(function(Clazz
,Clazz_doubleToInt
,Clazz_declarePackage
,Clazz_instanceOf
,Clazz_load
,Clazz_instantialize
,Clazz_decorateAsClass
,Clazz_floatToInt
,Clazz_makeConstructor
,Clazz_defineEnumConstant
,Clazz_exceptionOf
,Clazz_newIntArray
,Clazz_defineStatics
,Clazz_newFloatArray
,Clazz_declareType
,Clazz_prepareFields
,Clazz_superConstructor
,Clazz_newByteArray
,Clazz_declareInterface
,Clazz_p0p
,Clazz_pu$h
,Clazz_newShortArray
,Clazz_innerTypeInstance
,Clazz_isClassDefined
,Clazz_prepareCallback
,Clazz_newArray
,Clazz_castNullAs
,Clazz_floatToShort
,Clazz_superCall
,Clazz_decorateAsType
,Clazz_newBooleanArray
,Clazz_newCharArray
,Clazz_implementOf
,Clazz_newDoubleArray
,Clazz_overrideConstructor
,Clazz_supportsNativeObject
,Clazz_extendedObjectMethods
,Clazz_callingStackTraces
,Clazz_clone
,Clazz_doubleToShort
,Clazz_innerFunctions
,Clazz_getInheritedLevel
,Clazz_getParamsType
,Clazz_isAF
,Clazz_isAI
,Clazz_isAS
,Clazz_isASS
,Clazz_isAP
,Clazz_isAFloat
,Clazz_isAII
,Clazz_isAFF
,Clazz_isAFFF
,Clazz_tryToSearchAndExecute
,$_A
,$_Ab
,$_AB
,$_AC
,$_AD
,$_AF
,$_AI
,$_AL
,$_AS
,$_B
,$_C
,$_D
,$_E
,$_F
,$_G
,$_H
,$_I
,$_J
,$_K
,$_k
,$_L
,$_M
,$_N
,$_O
,$_P
,$_Q
,$_R
,$_S
,$_s
,$_T
,$_U
,$_V
,$_W
,$_X
,$_Y
,$_Z
){
var $t$;
//var c$;
___JmolDate="$Date: 2013-11-06 00:32:37 -0800 (Wed, 06 Nov 2013) $"
___fullJmolProperties="src/org/jmol/viewer/Jmol.properties"
___JmolVersion="13.3.9_dev_2013.11.05"
// JSmolJavaExt.js
// BH 11/4/2013 7:34:26 AM changing "var nativeClazz" to "var nativeClass" to avoid ANT replacement of "nativeClazz_" to "nativeClazz_"
// BH 10/19/2013 1:29:27 PM fixed String.$replace()
// BH 10/18/2013 6:09:23 PM fixed (Double|Float).valueOf(NaN).valueOf(), which should return NaN, not throw an error
// BH 10/12/2013 11:18:44 AM fixed bug in Double(String) and Float(String) that was returning typeof "string"
// BH 10/10/2013 2:40:20 PM  added Math.log10   

// BH 7/23/2013 7:24:01 AM fixing Number.shortValue() and Number.byteValue() for negative values
// BH 6/16/2013 1:31:30 PM adding /| in String.replace -- thank you David Koes
// BH 3/13/2013 12:49:23 PM setting Boolean.valueOf() "@" 
// BH 3/2/2013 10:46:45 PM removed Double.valueOf(String)
// BH 11/6/2012 8:26:33 PM added instanceof Int32Array in String.instantialize
// BH 10/13/2012 11:38:07 PM corrected Integer.parseInt to allow only +-0123456789; created Integer.parseIntRadix
// BH 11/1/2012 added Short
// BH 9/10/2012 6:27:21 AM added java.net.URL... classes
// BH 1/7/2013 7:40:06 AM added Clazz_dateToString

Math.log10 = function(a){ return Math.log(a) / 2.302585092994046 }

Clazz_dateToString = Date.prototype.toString

java.lang.Number=Number;
if(Clazz_supportsNativeObject){
for(var i=0;i<Clazz_extendedObjectMethods.length;i++){
var p=Clazz_extendedObjectMethods[i];
Number.prototype[p]=JavaObject.prototype[p];
}
}

Number.__CLASS_NAME__="Number";
Clazz_implementOf(Number,java.io.Serializable);
Number.equals=Clazz_innerFunctions.equals;
Number.getName=Clazz_innerFunctions.getName;


Number.serialVersionUID=Number.prototype.serialVersionUID=-8742448824652078965;

// HOWEVER this is not correct -- 0xffff should be -1. 
$_M(Number,"shortValue",
function(){
var x = Math.round(this)&0xffff;
return (this < 0 && x > 0 ? x - 0x10000 : x);
});

$_M(Number,"byteValue",
function(){
var x = Math.round(this)&0xff;
return (this < 0 && x > 0 ? x - 0x100 : x);
});

$_M(Number,"intValue",
function(){
return Math.round(this)&0xffffffff;
});

$_M(Number,"longValue",
function(){
return Math.round(this);
});

$_M(Number,"floatValue",
function(){
return this.valueOf();
});
$_M(Number,"doubleValue",
function(){
return parseFloat(this.valueOf());
});

$_V(Number,"hashCode",
function(){
return this.valueOf();
});

java.lang.Integer=Integer=function(){
Clazz_instantialize(this,arguments);
};
Clazz_decorateAsType(Integer,"Integer",Number,Comparable,null,true);
Integer.prototype.valueOf=function(){return 0;};
Integer.toString=Integer.prototype.toString=function(){
if(arguments.length!=0){
return""+arguments[0];
} else if(this===Integer){
return"class java.lang.Integer";
}
return""+this.valueOf();
};

/*

Clazz_makeConstructor(Integer,
function(){
this.valueOf=function(){
return 0;
};
});
*/


$_k(Integer,
function(value){
var v=Math.round(value)&0xffffffff;
this.valueOf=function(){
return v;
};
}); //BH
/*
Clazz_makeConstructor(Integer,
function(s){
var value=Integer.parseInt(s,10);
this.valueOf=function(){
return value;
};
},"String");
*/
Integer.serialVersionUID=Integer.prototype.serialVersionUID=1360826667806852920;
Integer.MIN_VALUE=Integer.prototype.MIN_VALUE=-0x80000000;
Integer.MAX_VALUE=Integer.prototype.MAX_VALUE=0x7fffffff;
Integer.TYPE=Integer.prototype.TYPE=Integer;


$_M(Integer,"bitCount",
function(i) {
  i = i - ((i >>> 1) & 0x55555555);
  i = (i & 0x33333333) + ((i >>> 2) & 0x33333333);
  i = (i + (i >>> 4)) & 0x0f0f0f0f;
  i = i + (i >>> 8);
  i = i + (i >>> 16);
  return i & 0x3f;
},"Number");
Integer.bitCount=Integer.prototype.bitCount;

$_M(Integer,"numberOfLeadingZeros",
function(i) {
 if (i == 0) return 32;
 var n = 1;
 if (i >>> 16 == 0) { n += 16; i <<= 16; }
 if (i >>> 24 == 0) { n +=  8; i <<=  8; }
 if (i >>> 28 == 0) { n +=  4; i <<=  4; }
 if (i >>> 30 == 0) { n +=  2; i <<=  2; }
 n -= i >>> 31;
 return n;
},"Number");
Integer.numberOfLeadingZeros=Integer.prototype.numberOfLeadingZeros;

$_M(Integer,"numberOfTrailingZeros",
function(i) {
  if (i == 0) return 32;
  var n = 31;
  var y = i <<16; if (y != 0) { n = n -16; i = y; }
  y = i << 8; if (y != 0) { n = n - 8; i = y; }
  y = i << 4; if (y != 0) { n = n - 4; i = y; }
  y = i << 2; if (y != 0) { n = n - 2; i = y; }
  return n - ((i << 1) >>> 31);
},"Number");
Integer.numberOfTrailingZeros=Integer.prototype.numberOfTrailingZeros;

$_M(Integer,"parseIntRadix",
function(s,radix){
if(s==null){
throw new NumberFormatException("null");
}if(radix<2){
throw new NumberFormatException("radix "+radix+" less than Character.MIN_RADIX");
}if(radix>36){
throw new NumberFormatException("radix "+radix+" greater than Character.MAX_RADIX");
}
if (radix == 10) {
	for (var i = s.length; --i >= 0;) {
	  var c = s.charCodeAt(i);
	  if (c >= 48 && c <= 57) continue;
	  if (i > 0 || c != 43 && c != 45)
		  throw new NumberFormatException("Not a Number : "+s);

	}
}
var integer=parseInt(s,radix);
if(isNaN(integer)){
throw new NumberFormatException("Not a Number : "+s);
}
return integer;
},"String, Number");
Integer.parseIntRadix=Integer.prototype.parseIntRadix;

$_M(Integer,"parseInt",
function(s){
return Integer.parseIntRadix(s,10);
},"String");
Integer.parseInt=Integer.prototype.parseInt;

/*
$_M(Integer,"$valueOf",
function(s){
return new Integer(Integer.parseIntRadix(s,10));
},"String");
*/

$_V(Integer,"$valueOf",
function(s){
return new Integer(s);
});

/*
$_M(Integer,"$valueOf",
function(s,r){
return new Integer(Integer.parseIntRadix(s,r));
},"String, Number");
*/

Integer.$valueOf=Integer.prototype.$valueOf;


$_V(Integer,"equals",
function(s){
if(s==null||!Clazz_instanceOf(s,Integer)){
return false;
}
return s.valueOf()==this.valueOf();
},"Object");
Integer.toHexString=Integer.prototype.toHexString=function(d){
if(d.valueOf)d=d.valueOf();
if (d < 0) {
var b = d & 0xFFFFFF;
var c = ((d>>24)&0xFF);
return c._numberToString(16) + (b = b._numberToString(16)).substring(b.length - 6);
}
return d._numberToString(16);};
Integer.toOctalString=Integer.prototype.toOctalString=function(d){if(d.valueOf)d=d.valueOf();return d._numberToString(8);};
Integer.toBinaryString=Integer.prototype.toBinaryString=function(d){if(d.valueOf)d=d.valueOf();return d._numberToString(2);};

Number.toString = Number.prototype.toString=function(a){
if (arguments.length == 0)return ""+a
return Integer.toHexString(a);
};



Integer.decode=$_M(Integer,"decode",
function(nm){
var radix=10;
var index=0;
var negative=false;
var result;
if(nm.startsWith("-")){
negative=true;
index++;
}if(nm.startsWith("0x",index)||nm.startsWith("0X",index)){
index+=2;
radix=16;
}else if(nm.startsWith("#",index)){
index++;
radix=16;
}else if(nm.startsWith("0",index)&&nm.length>1+index){
index++;
radix=8;
}if(nm.startsWith("-",index))throw new NumberFormatException("Negative sign in wrong position");
try{
result=Integer.$valueOf(nm.substring(index),radix);
result=negative?new Integer(-result.intValue()):result;
}catch(e){
if(Clazz_instanceOf(e,NumberFormatException)){
var constant=negative?String.instantialize("-"+nm.substring(index)):nm.substring(index);
result=Integer.$valueOf(constant,radix);
}else{
throw e;
}
}
return result;
},"~S");

$_V(Integer,"hashCode",
function(){
return this.valueOf();
});


java.lang.Long=Long=function(){
Clazz_instantialize(this,arguments);
};
Clazz_decorateAsType(Long,"Long",Number,Comparable,null,true);
Long.prototype.valueOf=function(){return 0;};
Long.toString=Long.prototype.toString=function(){
if(arguments.length!=0){
return""+arguments[0];
}else if(this===Long){
return"class java.lang.Long";
}
return""+this.valueOf();
};
Clazz_makeConstructor(Long,
function(){
this.valueOf=function(){
return 0;
};
});
Clazz_makeConstructor(Long,
function(value){
var v=Math.round(value);
this.valueOf=function(){
return v;
};
},"Number");
Clazz_makeConstructor(Long,
function(s){
var value=Long.parseLong(s,10);
this.valueOf=function(){
return value;
};
},"String");
Long.serialVersionUID=Long.prototype.serialVersionUID=4290774380558885855;
Long.MIN_VALUE=Long.prototype.MIN_VALUE=-0x8000000000000000;
Long.MAX_VALUE=Long.prototype.MAX_VALUE=0x7fffffffffffffff;
Long.TYPE=Long.prototype.TYPE=Long;

$_M(Long,"parseLong",
function(s,radix){
if(s==null){
throw new NumberFormatException("null");
}if(radix<2){
throw new NumberFormatException("radix "+radix+" less than Character.MIN_RADIX");
}if(radix>36){
throw new NumberFormatException("radix "+radix+" greater than Character.MAX_RADIX");
}
var longVal=parseInt(s,radix);
if(isNaN(longVal)){
throw new NumberFormatException("Not a Number : "+s);
}
return longVal;
},"String, Number");

$_M(Long,"parseLong",
function(s){
return Long.parseLong(s,10);
},"String");

Long.parseLong=Long.prototype.parseLong;

$_M(Long,"$valueOf",
function(s){
return new Long(Long.parseLong(s,10));
},"String");

$_M(Long,"$valueOf",
function(s){
return new Long(s);
},"Number");

$_M(Long,"$valueOf",
function(s,r){
return new Long(Long.parseLong(s,r));
},"String, Number");

Long.$valueOf=Long.prototype.$valueOf;
$_V(Long,"equals",
function(s){
if(s==null||!Clazz_instanceOf(s,Long)){
return false;
}
return s.valueOf()==this.valueOf();
},"Object");
Long.toHexString=Long.prototype.toHexString=function(i){
return i.toString(16);
};
Long.toOctalString=Long.prototype.toOctalString=function(i){
return i.toString(8);
};
Long.toBinaryString=Long.prototype.toBinaryString=function(i){
return i.toString(2);
};


Long.decode=$_M(Long,"decode",
function(nm){
var radix=10;
var index=0;
var negative=false;
var result;
if(nm.startsWith("-")){
negative=true;
index++;
}if(nm.startsWith("0x",index)||nm.startsWith("0X",index)){
index+=2;
radix=16;
}else if(nm.startsWith("#",index)){
index++;
radix=16;
}else if(nm.startsWith("0",index)&&nm.length>1+index){
index++;
radix=8;
}if(nm.startsWith("-",index))throw new NumberFormatException("Negative sign in wrong position");
try{
result=Long.$valueOf(nm.substring(index),radix);
result=negative?new Long(-result.longValue()):result;
}catch(e){
if(Clazz_instanceOf(e,NumberFormatException)){
var constant=negative?String.instantialize("-"+nm.substring(index)):nm.substring(index);
result=Long.$valueOf(constant,radix);
}else{
throw e;
}
}
return result;
},"~S");

java.lang.Short = Short = function () {
Clazz_instantialize (this, arguments);
};
Clazz_decorateAsType (Short, "Short", Number, Comparable, null, true);
Short.prototype.valueOf = function () { return 0; };
Short.toString = Short.prototype.toString = function () {
	if (arguments.length != 0) {
		return "" + arguments[0];
	} else if (this === Short) {
		return "class java.lang.Short"; // Short.class.toString
	}
	return "" + this.valueOf ();
};
/*
Clazz_makeConstructor (Short,
function () {
this.valueOf = function () {
	return 0;
};
});
*/

$_k (Short,
function (value) {
var v = Math.round (value) & 0xffffffff;
this.valueOf = function () {
	return v;
};
});

/*
Clazz_makeConstructor (Short,
function (s) {
var value = Short.parseShort (s, 10);
this.valueOf = function () {
	return value;
};
}, "String");
*/

Short.serialVersionUID = Short.prototype.serialVersionUID = 7515723908773894738;
Short.MIN_VALUE = Short.prototype.MIN_VALUE = -32768;
Short.MAX_VALUE = Short.prototype.MAX_VALUE = 32767;
Short.TYPE = Short.prototype.TYPE = Short;

$_M(Short, "parseShort",
function (s, radix) {
if (s == null) {
throw  new NumberFormatException ("null");
}if (radix < 2) {
throw  new NumberFormatException ("radix " + radix + " less than Character.MIN_RADIX");
}if (radix > 36) {
throw  new NumberFormatException ("radix " + radix + " greater than Character.MAX_RADIX");
}
var integer = parseInt (s, radix);
if(isNaN(integer)){
throw  new NumberFormatException ("Not a Number : " + s);
}
return integer;
}, "String, Number");
Short.parseShort = Short.prototype.parseShort;
$_M(Short, "parseShort",
function (s) {
return Short.parseShort (s, 10);
}, "String");

Short.parseShort = Short.prototype.parseShort;

/*
$_M(Short, "$valueOf",
function (s) {
return new Short(Short.parseShort (s, 10));
}, "String");
  */
  
$_V(Short, "$valueOf",
function (s) {
return new Short(s);
});

/*
$_M(Short, "$valueOf",
function (s, r) {
return new Short(Short.parseShort (s, r));
}, "String, Number");
  */
  
Short.$valueOf = Short.prototype.$valueOf;
$_V(Short, "equals",
function (s) {
if(s == null || !Clazz_instanceOf(s, Short) ){
	return false;
}
return s.valueOf()  == this.valueOf();
}, "Object");
Short.toHexString = Short.prototype.toHexString = function (i) {
	return i.toString (16);
};
Short.toOctalString = Short.prototype.toOctalString = function (i) {
	return i.toString (8);
};
Short.toBinaryString = Short.prototype.toBinaryString = function (i) {
	return i.toString (2);
};
Short.decode = $_M(Short, "decode",
function (nm) {
var radix = 10;
var index = 0;
var negative = false;
var result;
if (nm.startsWith ("-")) {
negative = true;
index++;
}if (nm.startsWith ("0x", index) || nm.startsWith ("0X", index)) {
index += 2;
radix = 16;
} else if (nm.startsWith ("#", index)) {
index++;
radix = 16;
} else if (nm.startsWith ("0", index) && nm.length > 1 + index) {
index++;
radix = 8;
}if (nm.startsWith ("-", index)) throw  new NumberFormatException ("Negative sign in wrong position");
try {
result = Short.$valueOf (nm.substring (index), radix);
result = negative ?  new Short (-result.shortValue ()) : result;
} catch (e) {
if (Clazz_instanceOf (e, NumberFormatException)) {
var constant = negative ?  String.instantialize ("-" + nm.substring (index)) : nm.substring (index);
result = Short.$valueOf (constant, radix);
} else {
throw e;
}
}
return result;
}, "~S");

java.lang.Float=Float=function(){
Clazz_instantialize(this,arguments);
};
Clazz_decorateAsType(Float,"Float",Number,Comparable,null,true);
Float.prototype.valueOf=function(){return 0;};
Float.toString=Float.prototype.toString=function(){
if(arguments.length!=0){
return""+arguments[0];
}else if(this===Float){
return"class java.lang.Float";
}
return""+this.valueOf();
};


/*
Clazz_makeConstructor(Float,
function(){

this.valueOf=function(){
return 0.0;
};
});
*/
$_k(Float,
function(value){
this.valueOf=function(){
return Float.parseFloat(value);
};
});
/*
Clazz_makeConstructor(Float,
function(s){
var value=null;
if(s!=null){
value=Float.parseFloat(s);
}else{
value=0;
}
this.valueOf=function(){
return value;
};
},"String");
*/

Float.serialVersionUID=Float.prototype.serialVersionUID=-2671257302660747028;
Float.MIN_VALUE=Float.prototype.MIN_VALUE=3.4028235e+38;
Float.MAX_VALUE=Float.prototype.MAX_VALUE=1.4e-45;
Float.NEGATIVE_INFINITY=Number.NEGATIVE_INFINITY;
Float.POSITIVE_INFINITY=Number.POSITIVE_INFINITY;
Float.NaN=Number.NaN;
Float.TYPE=Float.prototype.TYPE=Float;

$_M(Float,"parseFloat",
function(s){
if(s==null){
throw new NumberFormatException("null");
}
if (typeof s == "number")return s;  // important -- typeof NaN is "number" and is OK here
var floatVal=parseFloat(s);
if(isNaN(floatVal)){
throw new NumberFormatException("Not a Number : "+s);
}
return floatVal;
},"String");
Float.parseFloat=Float.prototype.parseFloat;

/*
$_M(Float,"$valueOf",
function(s){
return new Float(Float.parseFloat(s,10));
},"String");
*/

$_V(Float,"$valueOf",
function(s){
return new Float(s);
});

Float.$valueOf=Float.prototype.$valueOf;

$_M(Float,"isNaN",
function(num){
return isNaN(num);
},"Number");
Float.isNaN=Float.prototype.isNaN;
$_M(Float,"isInfinite",
function(num){
return!isFinite(num);
},"Number");
Float.isInfinite=Float.prototype.isInfinite;

$_V(Float,"equals",
function(s){
if(s==null||!Clazz_instanceOf(s,Float)){
return false;
}
return s.valueOf()==this.valueOf();
},"Object");

java.lang.Double=Double=function(){
Clazz_instantialize(this,arguments);
};
Clazz_decorateAsType(Double,"Double",Number,Comparable,null,true);
Double.prototype.valueOf=function(){return 0;};
Double.toString=Double.prototype.toString=function(){
if(arguments.length!=0){
return""+arguments[0];
}else if(this===Double){
return"class java.lang.Double";
}
return""+this.valueOf();
};
/*
Clazz_makeConstructor(Double,
function(){
this.valueOf=function(){
return 0.0;
};
});
*/
$_k(Double,
function(value){
this.valueOf=function(){
return Double.parseDouble(value);
};
}); // BH

/*

Clazz_makeConstructor(Double,
function(s){
var value=Double.parseDouble(s);
this.valueOf=function(){
return value;
};
},"String");
*/

Double.serialVersionUID=Double.prototype.serialVersionUID=-9172774392245257468;
Double.MIN_VALUE=Double.prototype.MIN_VALUE=4.9e-324;
Double.MAX_VALUE=Double.prototype.MAX_VALUE=1.7976931348623157e+308;
Double.NEGATIVE_INFINITY=Number.NEGATIVE_INFINITY;
Double.POSITIVE_INFINITY=Number.POSITIVE_INFINITY;
Double.NaN=Number.NaN;
Double.TYPE=Double.prototype.TYPE=Double;

$_M(Double,"isNaN",
function(num){
return isNaN(num);
},"Number");
Double.isNaN=Double.prototype.isNaN;
$_M(Double,"isInfinite",
function(num){
return!isFinite(num);
},"Number");
Double.isInfinite=Double.prototype.isInfinite;

$_M(Double,"parseDouble",
function(s){
if(s==null){
throw new NumberFormatException("null");
}
if (typeof s == "number")return s;  // important -- typeof NaN is "number" and is OK here
var doubleVal=parseFloat(s);
if(isNaN(doubleVal)){
throw new NumberFormatException("Not a Number : "+s);
}
return doubleVal;
},"String");
Double.parseDouble=Double.prototype.parseDouble;

/*
$_M(Double,"$valueOf",
function(s){
return new Double(this.parseDouble(s));
},"String");
*/

$_M(Double,"$valueOf",
function(v){
return new Double(v);
},"Number");

Double.$valueOf=Double.prototype.$valueOf;

$_V(Double,"equals",
function(s){
if(s==null||!Clazz_instanceOf(s,Double)){
return false;
}
return s.valueOf()==this.valueOf();
},"Object");

java.lang.Byte=Byte=function(){
Clazz_instantialize(this,arguments);
};
Clazz_decorateAsType(Byte,"Byte",Number,Comparable,null,true);
Byte.prototype.valueOf=function(){return 0;};
Byte.toString=Byte.prototype.toString=function(){
if(arguments.length!=0){
return""+arguments[0];
}else if(this===Byte){
return"class java.lang.Byte";
}
return""+this.valueOf();
};
Clazz_makeConstructor(Byte,
function(){
this.valueOf=function(){
return 0;
};
});
Clazz_makeConstructor(Byte,
function(value){
var v=Math.round(value)&0xffffffff;
this.valueOf=function(){
return v;
};
},"Number");
Clazz_makeConstructor(Byte,
function(s){
var value=Byte.parseByte(s,10);
this.valueOf=function(){
return value;
};
},"String");
Byte.serialVersionUID=Byte.prototype.serialVersionUID=-7183698231559129828;
Byte.MIN_VALUE=Byte.prototype.MIN_VALUE=-128;
Byte.MAX_VALUE=Byte.prototype.MAX_VALUE=127;
Byte.SIZE=Byte.prototype.SIZE=8;
Byte.TYPE=Byte.prototype.TYPE=Byte;

$_M(Byte,"parseByte",
function(s,radix){
if(s==null){
throw new NumberFormatException("null");
}if(radix<2){
throw new NumberFormatException("radix "+radix+" less than Character.MIN_RADIX");
}if(radix>36){
throw new NumberFormatException("radix "+radix+" greater than Character.MAX_RADIX");
}
var integer=parseInt(s,radix);
if(isNaN(integer)){
throw new NumberFormatException("Not a Number : "+s);
}
return integer;
},"String, Number");
Byte.parseByte=Byte.prototype.parseByte;
$_M(Byte,"parseByte",
function(s){
return Byte.parseByte(s,10);
},"String");

Byte.parseByte=Byte.prototype.parseByte;

$_M(Byte,"$valueOf",
function(s){
return new Byte(Byte.parseByte(s,10));
},"String");

$_M(Byte,"$valueOf",
function(s){
return new Byte(s);
},"Number");

$_M(Byte,"$valueOf",
function(s,r){
return new Byte(Byte.parseByte(s,r));
},"String, Number");

Byte.$valueOf=Byte.prototype.$valueOf;
$_V(Byte,"equals",
function(s){
if(s==null||!Clazz_instanceOf(s,Byte)){
return false;
}
return s.valueOf()==this.valueOf();
},"Object");
Byte.toHexString=Byte.prototype.toHexString=function(i){
return i.toString(16);
};
Byte.toOctalString=Byte.prototype.toOctalString=function(i){
return i.toString(8);
};
Byte.toBinaryString=Byte.prototype.toBinaryString=function(i){
return i.toString(2);
};
Byte.decode=$_M(Byte,"decode",
function(nm){
var radix=10;
var index=0;
var negative=false;
var result;
if(nm.startsWith("-")){
negative=true;
index++;
}if(nm.startsWith("0x",index)||nm.startsWith("0X",index)){
index+=2;
radix=16;
}else if(nm.startsWith("#",index)){
index++;
radix=16;
}else if(nm.startsWith("0",index)&&nm.length>1+index){
index++;
radix=8;
}if(nm.startsWith("-",index))throw new NumberFormatException("Negative sign in wrong position");
try{
result=Byte.$valueOf(nm.substring(index),radix);
result=negative?new Byte(-result.byteValue()):result;
}catch(e){
if(Clazz_instanceOf(e,NumberFormatException)){
var constant=negative?String.instantialize("-"+nm.substring(index)):nm.substring(index);
result=Byte.$valueOf(constant,radix);
}else{
throw e;
}
}
return result;
},"~S");

java.lang.B00lean = Boolean;
java.lang.Boolean = Boolean = function () {
	Clazz_instantialize (this, arguments);
};
if (Clazz_supportsNativeObject) {
	for (var i = 0; i < Clazz_extendedObjectMethods.length; i++) {
		var p = Clazz_extendedObjectMethods[i];
		Boolean.prototype[p] = JavaObject.prototype[p];
	}
}
Boolean.__CLASS_NAME__="Boolean";
Clazz_implementOf(Boolean,[java.io.Serializable,java.lang.Comparable]);
Boolean.equals=Clazz_innerFunctions.equals;
Boolean.getName=Clazz_innerFunctions.getName;
Boolean.serialVersionUID=Boolean.prototype.serialVersionUID=-3665804199014368530;

//Clazz_makeConstructor(Boolean,
//function(value){
//this.valueOf=function(){
//return value;
//};
//},"~B");

Clazz_overrideConstructor(Boolean,
function(s){
  var b = ((typeof s == "string" ? Boolean.toBoolean(s) : s) ? true : false);
  this.valueOf=function(){return b;};
},"~O");

Boolean.parseBoolean=$_M(Boolean,"parseBoolean",
function(s){
return Boolean.toBoolean(s);
},"~S");
$_M(Boolean,"booleanValue",
function(){
return this.valueOf();
});
Boolean.$valueOf=$_V(Boolean,"$valueOf",
function(b){
return(b?Boolean.TRUE:Boolean.FALSE);
});
Boolean.toString=$_M(Boolean,"toString",
function(b){
return b?"true":"false";
},"~B");
$_V(Boolean,"toString",
function(){
return this.valueOf()?"true":"false";
});
$_V(Boolean,"hashCode",
function(){
return this.valueOf()?1231:1237;
});
$_V(Boolean,"equals",
function(obj){
if(Clazz_instanceOf(obj,Boolean)){
return this.booleanValue()==obj.booleanValue();
}return false;
},"~O");
Boolean.getBoolean=$_M(Boolean,"getBoolean",
function(name){
var result=false;
try{
result=Boolean.toBoolean(System.getProperty(name));
}catch(e){
if(Clazz_instanceOf(e,IllegalArgumentException)){
}else if(Clazz_instanceOf(e,NullPointerException)){
}else{
throw e;
}
}
return result;
},"~S");
$_V(Boolean,"compareTo",
function(b){
return(b.value==this.value?0:(this.value?1:-1));
},"Boolean");
Boolean.toBoolean=$_M(Boolean,"toBoolean",
($fz=function(name){
return((name!=null)&&name.equalsIgnoreCase("true"));
},$fz.isPrivate=true,$fz),"~S");
Boolean.TRUE=Boolean.prototype.TRUE=new Boolean(true);
Boolean.FALSE=Boolean.prototype.FALSE=new Boolean(false);
Boolean.TYPE=Boolean.prototype.TYPE=Boolean;


Encoding=new Object();
Encoding.UTF8="utf-8";
Encoding.UTF16="utf-16";
Encoding.ASCII="ascii";


Encoding.guessEncoding=function(str){
if(str.charCodeAt(0)==0xEF&&str.charCodeAt(1)==0xBB&&str.charCodeAt(2)==0xBF){
return Encoding.UTF8;
}else if(str.charCodeAt(0)==0xFF&&str.charCodeAt(1)==0xFE){
return Encoding.UTF16;
}else{
return Encoding.ASCII;
}
};

Encoding.readUTF8=function(str){
var encoding=this.guessEncoding(str);
var startIdx=0;
if(encoding==Encoding.UTF8){
startIdx=3;
}else if(encoding==Encoding.UTF16){
startIdx=2;
}
var arrs=new Array();
for(var i=startIdx;i<str.length;i++){
var charCode=str.charCodeAt(i);
if(charCode<0x80){
arrs[arrs.length]=str.charAt(i);
}else if(charCode>0xc0&&charCode<0xe0){
var c1=charCode&0x1f;
i++;
var c2=str.charCodeAt(i)&0x3f;
var c=(c1<<6)+c2;
arrs[arrs.length]=String.fromCharCode(c);
}else if(charCode>=0xe0){
var c1=charCode&0x0f;
i++;
var c2=str.charCodeAt(i)&0x3f;
i++;
var c3=str.charCodeAt(i)&0x3f;
var c=(c1<<12)+(c2<<6)+c3;
arrs[arrs.length]=String.fromCharCode(c);
}
}
return arrs.join('');
};

Encoding.convert2UTF8=function(str){
var encoding=this.guessEncoding(str);
var startIdx=0;
if(encoding==Encoding.UTF8){
return str;
}else if(encoding==Encoding.UTF16){
startIdx=2;
}

var offset=0;
var arrs=new Array(offset+str.length-startIdx);

for(var i=startIdx;i<str.length;i++){
var charCode=str.charCodeAt(i);
if(charCode<0x80){
arrs[offset+i-startIdx]=str.charAt(i);
}else if(charCode<=0x07ff){
var c1=0xc0+((charCode&0x07c0)>>6);
var c2=0x80+(charCode&0x003f);
arrs[offset+i-startIdx]=String.fromCharCode(c1)+String.fromCharCode(c2);
}else{
var c1=0xe0+((charCode&0xf000)>>12);
var c2=0x80+((charCode&0x0fc0)>>6);
var c3=0x80+(charCode&0x003f);
arrs[offset+i-startIdx]=String.fromCharCode(c1)+String.fromCharCode(c2)+String.fromCharCode(c3);
}
}
return arrs.join('');
};
Encoding.base64Chars=new Array(
'A','B','C','D','E','F','G','H',
'I','J','K','L','M','N','O','P',
'Q','R','S','T','U','V','W','X',
'Y','Z','a','b','c','d','e','f',
'g','h','i','j','k','l','m','n',
'o','p','q','r','s','t','u','v',
'w','x','y','z','0','1','2','3',
'4','5','6','7','8','9','+','/'
);
Encoding.encodeBase64=function(str){
if(str==null||str.length==0)return str;
var b64=Encoding.base64Chars;
var length=str.length;
var index=0;
var buf=[];
var c0,c1,c2;
while(index<length){
c0=str.charCodeAt(index++);
buf[buf.length]=b64[c0>>2];
if(index<length){
c1=str.charCodeAt(index++);
buf[buf.length]=b64[((c0<<4)&0x30)|(c1>>4)];
if(index<length){
c2=str.charCodeAt(index++);
buf[buf.length]=b64[((c1<<2)&0x3c)|(c2>>6)];
buf[buf.length]=b64[c2&0x3F];
}else{
buf[buf.length]=b64[((c1<<2)&0x3c)];
buf[buf.length]='=';
}
}else{
buf[buf.length]=b64[(c0<<4)&0x30];
buf[buf.length]='=';
buf[buf.length]='=';
}
}
return buf.join('');
};
Encoding.decodeBase64=function(str){
if(str==null||str.length==0)return str;
var b64=Encoding.base64Chars;
var xb64=Encoding.xBase64Chars;
if(Encoding.xBase64Chars==null){
xb64=new Object();
for(var i=0;i<b64.length;i++){
xb64[b64[i]]=i;
}
Encoding.xBase64Chars=xb64;
}
var length=str.length;
var index=0;
var buf=[];
var c0,c1,c2,c3;
var c=0;
while(index<length&&c++<60000){
c0=xb64[str.charAt(index++)];
c1=xb64[str.charAt(index++)];
c2=xb64[str.charAt(index++)];
c3=xb64[str.charAt(index++)];
buf[buf.length]=String.fromCharCode(((c0<<2)&0xff)|c1>>4);
if(c2!=null){
buf[buf.length]=String.fromCharCode(((c1<<4)&0xff)|c2>>2);
if(c3!=null){
buf[buf.length]=String.fromCharCode(((c2<<6)&0xff)|c3);
}
}
}
return buf.join('');
};

if(String.prototype.$replace==null){
java.lang.String=String;
if(Clazz_supportsNativeObject){
for(var i=0;i<Clazz_extendedObjectMethods.length;i++){
var p=Clazz_extendedObjectMethods[i];
if("to$tring"==p||"toString"==p||"equals"==p||"hashCode"==p){
continue;
}
String.prototype[p]=JavaObject.prototype[p];
}
}

Clazz_implementOf(String,[java.io.Serializable,CharSequence,Comparable]);

String.getName=Clazz_innerFunctions.getName;

String.serialVersionUID=String.prototype.serialVersionUID=-6849794470754667710;

String.prototype.$replace=function(c1,c2){
	if (c1 == c2 || this.indexOf (c1) < 0) return "" + this;
	if (c1.length == 1) {
    if ("\\$.*+|?^{}()[]".indexOf(c1) >= 0) 	c1 = "\\" + c1;
  } else {    
    c1=c1.replace(/([\\\$\.\*\+\|\?\^\{\}\(\)\[\]])/g,function($0,$1){return"\\"+$1;});
  }
  return this.replace(new RegExp(c1,"gm"),c2);
};
String.prototype.$generateExpFunction=function(str){
var arr=[];
var orders=[];
var idx=0;
arr[0]="";
var i=0;
for(;i<str.length;i++){
var ch=str.charAt(i);
if(i!=str.length-1&&ch=='\\'){
i++;
var c=str.charAt(i);
if(c=='\\'){
arr[idx]+='\\';
}
arr[idx]+=c;
}else if(i!=str.length-1&&ch=='$'){
i++;
orders[idx]=parseInt(str.charAt(i));
idx++;
arr[idx]="";
}else if(ch=='\r'){
arr[idx]+="\\r";
}else if(ch=='\n'){
arr[idx]+="\\n";
}else if(ch=='\t'){
arr[idx]+="\\t";
}else if(ch=='\"'){
arr[idx]+="\\\"";
}else{
arr[idx]+=ch;
}
}
var funStr="f = function (";
var max=Math.max.apply({},orders);
for(i=0;i<=max;i++){
funStr+="$"+i;
if(i!=max){
funStr+=", ";
}
}
funStr+=") { return ";
for(i=0;i<arr.length-1;i++){
funStr+="\""+arr[i]+"\" + $"+orders[i]+" + ";
}
funStr+="\""+arr[i]+"\"; }";
var f=null;
eval(funStr)
return f;
};

String.prototype.replaceAll=function(exp,str){
var regExp=new RegExp(exp,"gm");
return this.replace(regExp,this.$generateExpFunction(str));
};
String.prototype.replaceFirst=function(exp,str){
var regExp=new RegExp(exp,"m");
return this.replace(regExp,this.$generateExpFunction(str));
};
String.prototype.matches=function(exp){
if(exp!=null){
exp="^("+exp+")$";
}
var regExp=new RegExp(exp,"gm");
var m=this.match(regExp);
return m!=null&&m.length!=0;
};
String.prototype.regionMatches=function(ignoreCase,toffset,
other,ooffset,len){

if(typeof ignoreCase=="number"
||(ignoreCase!=true&&ignoreCase!=false)){
len=ooffset;
ooffset=other;
other=toffset;
toffset=ignoreCase;
ignoreCase=false;
}
var to=toffset;
var po=ooffset;

if((ooffset<0)||(toffset<0)||(toffset>this.length-len)||
(ooffset>other.length-len)){
return false;
}
var s1=this.substring(toffset,toffset+len);
var s2=other.substring(ooffset,ooffset+len);
if(ignoreCase){
s1=s1.toLowerCase();
s2=s2.toLowerCase();
}
return s1==s2;
};
String.prototype.$plit=function(regex,limit){

if(limit!=null&&limit>0){
if(limit==1){
return this;
}
var regExp=new RegExp("("+regex+")","gm");
var count=1;
var s=this.replace(regExp,function($0,$1){
count++;
if(count==limit){
return"@@_@@";
}else if(count>limit){
return $0;
}else{
return $0;
}
});
regExp=new RegExp(regex,"gm");
var arr=this.split(regExp);
if(arr.length>limit){
arr[limit-1]=s.substring(s.indexOf("@@_@@")+5);
arr.length=limit;
}
return arr;
}else{
var regExp=new RegExp(regex,"gm");
return this.split(regExp);
}
};

String.prototype.trim=function(){
var len=this.length;
var st=0;

while((st<len)&&(this.charAt(st)<=' ')){
st++;
}
while((st<len)&&(this.charAt(len-1)<=' ')){
len--;
}
return((st>0)||(len<len))?this.substring(st,len):this;
};

String.prototype.trim=function(){
return this.replace(/^\s+/g,'').replace(/\s+$/g,'');
};


String.prototype.startsWith_string_number=function(prefix,toffset){
var to=toffset;
var po=0;
var pc=prefix.length;

if((toffset<0)||(toffset>this.length-pc)){
return false;
}
while(--pc>=0){
if(this.charAt(to++)!=prefix.charAt(po++)){
return false;
}
}
return true;
};

String.prototype.startsWith=function(prefix){
if(arguments.length==1){
return this.startsWith_string_number(arguments[0],0);
}else if(arguments.length==2){
return this.startsWith_string_number(arguments[0],arguments[1]);
}else{
return false;
}
};

String.prototype.endsWith=function(suffix){
return this.startsWith(suffix,this.length-suffix.length);
};

String.prototype.equals=function(anObject){
return this.valueOf()==anObject;
};

String.prototype.equalsIgnoreCase=function(anotherString){
return(anotherString==null)?false:(this==anotherString
||this.toLowerCase()==anotherString.toLowerCase());
};


String.prototype.hash=0;

String.prototype.hashCode=function(){
var h=this.hash;
if(h==0){
var off=0;
var len=this.length;
for(var i=0;i<len;i++){
h=31*h+this.charCodeAt(off++);
h&=0xffffffff;
}
this.hash=h;
}
return h;
};

String.prototype.getBytes=function(){
if(arguments.length==4){
return this.getChars(arguments[0],arguments[1],arguments[2],arguments[3]);
}
var s=this;
if(arguments.length==1){
var cs=arguments[0].toString().toLowerCase();
var charset=[
"utf-8","UTF8","us-ascii","iso-8859-1","8859_1","gb2312","gb18030","gbk"
];
var existed=false;
for(var i=0;i<charset.length;i++){
if(charset[i]==cs){
existed=true;
break;
}
}
if(!existed){
throw new java.io.UnsupportedEncodingException();
}
if(cs=="utf-8"||cs=="utf8"){
s=Encoding.convert2UTF8(this);
}
}
var arrs=new Array(s.length);
var c=0,ii=0;
for(var i=0;i<s.length;i++){
c=s.charCodeAt(i);
if(c>255){
arrs[ii]=0x1a;
arrs[ii+1]=c&0xff;
arrs[ii+2]=(c&0xff00)>>8;
ii+=2;
}else{
arrs[ii]=c;
}
ii++;
}
return arrs;
};

String.prototype.compareTo=function(anotherString){
if(anotherString==null){
throw new java.lang.NullPointerException();
}
var len1=this.length;
var len2=anotherString.length;
var n=Math.min(len1,len2);
var k=0;
while(k<n){
var c1=this.charCodeAt(k);
var c2=anotherString.charCodeAt(k);
if(c1!=c2){
return c1-c2;
}
k++;
}
return len1-len2;
};

String.prototype.toCharArray=function(){
var result=new Array(this.length);
for(var i=0;i<this.length;i++){
result[i]=this.charAt(i);
}
return result;
};
String.value0f=String.valueOf;
String.valueOf=function(o){
if(o=="undefined"){
return String.value0f();
}
if(o instanceof Array){
if(arguments.length==1){
return o.join('');
}else{
var off=arguments[1];
var len=arguments[2];
var oo=new Array(len);
for(var i=0;i<len;i++){
oo[i]=o[off+i];
}
return oo.join('');
}
}
return""+o;
};

String.prototype.subSequence=function(beginIndex,endIndex){
return this.substring(beginIndex,endIndex);
};

String.prototype.compareToIgnoreCase=function(str){
if(str==null){
throw new NullPointerException();
}
var s1=this.toUpperCase();
var s2=str.toUpperCase();
if(s1==s2){
return 0;
}else{
var s1=this.toLowerCase();
var s2=str.toLowerCase();
if(s1==s2){
return 0;
}else if(s1>s2){
return 1;
}else{
return-1;
}
}
};

String.prototype.contentEquals=function(sb){
if(this.length!=sb.length()){
return false;
}
var v=sb.getValue();
var i=0;
var j=0;
var n=this.length;
while(n--!=0){
if(this.charCodeAt(i++)!=v[j++]){
return false;
}
}
return true;
};

String.prototype.getChars=function(srcBegin,srcEnd,dst,dstBegin){
if(srcBegin<0){
throw new StringIndexOutOfBoundsException(srcBegin);
}
if(srcEnd>this.length){
throw new StringIndexOutOfBoundsException(srcEnd);
}
if(srcBegin>srcEnd){
throw new StringIndexOutOfBoundsException(srcEnd-srcBegin);
}
if(dst==null){
throw new NullPointerException();
}
for(var i=0;i<srcEnd-srcBegin;i++){
dst[dstBegin+i]=this.charAt(srcBegin+i);
}
};
String.prototype.$concat=String.prototype.concat;
String.prototype.concat=function(s){
if(s==null){
throw new NullPointerException();
}
return this.$concat(s);
};

String.prototype.$lastIndexOf=String.prototype.lastIndexOf;
String.prototype.lastIndexOf=function(s,last){
if(last!=null&&last+this.length<=0){
return-1;
}
if(last!=null){
return this.$lastIndexOf(s,last);
}else{
return this.$lastIndexOf(s);
}
};

String.prototype.intern=function(){
return this.valueOf();
};
String.copyValueOf=String.prototype.copyValueOf=function(){
if(arguments.length==1){
return String.instantialize(arguments[0]);
}else{
return String.instantialize(arguments[0],arguments[1],arguments[2]);
}
};
String.indexOf=function(source,sourceOffset,sourceCount,
target,targetOffset,targetCount,fromIndex){
if(fromIndex>=sourceCount){
return(targetCount==0?sourceCount:-1);
}
if(fromIndex<0){
fromIndex=0;
}
if(targetCount==0){
return fromIndex;
}

var first=target[targetOffset];
var i=sourceOffset+fromIndex;
var max=sourceOffset+(sourceCount-targetCount);

startSearchForFirstChar:
while(true){

while(i<=max&&source[i]!=first){
i++;
}
if(i>max){
return-1;
}


var j=i+1;
var end=j+targetCount-1;
var k=targetOffset+1;
while(j<end){
if(source[j++]!=target[k++]){
i++;

continue startSearchForFirstChar;
}
}
return i-sourceOffset;
}
};

/*


String.instantialize=function(){
if(arguments.length==0){
return new String();
}else if(arguments.length==1){
var x=arguments[0];
if(typeof x=="string"||x instanceof String){
return new String(x);
}else if(x instanceof Array){
if(x.length>0&&typeof x[0]=="number"){
var arr=new Array(x.length);
for(var i=0;i<x.length;i++){
arr[i]=String.fromCharCode(x[i]&0xff);
}
return Encoding.readUTF8(arr.join(''));
}
return x.join('');
}else if(x.__CLASS_NAME__=="StringBuffer"
||x.__CLASS_NAME__=="java.lang.StringBuffer"){
var value=x.shareValue();
var length=x.length();
var valueCopy=new Array(length);
for(var i=0;i<length;i++){
valueCopy[i]=value[i];
}
return valueCopy.join('')

}else{
return""+x;
}
}else if(arguments.length==2){
var x=arguments[0];
var hibyte=arguments[1];
if(typeof hibyte=="string"){
return String.instantialize(x,0,x.length,hibyte);
}else{
return String.instantialize(x,hibyte,0,x.length);
}
}else if(arguments.length==3){
var bytes=arguments[0];
var offset=arguments[1];
var length=arguments[2];
if(arguments[2]instanceof Array){
bytes=arguments[2];
offset=arguments[0];
length=arguments[1];
}
var arr=new Array(length);
if(offset<0||length+offset>bytes.length){
throw new IndexOutOfBoundsException();
}
if(length>0){
var isChar=(bytes[offset].length!=null);
if(isChar){
for(var i=0;i<length;i++){
arr[i]=bytes[offset+i];
}
}else{
for(var i=0;i<length;i++){
arr[i]=String.fromCharCode(bytes[offset+i]);
}
}
}
return arr.join('');
}else if(arguments.length==4){
var bytes=arguments[0];
var y=arguments[3];
if(typeof y=="string"||y instanceof String){
var offset=arguments[1];
var length=arguments[2];
var arr=new Array(length);
for(var i=0;i<length;i++){
arr[i]=bytes[offset+i];
if(typeof arr[i]=="number"){
arr[i]=String.fromCharCode(arr[i]&0xff);
}
}
var cs=y.toLowerCase();
if(cs=="utf-8"||cs=="utf8"){
return Encoding.readUTF8(arr.join(''));
}else{
return arr.join('');
}
}else{
var count=arguments[3];
var offset=arguments[2];
var hibyte=arguments[1];
var value=new Array(count);
if(hibyte==0){
for(var i=count;i-->0;){
value[i]=String.fromCharCode(bytes[i+offset]&0xff);
}
}else{
hibyte<<=8;
for(var i=count;i-->0;){
value[i]=String.fromCharCode(hibyte|(bytes[i+offset]&0xff));
}
}
return value.join('');
}
}else{
var s="";
for(var i=0;i<arguments.length;i++){
s+=arguments[i];
}
return s;
}
};


*/


String.instantialize=function(){
switch (arguments.length) {
case 0:
	return new String();
case 1:
	var x=arguments[0];
	if(typeof x=="string"||x instanceof String){
		return new String(x);
	}
	if(x instanceof Array || x instanceof Int32Array){
		if(x.length>0&&typeof x[0]=="number"){
			var arr=new Array(x.length);
			for(var i=0;i<x.length;i++){
				arr[i]=String.fromCharCode(x[i]&0xff);
			}
			return Encoding.readUTF8(arr.join(''));
		}
		return x.join('');
	}
	if(x.__CLASS_NAME__=="StringBuffer"||x.__CLASS_NAME__=="java.lang.StringBuffer"){
		var value=x.shareValue();
		var length=x.length();
		var valueCopy=new Array(length);
		for(var i=0;i<length;i++){
			valueCopy[i]=value[i];
		}
		return valueCopy.join('')
	}
	return""+x;
case 2:	
	var x=arguments[0];
	var hibyte=arguments[1];
	if(typeof hibyte=="string"){
		return String.instantialize(x,0,x.length,hibyte);
	}
	return String.instantialize(x,hibyte,0,x.length);
case 3:
	var bytes=arguments[0];
	var offset=arguments[1];
	var length=arguments[2];
	if(arguments[2]instanceof Array){
		bytes=arguments[2];
		offset=arguments[0];
		length=arguments[1];
	}
	var arr=new Array(length);
	if(offset<0||length+offset>bytes.length){
		throw new IndexOutOfBoundsException();
	}
	if(length>0){
		var isChar=(bytes[offset].length!=null);
		if(isChar){
			for(var i=0;i<length;i++){
				arr[i]=bytes[offset+i];
			}
		}else{
			for(var i=0;i<length;i++){
				arr[i]=String.fromCharCode(bytes[offset+i]);
			}
		}
	}
	return arr.join('');
case 4:
	var bytes=arguments[0];
	var y=arguments[3];
	if(typeof y=="string"||y instanceof String){
		var offset=arguments[1];
		var length=arguments[2];
		var arr=new Array(length);
		for(var i=0;i<length;i++){
			arr[i]=bytes[offset+i];
			if(typeof arr[i]=="number"){
				arr[i]=String.fromCharCode(arr[i]&0xff);
			}
		}
		var cs=y.toLowerCase();
		if(cs=="utf-8"||cs=="utf8"){
			return Encoding.readUTF8(arr.join(''));
		}
		return arr.join('');
	}
	var count=arguments[3];
	var offset=arguments[2];
	var hibyte=arguments[1];
	var value=new Array(count);
	if(hibyte==0){
		for(var i=count;i-->0;){
			value[i]=String.fromCharCode(bytes[i+offset]&0xff);
		}
	}else{
		hibyte<<=8;
		for(var i=count;i-->0;){
			value[i]=String.fromCharCode(hibyte|(bytes[i+offset]&0xff));
		}
	}
	return value.join('');
default:
	var s="";
	for(var i=0;i<arguments.length;i++){
		s+=arguments[i];
	}
	return s;
}
};


if(navigator.userAgent.toLowerCase().indexOf("chrome")!=-1){
String.prototype.toString=function(){
return this;
};
}

}
c$=$_C(function(){
this.value=0;
$_Z(this,arguments);
},java.lang,"Character",null,[java.io.Serializable,Comparable]);
$_K(c$,
function(value){
this.value=value;
},"~N");
$_M(c$,"charValue",
function(){
return this.value;
});
$_V(c$,"hashCode",
function(){
return(this.value).charCodeAt(0);
});
$_V(c$,"equals",
function(obj){
if($_O(obj,Character)){
return(this.value).charCodeAt(0)==((obj).charValue()).charCodeAt(0);
}return false;
},"~O");
$_V(c$,"compareTo",
function(c){
return(this.value).charCodeAt(0)-(c.value).charCodeAt(0);
},"Character");
c$.toLowerCase=$_M(c$,"toLowerCase",
function(c){
return(""+c).toLowerCase().charAt(0);
},"~N");
c$.toUpperCase=$_M(c$,"toUpperCase",
function(c){
return(""+c).toUpperCase().charAt(0);
},"~N");
c$.isDigit=$_M(c$,"isDigit",
function(c){
if(('0').charCodeAt (0) <= (c).charCodeAt (0) && (c).charCodeAt (0) <= ('9').charCodeAt(0))return true;
if((c).charCodeAt(0)<1632)return false;
return false;
},"~N");
c$.isUpperCase=$_M(c$,"isUpperCase",
function(c){
if(('A').charCodeAt (0) <= (c).charCodeAt (0) && (c).charCodeAt (0) <= ('Z').charCodeAt(0)){
return true;
}return false;
},"~N");
c$.isLowerCase=$_M(c$,"isLowerCase",
function(c){
if(('a').charCodeAt (0) <= (c).charCodeAt (0) && (c).charCodeAt (0) <= ('z').charCodeAt(0)){
return true;
}return false;
},"~N");
c$.isWhitespace=$_M(c$,"isWhitespace",
function(c){
if(((c).charCodeAt(0)>=0x1c&&(c).charCodeAt(0)<=0x20)||((c).charCodeAt(0)>=0x9&&(c).charCodeAt(0)<=0xd))return true;
if((c).charCodeAt(0)==0x1680)return true;
if((c).charCodeAt(0)<0x2000||(c).charCodeAt(0)==0x2007)return false;
return(c).charCodeAt(0)<=0x200b||(c).charCodeAt(0)==0x2028||(c).charCodeAt(0)==0x2029||(c).charCodeAt(0)==0x3000;
},"~N");
c$.isLetter=$_M(c$,"isLetter",
function(c){
if((('A').charCodeAt (0) <= (c).charCodeAt (0) && (c).charCodeAt (0) <= ('Z').charCodeAt (0)) || (('a').charCodeAt (0) <= (c).charCodeAt (0) && (c).charCodeAt (0) <= ('z').charCodeAt(0)))return true;
if((c).charCodeAt(0)<128)return false;
return false;
},"~N");
c$.isLetterOrDigit=$_M(c$,"isLetterOrDigit",
function(c){
return Character.isLetter(c)||Character.isDigit(c);
},"~N");
c$.isSpaceChar=$_M(c$,"isSpaceChar",
function(c){
if((c).charCodeAt(0)==0x20||(c).charCodeAt(0)==0xa0||(c).charCodeAt(0)==0x1680)return true;
if((c).charCodeAt(0)<0x2000)return false;
return(c).charCodeAt(0)<=0x200b||(c).charCodeAt(0)==0x2028||(c).charCodeAt(0)==0x2029||(c).charCodeAt(0)==0x202f||(c).charCodeAt(0)==0x3000;
},"~N");
c$.digit=$_M(c$,"digit",
function(c,radix){
if(radix>=2&&radix<=36){
if((c).charCodeAt(0)<128){
var result=-1;
if(('0').charCodeAt (0) <= (c).charCodeAt (0) && (c).charCodeAt (0) <= ('9').charCodeAt(0)){
result=(c).charCodeAt(0)-('0').charCodeAt(0);
}else if(('a').charCodeAt (0) <= (c).charCodeAt (0) && (c).charCodeAt (0) <= ('z').charCodeAt(0)){
result=(c).charCodeAt(0)-(87);
}else if(('A').charCodeAt (0) <= (c).charCodeAt (0) && (c).charCodeAt (0) <= ('Z').charCodeAt(0)){
result=(c).charCodeAt(0)-(55);
}return result<radix?result:-1;
}}return-1;
},"~N,~N");
$_V(c$,"toString",
function(){
var buf=[this.value];
return String.valueOf(buf);
});
c$.toString=$_V(c$,"toString",
function(c){
{
if(this===Character){
return"class java.lang.Character";
}
}return String.valueOf(c);
},"~N");
$_S(c$,
"MIN_VALUE",'\u0000',
"MAX_VALUE",'\uffff',
"MIN_RADIX",2,
"MAX_RADIX",36,
"TYPE",null);

java.lang.Character.TYPE=java.lang.Character.prototype.TYPE=java.lang.Character;
Array.getComponentType=function(){
return Object;
};c$=$_T(java.lang.reflect,"Array");
c$.newInstance=$_M(c$,"newInstance",
function(componentType,size){
return $_A(length);
},"Class,~N");

java.util.Date=Date;
Clazz_decorateAsType(java.util.Date,"java.util.Date",null,[java.io.Serializable,Cloneable,Comparable]);
java.util.Date.prototype.toString = Clazz_dateToString

$_M(java.util.Date,"clone",
function(){
return new Date(this.getTime());
});

$_M(java.util.Date,"before",
function(when){
return this.getTime()<when.getTime();
},"java.util.Date");
$_M(java.util.Date,"after",
function(when){
return this.getTime()>when.getTime();
},"java.util.Date");
$_M(java.util.Date,"equals",
function(obj){
return Clazz_instanceOf(obj,java.util.Date)&&this.getTime()==(obj).getTime();
},"Object");
$_M(java.util.Date,"compareTo",
function(anotherDate){
var thisTime=this.getTime();
var anotherTime=anotherDate.getTime();
return(thisTime<anotherTime?-1:(thisTime==anotherTime?0:1));
},"java.util.Date");
$_M(java.util.Date,"compareTo",
function(o){
return this.compareTo(o);
},"Object");
$_V(java.util.Date,"hashCode",
function(){
var ht=this.getTime();
return parseInt(ht)^parseInt((ht>>32));
});

c$=$_C(function(){
this.source=null;
$_Z(this,arguments);
},java.util,"EventObject",null,java.io.Serializable);
$_K(c$,
function(source){
if(source!=null)this.source=source;
else throw new IllegalArgumentException();
},"~O");
$_M(c$,"getSource",
function(){
return this.source;
});
$_V(c$,"toString",
function(){
return this.getClass().getName()+"[source="+String.valueOf(this.source)+']';
});
$_I(java.util,"EventListener");

c$=$_C(function(){
this.listener=null;
$_Z(this,arguments);
},java.util,"EventListenerProxy",null,java.util.EventListener);
$_K(c$,
function(listener){
this.listener=listener;
},"java.util.EventListener");
$_M(c$,"getListener",
function(){
return this.listener;
});
$_I(java.util,"Iterator");

$_I(java.util,"ListIterator",java.util.Iterator);
$_I(java.util,"Enumeration");
$_I(java.util,"Collection",Iterable);

$_I(java.util,"Set",java.util.Collection);
$_I(java.util,"Map");
$_I(java.util.Map,"Entry");

$_I(java.util,"List",java.util.Collection);

$_I(java.util,"Queue",java.util.Collection);
$_I(java.util,"RandomAccess");
c$=$_C(function(){
this.detailMessage=null;
this.cause=null;
this.stackTrace=null;
$_Z(this,arguments);
},java.lang,"Throwable",null,java.io.Serializable);
$_Y(c$,function(){
this.cause=this;
//alert("e0 "+ arguments.callee.caller.caller.caller.caller.caller)
});
$_K(c$,
function(){
this.fillInStackTrace();
});
$_K(c$,
function(message){
this.fillInStackTrace();
this.detailMessage=message;
},"~S");
$_K(c$,
function(message,cause){
this.fillInStackTrace();
this.detailMessage=message;
this.cause=cause;
},"~S,Throwable");
$_K(c$,
function(cause){
this.fillInStackTrace();
this.detailMessage=(cause==null?null:cause.toString());
this.cause=cause;
},"Throwable");
$_M(c$,"getMessage",
function(){
{
if(typeof this.message!="undefined"){
return this.message;
}
}return this.detailMessage;
});
$_M(c$,"getLocalizedMessage",
function(){
return this.getMessage();
});
$_M(c$,"getCause",
function(){
return(this.cause===this?null:this.cause);
});
$_M(c$,"initCause",
function(cause){
if(this.cause!==this)throw new IllegalStateException("Can't overwrite cause");
if(cause===this)throw new IllegalArgumentException("Self-causation not permitted");
this.cause=cause;
return this;
},"Throwable");
$_V(c$,"toString",
function(){
var s=this.getClass().getName();
var message=this.getLocalizedMessage();
return(message!=null)?(s+": "+message):s;
});
$_M(c$,"printStackTrace",
function(){
System.err.println(this);
for(var i=0;i<this.stackTrace.length;i++){
var t=this.stackTrace[i];
var x=t.methodName.indexOf("(");
var n=t.methodName.substring(0,x).replace(/\s+/g,"");
if(n!="construct"||t.nativeClazz==null
||Clazz_getInheritedLevel(t.nativeClazz,Throwable)<0){
System.err.println(t);
}
}
});
$_M(c$,"printStackTrace",
function(s){
this.printStackTrace();
},"java.io.PrintStream");
$_M(c$,"printStackTrace",
function(s){
this.printStackTrace();
},"java.io.PrintWriter");
$_M(c$,"fillInStackTrace",
function(){
this.stackTrace=new Array();
var caller=arguments.callee.caller;
var superCaller=null;
var callerList=new Array();
var index=Clazz_callingStackTraces.length-1;
var noLooping=true;
while(index>-1||caller!=null){
var clazzName=null;
var nativeClass=null;
if(!noLooping||caller==Clazz_tryToSearchAndExecute||caller==$_U||caller==null){
if(index<0){
break;
}
noLooping=true;
superCaller=Clazz_callingStackTraces[index].caller;
nativeClass=Clazz_callingStackTraces[index].owner;
index--;
}else{
superCaller=caller;
if(superCaller.claxxOwner!=null){
nativeClass=superCaller.claxxOwner;
}else if(superCaller.exClazz!=null){
nativeClass=superCaller.exClazz;
}
}
var st=new StackTraceElement(
((nativeClass!=null&&nativeClass.__CLASS_NAME__.length!=0)?
nativeClass.__CLASS_NAME__:"anonymous"),
((superCaller.exName==null)?"anonymous":superCaller.exName)
+" ("+Clazz_getParamsType(superCaller.arguments)+")",
null,-1);
st.nativeClazz=nativeClass;
this.stackTrace[this.stackTrace.length]=st;
for(var i=0;i<callerList.length;i++){
if(callerList[i]==superCaller){

var st=new StackTraceElement("lost","missing",null,-3);
st.nativeClazz=null;
this.stackTrace[this.stackTrace.length]=st;
noLooping=false;

}
}
if(superCaller!=null){
callerList[callerList.length]=superCaller;
}
caller=superCaller.arguments.callee.caller;
}
Clazz_initializingException=false;
return this;
});
$_M(c$,"setStackTrace",
function(stackTrace){
var defensiveCopy=stackTrace.clone();
for(var i=0;i<defensiveCopy.length;i++)if(defensiveCopy[i]==null)throw new NullPointerException("stackTrace["+i+"]");

this.stackTrace=defensiveCopy;
},"~A");

c$=$_C(function(){
this.declaringClass=null;
this.methodName=null;
this.fileName=null;
this.lineNumber=0;
$_Z(this,arguments);
},java.lang,"StackTraceElement",null,java.io.Serializable);
$_K(c$,
function(cls,method,file,line){
if(cls==null||method==null){
throw new NullPointerException();
}this.declaringClass=cls;
this.methodName=method;
this.fileName=file;
this.lineNumber=line;
},"~S,~S,~S,~N");
$_V(c$,"equals",
function(obj){
if(!($_O(obj,StackTraceElement))){
return false;
}var castObj=obj;
if((this.methodName==null)||(castObj.methodName==null)){
return false;
}if(!this.getMethodName().equals(castObj.getMethodName())){
return false;
}if(!this.getClassName().equals(castObj.getClassName())){
return false;
}var localFileName=this.getFileName();
if(localFileName==null){
if(castObj.getFileName()!=null){
return false;
}}else{
if(!localFileName.equals(castObj.getFileName())){
return false;
}}if(this.getLineNumber()!=castObj.getLineNumber()){
return false;
}return true;
},"~O");
$_M(c$,"getClassName",
function(){
return(this.declaringClass==null)?"<unknown class>":this.declaringClass;
});
$_M(c$,"getFileName",
function(){
return this.fileName;
});
$_M(c$,"getLineNumber",
function(){
return this.lineNumber;
});
$_M(c$,"getMethodName",
function(){
return(this.methodName==null)?"<unknown method>":this.methodName;
});
$_V(c$,"hashCode",
function(){
if(this.methodName==null){
return 0;
}return this.methodName.hashCode()^this.declaringClass.hashCode();
});
$_M(c$,"isNativeMethod",
function(){
return this.lineNumber==-2;
});
$_V(c$,"toString",
function(){
var buf=new StringBuilder(80);
buf.append(this.getClassName());
buf.append('.');
buf.append(this.getMethodName());
if(this.isNativeMethod()){
buf.append("(Native Method)");
}else{
var fName=this.getFileName();
if(fName==null){
buf.append("(Unknown Source)");
}else{
var lineNum=this.getLineNumber();
buf.append('(');
buf.append(fName);
if(lineNum>=0){
buf.append(':');
buf.append(lineNum);
}buf.append(')');
}}return buf.toString();
});

c$=$_T(java.lang,"Error",Throwable);

c$=$_T(java.lang,"LinkageError",Error);

c$=$_T(java.lang,"IncompatibleClassChangeError",LinkageError);

c$=$_T(java.lang,"AbstractMethodError",IncompatibleClassChangeError);

c$=$_T(java.lang,"AssertionError",Error);
$_K(c$,
function(detailMessage){
$_R(this,AssertionError,[String.valueOf(detailMessage),($_O(detailMessage,Throwable)?detailMessage:null)]);
},"~O");
$_K(c$,
function(detailMessage){
this.construct(String.valueOf(detailMessage));
},"~B");
$_K(c$,
function(detailMessage){
this.construct(String.valueOf(detailMessage));
},"~N");
$_K(c$,
function(detailMessage){
this.construct(Integer.toString(detailMessage));
},"~N");
$_K(c$,
function(detailMessage){
this.construct(Long.toString(detailMessage));
},"~N");
$_K(c$,
function(detailMessage){
this.construct(Float.toString(detailMessage));
},"~N");
$_K(c$,
function(detailMessage){
this.construct(Double.toString(detailMessage));
},"~N");

c$=$_T(java.lang,"ClassCircularityError",LinkageError);

c$=$_T(java.lang,"ClassFormatError",LinkageError);

c$=$_C(function(){
this.exception=null;
$_Z(this,arguments);
},java.lang,"ExceptionInInitializerError",LinkageError);
$_K(c$,
function(){
$_R(this,ExceptionInInitializerError);
this.initCause(null);
});
$_K(c$,
function(detailMessage){
$_R(this,ExceptionInInitializerError,[detailMessage]);
this.initCause(null);
},"~S");
$_K(c$,
function(exception){
$_R(this,ExceptionInInitializerError);
this.exception=exception;
this.initCause(exception);
},"Throwable");
$_M(c$,"getException",
function(){
return this.exception;
});
$_V(c$,"getCause",
function(){
return this.exception;
});

c$=$_T(java.lang,"IllegalAccessError",IncompatibleClassChangeError);

c$=$_T(java.lang,"InstantiationError",IncompatibleClassChangeError);

c$=$_T(java.lang,"VirtualMachineError",Error);

c$=$_T(java.lang,"InternalError",VirtualMachineError);

c$=$_T(java.lang,"NoClassDefFoundError",LinkageError);

c$=$_T(java.lang,"NoSuchFieldError",IncompatibleClassChangeError);

c$=$_T(java.lang,"NoSuchMethodError",IncompatibleClassChangeError);

c$=$_T(java.lang,"OutOfMemoryError",VirtualMachineError);

c$=$_T(java.lang,"StackOverflowError",VirtualMachineError);

c$=$_T(java.lang,"UnknownError",VirtualMachineError);

c$=$_T(java.lang,"UnsatisfiedLinkError",LinkageError);

c$=$_T(java.lang,"UnsupportedClassVersionError",ClassFormatError);

c$=$_T(java.lang,"VerifyError",LinkageError);

c$=$_T(java.lang,"ThreadDeath",Error);
$_K(c$,
function(){
$_R(this,ThreadDeath,[]);
});

c$=$_T(java.lang,"Exception",Throwable);

c$=$_T(java.lang,"RuntimeException",Exception);

c$=$_T(java.lang,"ArithmeticException",RuntimeException);

c$=$_T(java.lang,"IndexOutOfBoundsException",RuntimeException);

c$=$_T(java.lang,"ArrayIndexOutOfBoundsException",IndexOutOfBoundsException);
$_K(c$,
function(index){
$_R(this,ArrayIndexOutOfBoundsException,["Array index out of range: "+index]);
},"~N");

c$=$_T(java.lang,"ArrayStoreException",RuntimeException);

c$=$_T(java.lang,"ClassCastException",RuntimeException);

c$=$_C(function(){
this.ex=null;
$_Z(this,arguments);
},java.lang,"ClassNotFoundException",Exception);
$_K(c$,
function(){
$_R(this,ClassNotFoundException,[Clazz_castNullAs("Throwable")]);
});
$_K(c$,
function(detailMessage){
$_R(this,ClassNotFoundException,[detailMessage,null]);
},"~S");
$_K(c$,
function(detailMessage,exception){
$_R(this,ClassNotFoundException,[detailMessage]);
this.ex=exception;
},"~S,Throwable");
$_M(c$,"getException",
function(){
return this.ex;
});
$_V(c$,"getCause",
function(){
return this.ex;
});

c$=$_T(java.lang,"CloneNotSupportedException",Exception);

c$=$_T(java.lang,"IllegalAccessException",Exception);

c$=$_T(java.lang,"IllegalArgumentException",RuntimeException);
$_K(c$,
function(cause){
$_R(this,IllegalArgumentException,[(cause==null?null:cause.toString()),cause]);
},"Throwable");

c$=$_T(java.lang,"IllegalMonitorStateException",RuntimeException);

c$=$_T(java.lang,"IllegalStateException",RuntimeException);
$_K(c$,
function(cause){
$_R(this,IllegalStateException,[(cause==null?null:cause.toString()),cause]);
},"Throwable");

c$=$_T(java.lang,"IllegalThreadStateException",IllegalArgumentException);

c$=$_T(java.lang,"InstantiationException",Exception);

c$=$_T(java.lang,"InterruptedException",Exception);

c$=$_T(java.lang,"NegativeArraySizeException",RuntimeException);

c$=$_T(java.lang,"NoSuchFieldException",Exception);

c$=$_T(java.lang,"NoSuchMethodException",Exception);

c$=$_T(java.lang,"NullPointerException",RuntimeException);

c$=$_T(java.lang,"NumberFormatException",IllegalArgumentException);

c$=$_T(java.lang,"SecurityException",RuntimeException);
$_K(c$,
function(cause){
$_R(this,SecurityException,[(cause==null?null:cause.toString()),cause]);
},"Throwable");

c$=$_T(java.lang,"StringIndexOutOfBoundsException",IndexOutOfBoundsException);
$_K(c$,
function(index){
$_R(this,StringIndexOutOfBoundsException,["String index out of range: "+index]);
},"~N");

c$=$_T(java.lang,"UnsupportedOperationException",RuntimeException);
$_K(c$,
function(){
$_R(this,UnsupportedOperationException,[]);
});
$_K(c$,
function(cause){
$_R(this,UnsupportedOperationException,[(cause==null?null:cause.toString()),cause]);
},"Throwable");

c$=$_C(function(){
this.target=null;
$_Z(this,arguments);
},java.lang.reflect,"InvocationTargetException",Exception);
$_K(c$,
function(){
$_R(this,java.lang.reflect.InvocationTargetException,[Clazz_castNullAs("Throwable")]);
});
$_K(c$,
function(exception){
$_R(this,java.lang.reflect.InvocationTargetException,[null,exception]);
this.target=exception;
},"Throwable");
$_K(c$,
function(exception,detailMessage){
$_R(this,java.lang.reflect.InvocationTargetException,[detailMessage,exception]);
this.target=exception;
},"Throwable,~S");
$_M(c$,"getTargetException",
function(){
return this.target;
});
$_V(c$,"getCause",
function(){
return this.target;
});

c$=$_C(function(){
this.undeclaredThrowable=null;
$_Z(this,arguments);
},java.lang.reflect,"UndeclaredThrowableException",RuntimeException);
$_K(c$,
function(exception){
$_R(this,java.lang.reflect.UndeclaredThrowableException);
this.undeclaredThrowable=exception;
this.initCause(exception);
},"Throwable");
$_K(c$,
function(exception,detailMessage){
$_R(this,java.lang.reflect.UndeclaredThrowableException,[detailMessage]);
this.undeclaredThrowable=exception;
this.initCause(exception);
},"Throwable,~S");
$_M(c$,"getUndeclaredThrowable",
function(){
return this.undeclaredThrowable;
});
$_V(c$,"getCause",
function(){
return this.undeclaredThrowable;
});

c$=$_T(java.io,"IOException",Exception);


c$=$_T(java.io,"CharConversionException",java.io.IOException);

c$=$_T(java.io,"EOFException",java.io.IOException);

c$=$_T(java.io,"FileNotFoundException",java.io.IOException);

c$=$_C(function(){
this.bytesTransferred=0;
$_Z(this,arguments);
},java.io,"InterruptedIOException",java.io.IOException);

c$=$_T(java.io,"ObjectStreamException",java.io.IOException);

c$=$_C(function(){
this.classname=null;
$_Z(this,arguments);
},java.io,"InvalidClassException",java.io.ObjectStreamException);
$_K(c$,
function(className,detailMessage){
$_R(this,java.io.InvalidClassException,[detailMessage]);
this.classname=className;
},"~S,~S");
$_M(c$,"getMessage",
function(){
var msg=$_U(this,java.io.InvalidClassException,"getMessage",[]);
if(this.classname!=null){
msg=this.classname+';' + ' '+msg;
}return msg;
});

c$=$_T(java.io,"InvalidObjectException",java.io.ObjectStreamException);

c$=$_T(java.io,"NotActiveException",java.io.ObjectStreamException);

c$=$_T(java.io,"NotSerializableException",java.io.ObjectStreamException);

c$=$_C(function(){
this.eof=false;
this.length=0;
$_Z(this,arguments);
},java.io,"OptionalDataException",java.io.ObjectStreamException);

c$=$_T(java.io,"StreamCorruptedException",java.io.ObjectStreamException);

c$=$_T(java.io,"SyncFailedException",java.io.IOException);

c$=$_T(java.io,"UnsupportedEncodingException",java.io.IOException);

c$=$_T(java.io,"UTFDataFormatException",java.io.IOException);

c$=$_C(function(){
this.detail=null;
$_Z(this,arguments);
},java.io,"WriteAbortedException",java.io.ObjectStreamException);
$_K(c$,
function(detailMessage,rootCause){
$_R(this,java.io.WriteAbortedException,[detailMessage]);
this.detail=rootCause;
this.initCause(rootCause);
},"~S,Exception");
$_M(c$,"getMessage",
function(){
var msg=$_U(this,java.io.WriteAbortedException,"getMessage",[]);
if(this.detail!=null){
msg=msg+"; "+this.detail.toString();
}return msg;
});
$_V(c$,"getCause",
function(){
return this.detail;
});

c$=$_T(java.util,"ConcurrentModificationException",RuntimeException);
$_K(c$,
function(){
$_R(this,java.util.ConcurrentModificationException,[]);
});

c$=$_T(java.util,"EmptyStackException",RuntimeException);

c$=$_C(function(){
this.className=null;
this.key=null;
$_Z(this,arguments);
},java.util,"MissingResourceException",RuntimeException);
$_K(c$,
function(detailMessage,className,resourceName){
$_R(this,java.util.MissingResourceException,[detailMessage]);
this.className=className;
this.key=resourceName;
},"~S,~S,~S");
$_M(c$,"getClassName",
function(){
return this.className;
});
$_M(c$,"getKey",
function(){
return this.key;
});

c$=$_T(java.util,"NoSuchElementException",RuntimeException);

c$=$_T(java.util,"TooManyListenersException",Exception);

c$=$_T(java.lang,"Void");
$_S(c$,
"TYPE",null);
{
java.lang.Void.TYPE=java.lang.Void;
}$_I(java.lang.reflect,"GenericDeclaration");
$_I(java.lang.reflect,"AnnotatedElement");

c$=$_T(java.lang.reflect,"AccessibleObject",null,java.lang.reflect.AnnotatedElement);
$_K(c$,
function(){
});
$_M(c$,"isAccessible",
function(){
return false;
});
c$.setAccessible=$_M(c$,"setAccessible",
function(objects,flag){
return;
},"~A,~B");
$_M(c$,"setAccessible",
function(flag){
return;
},"~B");
$_V(c$,"isAnnotationPresent",
function(annotationType){
return false;
},"Class");
$_V(c$,"getDeclaredAnnotations",
function(){
return new Array(0);
});
$_V(c$,"getAnnotations",
function(){
return new Array(0);
});
$_V(c$,"getAnnotation",
function(annotationType){
return null;
},"Class");
c$.marshallArguments=$_M(c$,"marshallArguments",
function(parameterTypes,args){
return null;
},"~A,~A");
$_M(c$,"invokeV",
function(receiver,args){
return;
},"~O,~A");
$_M(c$,"invokeL",
function(receiver,args){
return null;
},"~O,~A");
$_M(c$,"invokeI",
function(receiver,args){
return 0;
},"~O,~A");
$_M(c$,"invokeJ",
function(receiver,args){
return 0;
},"~O,~A");
$_M(c$,"invokeF",
function(receiver,args){
return 0.0;
},"~O,~A");
$_M(c$,"invokeD",
function(receiver,args){
return 0.0;
},"~O,~A");
c$.emptyArgs=c$.prototype.emptyArgs=new Array(0);
$_I(java.lang.reflect,"InvocationHandler");
c$=$_I(java.lang.reflect,"Member");
$_S(c$,
"PUBLIC",0,
"DECLARED",1);

c$=$_T(java.lang.reflect,"Modifier");
$_K(c$,
function(){
});
c$.isAbstract=$_M(c$,"isAbstract",
function(modifiers){
return((modifiers&1024)!=0);
},"~N");
c$.isFinal=$_M(c$,"isFinal",
function(modifiers){
return((modifiers&16)!=0);
},"~N");
c$.isInterface=$_M(c$,"isInterface",
function(modifiers){
return((modifiers&512)!=0);
},"~N");
c$.isNative=$_M(c$,"isNative",
function(modifiers){
return((modifiers&256)!=0);
},"~N");
c$.isPrivate=$_M(c$,"isPrivate",
function(modifiers){
return((modifiers&2)!=0);
},"~N");
c$.isProtected=$_M(c$,"isProtected",
function(modifiers){
return((modifiers&4)!=0);
},"~N");
c$.isPublic=$_M(c$,"isPublic",
function(modifiers){
return((modifiers&1)!=0);
},"~N");
c$.isStatic=$_M(c$,"isStatic",
function(modifiers){
return((modifiers&8)!=0);
},"~N");
c$.isStrict=$_M(c$,"isStrict",
function(modifiers){
return((modifiers&2048)!=0);
},"~N");
c$.isSynchronized=$_M(c$,"isSynchronized",
function(modifiers){
return((modifiers&32)!=0);
},"~N");
c$.isTransient=$_M(c$,"isTransient",
function(modifiers){
return((modifiers&128)!=0);
},"~N");
c$.isVolatile=$_M(c$,"isVolatile",
function(modifiers){
return((modifiers&64)!=0);
},"~N");
c$.toString=$_M(c$,"toString",
function(modifiers){
var sb=new Array(0);
if(java.lang.reflect.Modifier.isPublic(modifiers))sb[sb.length]="public";
if(java.lang.reflect.Modifier.isProtected(modifiers))sb[sb.length]="protected";
if(java.lang.reflect.Modifier.isPrivate(modifiers))sb[sb.length]="private";
if(java.lang.reflect.Modifier.isAbstract(modifiers))sb[sb.length]="abstract";
if(java.lang.reflect.Modifier.isStatic(modifiers))sb[sb.length]="static";
if(java.lang.reflect.Modifier.isFinal(modifiers))sb[sb.length]="final";
if(java.lang.reflect.Modifier.isTransient(modifiers))sb[sb.length]="transient";
if(java.lang.reflect.Modifier.isVolatile(modifiers))sb[sb.length]="volatile";
if(java.lang.reflect.Modifier.isSynchronized(modifiers))sb[sb.length]="synchronized";
if(java.lang.reflect.Modifier.isNative(modifiers))sb[sb.length]="native";
if(java.lang.reflect.Modifier.isStrict(modifiers))sb[sb.length]="strictfp";
if(java.lang.reflect.Modifier.isInterface(modifiers))sb[sb.length]="interface";
if(sb.length>0){
return sb.join(" ");
}return"";
},"~N");
$_S(c$,
"PUBLIC",0x1,
"PRIVATE",0x2,
"PROTECTED",0x4,
"STATIC",0x8,
"FINAL",0x10,
"SYNCHRONIZED",0x20,
"VOLATILE",0x40,
"TRANSIENT",0x80,
"NATIVE",0x100,
"INTERFACE",0x200,
"ABSTRACT",0x400,
"STRICT",0x800,
"BRIDGE",0x40,
"VARARGS",0x80,
"SYNTHETIC",0x1000,
"ANNOTATION",0x2000,
"ENUM",0x4000);

c$=$_C(function(){
this.clazz=null;
this.parameterTypes=null;
this.exceptionTypes=null;
this.modifiers=0;
$_Z(this,arguments);
},java.lang.reflect,"Constructor",java.lang.reflect.AccessibleObject,[java.lang.reflect.GenericDeclaration,java.lang.reflect.Member]);
$_K(c$,
function(declaringClass,parameterTypes,checkedExceptions,modifiers){
$_R(this,java.lang.reflect.Constructor,[]);
this.clazz=declaringClass;
this.parameterTypes=parameterTypes;
this.exceptionTypes=checkedExceptions;
this.modifiers=modifiers;
},"Class,~A,~A,~N");
$_V(c$,"getTypeParameters",
function(){
return null;
});
$_M(c$,"toGenericString",
function(){
return null;
});
$_M(c$,"getGenericParameterTypes",
function(){
return null;
});
$_M(c$,"getGenericExceptionTypes",
function(){
return null;
});
$_M(c$,"getParameterAnnotations",
function(){
return null;
});
$_M(c$,"isVarArgs",
function(){
return false;
});
$_V(c$,"isSynthetic",
function(){
return false;
});
$_V(c$,"equals",
function(object){
if(object!=null&&$_O(object,java.lang.reflect.Constructor)){
var other=object;
if(this.getDeclaringClass()===other.getDeclaringClass()){
var params1=this.parameterTypes;
var params2=other.parameterTypes;
if(params1.length==params2.length){
for(var i=0;i<params1.length;i++){
if(params1[i]!==params2[i])return false;
}
return true;
}}}return false;
},"~O");
$_V(c$,"getDeclaringClass",
function(){
return this.clazz;
});
$_M(c$,"getExceptionTypes",
function(){
return this.exceptionTypes;
});
$_V(c$,"getModifiers",
function(){
return this.modifiers;
});
$_V(c$,"getName",
function(){
return this.getDeclaringClass().getName();
});
$_M(c$,"getParameterTypes",
function(){
return this.parameterTypes;
});
$_V(c$,"hashCode",
function(){
return this.getDeclaringClass().getName().hashCode();
});
$_M(c$,"newInstance",
function(args){
var instance=new this.clazz($_G);
$_Z(instance,args);
return instance;
},"~A");
$_V(c$,"toString",
function(){
return null;
});

c$=$_T(java.lang.reflect,"Field",java.lang.reflect.AccessibleObject,java.lang.reflect.Member);
$_V(c$,"isSynthetic",
function(){
return false;
});
$_M(c$,"toGenericString",
function(){
return null;
});
$_M(c$,"isEnumConstant",
function(){
return false;
});
$_M(c$,"getGenericType",
function(){
return null;
});
$_V(c$,"equals",
function(object){
return false;
},"~O");
$_V(c$,"getDeclaringClass",
function(){
return null;
});
$_V(c$,"getName",
function(){
return null;
});
$_M(c$,"getType",
function(){
return null;
});
$_V(c$,"hashCode",
function(){
return 0;
});
$_V(c$,"toString",
function(){
return null;
});

c$=$_C(function(){
this.clazz=null;
this.name=null;
this.returnType=null;
this.parameterTypes=null;
this.exceptionTypes=null;
this.modifiers=0;
$_Z(this,arguments);
},java.lang.reflect,"Method",java.lang.reflect.AccessibleObject,[java.lang.reflect.GenericDeclaration,java.lang.reflect.Member]);
$_K(c$,
function(declaringClass,name,parameterTypes,returnType,checkedExceptions,modifiers){
$_R(this,java.lang.reflect.Method,[]);
this.clazz=declaringClass;
this.name=name;
this.parameterTypes=parameterTypes;
this.returnType=returnType;
this.exceptionTypes=checkedExceptions;
this.modifiers=modifiers;
},"Class,~S,~A,Class,~A,~N");
$_V(c$,"getTypeParameters",
function(){
return null;
});
$_M(c$,"toGenericString",
function(){
return null;
});
$_M(c$,"getGenericParameterTypes",
function(){
return null;
});
$_M(c$,"getGenericExceptionTypes",
function(){
return null;
});
$_M(c$,"getGenericReturnType",
function(){
return null;
});
$_M(c$,"getParameterAnnotations",
function(){
return null;
});
$_M(c$,"isVarArgs",
function(){
return false;
});
$_M(c$,"isBridge",
function(){
return false;
});
$_V(c$,"isSynthetic",
function(){
return false;
});
$_M(c$,"getDefaultValue",
function(){
return null;
});
$_V(c$,"equals",
function(object){
if(object!=null&&$_O(object,java.lang.reflect.Method)){
var other=object;
if((this.getDeclaringClass()===other.getDeclaringClass())&&(this.getName()===other.getName())){
var params1=this.parameterTypes;
var params2=other.parameterTypes;
if(params1.length==params2.length){
for(var i=0;i<params1.length;i++){
if(params1[i]!==params2[i])return false;
}
return true;
}}}return false;
},"~O");
$_V(c$,"getDeclaringClass",
function(){
return this.clazz;
});
$_M(c$,"getExceptionTypes",
function(){
return this.exceptionTypes;
});
$_V(c$,"getModifiers",
function(){
return this.modifiers;
});
$_V(c$,"getName",
function(){
return this.name;
});
$_M(c$,"getParameterTypes",
function(){
return this.parameterTypes;
});
$_M(c$,"getReturnType",
function(){
return this.returnType;
});
$_V(c$,"hashCode",
function(){
return this.getDeclaringClass().getName().hashCode()^this.getName().hashCode();
});
$_M(c$,"invoke",
function(receiver,args){
var m=this.clazz.prototype[this.getName()];
if(m==null){
m=this.clazz[this.getName()];
}
if(m!=null){
m.apply(receiver,args);
}else{

}
},"~O,~A");
$_V(c$,"toString",
function(){
return null;
});



/*

these are all now included in core.z.js itself.


$_J("java.net");
c$=$_T(java.net,"URLEncoder");
c$.encode=$_M(c$,"encode",
function(s){
return encodeURIComponent(arguments[0]);
},"~S");
c$.encode=$_M(c$,"encode",
function(s,enc){
return encodeURIComponent(arguments[0]);
},"~S,~S");
$_S(c$,
"digits","0123456789ABCDEF");

c$=$_T(java.net,"MalformedURLException",java.io.IOException);




$_J("java.net");
$_L(null,"java.net.URLDecoder",["java.lang.NullPointerException"],function(){
c$=$_T(java.net,"URLDecoder");
c$.decode=$_M(c$,"decode",
function(s){
return decodeURIComponent(arguments[0]);
},"~S");
c$.decode=$_M(c$,"decode",
function(s,enc){
if(enc==null){
throw new NullPointerException();
}{
return decodeURIComponent(arguments[0]);
}return null;
},"~S,~S");
});

Clazz_declarePackage ("java.net");
Clazz_declareInterface (java.net, "URLStreamHandlerFactory");

Clazz_declarePackage ("java.net");
Clazz_load (null, "java.net.URLStreamHandler", ["java.lang.IllegalArgumentException", "$.SecurityException", "$.StringBuffer", "$.UnsupportedOperationException"], function () {
c$ = Clazz_declareType (java.net, "URLStreamHandler");
$_M(c$, "openConnection",
function (u, p) {
throw  new UnsupportedOperationException ("Method not implemented.");
}, "java.net.URL,java.net.Proxy");
$_M(c$, "parseURL",
function (u, spec, start, limit) {
var protocol = u.getProtocol ();
var authority = u.getAuthority ();
var userInfo = u.getUserInfo ();
var host = u.getHost ();
var port = u.getPort ();
var path = u.getPath ();
var query = u.getQuery ();
var ref = u.getRef ();
var isRelPath = false;
var queryOnly = false;
if (start < limit) {
var queryStart = spec.indexOf ('?');
queryOnly = queryStart == start;
if ((queryStart != -1) && (queryStart < limit)) {
query = spec.substring (queryStart + 1, limit);
if (limit > queryStart) limit = queryStart;
spec = spec.substring (0, queryStart);
}}var i = 0;
var isUNCName = (start <= limit - 4) && ((spec.charAt (start)).charCodeAt (0) == ('/').charCodeAt (0)) && ((spec.charAt (start + 1)).charCodeAt (0) == ('/').charCodeAt (0)) && ((spec.charAt (start + 2)).charCodeAt (0) == ('/').charCodeAt (0)) && ((spec.charAt (start + 3)).charCodeAt (0) == ('/').charCodeAt (0));
if (!isUNCName && (start <= limit - 2) && ((spec.charAt (start)).charCodeAt (0) == ('/').charCodeAt (0)) && ((spec.charAt (start + 1)).charCodeAt (0) == ('/').charCodeAt (0))) {
start += 2;
i = spec.indexOf ('/', start);
if (i < 0) {
i = spec.indexOf ('?', start);
if (i < 0) i = limit;
}host = authority = spec.substring (start, i);
var ind = authority.indexOf ('@');
if (ind != -1) {
userInfo = authority.substring (0, ind);
host = authority.substring (ind + 1);
} else {
userInfo = null;
}if (host != null) {
if (host.length > 0 && ((host.charAt (0)).charCodeAt (0) == ('[').charCodeAt (0))) {
throw  new IllegalArgumentException ("Invalid host: " + host);
} else {
ind = host.indexOf (':');
port = -1;
if (ind >= 0) {
if (host.length > (ind + 1)) {
port = Integer.parseInt (host.substring (ind + 1));
}host = host.substring (0, ind);
}}} else {
host = "";
}if (port < -1) throw  new IllegalArgumentException ("Invalid port number :" + port);
start = i;
if (authority != null && authority.length > 0) path = "";
}if (host == null) {
host = "";
}if (start < limit) {
if ((spec.charAt (start)).charCodeAt (0) == ('/').charCodeAt (0)) {
path = spec.substring (start, limit);
} else if (path != null && path.length > 0) {
isRelPath = true;
var ind = path.lastIndexOf ('/');
var seperator = "";
if (ind == -1 && authority != null) seperator = "/";
path = path.substring (0, ind + 1) + seperator + spec.substring (start, limit);
} else {
var seperator = (authority != null) ? "/" : "";
path = seperator + spec.substring (start, limit);
}} else if (queryOnly && path != null) {
var ind = path.lastIndexOf ('/');
if (ind < 0) ind = 0;
path = path.substring (0, ind) + "/";
}if (path == null) path = "";
if (isRelPath) {
while ((i = path.indexOf ("/./")) >= 0) {
path = path.substring (0, i) + path.substring (i + 2);
}
i = 0;
while ((i = path.indexOf ("/../", i)) >= 0) {
if (i > 0 && (limit = path.lastIndexOf ('/', i - 1)) >= 0 && (path.indexOf ("/../", limit) != 0)) {
path = path.substring (0, limit) + path.substring (i + 3);
i = 0;
} else {
i = i + 3;
}}
while (path.endsWith ("/..")) {
i = path.indexOf ("/..");
if ((limit = path.lastIndexOf ('/', i - 1)) >= 0) {
path = path.substring (0, limit + 1);
} else {
break;
}}
if (path.startsWith ("./") && path.length > 2) path = path.substring (2);
if (path.endsWith ("/.")) path = path.substring (0, path.length - 1);
}this.setURL (u, protocol, host, port, authority, userInfo, path, query, ref);
}, "java.net.URL,~S,~N,~N");
$_M(c$, "getDefaultPort",
function () {
return -1;
});
$_M(c$, "equals",
function (u1, u2) {
var ref1 = u1.getRef ();
var ref2 = u2.getRef ();
return (ref1 === ref2 || (ref1 != null && ref1.equals (ref2))) && this.sameFile (u1, u2);
}, "java.net.URL,java.net.URL");
$_V(c$, "hashCode",
function (u) {
var h = 0;
var protocol = u.getProtocol ();
if (protocol != null) h += protocol.hashCode ();
h += u.toString ().hashCode ();
var file = u.getFile ();
if (file != null) h += file.hashCode ();
if (u.getPort () == -1) h += this.getDefaultPort ();
 else h += u.getPort ();
var ref = u.getRef ();
if (ref != null) h += ref.hashCode ();
return h;
}, "java.net.URL");
$_M(c$, "sameFile",
function (u1, u2) {
if (!((u1.getProtocol () === u2.getProtocol ()) || (u1.getProtocol () != null && u1.getProtocol ().equalsIgnoreCase (u2.getProtocol ())))) return false;
if (!(u1.getFile () === u2.getFile () || (u1.getFile () != null && u1.getFile ().equals (u2.getFile ())))) return false;
var port1;
var port2;
port1 = (u1.getPort () != -1) ? u1.getPort () : u1.handler.getDefaultPort ();
port2 = (u2.getPort () != -1) ? u2.getPort () : u2.handler.getDefaultPort ();
if (port1 != port2) return false;
if (!this.hostsEqual (u1, u2)) return false;
return true;
}, "java.net.URL,java.net.URL");
$_M(c$, "hostsEqual",
function (u1, u2) {
if (u1.getHost () != null && u2.getHost () != null) return u1.getHost ().equalsIgnoreCase (u2.getHost ());
 else return u1.getHost () == null && u2.getHost () == null;
}, "java.net.URL,java.net.URL");
$_M(c$, "toExternalForm",
function (u) {
var len = u.getProtocol ().length + 1;
if (u.getAuthority () != null && u.getAuthority ().length > 0) len += 2 + u.getAuthority ().length;
if (u.getPath () != null) {
len += u.getPath ().length;
}if (u.getQuery () != null) {
len += 1 + u.getQuery ().length;
}if (u.getRef () != null) len += 1 + u.getRef ().length;
var result =  new StringBuffer (len);
result.append (u.getProtocol ());
result.append (":");
if (u.getAuthority () != null && u.getAuthority ().length > 0) {
result.append ("//");
result.append (u.getAuthority ());
}if (u.getPath () != null) {
result.append (u.getPath ());
}if (u.getQuery () != null) {
result.append ('?');
result.append (u.getQuery ());
}if (u.getRef () != null) {
result.append ("#");
result.append (u.getRef ());
}return result.toString ();
}, "java.net.URL");
$_M(c$, "setURL",
function (u, protocol, host, port, authority, userInfo, path, query, ref) {
if (this !== u.handler) {
throw  new SecurityException ("handler for url different from this handler");
}u.set (u.getProtocol (), host, port, authority, userInfo, path, query, ref);
}, "java.net.URL,~S,~S,~N,~S,~S,~S,~S,~S");
$_M(c$, "setURL",
function (u, protocol, host, port, file, ref) {
var authority = null;
var userInfo = null;
if (host != null && host.length != 0) {
authority = (port == -1) ? host : host + ":" + port;
var at = host.lastIndexOf ('@');
if (at != -1) {
userInfo = host.substring (0, at);
host = host.substring (at + 1);
}}var path = null;
var query = null;
if (file != null) {
var q = file.lastIndexOf ('?');
if (q != -1) {
query = file.substring (q + 1);
path = file.substring (0, q);
} else path = file;
}this.setURL (u, protocol, host, port, authority, userInfo, path, query, ref);
}, "java.net.URL,~S,~S,~N,~S,~S");
});

Clazz_declarePackage ("java.net");
c$ = Clazz_decorateAsClass (function () {
this.path = null;
this.query = null;
this.ref = null;
Clazz_instantialize (this, arguments);
}, java.net, "Parts");

Clazz_makeConstructor (c$,
function (file) {
var ind = file.indexOf ('#');
this.ref = ind < 0 ? null : file.substring (ind + 1);
file = ind < 0 ? file : file.substring (0, ind);
var q = file.lastIndexOf ('?');
if (q != -1) {
this.query = file.substring (q + 1);
this.path = file.substring (0, q);
} else {
this.path = file;
}}, "~S");
$_M(c$, "getPath",
function () {
return this.path;
});
$_M(c$, "getQuery",
function () {
return this.query;
});
$_M(c$, "getRef",
function () {
return this.ref;
});
                   
Clazz_declarePackage ("java.net");
Clazz_load (["java.util.Hashtable"], "java.net.URL", ["java.io.IOException", "java.lang.Character", "$.Error", "java.net.MalformedURLException", "$.Parts"], function () {
c$ = Clazz_decorateAsClass (function () {
this.protocol = null;
this.host = null;
this.port = -1;
this.file = null;
this.query = null;
this.authority = null;
this.path = null;
this.userInfo = null;
this.ref = null;
this.handler = null;
this.$hashCode = -1;
Clazz_instantialize (this, arguments);
}, java.net, "URL", null, java.io.Serializable);
Clazz_makeConstructor (c$,
function (protocol, host, port, file) {
this.construct (protocol, host, port, file, null);
}, "~S,~S,~N,~S");
Clazz_makeConstructor (c$,
function (protocol, host, file) {
this.construct (protocol, host, -1, file);
}, "~S,~S,~S");
Clazz_makeConstructor (c$,
function (protocol, host, port, file, handler) {
if (handler != null) {
var sm = System.getSecurityManager ();
if (sm != null) {
this.checkSpecifyHandler (sm);
}}protocol = protocol.toLowerCase ();
this.protocol = protocol;
if (host != null) {
if (host.indexOf (':') >= 0 && !host.startsWith ("[")) {
host = "[" + host + "]";
}this.host = host;
if (port < -1) {
throw  new java.net.MalformedURLException ("Invalid port number :" + port);
}this.port = port;
this.authority = (port == -1) ? host : host + ":" + port;
}var parts =  new java.net.Parts (file);
this.path = parts.getPath ();
this.query = parts.getQuery ();
if (this.query != null) {
this.file = this.path + "?" + this.query;
} else {
this.file = this.path;
}this.ref = parts.getRef ();
if (handler == null && (handler = java.net.URL.getURLStreamHandler (protocol)) == null) {
throw  new java.net.MalformedURLException ("unknown protocol: " + protocol);
}this.handler = handler;
}, "~S,~S,~N,~S,java.net.URLStreamHandler");
Clazz_makeConstructor (c$,
function (spec) {
this.construct (null, spec);
}, "~S");
Clazz_makeConstructor (c$,
function (context, spec) {
this.construct (context, spec, null);
}, "java.net.URL,~S");
Clazz_makeConstructor (c$,
function (context, spec, handler) {
var original = spec;
var i;
var limit;
var c;
var start = 0;
var newProtocol = null;
var aRef = false;
var isRelative = false;
if (handler != null) {
var sm = System.getSecurityManager ();
if (sm != null) {
this.checkSpecifyHandler (sm);
}}try {
limit = spec.length;
while ((limit > 0) && ((spec.charAt (limit - 1)).charCodeAt (0) <= (' ').charCodeAt (0))) {
limit--;
}
while ((start < limit) && ((spec.charAt (start)).charCodeAt (0) <= (' ').charCodeAt (0))) {
start++;
}
if (spec.regionMatches (true, start, "url:", 0, 4)) {
start += 4;
}if (start < spec.length && (spec.charAt (start)).charCodeAt (0) == ('#').charCodeAt (0)) {
aRef = true;
}for (i = start; !aRef && (i < limit) && ((c = (spec.charAt (i)).charCodeAt (0)) != ('/').charCodeAt (0)); i++) {
if (c == (':').charCodeAt (0)) {
var s = spec.substring (start, i).toLowerCase ();
if (this.isValidProtocol (s)) {
newProtocol = s;
start = i + 1;
}break;
}}
this.protocol = newProtocol;
if ((context != null) && ((newProtocol == null) || newProtocol.equalsIgnoreCase (context.protocol))) {
if (handler == null) {
handler = context.handler;
}if (context.path != null && context.path.startsWith ("/")) newProtocol = null;
if (newProtocol == null) {
this.protocol = context.protocol;
this.authority = context.authority;
this.userInfo = context.userInfo;
this.host = context.host;
this.port = context.port;
this.file = context.file;
this.path = context.path;
isRelative = true;
}}if (this.protocol == null) {
throw  new java.net.MalformedURLException ("no protocol: " + original);
}if (handler == null && (handler = java.net.URL.getURLStreamHandler (this.protocol)) == null) {
throw  new java.net.MalformedURLException ("unknown protocol: " + this.protocol);
}this.handler = handler;
i = spec.indexOf ('#', start);
if (i >= 0) {
this.ref = spec.substring (i + 1, limit);
limit = i;
}if (isRelative && start == limit) {
this.query = context.query;
if (this.ref == null) {
this.ref = context.ref;
}}
//Clazz_alert(["corz URL ", handler])
handler.parseURL (this, spec, start, limit);
} catch (e$$) {
if (Clazz_instanceOf (e$$, java.net.MalformedURLException)) {
var e = e$$;
{
throw e;
}
} else if (Clazz_instanceOf (e$$, Exception)) {
var e = e$$;
{
var exception =  new java.net.MalformedURLException (e.getMessage ());
exception.initCause (e);
throw exception;
}
} else {
throw e$$;
}
}
}, "java.net.URL,~S,java.net.URLStreamHandler");
$_M(c$, "isValidProtocol",
function (protocol) {
var len = protocol.length;
if (len < 1) return false;
var c = protocol.charAt (0);
if (!Character.isLetter (c)) return false;
for (var i = 1; i < len; i++) {
c = protocol.charAt (i);
if (!Character.isLetterOrDigit (c) && (c).charCodeAt (0) != ('.').charCodeAt (0) && (c).charCodeAt (0) != ('+').charCodeAt (0) && (c).charCodeAt (0) != ('-').charCodeAt (0)) {
return false;
}}
return true;
}, "~S");
$_M(c$, "checkSpecifyHandler",
function (sm) {
}, "SecurityManager");
$_M(c$, "set",
function (protocol, host, port, file, ref) {
{
this.protocol = protocol;
this.host = host;
this.authority = port == -1 ? host : host + ":" + port;
this.port = port;
this.file = file;
this.ref = ref;
this.$hashCode = -1;
var q = file.lastIndexOf ('?');
if (q != -1) {
this.query = file.substring (q + 1);
this.path = file.substring (0, q);
} else this.path = file;
}}, "~S,~S,~N,~S,~S");
$_M(c$, "set",
function (protocol, host, port, authority, userInfo, path, query, ref) {
{
this.protocol = protocol;
this.host = host;
this.port = port;
this.file = query == null ? path : path + "?" + query;
this.userInfo = userInfo;
this.path = path;
this.ref = ref;
this.$hashCode = -1;
this.query = query;
this.authority = authority;
}}, "~S,~S,~N,~S,~S,~S,~S,~S");
$_M(c$, "getQuery",
function () {
return this.query;
});
$_M(c$, "getPath",
function () {
return this.path;
});
$_M(c$, "getUserInfo",
function () {
return this.userInfo;
});
$_M(c$, "getAuthority",
function () {
return this.authority;
});
$_M(c$, "getPort",
function () {
return this.port;
});
$_M(c$, "getDefaultPort",
function () {
return this.handler.getDefaultPort ();
});
$_M(c$, "getProtocol",
function () {
return this.protocol;
});
$_M(c$, "getHost",
function () {
return this.host;
});
$_M(c$, "getFile",
function () {
return this.file;
});
$_M(c$, "getRef",
function () {
return this.ref;
});
$_V (c$, "equals",
function (obj) {
if (!(Clazz_instanceOf (obj, java.net.URL))) return false;
var u2 = obj;
return this.handler.equals (this, u2);
}, "~O");
$_V (c$, "hashCode",
function () {
if (this.$hashCode != -1) return this.$hashCode;
this.$hashCode = this.handler.hashCode (this);
return this.$hashCode;
});
$_M(c$, "sameFile",
function (other) {
return this.handler.sameFile (this, other);
}, "java.net.URL");
$_V (c$, "toString",
function () {
return this.toExternalForm ();
});
$_M(c$, "toExternalForm",
function () {
return this.handler.toExternalForm (this);
});
$_M(c$, "openConnection",
function () {
return this.handler.openConnection (this);
});
$_M(c$, "openStream",
function () {
return this.openConnection ().getInputStream ();
});
$_M(c$, "getContent",
function () {
return this.openConnection ().getContent ();
});
$_M(c$, "getContent",
function (classes) {
return this.openConnection ().getContent (classes);
}, "~A");
c$.setURLStreamHandlerFactory = $_M(c$, "setURLStreamHandlerFactory",
function (fac) {
{
if (java.net.URL.factory != null) {
throw  new Error ("factory already defined");
}var security = System.getSecurityManager ();
if (security != null) {
security.checkSetFactory ();
}java.net.URL.handlers.clear ();
($t$ = java.net.URL.factory = fac, java.net.URL.prototype.factory = java.net.URL.factory, $t$);
}}, "java.net.URLStreamHandlerFactory");
c$.getURLStreamHandler = $_M(c$, "getURLStreamHandler",
function (protocol) {
var handler = java.net.URL.handlers.get (protocol);
if (handler == null) {
if (java.net.URL.factory != null) {
handler = java.net.URL.factory.createURLStreamHandler (protocol);
}}return handler;
}, "~S");
Clazz_defineStatics (c$,
"factory", null);
c$.handlers = c$.prototype.handlers =  new java.util.Hashtable ();
c$.streamHandlerLock = c$.prototype.streamHandlerLock =  new JavaObject ();
});

*/

;(function() {

if (Jmol.debugCode)return;

Clazz_declarePackage ("JU");
Clazz_load (null, "JU.T3", ["java.lang.Float"], function () {
c$ = Clazz_decorateAsClass (function () {
this.x = 0;
this.y = 0;
this.z = 0;
Clazz_instantialize (this, arguments);
}, JU, "T3", null, java.io.Serializable);
Clazz_makeConstructor (c$, 
function () {
});
$_M(c$, "set", 
function (x, y, z) {
this.x = x;
this.y = y;
this.z = z;
}, "~N,~N,~N");
$_M(c$, "setA", 
function (t) {
this.x = t[0];
this.y = t[1];
this.z = t[2];
}, "~A");
$_M(c$, "setT", 
function (t1) {
this.x = t1.x;
this.y = t1.y;
this.z = t1.z;
}, "JU.T3");
$_M(c$, "add2", 
function (t1, t2) {
this.x = t1.x + t2.x;
this.y = t1.y + t2.y;
this.z = t1.z + t2.z;
}, "JU.T3,JU.T3");
$_M(c$, "add", 
function (t1) {
this.x += t1.x;
this.y += t1.y;
this.z += t1.z;
}, "JU.T3");
$_M(c$, "sub2", 
function (t1, t2) {
this.x = t1.x - t2.x;
this.y = t1.y - t2.y;
this.z = t1.z - t2.z;
}, "JU.T3,JU.T3");
$_M(c$, "sub", 
function (t1) {
this.x -= t1.x;
this.y -= t1.y;
this.z -= t1.z;
}, "JU.T3");
$_M(c$, "scale", 
function (s) {
this.x *= s;
this.y *= s;
this.z *= s;
}, "~N");
$_M(c$, "scaleAdd2", 
function (s, t1, t2) {
this.x = s * t1.x + t2.x;
this.y = s * t1.y + t2.y;
this.z = s * t1.z + t2.z;
}, "~N,JU.T3,JU.T3");
$_M(c$, "scaleAdd", 
function (s, t1) {
this.x = s * this.x + t1.x;
this.y = s * this.y + t1.y;
this.z = s * this.z + t1.z;
}, "~N,JU.T3");
$_M(c$, "dot", 
function (v) {
return this.x * v.x + this.y * v.y + this.z * v.z;
}, "JU.T3");
$_M(c$, "lengthSquared", 
function () {
return this.x * this.x + this.y * this.y + this.z * this.z;
});
$_M(c$, "length", 
function () {
return Math.sqrt (this.lengthSquared ());
});
$_M(c$, "normalize", 
function () {
var d = this.length ();
this.x /= d;
this.y /= d;
this.z /= d;
});
$_V(c$, "hashCode", 
function () {
var bits = 1;
bits = 31 * bits + JU.T3.floatToIntBits0 (this.x);
bits = 31 * bits + JU.T3.floatToIntBits0 (this.y);
bits = 31 * bits + JU.T3.floatToIntBits0 (this.z);
return (bits ^ (bits >> 32));
});
c$.floatToIntBits0 = $_M(c$, "floatToIntBits0", 
function (f) {
return (f == 0 ? 0 : Float.floatToIntBits (f));
}, "~N");
$_V(c$, "equals", 
function (t1) {
if (!(Clazz_instanceOf (t1, JU.T3))) return false;
var t2 = t1;
return (this.x == t2.x && this.y == t2.y && this.z == t2.z);
}, "~O");
$_V(c$, "toString", 
function () {
return "(" + this.x + ", " + this.y + ", " + this.z + ")";
});
});
Clazz_declarePackage ("JU");
c$ = Clazz_decorateAsClass (function () {
this.x = 0;
this.y = 0;
this.z = 0;
Clazz_instantialize (this, arguments);
}, JU, "T3i", null, java.io.Serializable);
Clazz_makeConstructor (c$, 
function () {
});
$_M(c$, "set", 
function (x, y, z) {
this.x = x;
this.y = y;
this.z = z;
}, "~N,~N,~N");
$_M(c$, "setT", 
function (t1) {
this.x = t1.x;
this.y = t1.y;
this.z = t1.z;
}, "JU.T3i");
$_M(c$, "add", 
function (t) {
this.x += t.x;
this.y += t.y;
this.z += t.z;
}, "JU.T3i");
$_M(c$, "scaleAdd", 
function (s, t1, t2) {
this.x = s * t1.x + t2.x;
this.y = s * t1.y + t2.y;
this.z = s * t1.z + t2.z;
}, "~N,JU.T3i,JU.T3i");
$_V(c$, "hashCode", 
function () {
return this.x ^ this.y ^ this.z;
});
$_V(c$, "equals", 
function (o) {
if (!(Clazz_instanceOf (o, JU.T3i))) return false;
var t = o;
return (this.x == t.x && this.y == t.y && this.z == t.z);
}, "~O");
$_V(c$, "toString", 
function () {
return "(" + this.x + ", " + this.y + ", " + this.z + ")";
});
Clazz_declarePackage ("JU");
Clazz_load (null, "JU.T3d", ["java.lang.Double"], function () {
c$ = Clazz_decorateAsClass (function () {
this.x = 0;
this.y = 0;
this.z = 0;
Clazz_instantialize (this, arguments);
}, JU, "T3d", null, java.io.Serializable);
Clazz_makeConstructor (c$, 
function () {
});
$_M(c$, "set", 
function (x, y, z) {
this.x = x;
this.y = y;
this.z = z;
}, "~N,~N,~N");
$_M(c$, "setA", 
function (t) {
this.x = t[0];
this.y = t[1];
this.z = t[2];
}, "~A");
$_M(c$, "setT", 
function (t1) {
this.x = t1.x;
this.y = t1.y;
this.z = t1.z;
}, "JU.T3d");
$_M(c$, "add2", 
function (t1, t2) {
this.x = t1.x + t2.x;
this.y = t1.y + t2.y;
this.z = t1.z + t2.z;
}, "JU.T3d,JU.T3d");
$_M(c$, "add", 
function (t1) {
this.x += t1.x;
this.y += t1.y;
this.z += t1.z;
}, "JU.T3d");
$_M(c$, "sub2", 
function (t1, t2) {
this.x = t1.x - t2.x;
this.y = t1.y - t2.y;
this.z = t1.z - t2.z;
}, "JU.T3d,JU.T3d");
$_M(c$, "sub", 
function (t1) {
this.x -= t1.x;
this.y -= t1.y;
this.z -= t1.z;
}, "JU.T3d");
$_M(c$, "scale", 
function (s) {
this.x *= s;
this.y *= s;
this.z *= s;
}, "~N");
$_M(c$, "scaleAdd", 
function (s, t1, t2) {
this.x = s * t1.x + t2.x;
this.y = s * t1.y + t2.y;
this.z = s * t1.z + t2.z;
}, "~N,JU.T3d,JU.T3d");
$_V(c$, "hashCode", 
function () {
var xbits = JU.T3d.doubleToLongBits0 (this.x);
var ybits = JU.T3d.doubleToLongBits0 (this.y);
var zbits = JU.T3d.doubleToLongBits0 (this.z);
return (xbits ^ (xbits >> 32) ^ ybits ^ (ybits >> 32) ^ zbits ^ (zbits >> 32));
});
c$.doubleToLongBits0 = $_M(c$, "doubleToLongBits0", 
function (d) {
return (d == 0 ? 0 : Double.doubleToLongBits (d));
}, "~N");
$_V(c$, "equals", 
function (t1) {
if (!(Clazz_instanceOf (t1, JU.T3d))) return false;
var t2 = t1;
return (this.x == t2.x && this.y == t2.y && this.z == t2.z);
}, "~O");
$_V(c$, "toString", 
function () {
return "(" + this.x + ", " + this.y + ", " + this.z + ")";
});
});
Clazz_declarePackage ("JU");
Clazz_load (["JU.T3"], "JU.P3", null, function () {
c$ = Clazz_declareType (JU, "P3", JU.T3);
c$.newP = $_M(c$, "newP", 
function (t) {
var p =  new JU.P3 ();
p.x = t.x;
p.y = t.y;
p.z = t.z;
return p;
}, "JU.T3");
c$.new3 = $_M(c$, "new3", 
function (x, y, z) {
var p =  new JU.P3 ();
p.x = x;
p.y = y;
p.z = z;
return p;
}, "~N,~N,~N");
$_M(c$, "distanceSquared", 
function (p1) {
var dx = this.x - p1.x;
var dy = this.y - p1.y;
var dz = this.z - p1.z;
return (dx * dx + dy * dy + dz * dz);
}, "JU.T3");
$_M(c$, "distance", 
function (p1) {
return Math.sqrt (this.distanceSquared (p1));
}, "JU.T3");
});
Clazz_declarePackage ("JU");
Clazz_load (["JU.T3i"], "JU.P3i", null, function () {
c$ = Clazz_declareType (JU, "P3i", JU.T3i);
c$.new3 = $_M(c$, "new3", 
function (x, y, z) {
var pt =  new JU.P3i ();
pt.x = x;
pt.y = y;
pt.z = z;
return pt;
}, "~N,~N,~N");
});
Clazz_declarePackage ("JU");
Clazz_load (["JU.T3"], "JU.V3", null, function () {
c$ = Clazz_declareType (JU, "V3", JU.T3);
c$.newV = $_M(c$, "newV", 
function (t) {
return JU.V3.new3 (t.x, t.y, t.z);
}, "JU.T3");
c$.newVsub = $_M(c$, "newVsub", 
function (t1, t2) {
return JU.V3.new3 (t1.x - t2.x, t1.y - t2.y, t1.z - t2.z);
}, "JU.T3,JU.T3");
c$.new3 = $_M(c$, "new3", 
function (x, y, z) {
var v =  new JU.V3 ();
v.x = x;
v.y = y;
v.z = z;
return v;
}, "~N,~N,~N");
$_M(c$, "cross", 
function (v1, v2) {
this.set (v1.y * v2.z - v1.z * v2.y, v1.z * v2.x - v1.x * v2.z, v1.x * v2.y - v1.y * v2.x);
}, "JU.V3,JU.V3");
$_M(c$, "angle", 
function (v1) {
var xx = this.y * v1.z - this.z * v1.y;
var yy = this.z * v1.x - this.x * v1.z;
var zz = this.x * v1.y - this.y * v1.x;
var cross = Math.sqrt (xx * xx + yy * yy + zz * zz);
return Math.abs (Math.atan2 (cross, this.dot (v1)));
}, "JU.V3");
});
Clazz_declarePackage ("JU");
Clazz_load (["JU.T3d"], "JU.V3d", null, function () {
c$ = Clazz_declareType (JU, "V3d", JU.T3d);
$_M(c$, "cross", 
function (v1, v2) {
this.set (v1.y * v2.z - v1.z * v2.y, v1.z * v2.x - v1.x * v2.z, v1.x * v2.y - v1.y * v2.x);
}, "JU.V3d,JU.V3d");
$_M(c$, "normalize", 
function () {
var d = this.length ();
this.x /= d;
this.y /= d;
this.z /= d;
});
$_M(c$, "dot", 
function (v) {
return this.x * v.x + this.y * v.y + this.z * v.z;
}, "JU.V3d");
$_M(c$, "lengthSquared", 
function () {
return this.x * this.x + this.y * this.y + this.z * this.z;
});
$_M(c$, "length", 
function () {
return Math.sqrt (this.lengthSquared ());
});
});
Clazz_declarePackage ("JU");
Clazz_load (null, "JU.M3", ["java.lang.ArrayIndexOutOfBoundsException", "JU.T3"], function () {
c$ = Clazz_decorateAsClass (function () {
this.m00 = 0;
this.m01 = 0;
this.m02 = 0;
this.m10 = 0;
this.m11 = 0;
this.m12 = 0;
this.m20 = 0;
this.m21 = 0;
this.m22 = 0;
Clazz_instantialize (this, arguments);
}, JU, "M3", null, java.io.Serializable);
Clazz_makeConstructor (c$, 
function () {
});
c$.newA = $_M(c$, "newA", 
function (v) {
var m =  new JU.M3 ();
m.setA (v);
return m;
}, "~A");
c$.newM = $_M(c$, "newM", 
function (m1) {
var m =  new JU.M3 ();
m.m00 = m1.m00;
m.m01 = m1.m01;
m.m02 = m1.m02;
m.m10 = m1.m10;
m.m11 = m1.m11;
m.m12 = m1.m12;
m.m20 = m1.m20;
m.m21 = m1.m21;
m.m22 = m1.m22;
return m;
}, "JU.M3");
$_V(c$, "toString", 
function () {
return "[\n  [" + this.m00 + "\t" + this.m01 + "\t" + this.m02 + "]" + "\n  [" + this.m10 + "\t" + this.m11 + "\t" + this.m12 + "]" + "\n  [" + this.m20 + "\t" + this.m21 + "\t" + this.m22 + "] ]";
});
$_M(c$, "setIdentity", 
function () {
this.m00 = 1.0;
this.m01 = 0.0;
this.m02 = 0.0;
this.m10 = 0.0;
this.m11 = 1.0;
this.m12 = 0.0;
this.m20 = 0.0;
this.m21 = 0.0;
this.m22 = 1.0;
});
$_M(c$, "setElement", 
function (row, column, value) {
if (row == 0) if (column == 0) this.m00 = value;
 else if (column == 1) this.m01 = value;
 else if (column == 2) this.m02 = value;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 2 and is " + column);
 else if (row == 1) if (column == 0) this.m10 = value;
 else if (column == 1) this.m11 = value;
 else if (column == 2) this.m12 = value;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 2 and is " + column);
 else if (row == 2) if (column == 0) this.m20 = value;
 else if (column == 1) this.m21 = value;
 else if (column == 2) this.m22 = value;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 2 and is " + column);
 else throw  new ArrayIndexOutOfBoundsException ("row must be 0 to 2 and is " + row);
}, "~N,~N,~N");
$_M(c$, "getElement", 
function (row, column) {
if (row == 0) if (column == 0) return this.m00;
 else if (column == 1) return this.m01;
 else if (column == 2) return this.m02;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 2 and is " + column);
 else if (row == 1) if (column == 0) return this.m10;
 else if (column == 1) return this.m11;
 else if (column == 2) return this.m12;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 2 and is " + column);
 else if (row == 2) if (column == 0) return this.m20;
 else if (column == 1) return this.m21;
 else if (column == 2) return this.m22;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 2 and is " + column);
 else throw  new ArrayIndexOutOfBoundsException ("row must be 0 to 2 and is " + row);
}, "~N,~N");
$_M(c$, "setRow", 
function (row, x, y, z) {
if (row == 0) {
this.m00 = x;
this.m01 = y;
this.m02 = z;
} else if (row == 1) {
this.m10 = x;
this.m11 = y;
this.m12 = z;
} else if (row == 2) {
this.m20 = x;
this.m21 = y;
this.m22 = z;
} else {
throw  new ArrayIndexOutOfBoundsException ("row must be 0 to 2 and is " + row);
}}, "~N,~N,~N,~N");
$_M(c$, "setRowV", 
function (row, v) {
if (row == 0) {
this.m00 = v.x;
this.m01 = v.y;
this.m02 = v.z;
} else if (row == 1) {
this.m10 = v.x;
this.m11 = v.y;
this.m12 = v.z;
} else if (row == 2) {
this.m20 = v.x;
this.m21 = v.y;
this.m22 = v.z;
} else {
throw  new ArrayIndexOutOfBoundsException ("row must be 0 to 2 and is " + row);
}}, "~N,JU.T3");
$_M(c$, "getRow", 
function (row, v) {
if (row == 0) {
v[0] = this.m00;
v[1] = this.m01;
v[2] = this.m02;
} else if (row == 1) {
v[0] = this.m10;
v[1] = this.m11;
v[2] = this.m12;
} else if (row == 2) {
v[0] = this.m20;
v[1] = this.m21;
v[2] = this.m22;
} else {
throw  new ArrayIndexOutOfBoundsException ("row must be 0 to 2 and is " + row);
}}, "~N,~A");
$_M(c$, "setRowA", 
function (row, v) {
if (row == 0) {
this.m00 = v[0];
this.m01 = v[1];
this.m02 = v[2];
} else if (row == 1) {
this.m10 = v[0];
this.m11 = v[1];
this.m12 = v[2];
} else if (row == 2) {
this.m20 = v[0];
this.m21 = v[1];
this.m22 = v[2];
} else {
throw  new ArrayIndexOutOfBoundsException ("row must be 0 to 2 and is " + row);
}}, "~N,~A");
$_M(c$, "setColumn", 
function (column, x, y, z) {
if (column == 0) {
this.m00 = x;
this.m10 = y;
this.m20 = z;
} else if (column == 1) {
this.m01 = x;
this.m11 = y;
this.m21 = z;
} else if (column == 2) {
this.m02 = x;
this.m12 = y;
this.m22 = z;
} else {
throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 2 and is " + column);
}}, "~N,~N,~N,~N");
$_M(c$, "setColumnV", 
function (column, v) {
if (column == 0) {
this.m00 = v.x;
this.m10 = v.y;
this.m20 = v.z;
} else if (column == 1) {
this.m01 = v.x;
this.m11 = v.y;
this.m21 = v.z;
} else if (column == 2) {
this.m02 = v.x;
this.m12 = v.y;
this.m22 = v.z;
} else {
throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 2 and is " + column);
}}, "~N,JU.V3");
$_M(c$, "setColumnA", 
function (column, v) {
if (column == 0) {
this.m00 = v[0];
this.m10 = v[1];
this.m20 = v[2];
} else if (column == 1) {
this.m01 = v[0];
this.m11 = v[1];
this.m21 = v[2];
} else if (column == 2) {
this.m02 = v[0];
this.m12 = v[1];
this.m22 = v[2];
} else {
throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 2 and is " + column);
}}, "~N,~A");
$_M(c$, "getColumnV", 
function (column, v) {
if (column == 0) {
v.x = this.m00;
v.y = this.m10;
v.z = this.m20;
} else if (column == 1) {
v.x = this.m01;
v.y = this.m11;
v.z = this.m21;
} else if (column == 2) {
v.x = this.m02;
v.y = this.m12;
v.z = this.m22;
} else {
throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 2 and is " + column);
}}, "~N,JU.V3");
$_M(c$, "getColumn", 
function (column, v) {
if (column == 0) {
v[0] = this.m00;
v[1] = this.m10;
v[2] = this.m20;
} else if (column == 1) {
v[0] = this.m01;
v[1] = this.m11;
v[2] = this.m21;
} else if (column == 2) {
v[0] = this.m02;
v[1] = this.m12;
v[2] = this.m22;
} else {
throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 2 and is " + column);
}}, "~N,~A");
$_M(c$, "add", 
function (m1) {
this.m00 += m1.m00;
this.m01 += m1.m01;
this.m02 += m1.m02;
this.m10 += m1.m10;
this.m11 += m1.m11;
this.m12 += m1.m12;
this.m20 += m1.m20;
this.m21 += m1.m21;
this.m22 += m1.m22;
}, "JU.M3");
$_M(c$, "sub", 
function (m1) {
this.m00 -= m1.m00;
this.m01 -= m1.m01;
this.m02 -= m1.m02;
this.m10 -= m1.m10;
this.m11 -= m1.m11;
this.m12 -= m1.m12;
this.m20 -= m1.m20;
this.m21 -= m1.m21;
this.m22 -= m1.m22;
}, "JU.M3");
$_M(c$, "transpose", 
function () {
var tmp = this.m01;
this.m01 = this.m10;
this.m10 = tmp;
tmp = this.m02;
this.m02 = this.m20;
this.m20 = tmp;
tmp = this.m12;
this.m12 = this.m21;
this.m21 = tmp;
});
$_M(c$, "transposeM", 
function (m1) {
this.setM (m1);
this.transpose ();
}, "JU.M3");
$_M(c$, "setAA", 
function (a1) {
this.setFromAxisAngle (a1.x, a1.y, a1.z, a1.angle);
}, "JU.A4");
$_M(c$, "setFromAxisAngle", 
function (x, y, z, angle) {
var n = Math.sqrt (x * x + y * y + z * z);
n = 1 / n;
x *= n;
y *= n;
z *= n;
var c = Math.cos (angle);
var s = Math.sin (angle);
var omc = 1.0 - c;
this.m00 = (c + x * x * omc);
this.m11 = (c + y * y * omc);
this.m22 = (c + z * z * omc);
var tmp1 = x * y * omc;
var tmp2 = z * s;
this.m01 = (tmp1 - tmp2);
this.m10 = (tmp1 + tmp2);
tmp1 = x * z * omc;
tmp2 = y * s;
this.m02 = (tmp1 + tmp2);
this.m20 = (tmp1 - tmp2);
tmp1 = y * z * omc;
tmp2 = x * s;
this.m12 = (tmp1 - tmp2);
this.m21 = (tmp1 + tmp2);
}, "~N,~N,~N,~N");
$_M(c$, "setM", 
function (m1) {
this.m00 = m1.m00;
this.m01 = m1.m01;
this.m02 = m1.m02;
this.m10 = m1.m10;
this.m11 = m1.m11;
this.m12 = m1.m12;
this.m20 = m1.m20;
this.m21 = m1.m21;
this.m22 = m1.m22;
}, "JU.M3");
$_M(c$, "setA", 
function (m) {
this.m00 = m[0];
this.m01 = m[1];
this.m02 = m[2];
this.m10 = m[3];
this.m11 = m[4];
this.m12 = m[5];
this.m20 = m[6];
this.m21 = m[7];
this.m22 = m[8];
}, "~A");
$_M(c$, "invertM", 
function (m1) {
this.setM (m1);
this.invert ();
}, "JU.M3");
$_M(c$, "invert", 
function () {
var s = this.determinant ();
if (s == 0.0) return;
s = 1 / s;
this.set (this.m11 * this.m22 - this.m12 * this.m21, this.m02 * this.m21 - this.m01 * this.m22, this.m01 * this.m12 - this.m02 * this.m11, this.m12 * this.m20 - this.m10 * this.m22, this.m00 * this.m22 - this.m02 * this.m20, this.m02 * this.m10 - this.m00 * this.m12, this.m10 * this.m21 - this.m11 * this.m20, this.m01 * this.m20 - this.m00 * this.m21, this.m00 * this.m11 - this.m01 * this.m10);
this.mulf (s);
});
$_M(c$, "determinant", 
function () {
return this.m00 * (this.m11 * this.m22 - this.m21 * this.m12) - this.m01 * (this.m10 * this.m22 - this.m20 * this.m12) + this.m02 * (this.m10 * this.m21 - this.m20 * this.m11);
});
$_M(c$, "setScale", 
function (scale) {
this.m00 = scale;
this.m01 = 0.0;
this.m02 = 0.0;
this.m10 = 0.0;
this.m11 = scale;
this.m12 = 0.0;
this.m20 = 0.0;
this.m21 = 0.0;
this.m22 = scale;
}, "~N");
$_M(c$, "rotX", 
function (angle) {
var c = Math.cos (angle);
var s = Math.sin (angle);
this.m00 = 1.0;
this.m01 = 0.0;
this.m02 = 0.0;
this.m10 = 0.0;
this.m11 = c;
this.m12 = -s;
this.m20 = 0.0;
this.m21 = s;
this.m22 = c;
}, "~N");
$_M(c$, "rotY", 
function (angle) {
var c = Math.cos (angle);
var s = Math.sin (angle);
this.m00 = c;
this.m01 = 0.0;
this.m02 = s;
this.m10 = 0.0;
this.m11 = 1.0;
this.m12 = 0.0;
this.m20 = -s;
this.m21 = 0.0;
this.m22 = c;
}, "~N");
$_M(c$, "rotZ", 
function (angle) {
var c = Math.cos (angle);
var s = Math.sin (angle);
this.m00 = c;
this.m01 = -s;
this.m02 = 0.0;
this.m10 = s;
this.m11 = c;
this.m12 = 0.0;
this.m20 = 0.0;
this.m21 = 0.0;
this.m22 = 1.0;
}, "~N");
$_M(c$, "mulf", 
function (scalar) {
this.m00 *= scalar;
this.m01 *= scalar;
this.m02 *= scalar;
this.m10 *= scalar;
this.m11 *= scalar;
this.m12 *= scalar;
this.m20 *= scalar;
this.m21 *= scalar;
this.m22 *= scalar;
}, "~N");
$_M(c$, "mul", 
function (m1) {
this.mul2 (this, m1);
}, "JU.M3");
$_M(c$, "mul2", 
function (m1, m2) {
this.set (m1.m00 * m2.m00 + m1.m01 * m2.m10 + m1.m02 * m2.m20, m1.m00 * m2.m01 + m1.m01 * m2.m11 + m1.m02 * m2.m21, m1.m00 * m2.m02 + m1.m01 * m2.m12 + m1.m02 * m2.m22, m1.m10 * m2.m00 + m1.m11 * m2.m10 + m1.m12 * m2.m20, m1.m10 * m2.m01 + m1.m11 * m2.m11 + m1.m12 * m2.m21, m1.m10 * m2.m02 + m1.m11 * m2.m12 + m1.m12 * m2.m22, m1.m20 * m2.m00 + m1.m21 * m2.m10 + m1.m22 * m2.m20, m1.m20 * m2.m01 + m1.m21 * m2.m11 + m1.m22 * m2.m21, m1.m20 * m2.m02 + m1.m21 * m2.m12 + m1.m22 * m2.m22);
}, "JU.M3,JU.M3");
$_V(c$, "equals", 
function (o) {
if (!(Clazz_instanceOf (o, JU.M3))) return false;
var m = o;
return this.m00 == m.m00 && this.m01 == m.m01 && this.m02 == m.m02 && this.m10 == m.m10 && this.m11 == m.m11 && this.m12 == m.m12 && this.m20 == m.m20 && this.m21 == m.m21 && this.m22 == m.m22;
}, "~O");
$_V(c$, "hashCode", 
function () {
return JU.T3.floatToIntBits0 (this.m00) ^ JU.T3.floatToIntBits0 (this.m01) ^ JU.T3.floatToIntBits0 (this.m02) ^ JU.T3.floatToIntBits0 (this.m10) ^ JU.T3.floatToIntBits0 (this.m11) ^ JU.T3.floatToIntBits0 (this.m12) ^ JU.T3.floatToIntBits0 (this.m20) ^ JU.T3.floatToIntBits0 (this.m21) ^ JU.T3.floatToIntBits0 (this.m22);
});
$_M(c$, "setZero", 
function () {
this.m00 = 0.0;
this.m01 = 0.0;
this.m02 = 0.0;
this.m10 = 0.0;
this.m11 = 0.0;
this.m12 = 0.0;
this.m20 = 0.0;
this.m21 = 0.0;
this.m22 = 0.0;
});
$_M(c$, "transform", 
function (t) {
this.transform2 (t, t);
}, "JU.T3");
$_M(c$, "transform2", 
function (t, result) {
result.set (this.m00 * t.x + this.m01 * t.y + this.m02 * t.z, this.m10 * t.x + this.m11 * t.y + this.m12 * t.z, this.m20 * t.x + this.m21 * t.y + this.m22 * t.z);
}, "JU.T3,JU.T3");
$_M(c$, "set", 
function (m00, m01, m02, m10, m11, m12, m20, m21, m22) {
this.m00 = m00;
this.m01 = m01;
this.m02 = m02;
this.m10 = m10;
this.m11 = m11;
this.m12 = m12;
this.m20 = m20;
this.m21 = m21;
this.m22 = m22;
}, "~N,~N,~N,~N,~N,~N,~N,~N,~N");
});
Clazz_declarePackage ("JU");
Clazz_load (null, "JU.T4", ["JU.T3"], function () {
c$ = Clazz_decorateAsClass (function () {
this.x = 0;
this.y = 0;
this.z = 0;
this.w = 0;
Clazz_instantialize (this, arguments);
}, JU, "T4", null, java.io.Serializable);
Clazz_makeConstructor (c$, 
function () {
});
$_M(c$, "set", 
function (x, y, z, w) {
this.x = x;
this.y = y;
this.z = z;
this.w = w;
}, "~N,~N,~N,~N");
$_M(c$, "scale", 
function (s) {
this.x *= s;
this.y *= s;
this.z *= s;
this.w *= s;
}, "~N");
$_V(c$, "hashCode", 
function () {
return JU.T3.floatToIntBits0 (this.x) ^ JU.T3.floatToIntBits0 (this.y) ^ JU.T3.floatToIntBits0 (this.z) ^ JU.T3.floatToIntBits0 (this.w);
});
$_V(c$, "equals", 
function (o) {
if (!(Clazz_instanceOf (o, JU.T4))) return false;
var t = o;
return (this.x == t.x && this.y == t.y && this.z == t.z && this.w == t.w);
}, "~O");
$_V(c$, "toString", 
function () {
return "(" + this.x + ", " + this.y + ", " + this.z + ", " + this.w + ")";
});
});
Clazz_declarePackage ("JU");
Clazz_load (["JU.T4"], "JU.P4", null, function () {
c$ = Clazz_declareType (JU, "P4", JU.T4);
c$.new4 = $_M(c$, "new4", 
function (x, y, z, w) {
var pt =  new JU.P4 ();
pt.set (x, y, z, w);
return pt;
}, "~N,~N,~N,~N");
c$.newPt = $_M(c$, "newPt", 
function (value) {
var pt =  new JU.P4 ();
pt.set (value.x, value.y, value.z, value.w);
return pt;
}, "JU.P4");
$_M(c$, "distance", 
function (p1) {
var dx = this.x - p1.x;
var dy = this.y - p1.y;
var dz = this.z - p1.z;
var dw = this.w - p1.w;
return Math.sqrt (dx * dx + dy * dy + dz * dz + dw * dw);
}, "JU.P4");
});
Clazz_declarePackage ("JU");
Clazz_load (null, "JU.M4", ["java.lang.ArrayIndexOutOfBoundsException", "JU.T3"], function () {
c$ = Clazz_decorateAsClass (function () {
this.m00 = 0;
this.m01 = 0;
this.m02 = 0;
this.m03 = 0;
this.m10 = 0;
this.m11 = 0;
this.m12 = 0;
this.m13 = 0;
this.m20 = 0;
this.m21 = 0;
this.m22 = 0;
this.m23 = 0;
this.m30 = 0;
this.m31 = 0;
this.m32 = 0;
this.m33 = 0;
Clazz_instantialize (this, arguments);
}, JU, "M4", null, java.io.Serializable);
c$.newA = $_M(c$, "newA", 
function (v) {
var m =  new JU.M4 ();
m.m00 = v[0];
m.m01 = v[1];
m.m02 = v[2];
m.m03 = v[3];
m.m10 = v[4];
m.m11 = v[5];
m.m12 = v[6];
m.m13 = v[7];
m.m20 = v[8];
m.m21 = v[9];
m.m22 = v[10];
m.m23 = v[11];
m.m30 = v[12];
m.m31 = v[13];
m.m32 = v[14];
m.m33 = v[15];
return m;
}, "~A");
c$.newM = $_M(c$, "newM", 
function (m1) {
var m =  new JU.M4 ();
m.m00 = m1.m00;
m.m01 = m1.m01;
m.m02 = m1.m02;
m.m03 = m1.m03;
m.m10 = m1.m10;
m.m11 = m1.m11;
m.m12 = m1.m12;
m.m13 = m1.m13;
m.m20 = m1.m20;
m.m21 = m1.m21;
m.m22 = m1.m22;
m.m23 = m1.m23;
m.m30 = m1.m30;
m.m31 = m1.m31;
m.m32 = m1.m32;
m.m33 = m1.m33;
return m;
}, "JU.M4");
c$.newMV = $_M(c$, "newMV", 
function (m1, t) {
var m =  new JU.M4 ();
m.setMV (m1, t);
return m;
}, "JU.M3,JU.V3");
$_M(c$, "setMV", 
function (m1, t) {
this.setM3 (m1);
this.setTranslation (t);
}, "JU.M3,JU.V3");
$_M(c$, "setAA", 
function (a1) {
this.setFromAxisAngle (a1.x, a1.y, a1.z, a1.angle);
}, "JU.A4");
$_M(c$, "setFromAxisAngle", 
function (x, y, z, angle) {
var n = Math.sqrt (x * x + y * y + z * z);
n = 1 / n;
x *= n;
y *= n;
z *= n;
var c = Math.cos (angle);
var s = Math.sin (angle);
var omc = 1.0 - c;
this.m00 = (c + x * x * omc);
this.m11 = (c + y * y * omc);
this.m22 = (c + z * z * omc);
var tmp1 = x * y * omc;
var tmp2 = z * s;
this.m01 = (tmp1 - tmp2);
this.m10 = (tmp1 + tmp2);
tmp1 = x * z * omc;
tmp2 = y * s;
this.m02 = (tmp1 + tmp2);
this.m20 = (tmp1 - tmp2);
tmp1 = y * z * omc;
tmp2 = x * s;
this.m12 = (tmp1 - tmp2);
this.m21 = (tmp1 + tmp2);
}, "~N,~N,~N,~N");
$_M(c$, "setM", 
function (m1) {
this.m00 = m1.m00;
this.m01 = m1.m01;
this.m02 = m1.m02;
this.m03 = m1.m03;
this.m10 = m1.m10;
this.m11 = m1.m11;
this.m12 = m1.m12;
this.m13 = m1.m13;
this.m20 = m1.m20;
this.m21 = m1.m21;
this.m22 = m1.m22;
this.m23 = m1.m23;
this.m30 = m1.m30;
this.m31 = m1.m31;
this.m32 = m1.m32;
this.m33 = m1.m33;
}, "JU.M4");
$_V(c$, "toString", 
function () {
return "[\n  [" + this.m00 + "\t" + this.m01 + "\t" + this.m02 + "\t" + this.m03 + "]" + "\n  [" + this.m10 + "\t" + this.m11 + "\t" + this.m12 + "\t" + this.m13 + "]" + "\n  [" + this.m20 + "\t" + this.m21 + "\t" + this.m22 + "\t" + this.m23 + "]" + "\n  [" + this.m30 + "\t" + this.m31 + "\t" + this.m32 + "\t" + this.m33 + "] ]";
});
$_M(c$, "setIdentity", 
function () {
this.m00 = 1.0;
this.m01 = 0.0;
this.m02 = 0.0;
this.m03 = 0.0;
this.m10 = 0.0;
this.m11 = 1.0;
this.m12 = 0.0;
this.m13 = 0.0;
this.m20 = 0.0;
this.m21 = 0.0;
this.m22 = 1.0;
this.m23 = 0.0;
this.m30 = 0.0;
this.m31 = 0.0;
this.m32 = 0.0;
this.m33 = 1.0;
});
$_M(c$, "setElement", 
function (row, column, value) {
if (row == 0) if (column == 0) this.m00 = value;
 else if (column == 1) this.m01 = value;
 else if (column == 2) this.m02 = value;
 else if (column == 3) this.m03 = value;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 3 and is " + column);
 else if (row == 1) if (column == 0) this.m10 = value;
 else if (column == 1) this.m11 = value;
 else if (column == 2) this.m12 = value;
 else if (column == 3) this.m13 = value;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 3 and is " + column);
 else if (row == 2) if (column == 0) this.m20 = value;
 else if (column == 1) this.m21 = value;
 else if (column == 2) this.m22 = value;
 else if (column == 3) this.m23 = value;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 3 and is " + column);
 else if (row == 3) if (column == 0) this.m30 = value;
 else if (column == 1) this.m31 = value;
 else if (column == 2) this.m32 = value;
 else if (column == 3) this.m33 = value;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 3 and is " + column);
 else throw  new ArrayIndexOutOfBoundsException ("row must be 0 to 2 and is " + row);
}, "~N,~N,~N");
$_M(c$, "getElement", 
function (row, column) {
if (row == 0) if (column == 0) return this.m00;
 else if (column == 1) return this.m01;
 else if (column == 2) return this.m02;
 else if (column == 3) return this.m03;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 3 and is " + column);
 else if (row == 1) if (column == 0) return this.m10;
 else if (column == 1) return this.m11;
 else if (column == 2) return this.m12;
 else if (column == 3) return this.m13;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 3 and is " + column);
 else if (row == 2) if (column == 0) return this.m20;
 else if (column == 1) return this.m21;
 else if (column == 2) return this.m22;
 else if (column == 3) return this.m23;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 3 and is " + column);
 else if (row == 3) if (column == 0) return this.m30;
 else if (column == 1) return this.m31;
 else if (column == 2) return this.m32;
 else if (column == 3) return this.m33;
 else throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 3 and is " + column);
 else throw  new ArrayIndexOutOfBoundsException ("row must be 0 to 3 and is " + row);
}, "~N,~N");
$_M(c$, "get", 
function (trans) {
trans.x = this.m03;
trans.y = this.m13;
trans.z = this.m23;
}, "JU.V3");
$_M(c$, "getRotationScale", 
function (m1) {
m1.m00 = this.m00;
m1.m01 = this.m01;
m1.m02 = this.m02;
m1.m10 = this.m10;
m1.m11 = this.m11;
m1.m12 = this.m12;
m1.m20 = this.m20;
m1.m21 = this.m21;
m1.m22 = this.m22;
}, "JU.M3");
$_M(c$, "setRotationScale", 
function (m1) {
this.m00 = m1.m00;
this.m01 = m1.m01;
this.m02 = m1.m02;
this.m10 = m1.m10;
this.m11 = m1.m11;
this.m12 = m1.m12;
this.m20 = m1.m20;
this.m21 = m1.m21;
this.m22 = m1.m22;
}, "JU.M3");
$_M(c$, "setRow", 
function (row, v) {
if (row == 0) {
this.m00 = v[0];
this.m01 = v[1];
this.m02 = v[2];
this.m03 = v[3];
} else if (row == 1) {
this.m10 = v[0];
this.m11 = v[1];
this.m12 = v[2];
this.m13 = v[3];
} else if (row == 2) {
this.m20 = v[0];
this.m21 = v[1];
this.m22 = v[2];
this.m23 = v[3];
} else if (row == 3) {
this.m30 = v[0];
this.m31 = v[1];
this.m32 = v[2];
this.m33 = v[3];
} else {
throw  new ArrayIndexOutOfBoundsException ("row must be 0 to 3 and is " + row);
}}, "~N,~A");
$_M(c$, "getRow", 
function (row, v) {
if (row == 0) {
v[0] = this.m00;
v[1] = this.m01;
v[2] = this.m02;
v[3] = this.m03;
} else if (row == 1) {
v[0] = this.m10;
v[1] = this.m11;
v[2] = this.m12;
v[3] = this.m13;
} else if (row == 2) {
v[0] = this.m20;
v[1] = this.m21;
v[2] = this.m22;
v[3] = this.m23;
} else if (row == 3) {
v[0] = this.m30;
v[1] = this.m31;
v[2] = this.m32;
v[3] = this.m33;
} else {
throw  new ArrayIndexOutOfBoundsException ("row must be 0 to 3 and is " + row);
}}, "~N,~A");
$_M(c$, "setColumn4", 
function (column, x, y, z, w) {
if (column == 0) {
this.m00 = x;
this.m10 = y;
this.m20 = z;
this.m30 = w;
} else if (column == 1) {
this.m01 = x;
this.m11 = y;
this.m21 = z;
this.m31 = w;
} else if (column == 2) {
this.m02 = x;
this.m12 = y;
this.m22 = z;
this.m32 = w;
} else if (column == 3) {
this.m03 = x;
this.m13 = y;
this.m23 = z;
this.m33 = w;
} else {
throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 3 and is " + column);
}}, "~N,~N,~N,~N,~N");
$_M(c$, "setColumn", 
function (column, v) {
if (column == 0) {
this.m00 = v[0];
this.m10 = v[1];
this.m20 = v[2];
this.m30 = v[3];
} else if (column == 1) {
this.m01 = v[0];
this.m11 = v[1];
this.m21 = v[2];
this.m31 = v[3];
} else if (column == 2) {
this.m02 = v[0];
this.m12 = v[1];
this.m22 = v[2];
this.m32 = v[3];
} else if (column == 3) {
this.m03 = v[0];
this.m13 = v[1];
this.m23 = v[2];
this.m33 = v[3];
} else {
throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 3 and is " + column);
}}, "~N,~A");
$_M(c$, "getColumn", 
function (column, v) {
if (column == 0) {
v[0] = this.m00;
v[1] = this.m10;
v[2] = this.m20;
v[3] = this.m30;
} else if (column == 1) {
v[0] = this.m01;
v[1] = this.m11;
v[2] = this.m21;
v[3] = this.m31;
} else if (column == 2) {
v[0] = this.m02;
v[1] = this.m12;
v[2] = this.m22;
v[3] = this.m32;
} else if (column == 3) {
v[0] = this.m03;
v[1] = this.m13;
v[2] = this.m23;
v[3] = this.m33;
} else {
throw  new ArrayIndexOutOfBoundsException ("column must be 0 to 3 and is " + column);
}}, "~N,~A");
$_M(c$, "sub", 
function (m1) {
this.m00 -= m1.m00;
this.m01 -= m1.m01;
this.m02 -= m1.m02;
this.m03 -= m1.m03;
this.m10 -= m1.m10;
this.m11 -= m1.m11;
this.m12 -= m1.m12;
this.m13 -= m1.m13;
this.m20 -= m1.m20;
this.m21 -= m1.m21;
this.m22 -= m1.m22;
this.m23 -= m1.m23;
this.m30 -= m1.m30;
this.m31 -= m1.m31;
this.m32 -= m1.m32;
this.m33 -= m1.m33;
}, "JU.M4");
$_M(c$, "transpose", 
function () {
var tmp = this.m01;
this.m01 = this.m10;
this.m10 = tmp;
tmp = this.m02;
this.m02 = this.m20;
this.m20 = tmp;
tmp = this.m03;
this.m03 = this.m30;
this.m30 = tmp;
tmp = this.m12;
this.m12 = this.m21;
this.m21 = tmp;
tmp = this.m13;
this.m13 = this.m31;
this.m31 = tmp;
tmp = this.m23;
this.m23 = this.m32;
this.m32 = tmp;
});
$_M(c$, "invertM", 
function (m1) {
this.setM (m1);
this.invert ();
}, "JU.M4");
$_M(c$, "invert", 
function () {
var s = this.determinant ();
if (s == 0.0) return;
s = 1 / s;
this.set (this.m11 * (this.m22 * this.m33 - this.m23 * this.m32) + this.m12 * (this.m23 * this.m31 - this.m21 * this.m33) + this.m13 * (this.m21 * this.m32 - this.m22 * this.m31), this.m21 * (this.m02 * this.m33 - this.m03 * this.m32) + this.m22 * (this.m03 * this.m31 - this.m01 * this.m33) + this.m23 * (this.m01 * this.m32 - this.m02 * this.m31), this.m31 * (this.m02 * this.m13 - this.m03 * this.m12) + this.m32 * (this.m03 * this.m11 - this.m01 * this.m13) + this.m33 * (this.m01 * this.m12 - this.m02 * this.m11), this.m01 * (this.m13 * this.m22 - this.m12 * this.m23) + this.m02 * (this.m11 * this.m23 - this.m13 * this.m21) + this.m03 * (this.m12 * this.m21 - this.m11 * this.m22), this.m12 * (this.m20 * this.m33 - this.m23 * this.m30) + this.m13 * (this.m22 * this.m30 - this.m20 * this.m32) + this.m10 * (this.m23 * this.m32 - this.m22 * this.m33), this.m22 * (this.m00 * this.m33 - this.m03 * this.m30) + this.m23 * (this.m02 * this.m30 - this.m00 * this.m32) + this.m20 * (this.m03 * this.m32 - this.m02 * this.m33), this.m32 * (this.m00 * this.m13 - this.m03 * this.m10) + this.m33 * (this.m02 * this.m10 - this.m00 * this.m12) + this.m30 * (this.m03 * this.m12 - this.m02 * this.m13), this.m02 * (this.m13 * this.m20 - this.m10 * this.m23) + this.m03 * (this.m10 * this.m22 - this.m12 * this.m20) + this.m00 * (this.m12 * this.m23 - this.m13 * this.m22), this.m13 * (this.m20 * this.m31 - this.m21 * this.m30) + this.m10 * (this.m21 * this.m33 - this.m23 * this.m31) + this.m11 * (this.m23 * this.m30 - this.m20 * this.m33), this.m23 * (this.m00 * this.m31 - this.m01 * this.m30) + this.m20 * (this.m01 * this.m33 - this.m03 * this.m31) + this.m21 * (this.m03 * this.m30 - this.m00 * this.m33), this.m33 * (this.m00 * this.m11 - this.m01 * this.m10) + this.m30 * (this.m01 * this.m13 - this.m03 * this.m11) + this.m31 * (this.m03 * this.m10 - this.m00 * this.m13), this.m03 * (this.m11 * this.m20 - this.m10 * this.m21) + this.m00 * (this.m13 * this.m21 - this.m11 * this.m23) + this.m01 * (this.m10 * this.m23 - this.m13 * this.m20), this.m10 * (this.m22 * this.m31 - this.m21 * this.m32) + this.m11 * (this.m20 * this.m32 - this.m22 * this.m30) + this.m12 * (this.m21 * this.m30 - this.m20 * this.m31), this.m20 * (this.m02 * this.m31 - this.m01 * this.m32) + this.m21 * (this.m00 * this.m32 - this.m02 * this.m30) + this.m22 * (this.m01 * this.m30 - this.m00 * this.m31), this.m30 * (this.m02 * this.m11 - this.m01 * this.m12) + this.m31 * (this.m00 * this.m12 - this.m02 * this.m10) + this.m32 * (this.m01 * this.m10 - this.m00 * this.m11), this.m00 * (this.m11 * this.m22 - this.m12 * this.m21) + this.m01 * (this.m12 * this.m20 - this.m10 * this.m22) + this.m02 * (this.m10 * this.m21 - this.m11 * this.m20));
this.mul (s);
});
$_M(c$, "determinant", 
function () {
return (this.m00 * this.m11 - this.m01 * this.m10) * (this.m22 * this.m33 - this.m23 * this.m32) - (this.m00 * this.m12 - this.m02 * this.m10) * (this.m21 * this.m33 - this.m23 * this.m31) + (this.m00 * this.m13 - this.m03 * this.m10) * (this.m21 * this.m32 - this.m22 * this.m31) + (this.m01 * this.m12 - this.m02 * this.m11) * (this.m20 * this.m33 - this.m23 * this.m30) - (this.m01 * this.m13 - this.m03 * this.m11) * (this.m20 * this.m32 - this.m22 * this.m30) + (this.m02 * this.m13 - this.m03 * this.m12) * (this.m20 * this.m31 - this.m21 * this.m30);
});
$_M(c$, "setM3", 
function (m1) {
this.m00 = m1.m00;
this.m01 = m1.m01;
this.m02 = m1.m02;
this.m03 = 0.0;
this.m10 = m1.m10;
this.m11 = m1.m11;
this.m12 = m1.m12;
this.m13 = 0.0;
this.m20 = m1.m20;
this.m21 = m1.m21;
this.m22 = m1.m22;
this.m23 = 0.0;
this.m30 = 0.0;
this.m31 = 0.0;
this.m32 = 0.0;
this.m33 = 1.0;
}, "JU.M3");
$_M(c$, "setA", 
function (m, i) {
this.m00 = m[i++];
this.m01 = m[i++];
this.m02 = m[i++];
this.m03 = m[i++];
this.m10 = m[i++];
this.m11 = m[i++];
this.m12 = m[i++];
this.m13 = m[i++];
this.m20 = m[i++];
this.m21 = m[i++];
this.m22 = m[i++];
this.m23 = m[i++];
this.m30 = m[i++];
this.m31 = m[i++];
this.m32 = m[i++];
this.m33 = m[i++];
}, "~A,~N");
$_M(c$, "setTranslation", 
function (trans) {
this.m03 = trans.x;
this.m13 = trans.y;
this.m23 = trans.z;
}, "JU.V3");
$_M(c$, "rotX", 
function (angle) {
var c = Math.cos (angle);
var s = Math.sin (angle);
this.m00 = 1.0;
this.m01 = 0.0;
this.m02 = 0.0;
this.m03 = 0.0;
this.m10 = 0.0;
this.m11 = c;
this.m12 = -s;
this.m13 = 0.0;
this.m20 = 0.0;
this.m21 = s;
this.m22 = c;
this.m23 = 0.0;
this.m30 = 0.0;
this.m31 = 0.0;
this.m32 = 0.0;
this.m33 = 1.0;
}, "~N");
$_M(c$, "rotY", 
function (angle) {
var c = Math.cos (angle);
var s = Math.sin (angle);
this.m00 = c;
this.m01 = 0.0;
this.m02 = s;
this.m03 = 0.0;
this.m10 = 0.0;
this.m11 = 1.0;
this.m12 = 0.0;
this.m13 = 0.0;
this.m20 = -s;
this.m21 = 0.0;
this.m22 = c;
this.m23 = 0.0;
this.m30 = 0.0;
this.m31 = 0.0;
this.m32 = 0.0;
this.m33 = 1.0;
}, "~N");
$_M(c$, "rotZ", 
function (angle) {
var c = Math.cos (angle);
var s = Math.sin (angle);
this.m00 = c;
this.m01 = -s;
this.m02 = 0.0;
this.m03 = 0.0;
this.m10 = s;
this.m11 = c;
this.m12 = 0.0;
this.m13 = 0.0;
this.m20 = 0.0;
this.m21 = 0.0;
this.m22 = 1.0;
this.m23 = 0.0;
this.m30 = 0.0;
this.m31 = 0.0;
this.m32 = 0.0;
this.m33 = 1.0;
}, "~N");
$_M(c$, "mul", 
function (scalar) {
this.m00 *= scalar;
this.m01 *= scalar;
this.m02 *= scalar;
this.m03 *= scalar;
this.m10 *= scalar;
this.m11 *= scalar;
this.m12 *= scalar;
this.m13 *= scalar;
this.m20 *= scalar;
this.m21 *= scalar;
this.m22 *= scalar;
this.m23 *= scalar;
this.m30 *= scalar;
this.m31 *= scalar;
this.m32 *= scalar;
this.m33 *= scalar;
}, "~N");
$_M(c$, "mulM4", 
function (m1) {
this.mul2 (this, m1);
}, "JU.M4");
$_M(c$, "mul2", 
function (m1, m2) {
this.set (m1.m00 * m2.m00 + m1.m01 * m2.m10 + m1.m02 * m2.m20 + m1.m03 * m2.m30, m1.m00 * m2.m01 + m1.m01 * m2.m11 + m1.m02 * m2.m21 + m1.m03 * m2.m31, m1.m00 * m2.m02 + m1.m01 * m2.m12 + m1.m02 * m2.m22 + m1.m03 * m2.m32, m1.m00 * m2.m03 + m1.m01 * m2.m13 + m1.m02 * m2.m23 + m1.m03 * m2.m33, m1.m10 * m2.m00 + m1.m11 * m2.m10 + m1.m12 * m2.m20 + m1.m13 * m2.m30, m1.m10 * m2.m01 + m1.m11 * m2.m11 + m1.m12 * m2.m21 + m1.m13 * m2.m31, m1.m10 * m2.m02 + m1.m11 * m2.m12 + m1.m12 * m2.m22 + m1.m13 * m2.m32, m1.m10 * m2.m03 + m1.m11 * m2.m13 + m1.m12 * m2.m23 + m1.m13 * m2.m33, m1.m20 * m2.m00 + m1.m21 * m2.m10 + m1.m22 * m2.m20 + m1.m23 * m2.m30, m1.m20 * m2.m01 + m1.m21 * m2.m11 + m1.m22 * m2.m21 + m1.m23 * m2.m31, m1.m20 * m2.m02 + m1.m21 * m2.m12 + m1.m22 * m2.m22 + m1.m23 * m2.m32, m1.m20 * m2.m03 + m1.m21 * m2.m13 + m1.m22 * m2.m23 + m1.m23 * m2.m33, m1.m30 * m2.m00 + m1.m31 * m2.m10 + m1.m32 * m2.m20 + m1.m33 * m2.m30, m1.m30 * m2.m01 + m1.m31 * m2.m11 + m1.m32 * m2.m21 + m1.m33 * m2.m31, m1.m30 * m2.m02 + m1.m31 * m2.m12 + m1.m32 * m2.m22 + m1.m33 * m2.m32, m1.m30 * m2.m03 + m1.m31 * m2.m13 + m1.m32 * m2.m23 + m1.m33 * m2.m33);
}, "JU.M4,JU.M4");
$_V(c$, "equals", 
function (o) {
if (!(Clazz_instanceOf (o, JU.M4))) return false;
var m = o;
return (this.m00 == m.m00 && this.m01 == m.m01 && this.m02 == m.m02 && this.m03 == m.m03 && this.m10 == m.m10 && this.m11 == m.m11 && this.m12 == m.m12 && this.m13 == m.m13 && this.m20 == m.m20 && this.m21 == m.m21 && this.m22 == m.m22 && this.m23 == m.m23 && this.m30 == m.m30 && this.m31 == m.m31 && this.m32 == m.m32 && this.m33 == m.m33);
}, "~O");
$_V(c$, "hashCode", 
function () {
return JU.T3.floatToIntBits0 (this.m00) ^ JU.T3.floatToIntBits0 (this.m01) ^ JU.T3.floatToIntBits0 (this.m02) ^ JU.T3.floatToIntBits0 (this.m03) ^ JU.T3.floatToIntBits0 (this.m10) ^ JU.T3.floatToIntBits0 (this.m11) ^ JU.T3.floatToIntBits0 (this.m12) ^ JU.T3.floatToIntBits0 (this.m13) ^ JU.T3.floatToIntBits0 (this.m20) ^ JU.T3.floatToIntBits0 (this.m21) ^ JU.T3.floatToIntBits0 (this.m22) ^ JU.T3.floatToIntBits0 (this.m23) ^ JU.T3.floatToIntBits0 (this.m30) ^ JU.T3.floatToIntBits0 (this.m31) ^ JU.T3.floatToIntBits0 (this.m32) ^ JU.T3.floatToIntBits0 (this.m33);
});
$_M(c$, "transformT2", 
function (vec, vecOut) {
vecOut.set (this.m00 * vec.x + this.m01 * vec.y + this.m02 * vec.z + this.m03 * vec.w, this.m10 * vec.x + this.m11 * vec.y + this.m12 * vec.z + this.m13 * vec.w, this.m20 * vec.x + this.m21 * vec.y + this.m22 * vec.z + this.m23 * vec.w, this.m30 * vec.x + this.m31 * vec.y + this.m32 * vec.z + this.m33 * vec.w);
}, "JU.T4,JU.T4");
$_M(c$, "transform4", 
function (vec) {
this.transformT2 (vec, vec);
}, "JU.T4");
$_M(c$, "transform2", 
function (point, pointOut) {
try {
pointOut.set (this.m00 * point.x + this.m01 * point.y + this.m02 * point.z + this.m03, this.m10 * point.x + this.m11 * point.y + this.m12 * point.z + this.m13, this.m20 * point.x + this.m21 * point.y + this.m22 * point.z + this.m23);
} catch (e) {
if (Clazz_exceptionOf (e, NullPointerException)) {
} else {
throw e;
}
}
}, "JU.T3,JU.T3");
$_M(c$, "transform", 
function (point) {
this.transform2 (point, point);
}, "JU.T3");
$_M(c$, "transformV2", 
function (normal, normalOut) {
normalOut.set (this.m00 * normal.x + this.m01 * normal.y + this.m02 * normal.z, this.m10 * normal.x + this.m11 * normal.y + this.m12 * normal.z, this.m20 * normal.x + this.m21 * normal.y + this.m22 * normal.z);
}, "JU.V3,JU.V3");
$_M(c$, "transformV", 
function (normal) {
this.transformV2 (normal, normal);
}, "JU.V3");
$_M(c$, "setZero", 
function () {
this.m00 = 0.0;
this.m01 = 0.0;
this.m02 = 0.0;
this.m03 = 0.0;
this.m10 = 0.0;
this.m11 = 0.0;
this.m12 = 0.0;
this.m13 = 0.0;
this.m20 = 0.0;
this.m21 = 0.0;
this.m22 = 0.0;
this.m23 = 0.0;
this.m30 = 0.0;
this.m31 = 0.0;
this.m32 = 0.0;
this.m33 = 0.0;
});
$_M(c$, "set", 
function (m00, m01, m02, m03, m10, m11, m12, m13, m20, m21, m22, m23, m30, m31, m32, m33) {
this.m00 = m00;
this.m01 = m01;
this.m02 = m02;
this.m03 = m03;
this.m10 = m10;
this.m11 = m11;
this.m12 = m12;
this.m13 = m13;
this.m20 = m20;
this.m21 = m21;
this.m22 = m22;
this.m23 = m23;
this.m30 = m30;
this.m31 = m31;
this.m32 = m32;
this.m33 = m33;
}, "~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");
});
Clazz_declarePackage ("JU");
Clazz_load (null, "JU.A4", ["JU.T3"], function () {
c$ = Clazz_decorateAsClass (function () {
this.x = 0;
this.y = 0;
this.z = 0;
this.angle = 0;
Clazz_instantialize (this, arguments);
}, JU, "A4", null, java.io.Serializable);
Clazz_makeConstructor (c$, 
function () {
this.z = 1.0;
});
c$.new4 = $_M(c$, "new4", 
function (x, y, z, angle) {
var a =  new JU.A4 ();
a.set4 (x, y, z, angle);
return a;
}, "~N,~N,~N,~N");
c$.newAA = $_M(c$, "newAA", 
function (a1) {
var a =  new JU.A4 ();
a.set4 (a1.x, a1.y, a1.z, a1.angle);
return a;
}, "JU.A4");
c$.newVA = $_M(c$, "newVA", 
function (axis, angle) {
var a =  new JU.A4 ();
a.setVA (axis, angle);
return a;
}, "JU.V3,~N");
$_M(c$, "setVA", 
function (axis, angle) {
this.x = axis.x;
this.y = axis.y;
this.z = axis.z;
this.angle = angle;
}, "JU.V3,~N");
$_M(c$, "set4", 
function (x, y, z, angle) {
this.x = x;
this.y = y;
this.z = z;
this.angle = angle;
}, "~N,~N,~N,~N");
$_M(c$, "setAA", 
function (a) {
this.x = a.x;
this.y = a.y;
this.z = a.z;
this.angle = a.angle;
}, "JU.A4");
$_M(c$, "setM", 
function (m1) {
this.setFromMat (m1.m00, m1.m01, m1.m02, m1.m10, m1.m11, m1.m12, m1.m20, m1.m21, m1.m22);
}, "JU.M3");
$_M(c$, "setFromMat", 
function (m00, m01, m02, m10, m11, m12, m20, m21, m22) {
var cos = (m00 + m11 + m22 - 1.0) * 0.5;
this.x = (m21 - m12);
this.y = (m02 - m20);
this.z = (m10 - m01);
var sin = 0.5 * Math.sqrt (this.x * this.x + this.y * this.y + this.z * this.z);
this.angle = Math.atan2 (sin, cos);
}, "~N,~N,~N,~N,~N,~N,~N,~N,~N");
$_V(c$, "toString", 
function () {
return "(" + this.x + ", " + this.y + ", " + this.z + ", " + this.angle + ")";
});
$_V(c$, "equals", 
function (o) {
if (!(Clazz_instanceOf (o, JU.A4))) return false;
var a1 = o;
return this.x == a1.x && this.y == a1.y && this.z == a1.z && this.angle == a1.angle;
}, "~O");
$_V(c$, "hashCode", 
function () {
return JU.T3.floatToIntBits0 (this.x) ^ JU.T3.floatToIntBits0 (this.y) ^ JU.T3.floatToIntBits0 (this.z) ^ JU.T3.floatToIntBits0 (this.angle);
});
});
Clazz_declarePackage ("JU");
Clazz_load (null, "JU.BS", ["java.lang.IndexOutOfBoundsException", "$.NegativeArraySizeException", "JU.SB"], function () {
c$ = Clazz_decorateAsClass (function () {
this.words = null;
this.wordsInUse = 0;
this.sizeIsSticky = false;
Clazz_instantialize (this, arguments);
}, JU, "BS", null, Cloneable);
c$.wordIndex = $_M(c$, "wordIndex", 
function (bitIndex) {
return bitIndex >> 5;
}, "~N");
$_M(c$, "recalculateWordsInUse", 
function () {
var i;
for (i = this.wordsInUse - 1; i >= 0; i--) if (this.words[i] != 0) break;

this.wordsInUse = i + 1;
});
Clazz_makeConstructor (c$, 
function () {
this.initWords (32);
this.sizeIsSticky = false;
});
c$.newN = $_M(c$, "newN", 
function (nbits) {
var bs =  new JU.BS ();
bs.init (nbits);
return bs;
}, "~N");
$_M(c$, "init", 
function (nbits) {
if (nbits < 0) throw  new NegativeArraySizeException ("nbits < 0: " + nbits);
this.initWords (nbits);
this.sizeIsSticky = true;
}, "~N");
$_M(c$, "initWords", 
function (nbits) {
this.words =  Clazz_newIntArray (JU.BS.wordIndex (nbits - 1) + 1, 0);
}, "~N");
$_M(c$, "ensureCapacity", 
function (wordsRequired) {
if (this.words.length < wordsRequired) {
var request = Math.max (2 * this.words.length, wordsRequired);
this.setLength (request);
this.sizeIsSticky = false;
}}, "~N");
$_M(c$, "expandTo", 
function (wordIndex) {
var wordsRequired = wordIndex + 1;
if (this.wordsInUse < wordsRequired) {
this.ensureCapacity (wordsRequired);
this.wordsInUse = wordsRequired;
}}, "~N");
$_M(c$, "set", 
function (bitIndex) {
if (bitIndex < 0) throw  new IndexOutOfBoundsException ("bitIndex < 0: " + bitIndex);
var wordIndex = JU.BS.wordIndex (bitIndex);
this.expandTo (wordIndex);
this.words[wordIndex] |= (1 << bitIndex);
}, "~N");
$_M(c$, "setBitTo", 
function (bitIndex, value) {
if (value) this.set (bitIndex);
 else this.clear (bitIndex);
}, "~N,~B");
$_M(c$, "setBits", 
function (fromIndex, toIndex) {
if (fromIndex == toIndex) return;
var startWordIndex = JU.BS.wordIndex (fromIndex);
var endWordIndex = JU.BS.wordIndex (toIndex - 1);
this.expandTo (endWordIndex);
var firstWordMask = -1 << fromIndex;
var lastWordMask = -1 >>> -toIndex;
if (startWordIndex == endWordIndex) {
this.words[startWordIndex] |= (firstWordMask & lastWordMask);
} else {
this.words[startWordIndex] |= firstWordMask;
for (var i = startWordIndex + 1; i < endWordIndex; i++) this.words[i] = -1;

this.words[endWordIndex] |= lastWordMask;
}}, "~N,~N");
$_M(c$, "clear", 
function (bitIndex) {
if (bitIndex < 0) throw  new IndexOutOfBoundsException ("bitIndex < 0: " + bitIndex);
var wordIndex = JU.BS.wordIndex (bitIndex);
if (wordIndex >= this.wordsInUse) return;
this.words[wordIndex] &= ~(1 << bitIndex);
this.recalculateWordsInUse ();
}, "~N");
$_M(c$, "clearBits", 
function (fromIndex, toIndex) {
if (fromIndex == toIndex) return;
var startWordIndex = JU.BS.wordIndex (fromIndex);
if (startWordIndex >= this.wordsInUse) return;
var endWordIndex = JU.BS.wordIndex (toIndex - 1);
if (endWordIndex >= this.wordsInUse) {
toIndex = this.length ();
endWordIndex = this.wordsInUse - 1;
}var firstWordMask = -1 << fromIndex;
var lastWordMask = -1 >>> -toIndex;
if (startWordIndex == endWordIndex) {
this.words[startWordIndex] &= ~(firstWordMask & lastWordMask);
} else {
this.words[startWordIndex] &= ~firstWordMask;
for (var i = startWordIndex + 1; i < endWordIndex; i++) this.words[i] = 0;

this.words[endWordIndex] &= ~lastWordMask;
}this.recalculateWordsInUse ();
}, "~N,~N");
$_M(c$, "clearAll", 
function () {
while (this.wordsInUse > 0) this.words[--this.wordsInUse] = 0;

});
$_M(c$, "get", 
function (bitIndex) {
if (bitIndex < 0) throw  new IndexOutOfBoundsException ("bitIndex < 0: " + bitIndex);
var wordIndex = JU.BS.wordIndex (bitIndex);
return (wordIndex < this.wordsInUse) && ((this.words[wordIndex] & (1 << bitIndex)) != 0);
}, "~N");
$_M(c$, "nextSetBit", 
function (fromIndex) {
if (fromIndex < 0) throw  new IndexOutOfBoundsException ("fromIndex < 0: " + fromIndex);
var u = JU.BS.wordIndex (fromIndex);
if (u >= this.wordsInUse) return -1;
var word = this.words[u] & (-1 << fromIndex);
while (true) {
if (word != 0) return (u * 32) + Integer.numberOfTrailingZeros (word);
if (++u == this.wordsInUse) return -1;
word = this.words[u];
}
}, "~N");
$_M(c$, "nextClearBit", 
function (fromIndex) {
if (fromIndex < 0) throw  new IndexOutOfBoundsException ("fromIndex < 0: " + fromIndex);
var u = JU.BS.wordIndex (fromIndex);
if (u >= this.wordsInUse) return fromIndex;
var word = ~this.words[u] & (-1 << fromIndex);
while (true) {
if (word != 0) return (u * 32) + Integer.numberOfTrailingZeros (word);
if (++u == this.wordsInUse) return this.wordsInUse * 32;
word = ~this.words[u];
}
}, "~N");
$_M(c$, "length", 
function () {
if (this.wordsInUse == 0) return 0;
return 32 * (this.wordsInUse - 1) + (32 - Integer.numberOfLeadingZeros (this.words[this.wordsInUse - 1]));
});
$_M(c$, "isEmpty", 
function () {
return this.wordsInUse == 0;
});
$_M(c$, "intersects", 
function (set) {
for (var i = Math.min (this.wordsInUse, set.wordsInUse) - 1; i >= 0; i--) if ((this.words[i] & set.words[i]) != 0) return true;

return false;
}, "JU.BS");
$_M(c$, "cardinality", 
function () {
var sum = 0;
for (var i = 0; i < this.wordsInUse; i++) sum += Integer.bitCount (this.words[i]);

return sum;
});
$_M(c$, "and", 
function (set) {
if (this === set) return;
while (this.wordsInUse > set.wordsInUse) this.words[--this.wordsInUse] = 0;

for (var i = 0; i < this.wordsInUse; i++) this.words[i] &= set.words[i];

this.recalculateWordsInUse ();
}, "JU.BS");
$_M(c$, "or", 
function (set) {
if (this === set) return;
var wordsInCommon = Math.min (this.wordsInUse, set.wordsInUse);
if (this.wordsInUse < set.wordsInUse) {
this.ensureCapacity (set.wordsInUse);
this.wordsInUse = set.wordsInUse;
}for (var i = 0; i < wordsInCommon; i++) this.words[i] |= set.words[i];

if (wordsInCommon < set.wordsInUse) System.arraycopy (set.words, wordsInCommon, this.words, wordsInCommon, this.wordsInUse - wordsInCommon);
}, "JU.BS");
$_M(c$, "xor", 
function (set) {
var wordsInCommon = Math.min (this.wordsInUse, set.wordsInUse);
if (this.wordsInUse < set.wordsInUse) {
this.ensureCapacity (set.wordsInUse);
this.wordsInUse = set.wordsInUse;
}for (var i = 0; i < wordsInCommon; i++) this.words[i] ^= set.words[i];

if (wordsInCommon < set.wordsInUse) System.arraycopy (set.words, wordsInCommon, this.words, wordsInCommon, set.wordsInUse - wordsInCommon);
this.recalculateWordsInUse ();
}, "JU.BS");
$_M(c$, "andNot", 
function (set) {
for (var i = Math.min (this.wordsInUse, set.wordsInUse) - 1; i >= 0; i--) this.words[i] &= ~set.words[i];

this.recalculateWordsInUse ();
}, "JU.BS");
$_V(c$, "hashCode", 
function () {
var h = 1234;
for (var i = this.wordsInUse; --i >= 0; ) h ^= this.words[i] * (i + 1);

return ((h >> 32) ^ h);
});
$_M(c$, "size", 
function () {
return this.words.length * 32;
});
$_V(c$, "equals", 
function (obj) {
if (!(Clazz_instanceOf (obj, JU.BS))) return false;
if (this === obj) return true;
var set = obj;
if (this.wordsInUse != set.wordsInUse) return false;
for (var i = 0; i < this.wordsInUse; i++) if (this.words[i] != set.words[i]) return false;

return true;
}, "~O");
$_V(c$, "clone", 
function () {
if (!this.sizeIsSticky && this.wordsInUse != this.words.length) this.setLength (this.wordsInUse);
return JU.BS.copy (this);
});
$_M(c$, "setLength", 
function (n) {
var a =  Clazz_newIntArray (n, 0);
System.arraycopy (this.words, 0, a, 0, Math.min (this.wordsInUse, n));
this.words = a;
}, "~N");
$_V(c$, "toString", 
function () {
var numBits = (this.wordsInUse > 128) ? this.cardinality () : this.wordsInUse * 32;
var b = JU.SB.newN (6 * numBits + 2);
b.appendC ('{');
var i = this.nextSetBit (0);
if (i != -1) {
b.appendI (i);
for (i = this.nextSetBit (i + 1); i >= 0; i = this.nextSetBit (i + 1)) {
var endOfRun = this.nextClearBit (i);
do {
b.append (", ").appendI (i);
} while (++i < endOfRun);
}
}b.appendC ('}');
return b.toString ();
});
c$.copy = $_M(c$, "copy", 
function (bitsetToCopy) {
var bs = null;
{
bs = Clazz_clone(bitsetToCopy);
}var wordCount = bitsetToCopy.wordsInUse;
if (wordCount == 0) {
bs.words = JU.BS.emptyBitmap;
} else {
bs.words =  Clazz_newIntArray (wordCount, 0);
System.arraycopy (bitsetToCopy.words, 0, bs.words, 0, wordCount);
}return bs;
}, "JU.BS");
$_M(c$, "cardinalityN", 
function (max) {
var n = this.cardinality ();
for (var i = this.length (); --i >= max; ) if (this.get (i)) n--;

return n;
}, "~N");
Clazz_defineStatics (c$,
"ADDRESS_BITS_PER_WORD", 5,
"BITS_PER_WORD", 32,
"WORD_MASK", 0xffffffff,
"emptyBitmap",  Clazz_newIntArray (0, 0));
});
Clazz_declarePackage ("JU");
c$ = Clazz_decorateAsClass (function () {
this.sb = null;
this.s = null;
Clazz_instantialize (this, arguments);
}, JU, "SB");
Clazz_makeConstructor (c$, 
function () {
{
this.s = "";
}});
c$.newN = $_M(c$, "newN", 
function (n) {
{
return new JU.SB();
}}, "~N");
c$.newS = $_M(c$, "newS", 
function (s) {
{
var sb = new JU.SB();
sb.s = s;
return sb;
}}, "~S");
$_M(c$, "append", 
function (s) {
{
this.s += s
}return this;
}, "~S");
$_M(c$, "appendC", 
function (c) {
{
this.s += c;
}return this;
}, "~S");
$_M(c$, "appendI", 
function (i) {
{
this.s += i
}return this;
}, "~N");
$_M(c$, "appendB", 
function (b) {
{
this.s += b
}return this;
}, "~B");
$_M(c$, "appendF", 
function (f) {
{
var sf = "" + f;
if (sf.indexOf(".") < 0 && sf.indexOf("e") < 0)
sf += ".0" ;
this.s += sf;
}return this;
}, "~N");
$_M(c$, "appendD", 
function (d) {
{
var sf = "" + d;
if (sf.indexOf(".") < 0 && sf.indexOf("e") < 0)
sf += ".0" ;
this.s += sf;
}return this;
}, "~N");
$_M(c$, "appendSB", 
function (buf) {
{
this.s += buf.s;
}return this;
}, "JU.SB");
$_M(c$, "appendO", 
function (data) {
{
this.s += data.toString();
}return this;
}, "~O");
$_M(c$, "appendCB", 
function (cb, off, len) {
{
for (var i = len,j=off; --i >= 0;)
this.s += cb[j++];
}}, "~A,~N,~N");
$_V(c$, "toString", 
function () {
{
return this.s;
}});
$_M(c$, "length", 
function () {
{
return this.s.length;
}});
$_M(c$, "indexOf", 
function (s) {
{
return this.s.indexOf(s);
}}, "~S");
$_M(c$, "charAt", 
function (i) {
{
return this.s.charAt(i);
}}, "~N");
$_M(c$, "setLength", 
function (n) {
{
this.s = this.s.substring(0, n);
}}, "~N");
$_M(c$, "lastIndexOf", 
function (s) {
{
return this.s.lastIndexOf(s);
}}, "~S");
$_M(c$, "indexOf2", 
function (s, i) {
{
return this.s.indexOf(s, i);
}}, "~S,~N");
$_M(c$, "substring", 
function (i) {
{
return this.s.substring(i);
}}, "~N");
$_M(c$, "substring2", 
function (i, j) {
{
return this.s.substring(i, j);
}}, "~N,~N");
$_M(c$, "toBytes", 
function (off, len) {
if (len < 0) len = this.length () - off;
var b =  Clazz_newByteArray (len, 0);
for (var i = off + len, j = i - off; --i >= off; ) b[--j] = (this.charAt (i)).charCodeAt (0);

return b;
}, "~N,~N");
Clazz_declarePackage ("JU");
Clazz_load (["java.lang.Boolean"], "JU.DF", ["java.lang.Double", "$.Float", "JU.PT", "$.SB"], function () {
c$ = Clazz_declareType (JU, "DF");
c$.setUseNumberLocalization = $_M(c$, "setUseNumberLocalization", 
function (TF) {
JU.DF.useNumberLocalization[0] = (TF ? Boolean.TRUE : Boolean.FALSE);
}, "~B");
c$.formatDecimalDbl = $_M(c$, "formatDecimalDbl", 
function (value, decimalDigits) {
if (decimalDigits == 2147483647 || value == -Infinity || value == Infinity || Double.isNaN (value)) return "" + value;
return JU.DF.formatDecimal (value, decimalDigits);
}, "~N,~N");
c$.formatDecimal = $_M(c$, "formatDecimal", 
function (value, decimalDigits) {
if (decimalDigits == 2147483647 || value == -Infinity || value == Infinity || Float.isNaN (value)) return "" + value;
var n;
if (decimalDigits < 0) {
decimalDigits = -decimalDigits;
if (decimalDigits > JU.DF.formattingStrings.length) decimalDigits = JU.DF.formattingStrings.length;
if (value == 0) return JU.DF.formattingStrings[decimalDigits] + "E+0";
n = 0;
var d;
if (Math.abs (value) < 1) {
n = 10;
d = value * 1e-10;
} else {
n = -10;
d = value * 1e10;
}var s = ("" + d).toUpperCase ();
var i = s.indexOf ("E");
n = JU.PT.parseInt (s.substring (i + 1)) + n;
return (i < 0 ? "" + value : JU.DF.formatDecimal (JU.PT.parseFloat (s.substring (0, i)), decimalDigits - 1) + "E" + (n >= 0 ? "+" : "") + n);
}if (decimalDigits >= JU.DF.formattingStrings.length) decimalDigits = JU.DF.formattingStrings.length - 1;
var s1 = ("" + value).toUpperCase ();
var isNeg = s1.startsWith ("-");
if (isNeg) s1 = s1.substring (1);
var pt = s1.indexOf (".");
if (pt < 0) return s1 + JU.DF.formattingStrings[decimalDigits].substring (1);
var pt1 = s1.indexOf ("E-");
if (pt1 > 0) {
n = JU.PT.parseInt (s1.substring (pt1 + 1));
s1 = "0." + "0000000000000000000000000000000000000000".substring (0, -n - 1) + s1.substring (0, 1) + s1.substring (2, pt1);
pt = 1;
}pt1 = s1.indexOf ("E");
if (pt1 > 0) {
n = JU.PT.parseInt (s1.substring (pt1 + 1));
s1 = s1.substring (0, 1) + s1.substring (2, pt1) + "0000000000000000000000000000000000000000";
s1 = s1.substring (0, n + 1) + "." + s1.substring (n + 1);
pt = s1.indexOf (".");
}var len = s1.length;
var pt2 = decimalDigits + pt + 1;
if (pt2 < len && s1.charAt (pt2) >= '5') {
return JU.DF.formatDecimal (value + (isNeg ? -1 : 1) * JU.DF.formatAdds[decimalDigits], decimalDigits);
}var sb = JU.SB.newS (s1.substring (0, (decimalDigits == 0 ? pt : ++pt)));
for (var i = 0; i < decimalDigits; i++, pt++) {
if (pt < len) sb.appendC (s1.charAt (pt));
 else sb.appendC ('0');
}
s1 = (isNeg ? "-" : "") + sb;
return (Boolean.TRUE.equals (JU.DF.useNumberLocalization[0]) ? s1 : s1.$replace (',', '.'));
}, "~N,~N");
c$.formatDecimalTrimmed = $_M(c$, "formatDecimalTrimmed", 
function (x, precision) {
var str = JU.DF.formatDecimalDbl (x, precision);
var m = str.length - 1;
var zero = '0';
while (m >= 0 && str.charAt (m) == zero) m--;

return str.substring (0, m + 1);
}, "~N,~N");
Clazz_defineStatics (c$,
"formattingStrings", ["0", "0.0", "0.00", "0.000", "0.0000", "0.00000", "0.000000", "0.0000000", "0.00000000", "0.000000000"],
"zeros", "0000000000000000000000000000000000000000",
"formatAdds", [0.5, 0.05, 0.005, 0.0005, 0.00005, 0.000005, 0.0000005, 0.00000005, 0.000000005, 0.0000000005]);
c$.useNumberLocalization = c$.prototype.useNumberLocalization = [Boolean.TRUE];
});
Clazz_declarePackage ("JU");
Clazz_load (null, "JU.PT", ["java.lang.Character", "$.Float", "JU.DF", "$.SB"], function () {
c$ = Clazz_declareType (JU, "PT");
c$.parseInt = $_M(c$, "parseInt", 
function (str) {
return JU.PT.parseIntNext (str, [0]);
}, "~S");
c$.parseIntNext = $_M(c$, "parseIntNext", 
function (str, next) {
var cch = str.length;
if (next[0] < 0 || next[0] >= cch) return -2147483648;
return JU.PT.parseIntChecked (str, cch, next);
}, "~S,~A");
c$.parseIntChecked = $_M(c$, "parseIntChecked", 
function (str, ichMax, next) {
var digitSeen = false;
var value = 0;
var ich = next[0];
if (ich < 0) return -2147483648;
var ch;
while (ich < ichMax && JU.PT.isWhiteSpace (str, ich)) ++ich;

var negative = false;
if (ich < ichMax && str.charCodeAt (ich) == 45) {
negative = true;
++ich;
}while (ich < ichMax && (ch = str.charCodeAt (ich)) >= 48 && ch <= 57) {
value = value * 10 + (ch - 48);
digitSeen = true;
++ich;
}
if (!digitSeen) value = -2147483648;
 else if (negative) value = -value;
next[0] = ich;
return value;
}, "~S,~N,~A");
c$.isWhiteSpace = $_M(c$, "isWhiteSpace", 
function (str, ich) {
var ch;
return (ich >= 0 && ((ch = str.charAt (ich)) == ' ' || ch == '\t' || ch == '\n'));
}, "~S,~N");
c$.parseFloatChecked = $_M(c$, "parseFloatChecked", 
function (str, ichMax, next, isStrict) {
var digitSeen = false;
var ich = next[0];
if (isStrict && str.indexOf ('\n') != str.lastIndexOf ('\n')) return NaN;
while (ich < ichMax && JU.PT.isWhiteSpace (str, ich)) ++ich;

var negative = false;
if (ich < ichMax && str.charAt (ich) == '-') {
++ich;
negative = true;
}var ch = 0;
var ival = 0;
var ival2 = 0;
while (ich < ichMax && (ch = str.charCodeAt (ich)) >= 48 && ch <= 57) {
ival = (ival * 10) + (ch - 48) * 1;
++ich;
digitSeen = true;
}
var isDecimal = false;
var iscale = 0;
var nzero = (ival == 0 ? -1 : 0);
if (ch == 46) {
isDecimal = true;
while (++ich < ichMax && (ch = str.charCodeAt (ich)) >= 48 && ch <= 57) {
digitSeen = true;
if (nzero < 0) {
if (ch == 48) {
nzero--;
continue;
}nzero = -nzero;
}if (iscale < JU.PT.decimalScale.length) {
ival2 = (ival2 * 10) + (ch - 48) * 1;
iscale++;
}}
}var value;
if (!digitSeen) {
value = NaN;
} else if (ival2 > 0) {
value = ival2 * JU.PT.decimalScale[iscale - 1];
if (nzero > 1) {
if (nzero - 2 < JU.PT.decimalScale.length) {
value *= JU.PT.decimalScale[nzero - 2];
} else {
value *= Math.pow (10, 1 - nzero);
}} else {
value += ival;
}} else {
value = ival;
}var isExponent = false;
if (ich < ichMax && (ch == 69 || ch == 101 || ch == 68)) {
isExponent = true;
if (++ich >= ichMax) return NaN;
ch = str.charCodeAt (ich);
if ((ch == 43) && (++ich >= ichMax)) return NaN;
next[0] = ich;
var exponent = JU.PT.parseIntChecked (str, ichMax, next);
if (exponent == -2147483648) return NaN;
if (exponent > 0 && exponent <= JU.PT.tensScale.length) value *= JU.PT.tensScale[exponent - 1];
 else if (exponent < 0 && -exponent <= JU.PT.decimalScale.length) value *= JU.PT.decimalScale[-exponent - 1];
 else if (exponent != 0) value *= Math.pow (10, exponent);
} else {
next[0] = ich;
}if (negative) value = -value;
if (value == Infinity) value = 3.4028235E38;
return (!isStrict || (!isExponent || isDecimal) && JU.PT.checkTrailingText (str, next[0], ichMax) ? value : NaN);
}, "~S,~N,~A,~B");
c$.checkTrailingText = $_M(c$, "checkTrailingText", 
function (str, ich, ichMax) {
var ch;
while (ich < ichMax && (Character.isWhitespace (ch = str.charAt (ich)) || ch == ';')) ++ich;

return (ich == ichMax);
}, "~S,~N,~N");
c$.parseFloatArray = $_M(c$, "parseFloatArray", 
function (str) {
return JU.PT.parseFloatArrayNext (str,  Clazz_newIntArray (1, 0), null, null, null);
}, "~S");
c$.parseFloatArrayInfested = $_M(c$, "parseFloatArrayInfested", 
function (tokens, data) {
var len = data.length;
var nTokens = tokens.length;
var n = 0;
var max = 0;
for (var i = 0; i >= 0 && i < len && n < nTokens; i++) {
var f;
while (Float.isNaN (f = JU.PT.parseFloat (tokens[n++])) && n < nTokens) {
}
if (!Float.isNaN (f)) data[(max = i)] = f;
if (n == nTokens) break;
}
return max + 1;
}, "~A,~A");
c$.parseFloatArrayNext = $_M(c$, "parseFloatArrayNext", 
function (str, next, f, strStart, strEnd) {
var n = 0;
var pt = next[0];
if (pt >= 0) {
if (strStart != null) {
var p = str.indexOf (strStart, pt);
if (p >= 0) next[0] = p + strStart.length;
}str = str.substring (next[0]);
pt = (strEnd == null ? -1 : str.indexOf (strEnd));
if (pt < 0) pt = str.length;
 else str = str.substring (0, pt);
next[0] += pt + 1;
var tokens = JU.PT.getTokens (str);
if (f == null) f =  Clazz_newFloatArray (tokens.length, 0);
n = JU.PT.parseFloatArrayInfested (tokens, f);
}if (f == null) return  Clazz_newFloatArray (0, 0);
for (var i = n; i < f.length; i++) f[i] = NaN;

return f;
}, "~S,~A,~A,~S,~S");
c$.parseFloatRange = $_M(c$, "parseFloatRange", 
function (str, ichMax, next) {
var cch = str.length;
if (ichMax > cch) ichMax = cch;
if (next[0] < 0 || next[0] >= ichMax) return NaN;
return JU.PT.parseFloatChecked (str, ichMax, next, false);
}, "~S,~N,~A");
c$.parseFloatNext = $_M(c$, "parseFloatNext", 
function (str, next) {
var cch = (str == null ? -1 : str.length);
if (next[0] < 0 || next[0] >= cch) return NaN;
return JU.PT.parseFloatChecked (str, cch, next, false);
}, "~S,~A");
c$.parseFloatStrict = $_M(c$, "parseFloatStrict", 
function (str) {
var cch = str.length;
if (cch == 0) return NaN;
return JU.PT.parseFloatChecked (str, cch, [0], true);
}, "~S");
c$.parseFloat = $_M(c$, "parseFloat", 
function (str) {
return JU.PT.parseFloatNext (str, [0]);
}, "~S");
c$.parseIntRadix = $_M(c$, "parseIntRadix", 
function (s, i) {
{
return Integer.parseIntRadix(s, i);
}}, "~S,~N");
c$.getTokens = $_M(c$, "getTokens", 
function (line) {
return JU.PT.getTokensAt (line, 0);
}, "~S");
c$.parseToken = $_M(c$, "parseToken", 
function (str) {
return JU.PT.parseTokenNext (str, [0]);
}, "~S");
c$.parseTrimmed = $_M(c$, "parseTrimmed", 
function (str) {
return JU.PT.parseTrimmedRange (str, 0, str.length);
}, "~S");
c$.parseTrimmedAt = $_M(c$, "parseTrimmedAt", 
function (str, ichStart) {
return JU.PT.parseTrimmedRange (str, ichStart, str.length);
}, "~S,~N");
c$.parseTrimmedRange = $_M(c$, "parseTrimmedRange", 
function (str, ichStart, ichMax) {
var cch = str.length;
if (ichMax < cch) cch = ichMax;
if (cch < ichStart) return "";
return JU.PT.parseTrimmedChecked (str, ichStart, cch);
}, "~S,~N,~N");
c$.getTokensAt = $_M(c$, "getTokensAt", 
function (line, ich) {
if (line == null) return null;
var cchLine = line.length;
if (ich < 0 || ich > cchLine) return null;
var tokenCount = JU.PT.countTokens (line, ich);
var tokens =  new Array (tokenCount);
var next =  Clazz_newIntArray (1, 0);
next[0] = ich;
for (var i = 0; i < tokenCount; ++i) tokens[i] = JU.PT.parseTokenChecked (line, cchLine, next);

return tokens;
}, "~S,~N");
c$.countTokens = $_M(c$, "countTokens", 
function (line, ich) {
var tokenCount = 0;
if (line != null) {
var ichMax = line.length;
while (true) {
while (ich < ichMax && JU.PT.isWhiteSpace (line, ich)) ++ich;

if (ich == ichMax) break;
++tokenCount;
do {
++ich;
} while (ich < ichMax && !JU.PT.isWhiteSpace (line, ich));
}
}return tokenCount;
}, "~S,~N");
c$.parseTokenNext = $_M(c$, "parseTokenNext", 
function (str, next) {
var cch = str.length;
if (next[0] < 0 || next[0] >= cch) return null;
return JU.PT.parseTokenChecked (str, cch, next);
}, "~S,~A");
c$.parseTokenRange = $_M(c$, "parseTokenRange", 
function (str, ichMax, next) {
var cch = str.length;
if (ichMax > cch) ichMax = cch;
if (next[0] < 0 || next[0] >= ichMax) return null;
return JU.PT.parseTokenChecked (str, ichMax, next);
}, "~S,~N,~A");
c$.parseTokenChecked = $_M(c$, "parseTokenChecked", 
function (str, ichMax, next) {
var ich = next[0];
while (ich < ichMax && JU.PT.isWhiteSpace (str, ich)) ++ich;

var ichNonWhite = ich;
while (ich < ichMax && !JU.PT.isWhiteSpace (str, ich)) ++ich;

next[0] = ich;
if (ichNonWhite == ich) return null;
return str.substring (ichNonWhite, ich);
}, "~S,~N,~A");
c$.parseTrimmedChecked = $_M(c$, "parseTrimmedChecked", 
function (str, ich, ichMax) {
while (ich < ichMax && JU.PT.isWhiteSpace (str, ich)) ++ich;

var ichLast = ichMax - 1;
while (ichLast >= ich && JU.PT.isWhiteSpace (str, ichLast)) --ichLast;

if (ichLast < ich) return "";
return str.substring (ich, ichLast + 1);
}, "~S,~N,~N");
c$.dVal = $_M(c$, "dVal", 
function (s) {
{
if(s==null){
throw new NumberFormatException("null");
}
var d=parseFloat(s);
if(isNaN(d))
throw new NumberFormatException("Not a Number : "+s);
return d
}}, "~S");
c$.fVal = $_M(c$, "fVal", 
function (s) {
{
return this.dVal(s);
}}, "~S");
c$.parseIntRange = $_M(c$, "parseIntRange", 
function (str, ichMax, next) {
var cch = str.length;
if (ichMax > cch) ichMax = cch;
if (next[0] < 0 || next[0] >= ichMax) return -2147483648;
return JU.PT.parseIntChecked (str, ichMax, next);
}, "~S,~N,~A");
c$.parseFloatArrayData = $_M(c$, "parseFloatArrayData", 
function (tokens, data) {
JU.PT.parseFloatArrayDataN (tokens, data, data.length);
}, "~A,~A");
c$.parseFloatArrayDataN = $_M(c$, "parseFloatArrayDataN", 
function (tokens, data, nData) {
for (var i = nData; --i >= 0; ) data[i] = (i >= tokens.length ? NaN : JU.PT.parseFloat (tokens[i]));

}, "~A,~A,~N");
c$.split = $_M(c$, "split", 
function (text, run) {
if (text.length == 0) return  new Array (0);
var n = 1;
var i = text.indexOf (run);
var lines;
var runLen = run.length;
if (i < 0 || runLen == 0) {
lines =  new Array (1);
lines[0] = text;
return lines;
}var len = text.length - runLen;
for (; i >= 0 && i < len; n++) i = text.indexOf (run, i + runLen);

lines =  new Array (n);
i = 0;
var ipt = 0;
var pt = 0;
for (; (ipt = text.indexOf (run, i)) >= 0 && pt + 1 < n; ) {
lines[pt++] = text.substring (i, ipt);
i = ipt + runLen;
}
if (text.indexOf (run, len) != len) len += runLen;
lines[pt] = text.substring (i, len);
return lines;
}, "~S,~S");
c$.getQuotedStringAt = $_M(c$, "getQuotedStringAt", 
function (line, ipt0) {
var next = [ipt0];
return JU.PT.getQuotedStringNext (line, next);
}, "~S,~N");
c$.getQuotedStringNext = $_M(c$, "getQuotedStringNext", 
function (line, next) {
var value = line;
var i = next[0];
if (i < 0 || (i = value.indexOf ("\"", i)) < 0) return "";
next[0] = ++i;
value = value.substring (i);
i = -1;
while (++i < value.length && value.charAt (i) != '"') if (value.charAt (i) == '\\') i++;

next[0] += i + 1;
return value.substring (0, i);
}, "~S,~A");
c$.isOneOf = $_M(c$, "isOneOf", 
function (key, semiList) {
if (semiList.length == 0) return false;
if (semiList.charAt (0) != ';') semiList = ";" + semiList + ";";
return key.indexOf (";") < 0 && semiList.indexOf (';' + key + ';') >= 0;
}, "~S,~S");
c$.getQuotedAttribute = $_M(c$, "getQuotedAttribute", 
function (info, name) {
var i = info.indexOf (name + "=");
return (i < 0 ? null : JU.PT.getQuotedStringAt (info, i));
}, "~S,~S");
c$.approx = $_M(c$, "approx", 
function (f, n) {
return Math.round (f * n) / n;
}, "~N,~N");
c$.simpleReplace = $_M(c$, "simpleReplace", 
function (str, strFrom, strTo) {
if (str == null || strFrom.length == 0 || str.indexOf (strFrom) < 0) return str;
var isOnce = (strTo.indexOf (strFrom) >= 0);
do {
str = str.$replace (strFrom, strTo);
} while (!isOnce && str.indexOf (strFrom) >= 0);
return str;
}, "~S,~S,~S");
c$.formatF = $_M(c$, "formatF", 
function (value, width, precision, alignLeft, zeroPad) {
return JU.PT.formatS (JU.DF.formatDecimal (value, precision), width, 0, alignLeft, zeroPad);
}, "~N,~N,~N,~B,~B");
c$.formatD = $_M(c$, "formatD", 
function (value, width, precision, alignLeft, zeroPad, allowOverflow) {
return JU.PT.formatS (JU.DF.formatDecimal (value, -1 - precision), width, 0, alignLeft, zeroPad);
}, "~N,~N,~N,~B,~B,~B");
c$.formatS = $_M(c$, "formatS", 
function (value, width, precision, alignLeft, zeroPad) {
if (value == null) return "";
var len = value.length;
if (precision != 2147483647 && precision > 0 && precision < len) value = value.substring (0, precision);
 else if (precision < 0 && len + precision >= 0) value = value.substring (len + precision + 1);
var padLength = width - value.length;
if (padLength <= 0) return value;
var isNeg = (zeroPad && !alignLeft && value.charAt (0) == '-');
var padChar = (zeroPad ? '0' : ' ');
var padChar0 = (isNeg ? '-' : padChar);
var sb =  new JU.SB ();
if (alignLeft) sb.append (value);
sb.appendC (padChar0);
for (var i = padLength; --i > 0; ) sb.appendC (padChar);

if (!alignLeft) sb.append (isNeg ? padChar + value.substring (1) : value);
return sb.toString ();
}, "~S,~N,~N,~B,~B");
c$.replaceAllCharacters = $_M(c$, "replaceAllCharacters", 
function (str, strFrom, strTo) {
for (var i = strFrom.length; --i >= 0; ) {
var chFrom = strFrom.substring (i, i + 1);
str = JU.PT.simpleReplace (str, chFrom, strTo);
}
return str;
}, "~S,~S,~S");
c$.trim = $_M(c$, "trim", 
function (str, chars) {
if (chars.length == 0) return str.trim ();
var len = str.length;
var k = 0;
while (k < len && chars.indexOf (str.charAt (k)) >= 0) k++;

var m = str.length - 1;
while (m > k && chars.indexOf (str.charAt (m)) >= 0) m--;

return str.substring (k, m + 1);
}, "~S,~S");
c$.trimQuotes = $_M(c$, "trimQuotes", 
function (value) {
return (value != null && value.length > 1 && value.startsWith ("\"") && value.endsWith ("\"") ? value.substring (1, value.length - 1) : value);
}, "~S");
c$.replaceAllCharacter = $_M(c$, "replaceAllCharacter", 
function (str, strFrom, chTo) {
if (str == null) return null;
for (var i = strFrom.length; --i >= 0; ) str = str.$replace (strFrom.charAt (i), chTo);

return str;
}, "~S,~S,~S");
c$.toJSON = $_M(c$, "toJSON", 
function (infoType, info) {
var sb =  new JU.SB ();
var sep = "";
if (info == null) return JU.PT.packageJSON (infoType, null);
if (Clazz_instanceOf (info, Integer) || Clazz_instanceOf (info, Float) || Clazz_instanceOf (info, Double)) return JU.PT.packageJSON (infoType, info.toString ());
if (Clazz_instanceOf (info, String)) return JU.PT.packageJSON (infoType, JU.PT.fixString (info));
if (JU.PT.isAS (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).append (JU.PT.fixString ((info)[i]));
sep = ",";
}
sb.append ("]");
return JU.PT.packageJSONSb (infoType, sb);
}if (JU.PT.isAI (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).appendI ((info)[i]);
sep = ",";
}
sb.append ("]");
return JU.PT.packageJSONSb (infoType, sb);
}if (JU.PT.isAF (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).appendF ((info)[i]);
sep = ",";
}
sb.append ("]");
return JU.PT.packageJSONSb (infoType, sb);
}if (JU.PT.isAD (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).appendD ((info)[i]);
sep = ",";
}
sb.append ("]");
return JU.PT.packageJSONSb (infoType, sb);
}if (JU.PT.isAP (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep);
JU.PT.addJsonTuple (sb, (info)[i]);
sep = ",";
}
sb.append ("]");
return JU.PT.packageJSONSb (infoType, sb);
}if (JU.PT.isASS (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).append (JU.PT.toJSON (null, (info)[i]));
sep = ",";
}
sb.append ("]");
return JU.PT.packageJSONSb (infoType, sb);
}if (JU.PT.isAII (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).append (JU.PT.toJSON (null, (info)[i]));
sep = ",";
}
sb.append ("]");
return JU.PT.packageJSONSb (infoType, sb);
}if (JU.PT.isAFF (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).append (JU.PT.toJSON (null, (info)[i]));
sep = ",";
}
sb.append ("]");
return JU.PT.packageJSONSb (infoType, sb);
}if (JU.PT.isAFFF (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).append (JU.PT.toJSON (null, (info)[i]));
sep = ",";
}
sb.append ("]");
return JU.PT.packageJSONSb (infoType, sb);
}if (Clazz_instanceOf (info, JU.List)) {
sb.append ("[ ");
var imax = (info).size ();
for (var i = 0; i < imax; i++) {
sb.append (sep).append (JU.PT.toJSON (null, (info).get (i)));
sep = ",";
}
sb.append (" ]");
return JU.PT.packageJSONSb (infoType, sb);
}if (Clazz_instanceOf (info, JU.M4)) {
var x =  Clazz_newFloatArray (4, 0);
var m4 = info;
sb.appendC ('[');
for (var i = 0; i < 4; i++) {
if (i > 0) sb.appendC (',');
m4.getRow (i, x);
sb.append (JU.PT.toJSON (null, x));
}
sb.appendC (']');
return JU.PT.packageJSONSb (infoType, sb);
}if (Clazz_instanceOf (info, JU.M3)) {
var x =  Clazz_newFloatArray (3, 0);
var m3 = info;
sb.appendC ('[');
for (var i = 0; i < 3; i++) {
if (i > 0) sb.appendC (',');
m3.getRow (i, x);
sb.append (JU.PT.toJSON (null, x));
}
sb.appendC (']');
return JU.PT.packageJSONSb (infoType, sb);
}if (Clazz_instanceOf (info, JU.T3)) {
JU.PT.addJsonTuple (sb, info);
return JU.PT.packageJSONSb (infoType, sb);
}if (Clazz_instanceOf (info, JU.A4)) {
sb.append ("[").appendF ((info).x).append (",").appendF ((info).y).append (",").appendF ((info).z).append (",").appendF (((info).angle * 180 / 3.141592653589793)).append ("]");
return JU.PT.packageJSONSb (infoType, sb);
}if (Clazz_instanceOf (info, JU.P4)) {
sb.append ("[").appendF ((info).x).append (",").appendF ((info).y).append (",").appendF ((info).z).append (",").appendF ((info).w).append ("]");
return JU.PT.packageJSONSb (infoType, sb);
}if (Clazz_instanceOf (info, java.util.Map)) {
sb.append ("{ ");
for (var key, $key = (info).keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) {
sb.append (sep).append (JU.PT.packageJSON (key, JU.PT.toJSON (null, (info).get (key))));
sep = ",";
}
sb.append (" }");
return JU.PT.packageJSONSb (infoType, sb);
}return JU.PT.packageJSON (infoType, JU.PT.fixString (info.toString ()));
}, "~S,~O");
c$.packageJSONSb = $_M(c$, "packageJSONSb", 
function (infoType, sb) {
return JU.PT.packageJSON (infoType, sb.toString ());
}, "~S,JU.SB");
c$.packageJSON = $_M(c$, "packageJSON", 
function (infoType, info) {
if (infoType == null) return info;
return "\"" + infoType + "\": " + info;
}, "~S,~S");
c$.fixString = $_M(c$, "fixString", 
function (s) {
{
if (typeof s == "undefined") return "null"
}if (s == null || s.indexOf ("{\"") == 0) return s;
s = JU.PT.simpleReplace (s, "\"", "''");
s = JU.PT.simpleReplace (s, "\n", " | ");
return "\"" + s + "\"";
}, "~S");
c$.addJsonTuple = $_M(c$, "addJsonTuple", 
function (sb, pt) {
sb.append ("[").appendF (pt.x).append (",").appendF (pt.y).append (",").appendF (pt.z).append ("]");
}, "JU.SB,JU.T3");
c$.isAS = $_M(c$, "isAS", 
function (x) {
{
return Clazz_isAS(x);
}}, "~O");
c$.isASS = $_M(c$, "isASS", 
function (x) {
{
return Clazz_isASS(x);
}}, "~O");
c$.isAP = $_M(c$, "isAP", 
function (x) {
{
return Clazz_isAP(x);
}}, "~O");
c$.isAF = $_M(c$, "isAF", 
function (x) {
{
return Clazz_isAF(x);
}}, "~O");
c$.isAFloat = $_M(c$, "isAFloat", 
function (x) {
{
return Clazz_isAFloat(x);
}}, "~O");
c$.isAD = $_M(c$, "isAD", 
function (x) {
{
return Clazz_isAF(x);
}}, "~O");
c$.isAB = $_M(c$, "isAB", 
function (x) {
{
return Clazz_isAI(x);
}}, "~O");
c$.isAI = $_M(c$, "isAI", 
function (x) {
{
return Clazz_isAI(x);
}}, "~O");
c$.isAII = $_M(c$, "isAII", 
function (x) {
{
return Clazz_isAII(x);
}}, "~O");
c$.isAFF = $_M(c$, "isAFF", 
function (x) {
{
return Clazz_isAFF(x);
}}, "~O");
c$.isAFFF = $_M(c$, "isAFFF", 
function (x) {
{
return Clazz_isAFFF(x);
}}, "~O");
c$.escapeUrl = $_M(c$, "escapeUrl", 
function (url) {
url = JU.PT.simpleReplace (url, "\n", "");
url = JU.PT.simpleReplace (url, "%", "%25");
url = JU.PT.simpleReplace (url, "#", "%23");
url = JU.PT.simpleReplace (url, "[", "%5B");
url = JU.PT.simpleReplace (url, "]", "%5D");
url = JU.PT.simpleReplace (url, " ", "%20");
return url;
}, "~S");
Clazz_defineStatics (c$,
"tensScale", [10, 100, 1000, 10000, 100000, 1000000],
"decimalScale", [0.1, 0.01, 0.001, 0.0001, 0.00001, 0.000001, 0.0000001, 0.00000001, 0.000000001],
"FLOAT_MIN_SAFE", 2E-45);
});
Clazz_declarePackage ("JU");
Clazz_load (null, "JU.AU", ["java.util.Arrays", "JU.List"], function () {
c$ = Clazz_declareType (JU, "AU");
c$.ensureLength = $_M(c$, "ensureLength", 
function (array, minimumLength) {
if (array != null && JU.AU.getLength (array) >= minimumLength) return array;
return JU.AU.arrayCopyObject (array, minimumLength);
}, "~O,~N");
c$.ensureLengthS = $_M(c$, "ensureLengthS", 
function (array, minimumLength) {
if (array != null && array.length >= minimumLength) return array;
return JU.AU.arrayCopyS (array, minimumLength);
}, "~A,~N");
c$.ensureLengthA = $_M(c$, "ensureLengthA", 
function (array, minimumLength) {
if (array != null && array.length >= minimumLength) return array;
return JU.AU.arrayCopyF (array, minimumLength);
}, "~A,~N");
c$.ensureLengthI = $_M(c$, "ensureLengthI", 
function (array, minimumLength) {
if (array != null && array.length >= minimumLength) return array;
return JU.AU.arrayCopyI (array, minimumLength);
}, "~A,~N");
c$.ensureLengthShort = $_M(c$, "ensureLengthShort", 
function (array, minimumLength) {
if (array != null && array.length >= minimumLength) return array;
return JU.AU.arrayCopyShort (array, minimumLength);
}, "~A,~N");
c$.ensureLengthByte = $_M(c$, "ensureLengthByte", 
function (array, minimumLength) {
if (array != null && array.length >= minimumLength) return array;
return JU.AU.arrayCopyByte (array, minimumLength);
}, "~A,~N");
c$.doubleLength = $_M(c$, "doubleLength", 
function (array) {
return JU.AU.arrayCopyObject (array, (array == null ? 16 : 2 * JU.AU.getLength (array)));
}, "~O");
c$.doubleLengthS = $_M(c$, "doubleLengthS", 
function (array) {
return JU.AU.arrayCopyS (array, (array == null ? 16 : 2 * array.length));
}, "~A");
c$.doubleLengthF = $_M(c$, "doubleLengthF", 
function (array) {
return JU.AU.arrayCopyF (array, (array == null ? 16 : 2 * array.length));
}, "~A");
c$.doubleLengthI = $_M(c$, "doubleLengthI", 
function (array) {
return JU.AU.arrayCopyI (array, (array == null ? 16 : 2 * array.length));
}, "~A");
c$.doubleLengthShort = $_M(c$, "doubleLengthShort", 
function (array) {
return JU.AU.arrayCopyShort (array, (array == null ? 16 : 2 * array.length));
}, "~A");
c$.doubleLengthByte = $_M(c$, "doubleLengthByte", 
function (array) {
return JU.AU.arrayCopyByte (array, (array == null ? 16 : 2 * array.length));
}, "~A");
c$.doubleLengthBool = $_M(c$, "doubleLengthBool", 
function (array) {
return JU.AU.arrayCopyBool (array, (array == null ? 16 : 2 * array.length));
}, "~A");
c$.deleteElements = $_M(c$, "deleteElements", 
function (array, firstElement, nElements) {
if (nElements == 0 || array == null) return array;
var oldLength = JU.AU.getLength (array);
if (firstElement >= oldLength) return array;
var n = oldLength - (firstElement + nElements);
if (n < 0) n = 0;
var t = JU.AU.newInstanceO (array, firstElement + n);
if (firstElement > 0) System.arraycopy (array, 0, t, 0, firstElement);
if (n > 0) System.arraycopy (array, firstElement + nElements, t, firstElement, n);
return t;
}, "~O,~N,~N");
c$.arrayCopyObject = $_M(c$, "arrayCopyObject", 
function (array, newLength) {
if (array == null) {
return null;
}var oldLength = JU.AU.getLength (array);
if (newLength == oldLength) return array;
var t = JU.AU.newInstanceO (array, newLength);
System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength);
return t;
}, "~O,~N");
c$.newInstanceO = $_M(c$, "newInstanceO", 
function (array, n) {
{
return new Array(n);
}}, "~O,~N");
c$.getLength = $_M(c$, "getLength", 
function (array) {
{
return array.length
}}, "~O");
c$.arrayCopyS = $_M(c$, "arrayCopyS", 
function (array, newLength) {
if (newLength < 0) newLength = array.length;
var t =  new Array (newLength);
if (array != null) {
var oldLength = array.length;
System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength);
}return t;
}, "~A,~N");
c$.arrayCopyII = $_M(c$, "arrayCopyII", 
function (array, newLength) {
var t = JU.AU.newInt2 (newLength);
if (array != null) {
var oldLength = array.length;
System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength);
}return t;
}, "~A,~N");
c$.arrayCopyPt = $_M(c$, "arrayCopyPt", 
function (array, newLength) {
if (newLength < 0) newLength = array.length;
var t =  new Array (newLength);
if (array != null) {
var oldLength = array.length;
System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength);
}return t;
}, "~A,~N");
c$.arrayCopyF = $_M(c$, "arrayCopyF", 
function (array, newLength) {
if (newLength < 0) newLength = array.length;
var t =  Clazz_newFloatArray (newLength, 0);
if (array != null) {
var oldLength = array.length;
System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength);
}return t;
}, "~A,~N");
c$.arrayCopyI = $_M(c$, "arrayCopyI", 
function (array, newLength) {
if (newLength < 0) newLength = array.length;
var t =  Clazz_newIntArray (newLength, 0);
if (array != null) {
var oldLength = array.length;
System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength);
}return t;
}, "~A,~N");
c$.arrayCopyRangeI = $_M(c$, "arrayCopyRangeI", 
function (array, i0, n) {
if (array == null) return null;
var oldLength = array.length;
if (n == -1) n = oldLength;
if (n == -2) n = Clazz_doubleToInt (oldLength / 2);
n = n - i0;
var t =  Clazz_newIntArray (n, 0);
System.arraycopy (array, i0, t, 0, n);
return t;
}, "~A,~N,~N");
c$.arrayCopyRangeRevI = $_M(c$, "arrayCopyRangeRevI", 
function (array, i0, n) {
if (array == null) return null;
var t = JU.AU.arrayCopyRangeI (array, i0, n);
if (n < 0) n = array.length;
for (var i = Clazz_doubleToInt (n / 2); --i >= 0; ) JU.AU.swapInt (t, i, n - 1 - i);

return t;
}, "~A,~N,~N");
c$.arrayCopyShort = $_M(c$, "arrayCopyShort", 
function (array, newLength) {
if (newLength < 0) newLength = array.length;
var t =  Clazz_newShortArray (newLength, 0);
if (array != null) {
var oldLength = array.length;
System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength);
}return t;
}, "~A,~N");
c$.arrayCopyByte = $_M(c$, "arrayCopyByte", 
function (array, newLength) {
if (newLength < 0) newLength = array.length;
var t =  Clazz_newByteArray (newLength, 0);
if (array != null) {
var oldLength = array.length;
System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength);
}return t;
}, "~A,~N");
c$.arrayCopyBool = $_M(c$, "arrayCopyBool", 
function (array, newLength) {
if (newLength < 0) newLength = array.length;
var t =  Clazz_newBooleanArray (newLength, false);
if (array != null) {
var oldLength = array.length;
System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength);
}return t;
}, "~A,~N");
c$.swapInt = $_M(c$, "swapInt", 
function (array, indexA, indexB) {
var t = array[indexA];
array[indexA] = array[indexB];
array[indexB] = t;
}, "~A,~N,~N");
c$.dumpArray = $_M(c$, "dumpArray", 
function (msg, A, x1, x2, y1, y2) {
var s = "dumpArray: " + msg + "\n";
for (var x = x1; x <= x2; x++) s += "\t*" + x + "*";

for (var y = y2; y >= y1; y--) {
s += "\n*" + y + "*";
for (var x = x1; x <= x2; x++) s += "\t" + (x < A.length && y < A[x].length ? A[x][y] : NaN);

}
return s;
}, "~S,~A,~N,~N,~N,~N");
c$.dumpIntArray = $_M(c$, "dumpIntArray", 
function (A, n) {
var str = "";
for (var i = 0; i < n; i++) str += " " + A[i];

return str;
}, "~A,~N");
c$.sortedItem = $_M(c$, "sortedItem", 
function (v, n) {
if (v.size () == 0) return null;
if (v.size () == 1) return v.get (0);
var keys = v.toArray ( new Array (v.size ()));
java.util.Arrays.sort (keys);
return keys[n % keys.length];
}, "JU.List,~N");
c$.createArrayOfArrayList = $_M(c$, "createArrayOfArrayList", 
function (size) {
return  new Array (size);
}, "~N");
c$.createArrayOfHashtable = $_M(c$, "createArrayOfHashtable", 
function (size) {
return  new Array (size);
}, "~N");
c$.swap = $_M(c$, "swap", 
function (o, i, j) {
var oi = o[i];
o[i] = o[j];
o[j] = oi;
}, "~A,~N,~N");
c$.newFloat2 = $_M(c$, "newFloat2", 
function (n) {
{
return Clazz_newArray(n, null);
}}, "~N");
c$.newInt2 = $_M(c$, "newInt2", 
function (n) {
{
return Clazz_newArray(n, null);
}}, "~N");
c$.newInt3 = $_M(c$, "newInt3", 
function (nx, ny) {
{
return Clazz_newArray(nx, null);
}}, "~N,~N");
c$.newFloat3 = $_M(c$, "newFloat3", 
function (nx, ny) {
{
return Clazz_newArray(nx, null);
}}, "~N,~N");
c$.newInt4 = $_M(c$, "newInt4", 
function (n) {
{
return Clazz_newArray(n, null);
}}, "~N");
c$.newShort2 = $_M(c$, "newShort2", 
function (n) {
{
return Clazz_newArray(n, null);
}}, "~N");
c$.newByte2 = $_M(c$, "newByte2", 
function (n) {
{
return Clazz_newArray(n, null);
}}, "~N");
c$.newDouble2 = $_M(c$, "newDouble2", 
function (n) {
{
return Clazz_newArray(n, null);
}}, "~N");
c$.removeMapKeys = $_M(c$, "removeMapKeys", 
function (map, root) {
var list =  new JU.List ();
for (var key, $key = map.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) if (key.startsWith (root)) list.addLast (key);

for (var i = list.size (); --i >= 0; ) map.remove (list.get (i));

return list.size ();
}, "java.util.Map,~S");
});
$_L(["java.util.Map"],"java.util.MapEntry",null,function(){
c$=$_C(function(){
this.key=null;
this.value=null;
$_Z(this,arguments);
},java.util,"MapEntry",null,[java.util.Map.Entry,Cloneable]);
$_K(c$,
function(theKey){
this.key=theKey;
},"~O");
$_K(c$,
function(theKey,theValue){
this.key=theKey;
this.value=theValue;
},"~O,~O");
$_M(c$,"clone",
function(){
try{
return $_U(this,java.util.MapEntry,"clone",[]);
}catch(e){
if($_O(e,CloneNotSupportedException)){
return null;
}else{
throw e;
}
}
});
$_V(c$,"equals",
function(object){
if(this===object){
return true;
}if($_O(object,java.util.Map.Entry)){
var entry=object;
return(this.key==null?entry.getKey()==null:this.key.equals(entry.getKey()))&&(this.value==null?entry.getValue()==null:this.value.equals(entry.getValue()));
}return false;
},"~O");
$_V(c$,"getKey",
function(){
return this.key;
});
$_V(c$,"getValue",
function(){
return this.value;
});
$_V(c$,"hashCode",
function(){
return(this.key==null?0:this.key.hashCode())^(this.value==null?0:this.value.hashCode());
});
$_V(c$,"setValue",
function(object){
var result=this.value;
this.value=object;
return result;
},"~O");
$_V(c$,"toString",
function(){
return this.key+"="+this.value;
});
$_I(java.util.MapEntry,"Type");
});
c$=$_T(java.util,"Dictionary");
$_K(c$,
function(){
});
$_L(["java.util.Collection"],"java.util.AbstractCollection",["java.lang.StringBuilder","$.UnsupportedOperationException","java.lang.reflect.Array"],function(){
c$=$_T(java.util,"AbstractCollection",null,java.util.Collection);
$_K(c$,
function(){
});
$_V(c$,"add",
function(object){
throw new UnsupportedOperationException();
},"~O");
$_V(c$,"addAll",
function(collection){
var result=false;
var it=collection.iterator();
while(it.hasNext()){
if(this.add(it.next())){
result=true;
}}
return result;
},"java.util.Collection");
$_V(c$,"clear",
function(){
var it=this.iterator();
while(it.hasNext()){
it.next();
it.remove();
}
});
$_V(c$,"contains",
function(object){
var it=this.iterator();
if(object!=null){
while(it.hasNext()){
if(object.equals(it.next())){
return true;
}}
}else{
while(it.hasNext()){
if(it.next()==null){
return true;
}}
}return false;
},"~O");
$_V(c$,"containsAll",
function(collection){
var it=collection.iterator();
while(it.hasNext()){
if(!this.contains(it.next())){
return false;
}}
return true;
},"java.util.Collection");
$_V(c$,"isEmpty",
function(){
return this.size()==0;
});
$_V(c$,"remove",
function(object){
var it=this.iterator();
if(object!=null){
while(it.hasNext()){
if(object.equals(it.next())){
it.remove();
return true;
}}
}else{
while(it.hasNext()){
if(it.next()==null){
it.remove();
return true;
}}
}return false;
},"~O");
$_V(c$,"removeAll",
function(collection){
var result=false;
var it=this.iterator();
while(it.hasNext()){
if(collection.contains(it.next())){
it.remove();
result=true;
}}
return result;
},"java.util.Collection");
$_V(c$,"retainAll",
function(collection){
var result=false;
var it=this.iterator();
while(it.hasNext()){
if(!collection.contains(it.next())){
it.remove();
result=true;
}}
return result;
},"java.util.Collection");
$_M(c$,"toArray",
function(){
var size=this.size();
var index=0;
var it=this.iterator();
var array=new Array(size);
while(index<size){
array[index++]=it.next();
}
return array;
});
$_M(c$,"toArray",
function(contents){
var size=this.size();
var index=0;
if(size>contents.length){
var ct=contents.getClass().getComponentType();
contents=java.lang.reflect.Array.newInstance(ct,size);
}for(var entry,$entry=this.iterator();$entry.hasNext()&&((entry=$entry.next())||true);){
contents[index++]=entry;
}
if(index<contents.length){
contents[index]=null;
}return contents;
},"~A");
$_V(c$,"toString",
function(){
if(this.isEmpty()){
return"[]";
}var buffer=new StringBuilder(this.size()*16);
buffer.append('[');
var it=this.iterator();
while(it.hasNext()){
var next=it.next();
if(next!==this){
buffer.append(next);
}else{
buffer.append("(this Collection)");
}if(it.hasNext()){
buffer.append(", ");
}}
buffer.append(']');
return buffer.toString();
});
});
$_L(null,"java.lang.AbstractStringBuilder",["java.io.InvalidObjectException","java.lang.ArrayIndexOutOfBoundsException","$.IndexOutOfBoundsException","$.NegativeArraySizeException","$.NullPointerException","$.StringIndexOutOfBoundsException"],function(){
c$=$_C(function(){
this.value=null;
this.count=0;
this.shared=false;
$_Z(this,arguments);
},java.lang,"AbstractStringBuilder");
$_M(c$,"getValue",
function(){
return this.value;
});
$_M(c$,"shareValue",
function(){
this.shared=true;
return this.value;
});
$_M(c$,"set",
function(val,len){
if(val==null)val=$_A(0,'\0');
if(val.length<len)throw new java.io.InvalidObjectException(("K0199"));
this.shared=false;
this.value=val;
this.count=len;
},"~A,~N");
$_K(c$,
function(){
this.value=$_A(16,'\0');
});
$_K(c$,
function(capacity){
if(capacity<0)throw new NegativeArraySizeException();
this.value=$_A(capacity,'\0');
},"~N");
$_K(c$,
function(string){
this.count=string.length;
this.shared=false;
this.value=$_A(this.count+16,'\0');
string.getChars(0,this.count,this.value,0);
},"~S");
$_M(c$,"enlargeBuffer",
($fz=function(min){
var twice=(this.value.length<<1)+2;
var newData=$_A(min>twice?min:twice,'\0');
System.arraycopy(this.value,0,newData,0,this.count);
this.value=newData;
this.shared=false;
},$fz.isPrivate=true,$fz),"~N");
$_M(c$,"appendNull",
function(){
var newSize=this.count+4;
if(newSize>this.value.length){
this.enlargeBuffer(newSize);
}else if(this.shared){
this.value=this.value.clone();
this.shared=false;
}this.value[this.count++]='n';
this.value[this.count++]='u';
this.value[this.count++]='l';
this.value[this.count++]='l';
});
$_M(c$,"append0",
function(chars){
var newSize=this.count+chars.length;
if(newSize>this.value.length){
this.enlargeBuffer(newSize);
}else if(this.shared){
this.value=this.value.clone();
this.shared=false;
}System.arraycopy(chars,0,this.value,this.count,chars.length);
this.count=newSize;
},"~A");
$_M(c$,"append0",
function(chars,start,length){
if(chars==null){
throw new NullPointerException();
}if(start>=0&&0<=length&&length<=chars.length-start){
var newSize=this.count+length;
if(newSize>this.value.length){
this.enlargeBuffer(newSize);
}else if(this.shared){
this.value=this.value.clone();
this.shared=false;
}System.arraycopy(chars,start,this.value,this.count,length);
this.count=newSize;
}else{
throw new ArrayIndexOutOfBoundsException();
}},"~A,~N,~N");
$_M(c$,"append0",
function(ch){
if(this.count==this.value.length){
this.enlargeBuffer(this.count+1);
}if(this.shared){
this.value=this.value.clone();
this.shared=false;
}this.value[this.count++]=ch;
},"~N");
$_M(c$,"append0",
function(string){
if(string==null){
this.appendNull();
return;
}var adding=string.length;
var newSize=this.count+adding;
if(newSize>this.value.length){
this.enlargeBuffer(newSize);
}else if(this.shared){
this.value=this.value.clone();
this.shared=false;
}string.getChars(0,adding,this.value,this.count);
this.count=newSize;
},"~S");
$_M(c$,"append0",
function(s,start,end){
if(s==null)s="null";
if(start<0||end<0||start>end||end>s.length())throw new IndexOutOfBoundsException();
this.append0(s.subSequence(start,end).toString());
},"CharSequence,~N,~N");
$_M(c$,"capacity",
function(){
return this.value.length;
});
$_M(c$,"charAt",
function(index){
if(index<0||index>=this.count)throw new StringIndexOutOfBoundsException(index);
return this.value[index];
},"~N");
$_M(c$,"delete0",
function(start,end){
if(start>=0){
if(end>this.count){
end=this.count;
}if(end==start){
return;
}if(end>start){
var length=this.count-end;
if(length>0){
if(!this.shared){
System.arraycopy(this.value,end,this.value,start,length);
}else{
var newData=$_A(this.value.length,'\0');
System.arraycopy(this.value,0,newData,0,start);
System.arraycopy(this.value,end,newData,start,length);
this.value=newData;
this.shared=false;
}}this.count-=end-start;
return;
}}throw new StringIndexOutOfBoundsException();
},"~N,~N");
$_M(c$,"deleteCharAt0",
function(location){
if(0>location||location>=this.count)throw new StringIndexOutOfBoundsException(location);
var length=this.count-location-1;
if(length>0){
if(!this.shared){
System.arraycopy(this.value,location+1,this.value,location,length);
}else{
var newData=$_A(this.value.length,'\0');
System.arraycopy(this.value,0,newData,0,location);
System.arraycopy(this.value,location+1,newData,location,length);
this.value=newData;
this.shared=false;
}}this.count--;
},"~N");
$_M(c$,"ensureCapacity",
function(min){
if(min>this.value.length){
this.enlargeBuffer(min);
}},"~N");
$_M(c$,"getChars",
function(start,end,dest,destStart){
if(start>this.count||end>this.count||start>end){
throw new StringIndexOutOfBoundsException();
}System.arraycopy(this.value,start,dest,destStart,end-start);
},"~N,~N,~A,~N");
$_M(c$,"insert0",
function(index,chars){
if(0>index||index>this.count){
throw new StringIndexOutOfBoundsException(index);
}if(chars.length!=0){
this.move(chars.length,index);
System.arraycopy(chars,0,this.value,index,chars.length);
this.count+=chars.length;
}},"~N,~A");
$_M(c$,"insert0",
function(index,chars,start,length){
if(0<=index&&index<=this.count){
if(start>=0&&0<=length&&length<=chars.length-start){
if(length!=0){
this.move(length,index);
System.arraycopy(chars,start,this.value,index,length);
this.count+=length;
}return;
}throw new StringIndexOutOfBoundsException("offset "+start+", len "+length+", array.length "+chars.length);
}throw new StringIndexOutOfBoundsException(index);
},"~N,~A,~N,~N");
$_M(c$,"insert0",
function(index,ch){
if(0>index||index>this.count){
throw new ArrayIndexOutOfBoundsException(index);
}this.move(1,index);
this.value[index]=ch;
this.count++;
},"~N,~N");
$_M(c$,"insert0",
function(index,string){
if(0<=index&&index<=this.count){
if(string==null)string="null";
var min=string.length;
if(min!=0){
this.move(min,index);
string.getChars(0,min,this.value,index);
this.count+=min;
}}else{
throw new StringIndexOutOfBoundsException(index);
}},"~N,~S");
$_M(c$,"insert0",
function(index,s,start,end){
if(s==null)s="null";
if(index<0||index>this.count||start<0||end<0||start>end||end>s.length())throw new IndexOutOfBoundsException();
this.insert0(index,s.subSequence(start,end).toString());
},"~N,CharSequence,~N,~N");
$_M(c$,"length",
function(){
return this.count;
});
$_M(c$,"move",
($fz=function(size,index){
var newSize;
if(this.value.length-this.count>=size){
if(!this.shared){
System.arraycopy(this.value,index,this.value,index+size,this.count-index);
return;
}newSize=this.value.length;
}else{
var a=this.count+size;
var b=(this.value.length<<1)+2;
newSize=a>b?a:b;
}var newData=$_A(newSize,'\0');
System.arraycopy(this.value,0,newData,0,index);
System.arraycopy(this.value,index,newData,index+size,this.count-index);
this.value=newData;
this.shared=false;
},$fz.isPrivate=true,$fz),"~N,~N");
$_M(c$,"replace0",
function(start,end,string){
if(start>=0){
if(end>this.count)end=this.count;
if(end>start){
var stringLength=string.length;
var diff=end-start-stringLength;
if(diff>0){
if(!this.shared){
System.arraycopy(this.value,end,this.value,start+stringLength,this.count-end);
}else{
var newData=$_A(this.value.length,'\0');
System.arraycopy(this.value,0,newData,0,start);
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}else{
var newData=$_A(this.value.length,'\0');
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this.value=newData;
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$_M(c$,"setLength",
function(length){
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if(this.shared){
var newData=$_A(this.value.length,'\0');
System.arraycopy(this.value,0,newData,0,this.count);
this.value=newData;
this.shared=false;
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}
}}}this.count=length;
},"~N");
$_M(c$,"substring",
function(start){
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this.shared=true;
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$_M(c$,"substring",
function(start,end){
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$_V(c$,"toString",
function(){
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if(this.count>=256&&this.count<=(this.value.length>>1))return String.instantialize(this.value,0,this.count);
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$_M(c$,"indexOf",
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$_M(c$,"indexOf",
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$_M(c$,"lastIndexOf",
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$_M(c$,"lastIndexOf",
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var firstChar=subString.charAt(0);
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var found=false;
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var o1=i;
var o2=0;
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}
if(o2==subCount)return i;
start=i-1;
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}return start<this.count?start:this.count;
}return-1;
},"~S,~N");
$_M(c$,"trimToSize",
function(){
if(this.count<this.value.length){
var newValue=$_A(this.count,'\0');
System.arraycopy(this.value,0,newValue,0,this.count);
this.value=newValue;
this.shared=false;
}});
$_S(c$,
"INITIAL_CAPACITY",16);
});
$_L(["java.lang.AbstractStringBuilder","$.Appendable"],"java.lang.StringBuilder",["java.lang.Double","$.Float","$.Long"],function(){
c$=$_T(java.lang,"StringBuilder",AbstractStringBuilder,[Appendable,CharSequence,java.io.Serializable]);
$_K(c$,
function(seq){
$_R(this,StringBuilder,[seq.toString()]);
},"CharSequence");
$_M(c$,"append",
function(b){
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return this;
},"~B");
$_M(c$,"append",
function(c){
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return this;
},"~N");
$_M(c$,"append",
function(i){
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return this;
},"~N");
$_M(c$,"append",
function(lng){
this.append0(Long.toString(lng));
return this;
},"~N");
$_M(c$,"append",
function(f){
this.append0(Float.toString(f));
return this;
},"~N");
$_M(c$,"append",
function(d){
this.append0(Double.toString(d));
return this;
},"~N");
$_M(c$,"append",
function(obj){
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this.appendNull();
}else{
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},"~O");
$_M(c$,"append",
function(str){
this.append0(str);
return this;
},"~S");
$_M(c$,"append",
function(sb){
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this.appendNull();
}else{
this.append0(sb.getValue(),0,sb.length());
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},"StringBuffer");
$_M(c$,"append",
function(ch){
this.append0(ch);
return this;
},"~A");
$_M(c$,"append",
function(str,offset,len){
this.append0(str,offset,len);
return this;
},"~A,~N,~N");
$_M(c$,"append",
function(csq){
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this.appendNull();
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this.append0(csq.toString());
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},"CharSequence");
$_M(c$,"append",
function(csq,start,end){
this.append0(csq,start,end);
return this;
},"CharSequence,~N,~N");
$_M(c$,"$delete",
function(start,end){
this.delete0(start,end);
return this;
},"~N,~N");
$_M(c$,"deleteCharAt",
function(index){
this.deleteCharAt0(index);
return this;
},"~N");
$_M(c$,"insert",
function(offset,b){
this.insert0(offset,b?"true":"false");
return this;
},"~N,~B");
$_M(c$,"insert",
function(offset,c){
this.insert0(offset,c);
return this;
},"~N,~N");
$_M(c$,"insert",
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this.insert0(offset,Integer.toString(i));
return this;
},"~N,~N");
$_M(c$,"insert",
function(offset,l){
this.insert0(offset,Long.toString(l));
return this;
},"~N,~N");
$_M(c$,"insert",
function(offset,f){
this.insert0(offset,Float.toString(f));
return this;
},"~N,~N");
$_M(c$,"insert",
function(offset,d){
this.insert0(offset,Double.toString(d));
return this;
},"~N,~N");
$_M(c$,"insert",
function(offset,obj){
this.insert0(offset,obj==null?"null":obj.toString());
return this;
},"~N,~O");
$_M(c$,"insert",
function(offset,str){
this.insert0(offset,str);
return this;
},"~N,~S");
$_M(c$,"insert",
function(offset,ch){
this.insert0(offset,ch);
return this;
},"~N,~A");
$_M(c$,"insert",
function(offset,str,strOffset,strLen){
this.insert0(offset,str,strOffset,strLen);
return this;
},"~N,~A,~N,~N");
$_M(c$,"insert",
function(offset,s){
this.insert0(offset,s==null?"null":s.toString());
return this;
},"~N,CharSequence");
$_M(c$,"insert",
function(offset,s,start,end){
this.insert0(offset,s,start,end);
return this;
},"~N,CharSequence,~N,~N");
$_M(c$,"replace",
function(start,end,str){
this.replace0(start,end,str);
return this;
},"~N,~N,~S");
$_M(c$,"reverse",
function(){
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return this;
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});
$_L(["java.lang.AbstractStringBuilder","$.Appendable"],"java.lang.StringBuffer",["java.lang.Character","$.Double","$.Float","$.Long"],function(){
c$=$_T(java.lang,"StringBuffer",AbstractStringBuilder,[Appendable,java.io.Serializable,CharSequence]);
$_K(c$,
function(cs){
if(cs==null){
throw new NullPointerException();
}
$_R(this,StringBuffer,[cs.toString()]);
},"CharSequence");
$_M(c$,"append",
function(b){
return this.append(b?"true":"false");
},"~B");
$_M(c$,"append",
function(ch){
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return this;
},"~N");
$_M(c$,"append",
function(d){
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},"~N");
$_M(c$,"append",
function(obj){
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this.appendNull();
}else{
this.append0(obj.toString());
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},"~O");
$_M(c$,"append",
function(string){
this.append0(string);
return this;
},"~S");
$_M(c$,"append",
function(sb){
if(sb==null){
this.appendNull();
}else{
{
this.append0(sb.getValue(),0,sb.length());
}}return this;
},"StringBuffer");
$_M(c$,"append",
function(chars){
this.append0(chars);
return this;
},"~A");
$_M(c$,"append",
function(chars,start,length){
this.append0(chars,start,length);
return this;
},"~A,~N,~N");
$_M(c$,"append",
function(s){
if(s==null){
this.appendNull();
}else{
this.append0(s.toString());
}return this;
},"CharSequence");
$_M(c$,"append",
function(s,start,end){
this.append0(s,start,end);
return this;
},"CharSequence,~N,~N");
$_M(c$,"appendCodePoint",
function(codePoint){
return this.append(Character.toChars(codePoint));
},"~N");
$_M(c$,"$delete",
function(start,end){
this.delete0(start,end);
return this;
},"~N,~N");
$_M(c$,"deleteCharAt",
function(location){
this.deleteCharAt0(location);
return this;
},"~N");
$_M(c$,"insert",
function(index,ch){
this.insert0(index,ch);
return this;
},"~N,~N");
$_M(c$,"insert",
function(index,b){
return this.insert(index,b?"true":"false");
},"~N,~B");
$_M(c$,"insert",
function(index,i){
return this.insert(index,Integer.toString(i));
},"~N,~N");
$_M(c$,"insert",
function(index,l){
return this.insert(index,Long.toString(l));
},"~N,~N");
$_M(c$,"insert",
function(index,d){
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},"~N,~N");
$_M(c$,"insert",
function(index,f){
return this.insert(index,Float.toString(f));
},"~N,~N");
$_M(c$,"insert",
function(index,obj){
return this.insert(index,obj==null?"null":obj.toString());
},"~N,~O");
$_M(c$,"insert",
function(index,string){
this.insert0(index,string);
return this;
},"~N,~S");
$_M(c$,"insert",
function(index,chars){
this.insert0(index,chars);
return this;
},"~N,~A");
$_M(c$,"insert",
function(index,chars,start,length){
this.insert0(index,chars,start,length);
return this;
},"~N,~A,~N,~N");
$_M(c$,"insert",
function(index,s){
this.insert0(index,s==null?"null":s.toString());
return this;
},"~N,CharSequence");
$_M(c$,"insert",
function(index,s,start,end){
this.insert0(index,s,start,end);
return this;
},"~N,CharSequence,~N,~N");
$_M(c$,"replace",
function(start,end,string){
this.replace0(start,end,string);
return this;
},"~N,~N,~S");
$_M(c$,"reverse",
function(){
this.reverse0();
return this;
});
$_V(c$,"subSequence",
function(start,end){
return $_U(this,StringBuffer,"substring",[start,end]);
},"~N,~N");
});
$_L(["java.util.AbstractCollection","$.Iterator","$.List","$.ListIterator","$.RandomAccess","$.NoSuchElementException"],"java.util.AbstractList",["java.lang.IllegalArgumentException","$.IllegalStateException","$.IndexOutOfBoundsException","$.UnsupportedOperationException","java.util.ConcurrentModificationException"],function(){
c$=$_C(function(){
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if(!$_D("java.util.AbstractList.SimpleListIterator")){
java.util.AbstractList.$AbstractList$SimpleListIterator$();
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if(!$_D("java.util.AbstractList.FullListIterator")){
java.util.AbstractList.$AbstractList$FullListIterator$();
}
$_Z(this,arguments);
},java.util,"AbstractList",java.util.AbstractCollection,java.util.List);
$_M(c$,"add",
function(location,object){
throw new UnsupportedOperationException();
},"~N,~O");
$_M(c$,"add",
function(object){
this.add(this.size(),object);
return true;
},"~O");
$_M(c$,"addAll",
function(location,collection){
var it=collection.iterator();
while(it.hasNext()){
this.add(location++,it.next());
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return!collection.isEmpty();
},"~N,java.util.Collection");
$_V(c$,"clear",
function(){
this.removeRange(0,this.size());
});
$_V(c$,"equals",
function(object){
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}if($_O(object,java.util.List)){
var list=object;
if(list.size()!=this.size()){
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var it2=list.iterator();
while(it1.hasNext()){
var e1=it1.next();
var e2=it2.next();
if(!(e1==null?e2==null:e1.equals(e2))){
return false;
}}
return true;
}return false;
},"~O");
$_V(c$,"hashCode",
function(){
var result=1;
var it=this.iterator();
while(it.hasNext()){
var object=it.next();
result=(31*result)+(object==null?0:object.hashCode());
}
return result;
});
$_V(c$,"indexOf",
function(object){
var it=this.listIterator();
if(object!=null){
while(it.hasNext()){
if(object.equals(it.next())){
return it.previousIndex();
}}
}else{
while(it.hasNext()){
if(it.next()==null){
return it.previousIndex();
}}
}return-1;
},"~O");
$_V(c$,"iterator",
function(){
return $_N(java.util.AbstractList.SimpleListIterator,this,null);
});
$_V(c$,"lastIndexOf",
function(object){
var it=this.listIterator(this.size());
if(object!=null){
while(it.hasPrevious()){
if(object.equals(it.previous())){
return it.nextIndex();
}}
}else{
while(it.hasPrevious()){
if(it.previous()==null){
return it.nextIndex();
}}
}return-1;
},"~O");
$_M(c$,"listIterator",
function(){
return this.listIterator(0);
});
$_M(c$,"listIterator",
function(location){
return $_N(java.util.AbstractList.FullListIterator,this,null,location);
},"~N");
$_M(c$,"remove",
function(location){
throw new UnsupportedOperationException();
},"~N");
$_M(c$,"removeRange",
function(start,end){
var it=this.listIterator(start);
for(var i=start;i<end;i++){
it.next();
it.remove();
}
},"~N,~N");
$_V(c$,"set",
function(location,object){
throw new UnsupportedOperationException();
},"~N,~O");
$_V(c$,"subList",
function(start,end){
if(0<=start&&end<=this.size()){
if(start<=end){
if($_O(this,java.util.RandomAccess)){
return new java.util.AbstractList.SubAbstractListRandomAccess(this,start,end);
}return new java.util.AbstractList.SubAbstractList(this,start,end);
}throw new IllegalArgumentException();
}throw new IndexOutOfBoundsException();
},"~N,~N");
c$.$AbstractList$SimpleListIterator$=function(){
$_H();
c$=$_C(function(){
$_B(this,arguments);
this.pos=-1;
this.expectedModCount=0;
this.lastPosition=-1;
$_Z(this,arguments);
},java.util.AbstractList,"SimpleListIterator",null,java.util.Iterator);
$_K(c$,
function(){
this.expectedModCount=this.b$["java.util.AbstractList"].modCount;
});
$_V(c$,"hasNext",
function(){
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});
$_V(c$,"next",
function(){
if(this.expectedModCount==this.b$["java.util.AbstractList"].modCount){
try{
var a=this.b$["java.util.AbstractList"].get(this.pos+1);
this.lastPosition=++this.pos;
return a;
}catch(e){
if($_O(e,IndexOutOfBoundsException)){
throw new java.util.NoSuchElementException();
}else{
throw e;
}
}
}throw new java.util.ConcurrentModificationException();
});
$_V(c$,"remove",
function(){
if(this.expectedModCount==this.b$["java.util.AbstractList"].modCount){
try{
this.b$["java.util.AbstractList"].remove(this.lastPosition);
}catch(e){
if($_O(e,IndexOutOfBoundsException)){
throw new IllegalStateException();
}else{
throw e;
}
}
if(this.b$["java.util.AbstractList"].modCount!=this.expectedModCount){
this.expectedModCount++;
}if(this.pos==this.lastPosition){
this.pos--;
}this.lastPosition=-1;
}else{
throw new java.util.ConcurrentModificationException();
}});
c$=$_P();
};
c$.$AbstractList$FullListIterator$=function(){
$_H();
c$=$_C(function(){
$_B(this,arguments);
$_Z(this,arguments);
},java.util.AbstractList,"FullListIterator",java.util.AbstractList.SimpleListIterator,java.util.ListIterator,$_N(java.util.AbstractList.SimpleListIterator,this,null,$_G));
$_K(c$,
function(a){
$_R(this,java.util.AbstractList.FullListIterator);
if(0<=a&&a<=this.b$["java.util.AbstractList"].size()){
this.pos=a-1;
}else{
throw new IndexOutOfBoundsException();
}},"~N");
$_V(c$,"add",
function(a){
if(this.expectedModCount==this.b$["java.util.AbstractList"].modCount){
try{
this.b$["java.util.AbstractList"].add(this.pos+1,a);
}catch(e){
if($_O(e,IndexOutOfBoundsException)){
throw new java.util.NoSuchElementException();
}else{
throw e;
}
}
this.pos++;
this.lastPosition=-1;
if(this.b$["java.util.AbstractList"].modCount!=this.expectedModCount){
this.expectedModCount++;
}}else{
throw new java.util.ConcurrentModificationException();
}},"~O");
$_V(c$,"hasPrevious",
function(){
return this.pos>=0;
});
$_V(c$,"nextIndex",
function(){
return this.pos+1;
});
$_V(c$,"previous",
function(){
if(this.expectedModCount==this.b$["java.util.AbstractList"].modCount){
try{
var a=this.b$["java.util.AbstractList"].get(this.pos);
this.lastPosition=this.pos;
this.pos--;
return a;
}catch(e){
if($_O(e,IndexOutOfBoundsException)){
throw new java.util.NoSuchElementException();
}else{
throw e;
}
}
}throw new java.util.ConcurrentModificationException();
});
$_V(c$,"previousIndex",
function(){
return this.pos;
});
$_V(c$,"set",
function(a){
if(this.expectedModCount==this.b$["java.util.AbstractList"].modCount){
try{
this.b$["java.util.AbstractList"].set(this.lastPosition,a);
}catch(e){
if($_O(e,IndexOutOfBoundsException)){
throw new IllegalStateException();
}else{
throw e;
}
}
}else{
throw new java.util.ConcurrentModificationException();
}},"~O");
c$=$_P();
};
$_H();
c$=$_T(java.util.AbstractList,"SubAbstractListRandomAccess",java.util.AbstractList.SubAbstractList,java.util.RandomAccess);
c$=$_P();
$_H();
c$=$_C(function(){
this.fullList=null;
this.offset=0;
this.$size=0;
$_Z(this,arguments);
},java.util.AbstractList,"SubAbstractList",java.util.AbstractList);
$_K(c$,
function(a,b,c){
$_R(this,java.util.AbstractList.SubAbstractList);
this.fullList=a;
this.modCount=this.fullList.modCount;
this.offset=b;
this.$size=c-b;
},"java.util.AbstractList,~N,~N");
$_M(c$,"add",
function(a,b){
if(this.modCount==this.fullList.modCount){
if(0<=a&&a<=this.$size){
this.fullList.add(a+this.offset,b);
this.$size++;
this.modCount=this.fullList.modCount;
}else{
throw new IndexOutOfBoundsException();
}}else{
throw new java.util.ConcurrentModificationException();
}},"~N,~O");
$_M(c$,"addAll",
function(a,b){
if(this.modCount==this.fullList.modCount){
if(0<=a&&a<=this.$size){
var c=this.fullList.addAll(a+this.offset,b);
if(c){
this.$size+=b.size();
this.modCount=this.fullList.modCount;
}return c;
}throw new IndexOutOfBoundsException();
}throw new java.util.ConcurrentModificationException();
},"~N,java.util.Collection");
$_M(c$,"addAll",
function(a){
if(this.modCount==this.fullList.modCount){
var b=this.fullList.addAll(this.offset+this.$size,a);
if(b){
this.$size+=a.size();
this.modCount=this.fullList.modCount;
}return b;
}throw new java.util.ConcurrentModificationException();
},"java.util.Collection");
$_M(c$,"get",
function(a){
if(this.modCount==this.fullList.modCount){
if(0<=a&&a<this.$size){
return this.fullList.get(a+this.offset);
}throw new IndexOutOfBoundsException();
}throw new java.util.ConcurrentModificationException();
},"~N");
$_V(c$,"iterator",
function(){
return this.listIterator(0);
});
$_M(c$,"listIterator",
function(a){
if(this.modCount==this.fullList.modCount){
if(0<=a&&a<=this.$size){
return new java.util.AbstractList.SubAbstractList.SubAbstractListIterator(this.fullList.listIterator(a+this.offset),this,this.offset,this.$size);
}throw new IndexOutOfBoundsException();
}throw new java.util.ConcurrentModificationException();
},"~N");
$_M(c$,"remove",
function(a){
if(this.modCount==this.fullList.modCount){
if(0<=a&&a<this.$size){
var b=this.fullList.remove(a+this.offset);
this.$size--;
this.modCount=this.fullList.modCount;
return b;
}throw new IndexOutOfBoundsException();
}throw new java.util.ConcurrentModificationException();
},"~N");
$_M(c$,"removeRange",
function(a,b){
if(a!=b){
if(this.modCount==this.fullList.modCount){
this.fullList.removeRange(a+this.offset,b+this.offset);
this.$size-=b-a;
this.modCount=this.fullList.modCount;
}else{
throw new java.util.ConcurrentModificationException();
}}},"~N,~N");
$_M(c$,"set",
function(a,b){
if(this.modCount==this.fullList.modCount){
if(0<=a&&a<this.$size){
return this.fullList.set(a+this.offset,b);
}throw new IndexOutOfBoundsException();
}throw new java.util.ConcurrentModificationException();
},"~N,~O");
$_V(c$,"size",
function(){
return this.$size;
});
$_M(c$,"sizeChanged",
function(a){
if(a){
this.$size++;
}else{
this.$size--;
}this.modCount=this.fullList.modCount;
},"~B");
$_H();
c$=$_C(function(){
this.subList=null;
this.iterator=null;
this.start=0;
this.end=0;
$_Z(this,arguments);
},java.util.AbstractList.SubAbstractList,"SubAbstractListIterator",null,java.util.ListIterator);
$_K(c$,
function(a,b,c,d){
this.iterator=a;
this.subList=b;
this.start=c;
this.end=this.start+d;
},"java.util.ListIterator,java.util.AbstractList.SubAbstractList,~N,~N");
$_M(c$,"add",
function(a){
this.iterator.add(a);
this.subList.sizeChanged(true);
this.end++;
},"~O");
$_V(c$,"hasNext",
function(){
return this.iterator.nextIndex()<this.end;
});
$_V(c$,"hasPrevious",
function(){
return this.iterator.previousIndex()>=this.start;
});
$_M(c$,"next",
function(){
if(this.iterator.nextIndex()<this.end){
return this.iterator.next();
}throw new java.util.NoSuchElementException();
});
$_M(c$,"nextIndex",
function(){
return this.iterator.nextIndex()-this.start;
});
$_M(c$,"previous",
function(){
if(this.iterator.previousIndex()>=this.start){
return this.iterator.previous();
}throw new java.util.NoSuchElementException();
});
$_M(c$,"previousIndex",
function(){
var a=this.iterator.previousIndex();
if(a>=this.start){
return a-this.start;
}return-1;
});
$_M(c$,"remove",
function(){
this.iterator.remove();
this.subList.sizeChanged(false);
this.end--;
});
$_M(c$,"set",
function(a){
this.iterator.set(a);
},"~O");
c$=$_P();
c$=$_P();
});
$_L(["java.util.AbstractList","$.List","$.RandomAccess"],"java.util.ArrayList",["java.lang.IllegalArgumentException","$.IndexOutOfBoundsException","java.lang.reflect.Array","java.util.Arrays"],function(){
c$=$_C(function(){
this.firstIndex=0;
this.lastIndex=0;
this.array=null;
$_Z(this,arguments);
},java.util,"ArrayList",java.util.AbstractList,[java.util.List,Cloneable,java.io.Serializable,java.util.RandomAccess]);

$_k(c$,
function(){
this.setup(0);
});

$_M(c$, "setup",
function(capacity){
$_R(this,java.util.ArrayList,[]);
this.firstIndex=this.lastIndex=0;
try{
this.array=this.newElementArray(capacity);
}catch(e){
if($_O(e,NegativeArraySizeException)){
throw new IllegalArgumentException();
}else{
throw e;
}
}
},"~N");
/*
$_K(c$,
function(collection){
$_R(this,java.util.ArrayList,[]);
var size=collection.size();
this.firstIndex=this.lastIndex=0;
this.array=this.newElementArray(size+(Math.floor(size/10)));
this.addAll(collection);
},"java.util.Collection");

*/

$_M(c$,"newElementArray",
($fz=function(size){
return new Array(size);
},$fz.isPrivate=true,$fz),"~N");

$_V(c$,"add",
function(location,object){

if (arguments.length == 1) {
	// coming from Java methods, e.g. Collections.list()
	// location is actually the object
	return this.add1(location);
}
var size=this.size();
if(0<location&&location<size){
if(this.firstIndex==0&&this.lastIndex==this.array.length){
this.growForInsert(location,1);
}else if((location<Math.floor(size/2)&&this.firstIndex>0)||this.lastIndex==this.array.length){
System.arraycopy(this.array,this.firstIndex,this.array,--this.firstIndex,location);
}else{
var index=location+this.firstIndex;
System.arraycopy(this.array,index,this.array,index+1,size-location);
this.lastIndex++;
}this.array[location+this.firstIndex]=object;
}else if(location==0){
if(this.firstIndex==0){
this.growAtFront(1);
}this.array[--this.firstIndex]=object;
}else if(location==size){
if(this.lastIndex==this.array.length){
this.growAtEnd(1);
}this.array[this.lastIndex++]=object;
}else{
throw new IndexOutOfBoundsException();
}this.modCount++;
},"~N,~O");

$_V(c$,"add1",
function(object){
if(this.lastIndex==this.array.length){
this.growAtEnd(1);
}this.array[this.lastIndex++]=object;
this.modCount++;
return true;
},"~O");

/* BH disallow addAll(int,List)
 * 
$_M(c$,"addAll",
function(location,collection){
var size=this.size();
if(location<0||location>size){
throw new IndexOutOfBoundsException();
}var growSize=collection.size();
if(0<location&&location<size){
if(this.array.length-size<growSize){
this.growForInsert(location,growSize);
}else if((location<Math.floor(size/2)&&this.firstIndex>0)||this.lastIndex>this.array.length-growSize){
var newFirst=this.firstIndex-growSize;
if(newFirst<0){
var index=location+this.firstIndex;
System.arraycopy(this.array,index,this.array,index-newFirst,size-location);
this.lastIndex-=newFirst;
newFirst=0;
}System.arraycopy(this.array,this.firstIndex,this.array,newFirst,location);
this.firstIndex=newFirst;
}else{
var index=location+this.firstIndex;
System.arraycopy(this.array,index,this.array,index+growSize,size-location);
this.lastIndex+=growSize;
}}else if(location==0){
this.growAtFront(growSize);
this.firstIndex-=growSize;
}else if(location==size){
if(this.lastIndex>this.array.length-growSize){
this.growAtEnd(growSize);
}this.lastIndex+=growSize;
}if(growSize>0){
var it=collection.iterator();
var index=location+this.firstIndex;
var end=index+growSize;
while(index<end){
this.array[index++]=it.next();
}
this.modCount++;
return true;
}return false;
},"~N,java.util.Collection");

 */

$_V(c$,"addAll",
function(collection){
var growSize=collection.size();
if(growSize>0){
	if(this.lastIndex>this.array.length-growSize){
		this.growAtEnd(growSize);
}
var it=collection.iterator();
var end=this.lastIndex+growSize;
while(this.lastIndex<end){
	this.array[this.lastIndex++]=it.next();
}
this.modCount++;
return true;
}return false;
},"java.util.Collection");

$_V(c$,"clear",
function(){
if(this.firstIndex!=this.lastIndex){
this.fill(this.firstIndex,this.lastIndex);
this.firstIndex=this.lastIndex=0;
this.modCount++;
}});

$_M(c$,"fill", function(i1, i2) { // BH
for (var i = i2; --i >= i1;)
this.array[i] = null;
},"~N,~N");

$_M(c$,"clone",
function(){
try{
var newList=$_U(this,java.util.ArrayList,"clone",[]);
newList.array=this.array.clone();
return newList;
}catch(e){
if($_O(e,CloneNotSupportedException)){
return null;
}else{
throw e;
}
}
});
$_V(c$,"contains",
function(object){
if(object!=null){
for(var i=this.firstIndex;i<this.lastIndex;i++){
if(object.equals(this.array[i])){
return true;
}}
}else{
for(var i=this.firstIndex;i<this.lastIndex;i++){
if(this.array[i]==null){
return true;
}}
}return false;
},"~O");
$_M(c$,"ensureCapacity",
function(minimumCapacity){
if(this.array.length<minimumCapacity){
if(this.firstIndex>0){
this.growAtFront(minimumCapacity-this.array.length);
}else{
this.growAtEnd(minimumCapacity-this.array.length);
}}},"~N");
$_V(c$,"get",
function(location){
if(0<=location&&location<this.size()){
return this.array[this.firstIndex+location];
}throw new IndexOutOfBoundsException();
},"~N");


$_M(c$,"growAtEnd",
($fz=function(required){
var size=this.size();
if(this.firstIndex>=required-(this.array.length-this.lastIndex)){
	var newLast=this.lastIndex-this.firstIndex;
	if(size>0){
		System.arraycopy(this.array,this.firstIndex,this.array,0,size);
		var start=newLast<this.firstIndex?this.firstIndex:newLast;
		this.fill(start,this.array.length);
	}
	this.firstIndex=0;
	this.lastIndex=newLast;
}else{
	var increment=Math.floor(size/2);
	if(required>increment){
		increment=required;
	}
	if(increment<12){
		increment=12;
	}
	var newArray=this.newElementArray(size+increment);
	if(size>0){
		System.arraycopy(this.array,this.firstIndex,newArray,this.firstIndex,size);
	}
	this.array=newArray;
}

},$fz.isPrivate=true,$fz),"~N");
$_M(c$,"growAtFront",
($fz=function(required){
var size=this.size();
if(this.array.length-this.lastIndex>=required){
var newFirst=this.array.length-size;
if(size>0){
System.arraycopy(this.array,this.firstIndex,this.array,newFirst,size);
var length=this.firstIndex+size>newFirst?newFirst:this.firstIndex+size;
this.fill(this.firstIndex,length);
}this.firstIndex=newFirst;
this.lastIndex=this.array.length;
}else{
var increment=Math.floor(size/2);
if(required>increment){
increment=required;
}if(increment<12){
increment=12;
}var newArray=this.newElementArray(size+increment);
if(size>0){
System.arraycopy(this.array,this.firstIndex,newArray,newArray.length-size,size);
}this.firstIndex=newArray.length-size;
this.lastIndex=newArray.length;
this.array=newArray;
}},$fz.isPrivate=true,$fz),"~N");
$_M(c$,"growForInsert",
($fz=function(location,required){
var size=this.size();
var increment=Math.floor(size/2);
if(required>increment){
increment=required;
}if(increment<12){
increment=12;
}var newArray=this.newElementArray(size+increment);
if(location<Math.floor(size/2)){
var newFirst=newArray.length-(size+required);
System.arraycopy(this.array,location,newArray,location+increment,size-location);
System.arraycopy(this.array,this.firstIndex,newArray,newFirst,location);
this.firstIndex=newFirst;
this.lastIndex=newArray.length;
}else{
System.arraycopy(this.array,this.firstIndex,newArray,0,location);
System.arraycopy(this.array,location,newArray,location+required,size-location);
this.firstIndex=0;
this.lastIndex+=required;
}this.array=newArray;
},$fz.isPrivate=true,$fz),"~N,~N");
$_V(c$,"indexOf",
function(object){
if(object!=null){
for(var i=this.firstIndex;i<this.lastIndex;i++){
if(object.equals(this.array[i])){
return i-this.firstIndex;
}}
}else{
for(var i=this.firstIndex;i<this.lastIndex;i++){
if(this.array[i]==null){
return i-this.firstIndex;
}}
}return-1;
},"~O");
$_V(c$,"isEmpty",
function(){
return this.lastIndex==this.firstIndex;
});
$_V(c$,"lastIndexOf",
function(object){
if(object!=null){
for(var i=this.lastIndex-1;i>=this.firstIndex;i--){
if(object.equals(this.array[i])){
return i-this.firstIndex;
}}
}else{
for(var i=this.lastIndex-1;i>=this.firstIndex;i--){
if(this.array[i]==null){
return i-this.firstIndex;
}}
}return-1;
},"~O");
$_V(c$,"remove",
function(location){
var result;
var size=this.size();
if(0<=location&&location<size){
if(location==size-1){
result=this.array[--this.lastIndex];
this.array[this.lastIndex]=null;
}else if(location==0){
result=this.array[this.firstIndex];
this.array[this.firstIndex++]=null;
}else{
var elementIndex=this.firstIndex+location;
result=this.array[elementIndex];
if(location<Math.floor(size/2)){
System.arraycopy(this.array,this.firstIndex,this.array,this.firstIndex+1,location);
this.array[this.firstIndex++]=null;
}else{
System.arraycopy(this.array,elementIndex+1,this.array,elementIndex,size-location-1);
this.array[--this.lastIndex]=null;
}}}else{
throw new IndexOutOfBoundsException();
}this.modCount++;
return result;
},"~N"); 

$_M(c$, "removeObject", function(o) {
	var i = this.indexOf(o);
	if (i < 0)return null;
	return this.remove(i);
}, "~O");

$_V(c$,"removeRange",
function(start,end){
if(start>=0&&start<=end&&end<=this.size()){
if(start==end){
return;
}var size=this.size();
if(end==size){
	this.fill(this.firstIndex+start,this.lastIndex);
this.lastIndex=this.firstIndex+start;
}else if(start==0){
	this.fill(this.firstIndex,this.firstIndex+end);
this.firstIndex+=end;
}else{
System.arraycopy(this.array,this.firstIndex+end,this.array,this.firstIndex+start,size-end);
var newLast=this.lastIndex+start-end;
this.fill(newLast,this.lastIndex);
this.lastIndex=newLast;
}this.modCount++;
}else{
throw new IndexOutOfBoundsException();
}},"~N,~N");
$_V(c$,"set",
function(location,object){
if(0<=location&&location<this.size()){
var result=this.array[this.firstIndex+location];
this.array[this.firstIndex+location]=object;
return result;
}throw new IndexOutOfBoundsException();
},"~N,~O");
$_V(c$,"size",
function(){
return this.lastIndex-this.firstIndex;
});
/*
$_M(c$,"toArray",
function(){
var size=this.size();
var result=new Array(size);
System.arraycopy(this.array,this.firstIndex,result,0,size);
return result;
});
*/

$_V(c$,"toArray",
function(contents){
var size=this.size();
if(!contents || size>contents.length)
	contents= new Array(size);
System.arraycopy(this.array,this.firstIndex,contents,0,size);
if(size<contents.length){
contents[size]=null;
}return contents;
},"~O");
$_M(c$,"trimToSize",
function(){
var size=this.size();
var newArray=this.newElementArray(size);
System.arraycopy(this.array,this.firstIndex,newArray,0,size);
this.array=newArray;
this.firstIndex=0;
this.lastIndex=this.array.length;
});
});
Clazz_declarePackage ("JU");
Clazz_load (["java.util.ArrayList"], "JU.List", null, function () {
c$ = Clazz_declareType (JU, "List", java.util.ArrayList);
$_M(c$, "addLast", 
function (v) {
{
return this.add1(v);
}}, "~O");
$_M(c$, "removeObj", 
function (v) {
{
return this.removeObject(v);
}}, "~O");
});
Clazz_declarePackage ("JU");
Clazz_load (["java.util.Hashtable"], "JU.CU", ["JU.P3", "$.PT"], function () {
c$ = Clazz_declareType (JU, "CU");
c$.toRGBHexString = $_M(c$, "toRGBHexString", 
function (c) {
var rgb = c.getRGB ();
if (rgb == 0) return "000000";
var r = "00" + Integer.toHexString ((rgb >> 16) & 0xFF);
r = r.substring (r.length - 2);
var g = "00" + Integer.toHexString ((rgb >> 8) & 0xFF);
g = g.substring (g.length - 2);
var b = "00" + Integer.toHexString (rgb & 0xFF);
b = b.substring (b.length - 2);
return r + g + b;
}, "javajs.api.GenericColor");
c$.toCSSString = $_M(c$, "toCSSString", 
function (c) {
var opacity = c.getOpacity255 ();
if (opacity == 255) return "#" + JU.CU.toRGBHexString (c);
var rgb = c.getRGB ();
return "rgba(" + ((rgb >> 16) & 0xFF) + "," + ((rgb >> 8) & 0xff) + "," + (rgb & 0xff) + "," + opacity / 255 + ")";
}, "javajs.api.GenericColor");
c$.getArgbFromString = $_M(c$, "getArgbFromString", 
function (strColor) {
var len = 0;
if (strColor == null || (len = strColor.length) == 0) return 0;
if (strColor.charAt (0) == '[' && strColor.charAt (len - 1) == ']') {
var check;
if (strColor.indexOf (",") >= 0) {
var tokens = JU.PT.split (strColor.substring (1, strColor.length - 1), ",");
if (tokens.length != 3) return 0;
var red = JU.PT.parseFloat (tokens[0]);
var grn = JU.PT.parseFloat (tokens[1]);
var blu = JU.PT.parseFloat (tokens[2]);
return JU.CU.colorTriadToFFRGB (red, grn, blu);
}switch (len) {
case 9:
check = "x";
break;
case 10:
check = "0x";
break;
default:
return 0;
}
if (strColor.indexOf (check) != 1) return 0;
strColor = "#" + strColor.substring (len - 7, len - 1);
len = 7;
}if (len == 7 && strColor.charAt (0) == '#') {
try {
return JU.PT.parseIntRadix (strColor.substring (1, 7), 16) | 0xFF000000;
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return 0;
} else {
throw e;
}
}
}var boxedArgb = JU.CU.mapJavaScriptColors.get (strColor.toLowerCase ());
return (boxedArgb == null ? 0 : boxedArgb.intValue ());
}, "~S");
c$.colorTriadToFFRGB = $_M(c$, "colorTriadToFFRGB", 
function (x, y, z) {
if (x <= 1 && y <= 1 && z <= 1) {
if (x > 0) x = x * 256 - 1;
if (y > 0) y = y * 256 - 1;
if (z > 0) z = z * 256 - 1;
}return JU.CU.rgb (Clazz_floatToInt (x), Clazz_floatToInt (y), Clazz_floatToInt (z));
}, "~N,~N,~N");
c$.rgb = $_M(c$, "rgb", 
function (red, grn, blu) {
return 0xFF000000 | (red << 16) | (grn << 8) | blu;
}, "~N,~N,~N");
c$.colorPtFromString = $_M(c$, "colorPtFromString", 
function (colorName, pt) {
return JU.CU.toRGBpt (JU.CU.getArgbFromString (colorName), pt);
}, "~S,JU.P3");
c$.colorPtFromInt2 = $_M(c$, "colorPtFromInt2", 
function (color) {
return JU.P3.new3 ((color >> 16) & 0xFF, (color >> 8) & 0xFF, color & 0xFF);
}, "~N");
c$.colorPtToFFRGB = $_M(c$, "colorPtToFFRGB", 
function (pt) {
return JU.CU.colorTriadToFFRGB (pt.x, pt.y, pt.z);
}, "JU.T3");
c$.toRGBpt = $_M(c$, "toRGBpt", 
function (color, pt) {
pt.x = (color >> 16) & 0xFF;
pt.y = (color >> 8) & 0xFF;
pt.z = color & 0xFF;
return pt;
}, "~N,JU.P3");
c$.toRGB3f = $_M(c$, "toRGB3f", 
function (c, f) {
f[0] = ((c >> 16) & 0xFF) / 255;
f[1] = ((c >> 8) & 0xFF) / 255;
f[2] = (c & 0xFF) / 255;
}, "~N,~A");
c$.toFFGGGfromRGB = $_M(c$, "toFFGGGfromRGB", 
function (rgb) {
var grey = (Clazz_doubleToInt (((2989 * ((rgb >> 16) & 0xFF)) + (5870 * ((rgb >> 8) & 0xFF)) + (1140 * (rgb & 0xFF)) + 5000) / 10000)) & 0xFFFFFF;
return JU.CU.rgb (grey, grey, grey);
}, "~N");
Clazz_defineStatics (c$,
"colorNames", ["black", "pewhite", "pecyan", "pepurple", "pegreen", "peblue", "peviolet", "pebrown", "pepink", "peyellow", "pedarkgreen", "peorange", "pelightblue", "pedarkcyan", "pedarkgray", "aliceblue", "antiquewhite", "aqua", "aquamarine", "azure", "beige", "bisque", "blanchedalmond", "blue", "blueviolet", "brown", "burlywood", "cadetblue", "chartreuse", "chocolate", "coral", "cornflowerblue", "cornsilk", "crimson", "cyan", "darkblue", "darkcyan", "darkgoldenrod", "darkgray", "darkgreen", "darkkhaki", "darkmagenta", "darkolivegreen", "darkorange", "darkorchid", "darkred", "darksalmon", "darkseagreen", "darkslateblue", "darkslategray", "darkturquoise", "darkviolet", "deeppink", "deepskyblue", "dimgray", "dodgerblue", "firebrick", "floralwhite", "forestgreen", "fuchsia", "gainsboro", "ghostwhite", "gold", "goldenrod", "gray", "green", "greenyellow", "honeydew", "hotpink", "indianred", "indigo", "ivory", "khaki", "lavender", "lavenderblush", "lawngreen", "lemonchiffon", "lightblue", "lightcoral", "lightcyan", "lightgoldenrodyellow", "lightgreen", "lightgrey", "lightpink", "lightsalmon", "lightseagreen", "lightskyblue", "lightslategray", "lightsteelblue", "lightyellow", "lime", "limegreen", "linen", "magenta", "maroon", "mediumaquamarine", "mediumblue", "mediumorchid", "mediumpurple", "mediumseagreen", "mediumslateblue", "mediumspringgreen", "mediumturquoise", "mediumvioletred", "midnightblue", "mintcream", "mistyrose", "moccasin", "navajowhite", "navy", "oldlace", "olive", "olivedrab", "orange", "orangered", "orchid", "palegoldenrod", "palegreen", "paleturquoise", "palevioletred", "papayawhip", "peachpuff", "peru", "pink", "plum", "powderblue", "purple", "red", "rosybrown", "royalblue", "saddlebrown", "salmon", "sandybrown", "seagreen", "seashell", "sienna", "silver", "skyblue", "slateblue", "slategray", "snow", "springgreen", "steelblue", "tan", "teal", "thistle", "tomato", "turquoise", "violet", "wheat", "white", "whitesmoke", "yellow", "yellowgreen", "bluetint", "greenblue", "greentint", "grey", "pinktint", "redorange", "yellowtint"],
"colorArgbs", [0xFF000000, 0xFFffffff, 0xFF00ffff, 0xFFd020ff, 0xFF00ff00, 0xFF6060ff, 0xFFff80c0, 0xFFa42028, 0xFFffd8d8, 0xFFffff00, 0xFF00c000, 0xFFffb000, 0xFFb0b0ff, 0xFF00a0a0, 0xFF606060, 0xFFF0F8FF, 0xFFFAEBD7, 0xFF00FFFF, 0xFF7FFFD4, 0xFFF0FFFF, 0xFFF5F5DC, 0xFFFFE4C4, 0xFFFFEBCD, 0xFF0000FF, 0xFF8A2BE2, 0xFFA52A2A, 0xFFDEB887, 0xFF5F9EA0, 0xFF7FFF00, 0xFFD2691E, 0xFFFF7F50, 0xFF6495ED, 0xFFFFF8DC, 0xFFDC143C, 0xFF00FFFF, 0xFF00008B, 0xFF008B8B, 0xFFB8860B, 0xFFA9A9A9, 0xFF006400, 0xFFBDB76B, 0xFF8B008B, 0xFF556B2F, 0xFFFF8C00, 0xFF9932CC, 0xFF8B0000, 0xFFE9967A, 0xFF8FBC8F, 0xFF483D8B, 0xFF2F4F4F, 0xFF00CED1, 0xFF9400D3, 0xFFFF1493, 0xFF00BFFF, 0xFF696969, 0xFF1E90FF, 0xFFB22222, 0xFFFFFAF0, 0xFF228B22, 0xFFFF00FF, 0xFFDCDCDC, 0xFFF8F8FF, 0xFFFFD700, 0xFFDAA520, 0xFF808080, 0xFF008000, 0xFFADFF2F, 0xFFF0FFF0, 0xFFFF69B4, 0xFFCD5C5C, 0xFF4B0082, 0xFFFFFFF0, 0xFFF0E68C, 0xFFE6E6FA, 0xFFFFF0F5, 0xFF7CFC00, 0xFFFFFACD, 0xFFADD8E6, 0xFFF08080, 0xFFE0FFFF, 0xFFFAFAD2, 0xFF90EE90, 0xFFD3D3D3, 0xFFFFB6C1, 0xFFFFA07A, 0xFF20B2AA, 0xFF87CEFA, 0xFF778899, 0xFFB0C4DE, 0xFFFFFFE0, 0xFF00FF00, 0xFF32CD32, 0xFFFAF0E6, 0xFFFF00FF, 0xFF800000, 0xFF66CDAA, 0xFF0000CD, 0xFFBA55D3, 0xFF9370DB, 0xFF3CB371, 0xFF7B68EE, 0xFF00FA9A, 0xFF48D1CC, 0xFFC71585, 0xFF191970, 0xFFF5FFFA, 0xFFFFE4E1, 0xFFFFE4B5, 0xFFFFDEAD, 0xFF000080, 0xFFFDF5E6, 0xFF808000, 0xFF6B8E23, 0xFFFFA500, 0xFFFF4500, 0xFFDA70D6, 0xFFEEE8AA, 0xFF98FB98, 0xFFAFEEEE, 0xFFDB7093, 0xFFFFEFD5, 0xFFFFDAB9, 0xFFCD853F, 0xFFFFC0CB, 0xFFDDA0DD, 0xFFB0E0E6, 0xFF800080, 0xFFFF0000, 0xFFBC8F8F, 0xFF4169E1, 0xFF8B4513, 0xFFFA8072, 0xFFF4A460, 0xFF2E8B57, 0xFFFFF5EE, 0xFFA0522D, 0xFFC0C0C0, 0xFF87CEEB, 0xFF6A5ACD, 0xFF708090, 0xFFFFFAFA, 0xFF00FF7F, 0xFF4682B4, 0xFFD2B48C, 0xFF008080, 0xFFD8BFD8, 0xFFFF6347, 0xFF40E0D0, 0xFFEE82EE, 0xFFF5DEB3, 0xFFFFFFFF, 0xFFF5F5F5, 0xFFFFFF00, 0xFF9ACD32, 0xFFAFD7FF, 0xFF2E8B57, 0xFF98FFB3, 0xFF808080, 0xFFFFABBB, 0xFFFF4500, 0xFFF6F675]);
c$.mapJavaScriptColors = c$.prototype.mapJavaScriptColors =  new java.util.Hashtable ();
{
for (var i = JU.CU.colorNames.length; --i >= 0; ) JU.CU.mapJavaScriptColors.put (JU.CU.colorNames[i], Integer.$valueOf (JU.CU.colorArgbs[i]));

}});
Clazz_declarePackage ("javajs.api");
Clazz_declareInterface (javajs.api, "FontManager");
Clazz_declarePackage ("javajs.api");
Clazz_declareInterface (javajs.api, "GenericMenuInterface");
Clazz_declarePackage ("javajs.awt");
Clazz_load (null, "javajs.awt.Font", ["JU.AU"], function () {
c$ = Clazz_decorateAsClass (function () {
this.fid = 0;
this.fontFace = null;
this.fontStyle = null;
this.fontSizeNominal = 0;
this.idFontFace = 0;
this.idFontStyle = 0;
this.fontSize = 0;
this.font = null;
this.fontMetrics = null;
this.manager = null;
this.ascent = 0;
this.descent = 0;
this.isBold = false;
this.isItalic = false;
Clazz_instantialize (this, arguments);
}, javajs.awt, "Font");
Clazz_makeConstructor (c$, 
function (manager, fid, idFontFace, idFontStyle, fontSize, fontSizeNominal, graphics) {
this.manager = manager;
this.fid = fid;
this.fontFace = javajs.awt.Font.fontFaces[idFontFace];
this.fontStyle = javajs.awt.Font.fontStyles[idFontStyle];
this.idFontFace = idFontFace;
this.idFontStyle = idFontStyle;
this.fontSize = fontSize;
this.isBold = (idFontStyle & 1) == 1;
this.isItalic = (idFontStyle & 2) == 2;
this.fontSizeNominal = fontSizeNominal;
this.font = manager.newFont (javajs.awt.Font.fontFaces[idFontFace], this.isBold, this.isItalic, fontSize);
this.fontMetrics = manager.getFontMetrics (this, graphics);
this.descent = manager.getFontDescent (this.fontMetrics);
this.ascent = manager.getFontAscent (this.fontMetrics);
}, "javajs.api.FontManager,~N,~N,~N,~N,~N,~O");
c$.getFont3D = $_M(c$, "getFont3D", 
function (fontID) {
return javajs.awt.Font.font3ds[fontID & 0xFF];
}, "~N");
c$.createFont3D = $_M(c$, "createFont3D", 
function (fontface, fontstyle, fontsize, fontsizeNominal, manager, graphicsForMetrics) {
if (fontsize > 0xFF) fontsize = 0xFF;
var fontsizeX16 = (Clazz_floatToInt (fontsize)) << 4;
var fontkey = ((fontface & 3) | ((fontstyle & 3) << 2) | (fontsizeX16 << 4));
for (var i = javajs.awt.Font.fontkeyCount; --i > 0; ) if (fontkey == javajs.awt.Font.fontkeys[i] && javajs.awt.Font.font3ds[i].fontSizeNominal == fontsizeNominal) return javajs.awt.Font.font3ds[i];

var fontIndexNext = ($t$ = javajs.awt.Font.fontkeyCount ++, javajs.awt.Font.prototype.fontkeyCount = javajs.awt.Font.fontkeyCount, $t$);
if (fontIndexNext == javajs.awt.Font.fontkeys.length) ($t$ = javajs.awt.Font.fontkeys = JU.AU.arrayCopyI (javajs.awt.Font.fontkeys, fontIndexNext + 8), javajs.awt.Font.prototype.fontkeys = javajs.awt.Font.fontkeys, $t$);
($t$ = javajs.awt.Font.font3ds = JU.AU.arrayCopyObject (javajs.awt.Font.font3ds, fontIndexNext + 8), javajs.awt.Font.prototype.font3ds = javajs.awt.Font.font3ds, $t$);
var font3d =  new javajs.awt.Font (manager, fontIndexNext, fontface, fontstyle, fontsize, fontsizeNominal, graphicsForMetrics);
javajs.awt.Font.font3ds[fontIndexNext] = font3d;
javajs.awt.Font.fontkeys[fontIndexNext] = fontkey;
return font3d;
}, "~N,~N,~N,~N,javajs.api.FontManager,~O");
c$.getFontFaceID = $_M(c$, "getFontFaceID", 
function (fontface) {
return ("Monospaced".equalsIgnoreCase (fontface) ? 2 : "Serif".equalsIgnoreCase (fontface) ? 1 : 0);
}, "~S");
c$.getFontStyleID = $_M(c$, "getFontStyleID", 
function (fontstyle) {
for (var i = 4; --i >= 0; ) if (javajs.awt.Font.fontStyles[i].equalsIgnoreCase (fontstyle)) return i;

return -1;
}, "~S");
$_M(c$, "getAscent", 
function () {
return this.ascent;
});
$_M(c$, "getDescent", 
function () {
return this.descent;
});
$_M(c$, "getHeight", 
function () {
return this.getAscent () + this.getDescent ();
});
$_M(c$, "getFontMetrics", 
function () {
return this.fontMetrics;
});
$_M(c$, "stringWidth", 
function (text) {
return this.manager.fontStringWidth (this, text);
}, "~S");
$_M(c$, "getInfo", 
function () {
return this.fontSizeNominal + " " + this.fontFace + " " + this.fontStyle;
});
Clazz_defineStatics (c$,
"FONT_ALLOCATION_UNIT", 8,
"fontkeyCount", 1,
"fontkeys",  Clazz_newIntArray (8, 0));
c$.font3ds = c$.prototype.font3ds =  new Array (8);
Clazz_defineStatics (c$,
"FONT_FACE_SANS", 0,
"FONT_FACE_SERIF", 1,
"FONT_FACE_MONO", 2,
"fontFaces", ["SansSerif", "Serif", "Monospaced", ""],
"FONT_STYLE_PLAIN", 0,
"FONT_STYLE_BOLD", 1,
"FONT_STYLE_ITALIC", 2,
"FONT_STYLE_BOLDITALIC", 3,
"fontStyles", ["Plain", "Bold", "Italic", "BoldItalic"]);
});
Clazz_declarePackage ("java.net");
c$ = Clazz_decorateAsClass (function () {
this.path = null;
this.query = null;
this.ref = null;
Clazz_instantialize (this, arguments);
}, java.net, "Parts");
Clazz_makeConstructor (c$, 
function (file) {
var ind = file.indexOf ('#');
this.ref = ind < 0 ? null : file.substring (ind + 1);
file = ind < 0 ? file : file.substring (0, ind);
var q = file.lastIndexOf ('?');
if (q != -1) {
this.query = file.substring (q + 1);
this.path = file.substring (0, q);
} else {
this.path = file;
}}, "~S");
$_M(c$, "getPath", 
function () {
return this.path;
});
$_M(c$, "getQuery", 
function () {
return this.query;
});
$_M(c$, "getRef", 
function () {
return this.ref;
});
$_L(["java.util.AbstractCollection","$.Set"],"java.util.AbstractSet",null,function(){
c$=$_T(java.util,"AbstractSet",java.util.AbstractCollection,java.util.Set);
$_V(c$,"equals",
function(object){
if(this===object){
return true;
}if($_O(object,java.util.Set)){
var s=object;
return this.size()==s.size()&&this.containsAll(s);
}return false;
},"~O");
$_V(c$,"hashCode",
function(){
var result=0;
var it=this.iterator();
while(it.hasNext()){
var next=it.next();
result+=next==null?0:next.hashCode();
}
return result;
});
$_V(c$,"removeAll",
function(collection){
var result=false;
if(this.size()<=collection.size()){
var it=this.iterator();
while(it.hasNext()){
if(collection.contains(it.next())){
it.remove();
result=true;
}}
}else{
var it=collection.iterator();
while(it.hasNext()){
result=this.remove(it.next())||result;
}
}return result;
},"java.util.Collection");
});
// BH adjusted to have only one sort method.

$_L(["java.util.AbstractList","$.RandomAccess"],"java.util.Arrays",["java.lang.ArrayIndexOutOfBoundsException","$.IllegalArgumentException","$.NullPointerException"],function(){
c$=$_T(java.util,"Arrays");

c$.sort=$_V(c$,"sort",
function(a,c,d,e){
  switch (arguments.length) {
  case 1:
    var aux=a.sort(function(o1,o2){
      if(typeof o1=="string"||o1 instanceof Comparable){
        return o1.compareTo(o2);
      }
      return o1-o2;
      });
    for(var i=0;i<a.length;i++){
      a[i]=aux[i];
    }
    return;
  case 2:
    var aux=a.sort(function(o1,o2){
      if(c!=null){
        return c.compare(o1,o2);
      }else if(typeof o1=="string"||o1 instanceof Comparable){
        return o1.compareTo(o2);
      }
      return o1-o2;
      });
    for(var i=0;i<a.length;i++){
      a[i]=aux[i];
    }
    return;
  case 3:
    var fromIndex = c;
    var toIndex = d;
    this.rangeCheck(a.length,fromIndex,toIndex);
    var aux=new Array();
    for(var i=fromIndex;i<toIndex;i++){
      aux[i-fromIndex]=a[i];
    }
    aux=aux.sort(function(o1,o2){
      if(typeof o1=="string"||o1 instanceof Comparable){
        return o1.compareTo(o2);
      }
      return o1-o2;
      });
    for(var i=fromIndex;i<toIndex;i++){
      a[i]=aux[i-fromIndex];
    }
    return;
  case 4:  
    var fromIndex = c;
    var toIndex = d;
    c = e;
    this.rangeCheck(a.length,fromIndex,toIndex);
    var aux=new Array();
    for(var i=fromIndex;i<toIndex;i++){
      aux[i-fromIndex]=a[i];
    }
    aux=aux.sort(function(o1,o2){
      if(c!=null){
        return c.compare(o1,o2);
      }else if(typeof o1=="string"||o1 instanceof Comparable){
        return o1.compareTo(o2);
      }
      return o1-o2;
      });
    for(var i=fromIndex;i<toIndex;i++){
      a[i]=aux[i-fromIndex];
    }
  }
});

c$.rangeCheck=$_M(c$,"rangeCheck",
($fz=function(arrayLen,fromIndex,toIndex){
if(fromIndex>toIndex)throw new IllegalArgumentException("fromIndex("+fromIndex+") > toIndex("+toIndex+")");
if(fromIndex<0)throw new ArrayIndexOutOfBoundsException(fromIndex);
if(toIndex>arrayLen)throw new ArrayIndexOutOfBoundsException(toIndex);
},$fz.isPrivate=true,$fz),"~N,~N,~N");
c$.binarySearch=$_M(c$,"binarySearch",
function(a,key){
var low=0;
var high=a.length-1;
while(low<=high){
var mid=(low+high)>>1;
var midVal=a[mid];
if(midVal<key)low=mid+1;
else if(midVal>key)high=mid-1;
else return mid;
}
return-(low+1);
},"~A,~N");
c$.binarySearch=$_M(c$,"binarySearch",
function(a,key){
var low=0;
var high=a.length-1;
while(low<=high){
var mid=(low+high)>>1;
var midVal=a[mid];
var cmp=(midVal).compareTo(key);
if(cmp<0)low=mid+1;
else if(cmp>0)high=mid-1;
else return mid;
}
return-(low+1);
},"~A,~O");
c$.binarySearch=$_M(c$,"binarySearch",
function(a,key,c){
if(c==null)return java.util.Arrays.binarySearch(a,key);
var low=0;
var high=a.length-1;
while(low<=high){
var mid=(low+high)>>1;
var midVal=a[mid];
var cmp=c.compare(midVal,key);
if(cmp<0)low=mid+1;
else if(cmp>0)high=mid-1;
else return mid;
}
return-(low+1);
},"~A,~O,java.util.Comparator");
c$.equals=$_M(c$,"equals",
function(a,a2){
if(a===a2)return true;
if(a==null||a2==null)return false;
var length=a.length;
if(a2.length!=length)return false;
for(var i=0;i<length;i++){
var o1=a[i];
var o2=a2[i];
{
if(!(o1==null?o2==null:(o1.equals==null?o1==o2:o1.equals(o2))))return false;
}}
return true;
},"~A,~A");

c$.fill=$_V(c$,"fill",
function(a,fromIndex,toIndex,val){
if (arguments.length == 2) {
		val = fromIndex;
		fromIndex = 0;
		toIndex = a.length;
	}	
	java.util.Arrays.rangeCheck(a.length,fromIndex,toIndex);
	for(var i=fromIndex;i<toIndex;i++)a[i]=val;
});

c$.asList=$_M(c$,"asList",
function(a){
return new java.util.Arrays.ArrayList(a);
},"~A");
$_H();
c$=$_C(function(){
this.a=null;
$_Z(this,arguments);
},java.util.Arrays,"ArrayList",java.util.AbstractList,[java.util.RandomAccess,java.io.Serializable]);
$_K(c$,
function(a){
$_R(this,java.util.Arrays.ArrayList,[]);
if(a==null)throw new NullPointerException();
this.a=a;
},"~A");
$_V(c$,"size",
function(){
return this.a.length;
});
$_M(c$,"toArray",
function(){
return this.a.clone();
});
$_V(c$,"get",
function(a){
return this.a[a];
},"~N");
$_V(c$,"set",
function(a,b){
var c=this.a[a];
this.a[a]=b;
return c;
},"~N,~O");
$_V(c$,"indexOf",
function(a){
if(a==null){
for(var b=0;b<this.a.length;b++)if(this.a[b]==null)return b;

}else{
for(var b=0;b<this.a.length;b++)if(a.equals(this.a[b]))return b;

}return-1;
},"~O");
$_V(c$,"contains",
function(a){
return this.indexOf(a)!=-1;
},"~O");
c$=$_P();
$_S(c$,
"INSERTIONSORT_THRESHOLD",7);
});
$_L(["java.util.Map"],"java.util.AbstractMap",["java.lang.StringBuilder","$.UnsupportedOperationException","java.util.AbstractCollection","$.AbstractSet","$.Iterator"],function(){
c$=$_C(function(){
this.$keySet=null;
this.valuesCollection=null;
$_Z(this,arguments);
},java.util,"AbstractMap",null,java.util.Map);
$_K(c$,
function(){
});
$_V(c$,"clear",
function(){
this.entrySet().clear();
});
$_V(c$,"containsKey",
function(key){
var it=this.entrySet().iterator();
if(key!=null){
while(it.hasNext()){
if(key.equals(it.next().getKey())){
return true;
}}
}else{
while(it.hasNext()){
if(it.next().getKey()==null){
return true;
}}
}return false;
},"~O");
$_V(c$,"containsValue",
function(value){
var it=this.entrySet().iterator();
if(value!=null){
while(it.hasNext()){
if(value.equals(it.next().getValue())){
return true;
}}
}else{
while(it.hasNext()){
if(it.next().getValue()==null){
return true;
}}
}return false;
},"~O");
$_V(c$,"equals",
function(object){
if(this===object){
return true;
}if($_O(object,java.util.Map)){
var map=object;
if(this.size()!=map.size()){
return false;
}var objectSet=map.entrySet();
var it=this.entrySet().iterator();
while(it.hasNext()){
if(!objectSet.contains(it.next())){
return false;
}}
return true;
}return false;
},"~O");
$_V(c$,"get",
function(key){
var it=this.entrySet().iterator();
if(key!=null){
while(it.hasNext()){
var entry=it.next();
if(key.equals(entry.getKey())){
return entry.getValue();
}}
}else{
while(it.hasNext()){
var entry=it.next();
if(entry.getKey()==null){
return entry.getValue();
}}
}return null;
},"~O");
$_V(c$,"hashCode",
function(){
var result=0;
var it=this.entrySet().iterator();
while(it.hasNext()){
result+=it.next().hashCode();
}
return result;
});
$_V(c$,"isEmpty",
function(){
return this.size()==0;
});
$_V(c$,"keySet",
function(){
if(this.$keySet==null){
this.$keySet=(($_D("java.util.AbstractMap$1")?0:java.util.AbstractMap.$AbstractMap$1$()),$_N(java.util.AbstractMap$1,this,null));
}return this.$keySet;
});
$_V(c$,"put",
function(key,value){
throw new UnsupportedOperationException();
},"~O,~O");
$_V(c$,"putAll",
function(map){
for(var entry,$entry=map.entrySet().iterator();$entry.hasNext()&&((entry=$entry.next())||true);){
this.put(entry.getKey(),entry.getValue());
}
},"java.util.Map");
$_V(c$,"remove",
function(key){
var it=this.entrySet().iterator();
if(key!=null){
while(it.hasNext()){
var entry=it.next();
if(key.equals(entry.getKey())){
it.remove();
return entry.getValue();
}}
}else{
while(it.hasNext()){
var entry=it.next();
if(entry.getKey()==null){
it.remove();
return entry.getValue();
}}
}return null;
},"~O");
$_V(c$,"size",
function(){
return this.entrySet().size();
});
$_V(c$,"toString",
function(){
if(this.isEmpty()){
return"{}";
}var buffer=new StringBuilder(this.size()*28);
buffer.append('{');
var it=this.entrySet().iterator();
while(it.hasNext()){
var entry=it.next();
var key=entry.getKey();
if(key!==this){
buffer.append(key);
}else{
buffer.append("(this Map)");
}buffer.append('=');
var value=entry.getValue();
if(value!==this){
buffer.append(value);
}else{
buffer.append("(this Map)");
}if(it.hasNext()){
buffer.append(", ");
}}
buffer.append('}');
return buffer.toString();
});
$_V(c$,"values",
function(){
if(this.valuesCollection==null){
this.valuesCollection=(($_D("java.util.AbstractMap$2")?0:java.util.AbstractMap.$AbstractMap$2$()),$_N(java.util.AbstractMap$2,this,null));
}return this.valuesCollection;
});
$_M(c$,"clone",
function(){
var result=$_U(this,java.util.AbstractMap,"clone",[]);
result.$keySet=null;
result.valuesCollection=null;
return result;
});
c$.$AbstractMap$1$=function(){
$_H();
c$=$_W(java.util,"AbstractMap$1",java.util.AbstractSet);
$_V(c$,"contains",
function(object){
return this.b$["java.util.AbstractMap"].containsKey(object);
},"~O");
$_V(c$,"size",
function(){
return this.b$["java.util.AbstractMap"].size();
});
$_V(c$,"iterator",
function(){
return(($_D("java.util.AbstractMap$1$1")?0:java.util.AbstractMap.$AbstractMap$1$1$()),$_N(java.util.AbstractMap$1$1,this,null));
});
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$_M(c$,"toArray",
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$_V(c$,"addAll",
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$_M(c$,"next",
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$_M(c$,"remove",
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$_M(c$,"hasPrevious",
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$_M(c$,"previous",
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$_M(c$,"nextIndex",
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$_M(c$,"previousIndex",
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$_M(c$,"set",
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c$=$_P();
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c$=$_C(function(){
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$_M(c$,"addAll",
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$_M(c$,"get",
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java.util.Collections.checkType(f.getValue(),this.valueType);
c[e]=f;
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c$=$_P();
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if(!$_D("java.util.Hashtable.HashEnumerator")){
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c$.newEntry=$_M(c$,"newEntry",
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$_k(c$,
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this.elementData=this.newElementArray(11);
this.firstSlot=this.elementData.length;
this.loadFactor=0.75;
this.computeMaxSize();
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$_M(c$,"newElementArray",
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$_V(c$,"clear",
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this.modCount++;
});
$_M(c$,"clone",
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try{
var hashtable=$_U(this,java.util.Hashtable,"clone",[]);
hashtable.elementData=this.elementData.clone();
var entry;
for(var i=this.elementData.length;--i>=0;){
if((entry=this.elementData[i])!=null){
hashtable.elementData[i]=entry.clone();
}}
return hashtable;
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throw e;
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}
});
$_M(c$,"computeMaxSize",
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$_M(c$,"contains",
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}
return false;
},"~O");
$_V(c$,"containsKey",
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},"~O");
$_V(c$,"containsValue",
function(value){
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},"~O");
$_V(c$,"elements",
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}return $_N(java.util.Hashtable.HashEnumerator,this,null,false);
});
$_V(c$,"entrySet",
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});
$_V(c$,"equals",
function(object){
if(this===object){
return true;
}if($_O(object,java.util.Map)){
var map=object;
if(this.size()!=map.size()){
return false;
}var entries=this.entrySet();
for(var e,$e=map.entrySet().iterator();$e.hasNext()&&((e=$e.next())||true);){
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return false;
}}
return true;
}return false;
},"~O");
$_V(c$,"get",
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var hash=key.hashCode();
var index=(hash&0x7FFFFFFF)%this.elementData.length;
var entry=this.elementData[index];
while(entry!=null){
if(entry.equalsKey(key,hash)){
return entry.value;
}entry=entry.next;
}
return null;
},"~O");
$_M(c$,"getEntry",
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var hash=key.hashCode();
var index=(hash&0x7FFFFFFF)%this.elementData.length;
var entry=this.elementData[index];
while(entry!=null){
if(entry.equalsKey(key,hash)){
return entry;
}entry=entry.next;
}
return null;
},"~O");
$_V(c$,"hashCode",
function(){
var result=0;
var it=this.entrySet().iterator();
while(it.hasNext()){
var entry=it.next();
var key=entry.getKey();
var value=entry.getValue();
var hash=(key!==this?key.hashCode():0)^(value!==this?(value!=null?value.hashCode():0):0);
result+=hash;
}
return result;
});
$_V(c$,"isEmpty",
function(){
return this.elementCount==0;
});
$_V(c$,"keys",
function(){
if(this.elementCount==0){
return java.util.Hashtable.EMPTY_ENUMERATION;
}return $_N(java.util.Hashtable.HashEnumerator,this,null,true);
});
$_V(c$,"keySet",
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return new java.util.Collections.SynchronizedSet((($_D("java.util.Hashtable$3")?0:java.util.Hashtable.$Hashtable$3$()),$_N(java.util.Hashtable$3,this,null)),this);
});
$_V(c$,"put",
function(key,value){
if(key!=null&&value!=null){
	// BH added ability to use a non-Java key for HTML elements, for example.
	if(!key.hashCode) {
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		  key.hashCode = function(){return hc};
		  key.equals = function(a){return this.hashCode() == a.hashCode()};
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var hash=key.hashCode();
var index=(hash&0x7FFFFFFF)%this.elementData.length;
var entry=this.elementData[index];
while(entry!=null&&!entry.equalsKey(key,hash)){
entry=entry.next;
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if(entry==null){
this.modCount++;
if(++this.elementCount>this.threshold){
this.rehash();
index=(hash&0x7FFFFFFF)%this.elementData.length;
}if(index<this.firstSlot){
this.firstSlot=index;
}if(index>this.lastSlot){
this.lastSlot=index;
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entry=java.util.Hashtable.newEntry(key,value,hash);
entry.next=this.elementData[index];
this.elementData[index]=entry;
return null;
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entry.value=value;
return result;
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},"~O,~O");
$_V(c$,"putAll",
function(map){
for(var entry,$entry=map.entrySet().iterator();$entry.hasNext()&&((entry=$entry.next())||true);){
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},"java.util.Map");

$_M(c$,"rehash",
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var length=(this.elementData.length<<1)+1;
if(length==0){
length=1;
}var newFirst=length;
var newLast=-1;
var newData=this.newElementArray(length);
for(var i=this.lastSlot+1;--i>=this.firstSlot;){
var entry=this.elementData[i];
while(entry!=null){
var index=(entry.getKeyHash()&0x7FFFFFFF)%length;
if(index<newFirst){
newFirst=index;
}if(index>newLast){
newLast=index;
}var next=entry.next;
entry.next=newData[index];
newData[index]=entry;
entry=next;
}
}
this.firstSlot=newFirst;
this.lastSlot=newLast;
this.elementData=newData;
this.computeMaxSize();
});
$_V(c$,"remove",
function(key){
var hash=key.hashCode();
var index=(hash&0x7FFFFFFF)%this.elementData.length;
var last=null;
var entry=this.elementData[index];
while(entry!=null&&!entry.equalsKey(key,hash)){
last=entry;
entry=entry.next;
}
if(entry!=null){
this.modCount++;
if(last==null){
this.elementData[index]=entry.next;
}else{
last.next=entry.next;
}this.elementCount--;
var result=entry.value;
entry.value=null;
return result;
}return null;
},"~O");
$_V(c$,"size",
function(){
return this.elementCount;
});
$_V(c$,"toString",
function(){
if(this.isEmpty()){
return"{}";
}var buffer=new StringBuilder(this.size()*28);
buffer.append('{');
for(var i=this.lastSlot;i>=this.firstSlot;i--){
var entry=this.elementData[i];
while(entry!=null){
if(entry.key!==this){
buffer.append(entry.key);
}else{
buffer.append("(this Map)");
}buffer.append('=');
if(entry.value!==this){
buffer.append(entry.value);
}else{
buffer.append("(this Map)");
}buffer.append(", ");
entry=entry.next;
}
}
if(this.elementCount>0){
buffer.setLength(buffer.length()-2);
}buffer.append('}');
return buffer.toString();
});
$_V(c$,"values",
function(){
return new java.util.Collections.SynchronizedCollection((($_D("java.util.Hashtable$4")?0:java.util.Hashtable.$Hashtable$4$()),$_N(java.util.Hashtable$4,this,null)),this);
});
c$.$Hashtable$HashIterator$=function(){
$_H();
c$=$_C(function(){
$_B(this,arguments);
this.position=0;
this.expectedModCount=0;
this.type=null;
this.lastEntry=null;
this.lastPosition=0;
this.canRemove=false;
$_Z(this,arguments);
},java.util.Hashtable,"HashIterator",null,java.util.Iterator);
$_K(c$,
function(a){
this.type=a;
this.position=this.b$["java.util.Hashtable"].lastSlot;
this.expectedModCount=this.b$["java.util.Hashtable"].modCount;
},"java.util.MapEntry.Type");
$_V(c$,"hasNext",
function(){
if(this.lastEntry!=null&&this.lastEntry.next!=null){
return true;
}while(this.position>=this.b$["java.util.Hashtable"].firstSlot){
if(this.b$["java.util.Hashtable"].elementData[this.position]==null){
this.position--;
}else{
return true;
}}
return false;
});
$_V(c$,"next",
function(){
if(this.expectedModCount==this.b$["java.util.Hashtable"].modCount){
if(this.lastEntry!=null){
this.lastEntry=this.lastEntry.next;
}if(this.lastEntry==null){
while(this.position>=this.b$["java.util.Hashtable"].firstSlot&&(this.lastEntry=this.b$["java.util.Hashtable"].elementData[this.position])==null){
this.position--;
}
if(this.lastEntry!=null){
this.lastPosition=this.position;
this.position--;
}}if(this.lastEntry!=null){
this.canRemove=true;
return this.type.get(this.lastEntry);
}throw new java.util.NoSuchElementException();
}throw new java.util.ConcurrentModificationException();
});
$_V(c$,"remove",
function(){
if(this.expectedModCount==this.b$["java.util.Hashtable"].modCount){
if(this.canRemove){
this.canRemove=false;
{
var a=false;
var b=this.b$["java.util.Hashtable"].elementData[this.lastPosition];
if(b===this.lastEntry){
this.b$["java.util.Hashtable"].elementData[this.lastPosition]=b.next;
a=true;
}else{
while(b!=null&&b.next!==this.lastEntry){
b=b.next;
}
if(b!=null){
b.next=this.lastEntry.next;
a=true;
}}if(a){
this.b$["java.util.Hashtable"].modCount++;
this.b$["java.util.Hashtable"].elementCount--;
this.expectedModCount++;
return;
}}}else{
throw new IllegalStateException();
}}throw new java.util.ConcurrentModificationException();
});
c$=$_P();
};
c$.$Hashtable$HashEnumerator$=function(){
$_H();
c$=$_C(function(){
$_B(this,arguments);
this.key=false;
this.start=0;
this.entry=null;
$_Z(this,arguments);
},java.util.Hashtable,"HashEnumerator",null,java.util.Enumeration);
$_K(c$,
function(a){
this.key=a;
this.start=this.b$["java.util.Hashtable"].lastSlot+1;
},"~B");
$_V(c$,"hasMoreElements",
function(){
if(this.entry!=null){
return true;
}while(--this.start>=this.b$["java.util.Hashtable"].firstSlot){
if(this.b$["java.util.Hashtable"].elementData[this.start]!=null){
this.entry=this.b$["java.util.Hashtable"].elementData[this.start];
return true;
}}
return false;
});
$_V(c$,"nextElement",
function(){
if(this.hasMoreElements()){
var a=this.key?this.entry.key:this.entry.value;
this.entry=this.entry.next;
return a;
}throw new java.util.NoSuchElementException();
});
c$=$_P();
};
c$.$Hashtable$2$=function(){
$_H();
c$=$_W(java.util,"Hashtable$2",java.util.AbstractSet);
$_V(c$,"size",
function(){
return this.b$["java.util.Hashtable"].elementCount;
});
$_V(c$,"clear",
function(){
this.b$["java.util.Hashtable"].clear();
});
$_V(c$,"remove",
function(object){
if(this.contains(object)){
this.b$["java.util.Hashtable"].remove((object).getKey());
return true;
}return false;
},"~O");
$_M(c$,"contains",
function(object){
var entry=this.b$["java.util.Hashtable"].getEntry((object).getKey());
return object.equals(entry);
},"~O");
$_M(c$,"iterator",
function(){
return $_N(java.util.Hashtable.HashIterator,this,null,(($_D("java.util.Hashtable$2$1")?0:java.util.Hashtable.$Hashtable$2$1$()),$_N(java.util.Hashtable$2$1,this,null)));
});
c$=$_P();
};
c$.$Hashtable$2$1$=function(){
$_H();
c$=$_W(java.util,"Hashtable$2$1",null,java.util.MapEntry.Type);
$_V(c$,"get",
function(entry){
return entry;
},"java.util.MapEntry");
c$=$_P();
};
c$.$Hashtable$3$=function(){
$_H();
c$=$_W(java.util,"Hashtable$3",java.util.AbstractSet);
$_V(c$,"contains",
function(object){
return this.b$["java.util.Hashtable"].containsKey(object);
},"~O");
$_V(c$,"size",
function(){
return this.b$["java.util.Hashtable"].elementCount;
});
$_V(c$,"clear",
function(){
this.b$["java.util.Hashtable"].clear();
});
$_V(c$,"remove",
function(key){
if(this.b$["java.util.Hashtable"].containsKey(key)){
this.b$["java.util.Hashtable"].remove(key);
return true;
}return false;
},"~O");
$_V(c$,"iterator",
function(){
return $_N(java.util.Hashtable.HashIterator,this,null,(($_D("java.util.Hashtable$3$1")?0:java.util.Hashtable.$Hashtable$3$1$()),$_N(java.util.Hashtable$3$1,this,null)));
});
c$=$_P();
};
c$.$Hashtable$3$1$=function(){
$_H();
c$=$_W(java.util,"Hashtable$3$1",null,java.util.MapEntry.Type);
$_V(c$,"get",
function(entry){
return entry.key;
},"java.util.MapEntry");
c$=$_P();
};
c$.$Hashtable$4$=function(){
$_H();
c$=$_W(java.util,"Hashtable$4",java.util.AbstractCollection);
$_V(c$,"contains",
function(object){
return this.b$["java.util.Hashtable"].contains(object);
},"~O");
$_V(c$,"size",
function(){
return this.b$["java.util.Hashtable"].elementCount;
});
$_V(c$,"clear",
function(){
this.b$["java.util.Hashtable"].clear();
});
$_V(c$,"iterator",
function(){
return $_N(java.util.Hashtable.HashIterator,this,null,(($_D("java.util.Hashtable$4$1")?0:java.util.Hashtable.$Hashtable$4$1$()),$_N(java.util.Hashtable$4$1,this,null)));
});
c$=$_P();
};
c$.$Hashtable$4$1$=function(){
$_H();
c$=$_W(java.util,"Hashtable$4$1",null,java.util.MapEntry.Type);
$_V(c$,"get",
function(entry){
return entry.value;
},"java.util.MapEntry");
c$=$_P();
};
c$.$Hashtable$1$=function(){
$_H();
c$=$_W(java.util,"Hashtable$1",null,java.util.Enumeration);
$_V(c$,"hasMoreElements",
function(){
return false;
});
$_V(c$,"nextElement",
function(){
throw new java.util.NoSuchElementException();
});
c$=$_P();
};
$_H();
c$=$_C(function(){
this.next=null;
this.hashcode=0;
$_Z(this,arguments);
},java.util.Hashtable,"Entry",java.util.MapEntry);
$_k(c$,
function(a,b){
	// _k for @j2sOverride
this.key = a;
this.value = b;
//$_R(this,java.util.Hashtable.Entry,[a,b]);
this.hashcode=a.hashCode();
});
$_M(c$,"clone",
function(){
var a=$_U(this,java.util.Hashtable.Entry,"clone",[]);
if(this.next!=null){
a.next=this.next.clone();

}
return a;
});
$_V(c$,"setValue",
function(a){
if(a==null){
throw new NullPointerException();
}var b=this.value;
this.value=a;
return b;
},"~O");
$_M(c$,"getKeyHash",
function(){
return this.key.hashCode();
});
$_M(c$,"equalsKey",
function(a,b){
return this.hashcode==a.hashCode()&&this.key.equals(a);
},"~O,~N");
$_V(c$,"toString",
function(){
return this.key+"="+this.value;
});
c$=$_P();
c$.EMPTY_ENUMERATION=c$.prototype.EMPTY_ENUMERATION=(($_D("java.util.Hashtable$1")?0:java.util.Hashtable.$Hashtable$1$()),$_N(java.util.Hashtable$1,this,null));
});
Clazz_declarePackage ("javajs.awt");
c$ = Clazz_decorateAsClass (function () {
this.width = 0;
this.height = 0;
Clazz_instantialize (this, arguments);
}, javajs.awt, "Dimension");
Clazz_makeConstructor (c$, 
function (w, h) {
this.set (w, h);
}, "~N,~N");
$_M(c$, "set", 
function (w, h) {
this.width = w;
this.height = h;
return this;
}, "~N,~N");
Clazz_load (null, "java.io.InputStream", ["java.io.IOException", "java.lang.IndexOutOfBoundsException", "$.NullPointerException"], function () {
c$ = Clazz_declareType (java.io, "InputStream");
$_M(c$, "read", 
function (b, off, len) {
if (b == null) {
throw  new NullPointerException ();
} else if (off < 0 || len < 0 || len > b.length - off) {
throw  new IndexOutOfBoundsException ();
} else if (len == 0) {
return 0;
}var c = this.readByteAsInt ();
if (c == -1) {
return -1;
}b[off] = c;
var i = 1;
try {
for (; i < len; i++) {
c = this.readByteAsInt ();
if (c == -1) {
break;
}b[off + i] = c;
}
} catch (ee) {
if (Clazz_exceptionOf (ee, java.io.IOException)) {
} else {
throw ee;
}
}
return i;
}, "~A,~N,~N");
$_M(c$, "skip", 
function (n) {
var remaining = n;
var nr;
if (java.io.InputStream.skipBuffer == null) ($t$ = java.io.InputStream.skipBuffer =  Clazz_newByteArray (2048, 0), java.io.InputStream.prototype.skipBuffer = java.io.InputStream.skipBuffer, $t$);
var localSkipBuffer = java.io.InputStream.skipBuffer;
if (n <= 0) {
return 0;
}while (remaining > 0) {
nr = this.read (localSkipBuffer, 0, Math.min (2048, remaining));
if (nr < 0) {
break;
}remaining -= nr;
}
return n - remaining;
}, "~N");
$_M(c$, "available", 
function () {
return 0;
});
$_M(c$, "close", 
function () {
});
$_M(c$, "mark", 
function (readlimit) {
}, "~N");
$_M(c$, "reset", 
function () {
throw  new java.io.IOException ("mark/reset not supported");
});
$_M(c$, "markSupported", 
function () {
return false;
});
$_M(c$, "resetStream", 
function () {
});
Clazz_defineStatics (c$,
"SKIP_BUFFER_SIZE", 2048,
"skipBuffer", null);
});
Clazz_load (["java.io.InputStream"], "java.io.ByteArrayInputStream", ["java.lang.IndexOutOfBoundsException", "$.NullPointerException"], function () {
c$ = Clazz_decorateAsClass (function () {
this.buf = null;
this.pos = 0;
this.$mark = 0;
this.count = 0;
Clazz_instantialize (this, arguments);
}, java.io, "ByteArrayInputStream", java.io.InputStream);
Clazz_makeConstructor (c$, 
function (buf) {
Clazz_superConstructor (this, java.io.ByteArrayInputStream, []);
this.buf = buf;
this.pos = 0;
this.count = buf.length;
}, "~A");
$_V(c$, "readByteAsInt", 
function () {
return (this.pos < this.count) ? (this.buf[this.pos++] & 0xff) : -1;
});
$_V(c$, "read", 
function (b, off, len) {
if (b == null) {
throw  new NullPointerException ();
} else if (off < 0 || len < 0 || len > b.length - off) {
throw  new IndexOutOfBoundsException ();
}if (this.pos >= this.count) {
return -1;
}var avail = this.count - this.pos;
if (len > avail) {
len = avail;
}if (len <= 0) {
return 0;
}System.arraycopy (this.buf, this.pos, b, off, len);
this.pos += len;
return len;
}, "~A,~N,~N");
$_V(c$, "skip", 
function (n) {
var k = this.count - this.pos;
if (n < k) {
k = n < 0 ? 0 : n;
}this.pos += k;
return k;
}, "~N");
$_V(c$, "available", 
function () {
return this.count - this.pos;
});
$_V(c$, "markSupported", 
function () {
return true;
});
$_V(c$, "mark", 
function (readAheadLimit) {
this.$mark = this.pos;
}, "~N");
$_V(c$, "resetStream", 
function () {
});
$_V(c$, "reset", 
function () {
this.pos = this.$mark;
});
$_V(c$, "close", 
function () {
});
});
Clazz_load (["java.io.InputStream"], "java.io.FilterInputStream", null, function () {
c$ = Clazz_decorateAsClass (function () {
this.$in = null;
Clazz_instantialize (this, arguments);
}, java.io, "FilterInputStream", java.io.InputStream);
Clazz_makeConstructor (c$, 
function ($in) {
Clazz_superConstructor (this, java.io.FilterInputStream, []);
this.$in = $in;
}, "java.io.InputStream");
$_M(c$, "readByteAsInt", 
function () {
return this.$in.readByteAsInt ();
});
$_M(c$, "read", 
function (b, off, len) {
return this.$in.read (b, off, len);
}, "~A,~N,~N");
$_M(c$, "skip", 
function (n) {
return this.$in.skip (n);
}, "~N");
$_M(c$, "available", 
function () {
return this.$in.available ();
});
$_M(c$, "close", 
function () {
this.$in.close ();
});
$_M(c$, "mark", 
function (readlimit) {
this.$in.mark (readlimit);
}, "~N");
$_M(c$, "reset", 
function () {
this.$in.reset ();
});
$_M(c$, "markSupported", 
function () {
return this.$in.markSupported ();
});
});
Clazz_load (["java.io.FilterInputStream"], "java.io.BufferedInputStream", ["java.io.IOException", "java.lang.IndexOutOfBoundsException"], function () {
c$ = Clazz_decorateAsClass (function () {
this.buf = null;
this.count = 0;
this.pos = 0;
this.markpos = -1;
this.marklimit = 0;
Clazz_instantialize (this, arguments);
}, java.io, "BufferedInputStream", java.io.FilterInputStream);
$_M(c$, "getInIfOpen", 
function () {
var input = this.$in;
if (input == null) throw  new java.io.IOException ("Stream closed");
return input;
});
$_M(c$, "getBufIfOpen", 
function () {
var buffer = this.buf;
if (buffer == null) throw  new java.io.IOException ("Stream closed");
return buffer;
});
$_V(c$, "resetStream", 
function () {
});
Clazz_makeConstructor (c$, 
function ($in) {
Clazz_superConstructor (this, java.io.BufferedInputStream, [$in]);
this.buf =  Clazz_newByteArray (java.io.BufferedInputStream.defaultBufferSize, 0);
}, "java.io.InputStream");
$_M(c$, "fill", 
function () {
var buffer = this.getBufIfOpen ();
if (this.markpos < 0) this.pos = 0;
 else if (this.pos >= buffer.length) if (this.markpos > 0) {
var sz = this.pos - this.markpos;
System.arraycopy (buffer, this.markpos, buffer, 0, sz);
this.pos = sz;
this.markpos = 0;
} else if (buffer.length >= this.marklimit) {
this.markpos = -1;
this.pos = 0;
} else {
var nsz = this.pos * 2;
if (nsz > this.marklimit) nsz = this.marklimit;
var nbuf =  Clazz_newByteArray (nsz, 0);
System.arraycopy (buffer, 0, nbuf, 0, this.pos);
buffer = this.buf = nbuf;
}this.count = this.pos;
var n = this.getInIfOpen ().read (buffer, this.pos, buffer.length - this.pos);
if (n > 0) this.count = n + this.pos;
});
$_V(c$, "readByteAsInt", 
function () {
if (this.pos >= this.count) {
this.fill ();
if (this.pos >= this.count) return -1;
}return this.getBufIfOpen ()[this.pos++] & 0xff;
});
$_M(c$, "read1", 
function (b, off, len) {
var avail = this.count - this.pos;
if (avail <= 0) {
if (len >= this.getBufIfOpen ().length && this.markpos < 0) {
return this.getInIfOpen ().read (b, off, len);
}this.fill ();
avail = this.count - this.pos;
if (avail <= 0) return -1;
}var cnt = (avail < len) ? avail : len;
System.arraycopy (this.getBufIfOpen (), this.pos, b, off, cnt);
this.pos += cnt;
return cnt;
}, "~A,~N,~N");
$_V(c$, "read", 
function (b, off, len) {
this.getBufIfOpen ();
if ((off | len | (off + len) | (b.length - (off + len))) < 0) {
throw  new IndexOutOfBoundsException ();
} else if (len == 0) {
return 0;
}var n = 0;
for (; ; ) {
var nread = this.read1 (b, off + n, len - n);
if (nread <= 0) return (n == 0) ? nread : n;
n += nread;
if (n >= len) return n;
var input = this.$in;
if (input != null && input.available () <= 0) return n;
}
}, "~A,~N,~N");
$_V(c$, "skip", 
function (n) {
this.getBufIfOpen ();
if (n <= 0) {
return 0;
}var avail = this.count - this.pos;
if (avail <= 0) {
if (this.markpos < 0) return this.getInIfOpen ().skip (n);
this.fill ();
avail = this.count - this.pos;
if (avail <= 0) return 0;
}var skipped = (avail < n) ? avail : n;
this.pos += skipped;
return skipped;
}, "~N");
$_V(c$, "available", 
function () {
var n = this.count - this.pos;
var avail = this.getInIfOpen ().available ();
return n > (2147483647 - avail) ? 2147483647 : n + avail;
});
$_V(c$, "mark", 
function (readlimit) {
this.marklimit = readlimit;
this.markpos = this.pos;
}, "~N");
$_V(c$, "reset", 
function () {
this.getBufIfOpen ();
if (this.markpos < 0) throw  new java.io.IOException ("Resetting to invalid mark");
this.pos = this.markpos;
});
$_V(c$, "markSupported", 
function () {
return true;
});
$_V(c$, "close", 
function () {
var input = this.$in;
this.$in = null;
if (input != null) input.close ();
return;
});
Clazz_defineStatics (c$,
"defaultBufferSize", 8192);
});
Clazz_load (["java.io.Closeable"], "java.io.Reader", ["java.io.IOException", "java.lang.IllegalArgumentException", "$.NullPointerException"], function () {
c$ = Clazz_decorateAsClass (function () {
this.lock = null;
this.skipBuffer = null;
Clazz_instantialize (this, arguments);
}, java.io, "Reader", null, java.io.Closeable);
Clazz_makeConstructor (c$, 
function (lock) {
if (lock == null) {
throw  new NullPointerException ();
}this.lock = lock;
}, "~O");
$_M(c$, "skip", 
function (n) {
if (n < 0) throw  new IllegalArgumentException ("skip value is negative");
var nn = Math.min (n, 8192);
{
if ((this.skipBuffer == null) || (this.skipBuffer.length < nn)) this.skipBuffer =  Clazz_newCharArray (nn, '\0');
var r = n;
while (r > 0) {
var nc = this.read (this.skipBuffer, 0, Math.min (r, nn));
if (nc == -1) break;
r -= nc;
}
return n - r;
}}, "~N");
$_M(c$, "ready", 
function () {
return false;
});
$_M(c$, "markSupported", 
function () {
return false;
});
$_M(c$, "mark", 
function (readAheadLimit) {
throw  new java.io.IOException ("mark() not supported");
}, "~N");
$_M(c$, "reset", 
function () {
throw  new java.io.IOException ("reset() not supported");
});
Clazz_defineStatics (c$,
"maxSkipBufferSize", 8192);
});
Clazz_load (["java.io.Reader"], "java.io.InputStreamReader", ["java.lang.NullPointerException"], function () {
c$ = Clazz_decorateAsClass (function () {
this.$in = null;
this.isOpen = true;
this.charsetName = null;
this.isUTF8 = false;
this.bytearr = null;
this.pos = 0;
Clazz_instantialize (this, arguments);
}, java.io, "InputStreamReader", java.io.Reader);
Clazz_makeConstructor (c$, 
function ($in, charsetName) {
Clazz_superConstructor (this, java.io.InputStreamReader, [$in]);
this.$in = $in;
this.charsetName = charsetName;
if (!(this.isUTF8 = "UTF-8".equals (charsetName)) && !"ISO-8859-1".equals (charsetName)) throw  new NullPointerException ("charsetName");
}, "java.io.InputStream,~S");
$_M(c$, "getEncoding", 
function () {
return this.charsetName;
});
$_V(c$, "read", 
function (cbuf, offset, length) {
if (this.bytearr == null || this.bytearr.length < length) this.bytearr =  Clazz_newByteArray (length, 0);
var c;
var char2;
var char3;
var byteCount = 0;
var charCount = offset;
var byteLen = this.$in.read (this.bytearr, this.pos, length - this.pos);
var nAvail = this.$in.available ();
if (byteLen < 0) return -1;
var nMax = byteLen;
while (byteCount < nMax) {
c = this.bytearr[byteCount] & 0xff;
if (this.isUTF8) switch (c >> 4) {
case 0xC:
case 0xD:
if (byteCount + 1 >= byteLen) {
if (nAvail >= 1) {
nMax = byteCount;
continue;
}} else if (((char2 = this.bytearr[byteCount + 1]) & 0xC0) == 0x80) {
cbuf[charCount++] = String.fromCharCode (((c & 0x1F) << 6) | (char2 & 0x3F));
byteCount += 2;
continue;
}this.isUTF8 = false;
break;
case 0xE:
if (byteCount + 2 >= byteLen) {
if (nAvail >= 2) {
nMax = byteCount;
continue;
}} else if (((char2 = this.bytearr[byteCount + 1]) & 0xC0) == 0x80 && ((char3 = this.bytearr[byteCount + 2]) & 0xC0) == 0x80) {
cbuf[charCount++] = String.fromCharCode (((c & 0x0F) << 12) | ((char2 & 0x3F) << 6) | (char3 & 0x3F));
byteCount += 3;
continue;
}this.isUTF8 = false;
break;
}
byteCount++;
cbuf[charCount++] = String.fromCharCode (c);
}
this.pos = byteLen - byteCount;
for (var i = 0; i < this.pos; i++) {
this.bytearr[i] = this.bytearr[byteCount++];
}
return charCount - offset;
}, "~A,~N,~N");
$_V(c$, "ready", 
function () {
return this.isOpen;
});
$_V(c$, "close", 
function () {
this.$in.close ();
this.isOpen = false;
});
});
Clazz_load (["java.io.Reader"], "java.io.BufferedReader", ["java.io.IOException", "java.lang.IllegalArgumentException", "$.IndexOutOfBoundsException", "JU.SB"], function () {
c$ = Clazz_decorateAsClass (function () {
this.$in = null;
this.cb = null;
this.nChars = 0;
this.nextChar = 0;
this.markedChar = -1;
this.readAheadLimit = 0;
this.skipLF = false;
this.markedSkipLF = false;
Clazz_instantialize (this, arguments);
}, java.io, "BufferedReader", java.io.Reader);
$_M(c$, "setSize", 
function (sz) {
if (sz <= 0) throw  new IllegalArgumentException ("Buffer size <= 0");
this.cb =  Clazz_newCharArray (sz, '\0');
this.nextChar = this.nChars = 0;
}, "~N");
Clazz_makeConstructor (c$, 
function ($in) {
Clazz_superConstructor (this, java.io.BufferedReader, [$in]);
this.$in = $in;
this.setSize (java.io.BufferedReader.defaultCharBufferSize);
}, "java.io.Reader");
$_M(c$, "ensureOpen", 
function () {
if (this.$in == null) throw  new java.io.IOException ("Stream closed");
});
$_M(c$, "fill", 
function () {
var dst;
if (this.markedChar <= -1) {
dst = 0;
} else {
var delta = this.nextChar - this.markedChar;
if (delta >= this.readAheadLimit) {
this.markedChar = -2;
this.readAheadLimit = 0;
dst = 0;
} else {
if (this.readAheadLimit <= this.cb.length) {
System.arraycopy (this.cb, this.markedChar, this.cb, 0, delta);
this.markedChar = 0;
dst = delta;
} else {
var ncb =  Clazz_newCharArray (this.readAheadLimit, '\0');
System.arraycopy (this.cb, this.markedChar, ncb, 0, delta);
this.cb = ncb;
this.markedChar = 0;
dst = delta;
}this.nextChar = this.nChars = delta;
}}var n;
do {
n = this.$in.read (this.cb, dst, this.cb.length - dst);
} while (n == 0);
if (n > 0) {
this.nChars = dst + n;
this.nextChar = dst;
}});
$_M(c$, "read1", 
function (cbuf, off, len) {
if (this.nextChar >= this.nChars) {
if (len >= this.cb.length && this.markedChar <= -1 && !this.skipLF) {
return this.$in.read (cbuf, off, len);
}this.fill ();
}if (this.nextChar >= this.nChars) return -1;
if (this.skipLF) {
this.skipLF = false;
if (this.cb[this.nextChar] == '\n') {
this.nextChar++;
if (this.nextChar >= this.nChars) this.fill ();
if (this.nextChar >= this.nChars) return -1;
}}var n = Math.min (len, this.nChars - this.nextChar);
System.arraycopy (this.cb, this.nextChar, cbuf, off, n);
this.nextChar += n;
return n;
}, "~A,~N,~N");
$_M(c$, "read", 
function (cbuf, off, len) {
{
this.ensureOpen ();
if ((off < 0) || (off > cbuf.length) || (len < 0) || ((off + len) > cbuf.length) || ((off + len) < 0)) {
throw  new IndexOutOfBoundsException ();
} else if (len == 0) {
return 0;
}var n = this.read1 (cbuf, off, len);
if (n <= 0) return n;
while ((n < len) && this.$in.ready ()) {
var n1 = this.read1 (cbuf, off + n, len - n);
if (n1 <= 0) break;
n += n1;
}
return n;
}}, "~A,~N,~N");
$_M(c$, "readLine1", 
function (ignoreLF) {
var s = null;
var startChar;
{
this.ensureOpen ();
var omitLF = ignoreLF || this.skipLF;
for (; ; ) {
if (this.nextChar >= this.nChars) this.fill ();
if (this.nextChar >= this.nChars) {
if (s != null && s.length () > 0) return s.toString ();
return null;
}var eol = false;
var c = String.fromCharCode (0);
var i;
if (omitLF && (this.cb[this.nextChar] == '\n')) this.nextChar++;
this.skipLF = false;
omitLF = false;
charLoop : for (i = this.nextChar; i < this.nChars; i++) {
c = this.cb[i];
if ((c == '\n') || (c == '\r')) {
eol = true;
break charLoop;
}}
startChar = this.nextChar;
this.nextChar = i;
if (eol) {
var str;
if (s == null) {
str =  String.instantialize (this.cb, startChar, i - startChar);
} else {
s.appendCB (this.cb, startChar, i - startChar);
str = s.toString ();
}this.nextChar++;
if (c == '\r') {
this.skipLF = true;
}return str;
}if (s == null) s = JU.SB.newN (java.io.BufferedReader.defaultExpectedLineLength);
s.appendCB (this.cb, startChar, i - startChar);
}
}}, "~B");
$_M(c$, "readLine", 
function () {
return this.readLine1 (false);
});
$_V(c$, "skip", 
function (n) {
if (n < 0) {
throw  new IllegalArgumentException ("skip value is negative");
}{
this.ensureOpen ();
var r = n;
while (r > 0) {
if (this.nextChar >= this.nChars) this.fill ();
if (this.nextChar >= this.nChars) break;
if (this.skipLF) {
this.skipLF = false;
if (this.cb[this.nextChar] == '\n') {
this.nextChar++;
}}var d = this.nChars - this.nextChar;
if (r <= d) {
this.nextChar += r;
r = 0;
break;
}r -= d;
this.nextChar = this.nChars;
}
return n - r;
}}, "~N");
$_M(c$, "ready", 
function () {
{
this.ensureOpen ();
if (this.skipLF) {
if (this.nextChar >= this.nChars && this.$in.ready ()) {
this.fill ();
}if (this.nextChar < this.nChars) {
if (this.cb[this.nextChar] == '\n') this.nextChar++;
this.skipLF = false;
}}return (this.nextChar < this.nChars) || this.$in.ready ();
}});
$_V(c$, "markSupported", 
function () {
return true;
});
$_V(c$, "mark", 
function (readAheadLimit) {
if (readAheadLimit < 0) {
throw  new IllegalArgumentException ("Read-ahead limit < 0");
}{
this.ensureOpen ();
this.readAheadLimit = readAheadLimit;
this.markedChar = this.nextChar;
this.markedSkipLF = this.skipLF;
}}, "~N");
$_V(c$, "reset", 
function () {
{
this.ensureOpen ();
if (this.markedChar < 0) throw  new java.io.IOException ((this.markedChar == -2) ? "Mark invalid" : "Stream not marked");
this.nextChar = this.markedChar;
this.skipLF = this.markedSkipLF;
}});
$_M(c$, "close", 
function () {
{
if (this.$in == null) return;
this.$in.close ();
this.$in = null;
this.cb = null;
}});
Clazz_defineStatics (c$,
"INVALIDATED", -2,
"UNMARKED", -1,
"defaultCharBufferSize", 8192,
"defaultExpectedLineLength", 80);
});
Clazz_load (["java.io.Reader"], "java.io.StringReader", ["java.io.IOException", "java.lang.IllegalArgumentException", "$.IndexOutOfBoundsException"], function () {
c$ = Clazz_decorateAsClass (function () {
this.str = null;
this.length = 0;
this.next = 0;
this.$mark = 0;
Clazz_instantialize (this, arguments);
}, java.io, "StringReader", java.io.Reader);
Clazz_makeConstructor (c$, 
function (s) {
Clazz_superConstructor (this, java.io.StringReader, [s]);
this.str = s;
this.length = s.length;
}, "~S");
$_M(c$, "ensureOpen", 
function () {
if (this.str == null) throw  new java.io.IOException ("Stream closed");
});
$_V(c$, "read", 
function (cbuf, off, len) {
{
this.ensureOpen ();
if ((off < 0) || (off > cbuf.length) || (len < 0) || ((off + len) > cbuf.length) || ((off + len) < 0)) {
throw  new IndexOutOfBoundsException ();
} else if (len == 0) {
return 0;
}if (this.next >= this.length) return -1;
var n = Math.min (this.length - this.next, len);
this.str.getChars (this.next, this.next + n, cbuf, off);
this.next += n;
return n;
}}, "~A,~N,~N");
$_V(c$, "skip", 
function (ns) {
{
this.ensureOpen ();
if (this.next >= this.length) return 0;
var n = Math.min (this.length - this.next, ns);
n = Math.max (-this.next, n);
this.next += n;
return n;
}}, "~N");
$_V(c$, "ready", 
function () {
{
this.ensureOpen ();
return true;
}});
$_V(c$, "markSupported", 
function () {
return true;
});
$_V(c$, "mark", 
function (readAheadLimit) {
if (readAheadLimit < 0) {
throw  new IllegalArgumentException ("Read-ahead limit < 0");
}{
this.ensureOpen ();
this.$mark = this.next;
}}, "~N");
$_V(c$, "reset", 
function () {
{
this.ensureOpen ();
this.next = this.$mark;
}});
$_V(c$, "close", 
function () {
this.str = null;
});
});
Clazz_load (["java.io.Closeable", "$.Flushable"], "java.io.OutputStream", ["java.lang.IndexOutOfBoundsException", "$.NullPointerException"], function () {
c$ = Clazz_declareType (java.io, "OutputStream", null, [java.io.Closeable, java.io.Flushable]);
$_M(c$, "write", 
function (b, off, len) {
if (b == null) {
throw  new NullPointerException ();
} else if ((off < 0) || (off > b.length) || (len < 0) || ((off + len) > b.length) || ((off + len) < 0)) {
throw  new IndexOutOfBoundsException ();
} else if (len == 0) {
return;
}for (var i = 0; i < len; i++) {
this.writeByteAsInt (b[off + i]);
}
}, "~A,~N,~N");
$_V(c$, "flush", 
function () {
});
$_V(c$, "close", 
function () {
});
});
Clazz_load (["java.io.OutputStream"], "java.io.ByteArrayOutputStream", ["java.lang.IllegalArgumentException", "$.IndexOutOfBoundsException", "$.OutOfMemoryError"], function () {
c$ = Clazz_decorateAsClass (function () {
this.buf = null;
this.count = 0;
Clazz_instantialize (this, arguments);
}, java.io, "ByteArrayOutputStream", java.io.OutputStream);
Clazz_makeConstructor (c$, 
function () {
this.construct (32);
});
Clazz_makeConstructor (c$, 
function (size) {
Clazz_superConstructor (this, java.io.ByteArrayOutputStream, []);
if (size < 0) {
throw  new IllegalArgumentException ("Negative initial size: " + size);
}this.buf =  Clazz_newByteArray (size, 0);
}, "~N");
$_M(c$, "ensureCapacity", 
function (minCapacity) {
if (minCapacity - this.buf.length > 0) this.grow (minCapacity);
}, "~N");
$_M(c$, "grow", 
function (minCapacity) {
var oldCapacity = this.buf.length;
var newCapacity = oldCapacity << 1;
if (newCapacity - minCapacity < 0) newCapacity = minCapacity;
if (newCapacity < 0) {
if (minCapacity < 0) throw  new OutOfMemoryError ();
newCapacity = minCapacity;
}this.buf = java.io.ByteArrayOutputStream.arrayCopyByte (this.buf, newCapacity);
}, "~N");
c$.arrayCopyByte = $_M(c$, "arrayCopyByte", 
function (array, newLength) {
var t =  Clazz_newByteArray (newLength, 0);
System.arraycopy (array, 0, t, 0, array.length < newLength ? array.length : newLength);
return t;
}, "~A,~N");
$_V(c$, "writeByteAsInt", 
function (b) {
this.ensureCapacity (this.count + 1);
this.buf[this.count] = b;
this.count += 1;
}, "~N");
$_M(c$, "write", 
function (b, off, len) {
if ((off < 0) || (off > b.length) || (len < 0) || ((off + len) - b.length > 0)) {
throw  new IndexOutOfBoundsException ();
}this.ensureCapacity (this.count + len);
System.arraycopy (b, off, this.buf, this.count, len);
this.count += len;
}, "~A,~N,~N");
$_M(c$, "writeTo", 
function (out) {
out.write (this.buf, 0, this.count);
}, "java.io.OutputStream");
$_M(c$, "reset", 
function () {
this.count = 0;
});
$_M(c$, "toByteArray", 
function () {
return (this.count == this.buf.length ? this.buf : java.io.ByteArrayOutputStream.arrayCopyByte (this.buf, this.count));
});
$_M(c$, "size", 
function () {
return this.count;
});
$_V(c$, "toString", 
function () {
return  String.instantialize (this.buf, 0, this.count);
});
$_V(c$, "close", 
function () {
});
});
Clazz_declarePackage ("java.net");
Clazz_load (["java.io.IOException"], "java.net.MalformedURLException", null, function () {
c$ = Clazz_declareType (java.net, "MalformedURLException", java.io.IOException);
Clazz_makeConstructor (c$, 
function () {
Clazz_superConstructor (this, java.net.MalformedURLException, []);
});
});
$_J("java.net");
c$=$_T(java.net,"URLEncoder");
c$.encode=$_M(c$,"encode",
function(s){
return encodeURIComponent(arguments[0]);
},"~S");
c$.encode=$_M(c$,"encode",
function(s,enc){
return encodeURIComponent(arguments[0]);
},"~S,~S");
$_S(c$,
"digits","0123456789ABCDEF");
$_J("java.net");
$_L(null,"java.net.URLDecoder",["java.lang.NullPointerException"],function(){
c$=$_T(java.net,"URLDecoder");
c$.decode=$_M(c$,"decode",
function(s){
return decodeURIComponent(arguments[0]);
},"~S");
c$.decode=$_M(c$,"decode",
function(s,enc){
if(enc==null){
throw new NullPointerException();
}{
return decodeURIComponent(arguments[0]);
}return null;
},"~S,~S");
});
Clazz_declarePackage ("java.net");
Clazz_declareInterface (java.net, "URLStreamHandlerFactory");
Clazz_declarePackage ("java.net");
Clazz_load (null, "java.net.URLStreamHandler", ["java.lang.IllegalArgumentException", "$.SecurityException", "$.UnsupportedOperationException"], function () {
c$ = Clazz_declareType (java.net, "URLStreamHandler");
$_M(c$, "openConnectionProxy", 
function (u, p) {
throw  new UnsupportedOperationException ("Method not implemented.");
}, "java.net.URL,java.net.Proxy");
$_M(c$, "parseURL", 
function (u, spec, start, limit) {
var protocol = u.getProtocol ();
var authority = u.getAuthority ();
var userInfo = u.getUserInfo ();
var host = u.getHost ();
var port = u.getPort ();
var path = u.getPath ();
var query = u.getQuery ();
var ref = u.getRef ();
var isRelPath = false;
var queryOnly = false;
if (start < limit) {
var queryStart = spec.indexOf ('?');
queryOnly = queryStart == start;
if ((queryStart != -1) && (queryStart < limit)) {
query = spec.substring (queryStart + 1, limit);
if (limit > queryStart) limit = queryStart;
spec = spec.substring (0, queryStart);
}}var i = 0;
var isUNCName = (start <= limit - 4) && (spec.charAt (start) == '/') && (spec.charAt (start + 1) == '/') && (spec.charAt (start + 2) == '/') && (spec.charAt (start + 3) == '/');
if (!isUNCName && (start <= limit - 2) && (spec.charAt (start) == '/') && (spec.charAt (start + 1) == '/')) {
start += 2;
i = spec.indexOf ('/', start);
if (i < 0) {
i = spec.indexOf ('?', start);
if (i < 0) i = limit;
}host = authority = spec.substring (start, i);
var ind = authority.indexOf ('@');
if (ind != -1) {
userInfo = authority.substring (0, ind);
host = authority.substring (ind + 1);
} else {
userInfo = null;
}if (host != null) {
if (host.length > 0 && (host.charAt (0) == '[')) {
throw  new IllegalArgumentException ("Invalid host: " + host);
}ind = host.indexOf (':');
port = -1;
if (ind >= 0) {
if (host.length > (ind + 1)) {
port = Integer.parseInt (host.substring (ind + 1));
}host = host.substring (0, ind);
}} else {
host = "";
}if (port < -1) throw  new IllegalArgumentException ("Invalid port number :" + port);
start = i;
if (authority.length > 0) path = "";
}if (host == null) {
host = "";
}if (start < limit) {
if (spec.charAt (start) == '/') {
path = spec.substring (start, limit);
} else if (path != null && path.length > 0) {
isRelPath = true;
var ind = path.lastIndexOf ('/');
var seperator = "";
if (ind == -1 && authority != null) seperator = "/";
path = path.substring (0, ind + 1) + seperator + spec.substring (start, limit);
} else {
var seperator = (authority != null) ? "/" : "";
path = seperator + spec.substring (start, limit);
}} else if (queryOnly && path != null) {
var ind = path.lastIndexOf ('/');
if (ind < 0) ind = 0;
path = path.substring (0, ind) + "/";
}if (path == null) path = "";
if (isRelPath) {
while ((i = path.indexOf ("/./")) >= 0) {
path = path.substring (0, i) + path.substring (i + 2);
}
i = 0;
while ((i = path.indexOf ("/../", i)) >= 0) {
if (i > 0 && (limit = path.lastIndexOf ('/', i - 1)) >= 0 && (path.indexOf ("/../", limit) != 0)) {
path = path.substring (0, limit) + path.substring (i + 3);
i = 0;
} else {
i = i + 3;
}}
while (path.endsWith ("/..")) {
i = path.indexOf ("/..");
if ((limit = path.lastIndexOf ('/', i - 1)) >= 0) {
path = path.substring (0, limit + 1);
} else {
break;
}}
if (path.startsWith ("./") && path.length > 2) path = path.substring (2);
if (path.endsWith ("/.")) path = path.substring (0, path.length - 1);
}this.setURL (u, protocol, host, port, authority, userInfo, path, query, ref);
}, "java.net.URL,~S,~N,~N");
$_M(c$, "getDefaultPort", 
function () {
return -1;
});
$_M(c$, "equals2", 
function (u1, u2) {
var ref1 = u1.getRef ();
var ref2 = u2.getRef ();
return (ref1 === ref2 || (ref1 != null && ref1.equals (ref2))) && this.sameFile (u1, u2);
}, "java.net.URL,java.net.URL");
$_M(c$, "hashCode", 
function (u) {
var h = 0;
var protocol = u.getProtocol ();
if (protocol != null) h += protocol.hashCode ();
h += u.toString ().hashCode ();
var file = u.getFile ();
if (file != null) h += file.hashCode ();
if (u.getPort () == -1) h += this.getDefaultPort ();
 else h += u.getPort ();
var ref = u.getRef ();
if (ref != null) h += ref.hashCode ();
return h;
}, "java.net.URL");
$_M(c$, "sameFile", 
function (u1, u2) {
if (!((u1.getProtocol () === u2.getProtocol ()) || (u1.getProtocol () != null && u1.getProtocol ().equalsIgnoreCase (u2.getProtocol ())))) return false;
if (!(u1.getFile () === u2.getFile () || (u1.getFile () != null && u1.getFile ().equals (u2.getFile ())))) return false;
var port1;
var port2;
port1 = (u1.getPort () != -1) ? u1.getPort () : u1.handler.getDefaultPort ();
port2 = (u2.getPort () != -1) ? u2.getPort () : u2.handler.getDefaultPort ();
if (port1 != port2) return false;
if (!this.hostsEqual (u1, u2)) return false;
return true;
}, "java.net.URL,java.net.URL");
$_M(c$, "hostsEqual", 
function (u1, u2) {
if (u1.getHost () != null && u2.getHost () != null) return u1.getHost ().equalsIgnoreCase (u2.getHost ());
return u1.getHost () == null && u2.getHost () == null;
}, "java.net.URL,java.net.URL");
$_M(c$, "toExternalForm", 
function (u) {
return "";
}, "java.net.URL");
$_M(c$, "setURL", 
function (u, protocol, host, port, authority, userInfo, path, query, ref) {
if (this !== u.handler) {
throw  new SecurityException ("handler for url different from this handler");
}u.set (u.getProtocol (), host, port, authority, userInfo, path, query, ref);
}, "java.net.URL,~S,~S,~N,~S,~S,~S,~S,~S");
$_M(c$, "setURLDeprecated", 
function (u, protocol, host, port, file, ref) {
var authority = null;
var userInfo = null;
if (host != null && host.length != 0) {
authority = (port == -1) ? host : host + ":" + port;
var at = host.lastIndexOf ('@');
if (at != -1) {
userInfo = host.substring (0, at);
host = host.substring (at + 1);
}}var path = null;
var query = null;
if (file != null) {
var q = file.lastIndexOf ('?');
if (q != -1) {
query = file.substring (q + 1);
path = file.substring (0, q);
} else path = file;
}this.setURL (u, protocol, host, port, authority, userInfo, path, query, ref);
}, "java.net.URL,~S,~S,~N,~S,~S");
});
Clazz_declarePackage ("java.net");
Clazz_load (["java.util.Hashtable"], "java.net.URL", ["java.io.IOException", "java.lang.Character", "$.Error", "java.net.MalformedURLException"], function () {
c$ = Clazz_decorateAsClass (function () {
this.protocol = null;
this.host = null;
this.port = -1;
this.file = null;
this.query = null;
this.authority = null;
this.path = null;
this.userInfo = null;
this.ref = null;
this.handler = null;
this.$hashCode = -1;
Clazz_instantialize (this, arguments);
}, java.net, "URL", null, java.io.Serializable);
Clazz_makeConstructor (c$, 
function (context, spec, handler) {
var original = spec;
var i;
var limit;
var c;
var start = 0;
var newProtocol = null;
var aRef = false;
var isRelative = false;
if (handler != null) {
var sm = System.getSecurityManager ();
if (sm != null) {
this.checkSpecifyHandler (sm);
}}try {
limit = spec.length;
while ((limit > 0) && (spec.charAt (limit - 1) <= ' ')) {
limit--;
}
while ((start < limit) && (spec.charAt (start) <= ' ')) {
start++;
}
if (spec.regionMatches (true, start, "url:", 0, 4)) {
start += 4;
}if (start < spec.length && spec.charAt (start) == '#') {
aRef = true;
}for (i = start; !aRef && (i < limit) && ((c = spec.charCodeAt (i)) != 47); i++) {
if (c == 58) {
var s = spec.substring (start, i).toLowerCase ();
if (this.isValidProtocol (s)) {
newProtocol = s;
start = i + 1;
}break;
}}
this.protocol = newProtocol;
if ((context != null) && ((newProtocol == null) || newProtocol.equalsIgnoreCase (context.protocol))) {
if (handler == null) {
handler = context.handler;
}if (context.path != null && context.path.startsWith ("/")) newProtocol = null;
if (newProtocol == null) {
this.protocol = context.protocol;
this.authority = context.authority;
this.userInfo = context.userInfo;
this.host = context.host;
this.port = context.port;
this.file = context.file;
this.path = context.path;
isRelative = true;
}}if (this.protocol == null) {
throw  new java.net.MalformedURLException ("no protocol: " + original);
}if (handler == null && (handler = java.net.URL.getURLStreamHandler (this.protocol)) == null) {
throw  new java.net.MalformedURLException ("unknown protocol: " + this.protocol);
}this.handler = handler;
i = spec.indexOf ('#', start);
if (i >= 0) {
this.ref = spec.substring (i + 1, limit);
limit = i;
}if (isRelative && start == limit) {
this.query = context.query;
if (this.ref == null) {
this.ref = context.ref;
}}handler.parseURL (this, spec, start, limit);
} catch (e$$) {
if (Clazz_exceptionOf (e$$, java.net.MalformedURLException)) {
var e = e$$;
{
throw e;
}
} else if (Clazz_exceptionOf (e$$, Exception)) {
var e = e$$;
{
var exception =  new java.net.MalformedURLException (e.getMessage ());
exception.initCause (e);
throw exception;
}
} else {
throw e$$;
}
}
}, "java.net.URL,~S,java.net.URLStreamHandler");
$_M(c$, "isValidProtocol", 
function (protocol) {
var len = protocol.length;
if (len < 1) return false;
var c = protocol.charAt (0);
if (!Character.isLetter (c)) return false;
for (var i = 1; i < len; i++) {
c = protocol.charAt (i);
if (!Character.isLetterOrDigit (c) && c != '.' && c != '+' && c != '-') {
return false;
}}
return true;
}, "~S");
$_M(c$, "checkSpecifyHandler", 
function (sm) {
}, "SecurityManager");
$_M(c$, "set5", 
function (protocol, host, port, file, ref) {
{
this.protocol = protocol;
this.host = host;
this.authority = port == -1 ? host : host + ":" + port;
this.port = port;
this.file = file;
this.ref = ref;
this.$hashCode = -1;
var q = file.lastIndexOf ('?');
if (q != -1) {
this.query = file.substring (q + 1);
this.path = file.substring (0, q);
} else this.path = file;
}}, "~S,~S,~N,~S,~S");
$_M(c$, "set", 
function (protocol, host, port, authority, userInfo, path, query, ref) {
{
this.protocol = protocol;
this.host = host;
this.port = port;
this.file = query == null ? path : path + "?" + query;
this.userInfo = userInfo;
this.path = path;
this.ref = ref;
this.$hashCode = -1;
this.query = query;
this.authority = authority;
}}, "~S,~S,~N,~S,~S,~S,~S,~S");
$_M(c$, "getQuery", 
function () {
return this.query;
});
$_M(c$, "getPath", 
function () {
return this.path;
});
$_M(c$, "getUserInfo", 
function () {
return this.userInfo;
});
$_M(c$, "getAuthority", 
function () {
return this.authority;
});
$_M(c$, "getPort", 
function () {
return this.port;
});
$_M(c$, "getDefaultPort", 
function () {
return this.handler.getDefaultPort ();
});
$_M(c$, "getProtocol", 
function () {
return this.protocol;
});
$_M(c$, "getHost", 
function () {
return this.host;
});
$_M(c$, "getFile", 
function () {
return this.file;
});
$_M(c$, "getRef", 
function () {
return this.ref;
});
$_V(c$, "equals", 
function (obj) {
if (!(Clazz_instanceOf (obj, java.net.URL))) return false;
var u2 = obj;
return this.handler.equals2 (this, u2);
}, "~O");
$_V(c$, "hashCode", 
function () {
if (this.$hashCode != -1) return this.$hashCode;
this.$hashCode = this.handler.hashCode (this);
return this.$hashCode;
});
$_M(c$, "sameFile", 
function (other) {
return this.handler.sameFile (this, other);
}, "java.net.URL");
$_V(c$, "toString", 
function () {
return this.toExternalForm ();
});
$_M(c$, "toExternalForm", 
function () {
return this.handler.toExternalForm (this);
});
$_M(c$, "openConnection", 
function () {
return this.handler.openConnection (this);
});
$_M(c$, "openStream", 
function () {
return this.openConnection ().getInputStream ();
});
$_M(c$, "getContent", 
function () {
return this.openConnection ().getInputStream ();
});
c$.setURLStreamHandlerFactory = $_M(c$, "setURLStreamHandlerFactory", 
function (fac) {
{
if (java.net.URL.factory != null) {
throw  new Error ("factory already defined");
}var security = System.getSecurityManager ();
if (security != null) {
security.checkSetFactory ();
}java.net.URL.handlers.clear ();
($t$ = java.net.URL.factory = fac, java.net.URL.prototype.factory = java.net.URL.factory, $t$);
}}, "java.net.URLStreamHandlerFactory");
c$.getURLStreamHandler = $_M(c$, "getURLStreamHandler", 
function (protocol) {
var handler = java.net.URL.handlers.get (protocol);
if (handler == null) {
if (java.net.URL.factory != null) {
handler = java.net.URL.factory.createURLStreamHandler (protocol);
}}return handler;
}, "~S");
Clazz_defineStatics (c$,
"factory", null);
c$.handlers = c$.prototype.handlers =  new java.util.Hashtable ();
c$.streamHandlerLock = c$.prototype.streamHandlerLock =  new JavaObject ();
});
Clazz_declarePackage ("java.net");
Clazz_load (null, "java.net.URLConnection", ["java.lang.IllegalStateException", "$.NullPointerException", "java.net.UnknownServiceException", "JU.List"], function () {
c$ = Clazz_decorateAsClass (function () {
this.url = null;
this.doInput = true;
this.doOutput = false;
this.connected = false;
this.requests = null;
Clazz_instantialize (this, arguments);
}, java.net, "URLConnection");
$_M(c$, "setDoInput", 
function (doinput) {
if (this.connected) throw  new IllegalStateException ("Already connected");
this.doInput = doinput;
}, "~B");
$_M(c$, "getDoInput", 
function () {
return this.doInput;
});
$_M(c$, "setDoOutput", 
function (dooutput) {
if (this.connected) throw  new IllegalStateException ("Already connected");
this.doOutput = dooutput;
}, "~B");
$_M(c$, "getDoOutput", 
function () {
return this.doOutput;
});
Clazz_makeConstructor (c$, 
function (url) {
this.url = url;
}, "java.net.URL");
$_M(c$, "getURL", 
function () {
return this.url;
});
$_M(c$, "getInputStream", 
function () {
throw  new java.net.UnknownServiceException ("protocol doesn't support input");
});
$_M(c$, "getOutputStream", 
function () {
throw  new java.net.UnknownServiceException ("protocol doesn't support output");
});
$_M(c$, "setRequestProperty", 
function (key, value) {
if (this.connected) throw  new IllegalStateException ("Already connected");
if (key == null) throw  new NullPointerException ("key is null");
if (this.requests == null) this.requests =  new JU.List ();
for (var i = this.requests.size (); --i >= 0; ) if (this.requests.get (i)[0].equals (key)) {
this.requests.get (i)[1] = value;
return;
}
this.requests.addLast ([key, value]);
}, "~S,~S");
});
Clazz_declarePackage ("JU");
Clazz_load (["java.net.URLConnection"], "JU.AjaxURLConnection", null, function () {
c$ = Clazz_decorateAsClass (function () {
this.bytesOut = null;
this.postOut = "";
Clazz_instantialize (this, arguments);
}, JU, "AjaxURLConnection", java.net.URLConnection);
$_M(c$, "doAjax", 
function () {
{
return Jmol._doAjax(this.url, this.postOut, this.bytesOut);
}});
$_V(c$, "connect", 
function () {
});
$_M(c$, "outputBytes", 
function (bytes) {
this.bytesOut = bytes;
}, "~A");
$_M(c$, "outputString", 
function (post) {
this.postOut = post;
}, "~S");
$_M(c$, "getSB", 
function () {
return this.doAjax ();
});
});
Clazz_declarePackage ("JU");
Clazz_load (["java.net.URLStreamHandlerFactory", "java.util.Hashtable"], "JU.AjaxURLStreamHandlerFactory", ["JU.AjaxURLStreamHandler"], function () {
c$ = Clazz_decorateAsClass (function () {
this.htFactories = null;
Clazz_instantialize (this, arguments);
}, JU, "AjaxURLStreamHandlerFactory", null, java.net.URLStreamHandlerFactory);
Clazz_prepareFields (c$, function () {
this.htFactories =  new java.util.Hashtable ();
});
$_V(c$, "createURLStreamHandler", 
function (protocol) {
var fac = this.htFactories.get (protocol);
if (fac == null) this.htFactories.put (protocol, fac =  new JU.AjaxURLStreamHandler (protocol));
return (fac.protocol == null ? null : fac);
}, "~S");
});
Clazz_declarePackage ("JU");
Clazz_load (["java.net.URLStreamHandler"], "JU.AjaxURLStreamHandler", ["JU.AjaxURLConnection", "$.SB"], function () {
c$ = Clazz_decorateAsClass (function () {
this.protocol = null;
Clazz_instantialize (this, arguments);
}, JU, "AjaxURLStreamHandler", java.net.URLStreamHandler);
Clazz_makeConstructor (c$, 
function (protocol) {
Clazz_superConstructor (this, JU.AjaxURLStreamHandler, []);
this.protocol = protocol;
}, "~S");
$_V(c$, "openConnection", 
function (url) {
return  new JU.AjaxURLConnection (url);
}, "java.net.URL");
$_V(c$, "toExternalForm", 
function (u) {
var result =  new JU.SB ();
result.append (u.getProtocol ());
result.append (":");
if (u.getAuthority () != null && u.getAuthority ().length > 0) {
result.append ("//");
result.append (u.getAuthority ());
}if (u.getPath () != null) {
result.append (u.getPath ());
}if (u.getQuery () != null) {
result.append ("?");
result.append (u.getQuery ());
}if (u.getRef () != null) {
result.append ("#");
result.append (u.getRef ());
}return result.toString ();
}, "java.net.URL");
});
$_J("java.text");
c$=$_C(function(){
this.pattern=null;
$_Z(this,arguments);
},java.text,"MessageFormat");
$_K(c$,
function(pattern){
this.pattern=pattern;
},"~S");
$_K(c$,
function(pattern,locale){
this.pattern=pattern;
},"~S,java.util.Locale");
c$.format=$_M(c$,"format",
function(pattern,args){
return pattern.replace(/\{(\d+)\}/g,function($0,$1){
var i=parseInt($1);
if(args==null)return null;
return args[i];
});
},"~S,~A");
$_M(c$,"format",
function(obj){
return java.text.MessageFormat.format(this.pattern,[obj]);
},"~O");
$_L(null,"java.util.Random",["java.lang.IllegalArgumentException"],function(){
c$=$_C(function(){
this.haveNextNextGaussian=false;
this.seed=0;
this.nextNextGaussian=0;
$_Z(this,arguments);
},java.util,"Random",null,java.io.Serializable);
$_K(c$,
function(){
this.setSeed(System.currentTimeMillis());
});
$_K(c$,
function(seed){
this.setSeed(seed);
},"~N");
$_M(c$,"next",
function(bits){
this.seed=(this.seed*25214903917+0xb)&(281474976710655);
return(this.seed>>>(48-bits));
},"~N");
$_M(c$,"nextBoolean",
function(){
return Math.random()>0.5;
});
$_M(c$,"nextBytes",
function(buf){
for(var i=0;i<bytes.length;i++){
bytes[i]=Math.round(0x100*Math.random());
}
},"~A");
$_M(c$,"nextDouble",
function(){
return Math.random();
});
$_M(c$,"nextFloat",
function(){
return Math.random();
});
$_M(c$,"nextGaussian",
function(){
if(this.haveNextNextGaussian){
this.haveNextNextGaussian=false;
return this.nextNextGaussian;
}var v1;
var v2;
var s;
do{
v1=2*this.nextDouble()-1;
v2=2*this.nextDouble()-1;
s=v1*v1+v2*v2;
}while(s>=1);
var norm=Math.sqrt(-2*Math.log(s)/s);
this.nextNextGaussian=v2*norm;
this.haveNextNextGaussian=true;
return v1*norm;
});
$_M(c$,"nextInt",
function(){
return Math.ceil(0xffff*Math.random())-0x8000;
});
$_M(c$,"nextInt",
function(n){
if(n>0){
if((n&-n)==n){
return((n*this.next(31))>>31);
}var bits;
var val;
do{
bits=this.next(31);
val=bits%n;
}while(bits-val+(n-1)<0);
return val;
}throw new IllegalArgumentException();
},"~N");
$_M(c$,"nextLong",
function(){
return Math.ceil(0xffffffff*Math.random())-0x80000000;
});
$_M(c$,"setSeed",
function(seed){
this.seed=(seed^25214903917)&(281474976710655);
this.haveNextNextGaussian=false;
},"~N");
$_S(c$,
"multiplier",0x5deece66d);
});
Clazz_declarePackage ("J.util");
Clazz_declareInterface (J.util, "LoggerInterface");
Clazz_declarePackage ("J.util");
Clazz_load (["J.util.LoggerInterface"], "J.util.DefaultLogger", ["J.util.Logger"], function () {
c$ = Clazz_declareType (J.util, "DefaultLogger", null, J.util.LoggerInterface);
$_M(c$, "log", 
function (out, level, txt, e) {
if (out === System.err) System.out.flush ();
if ((out != null) && ((txt != null) || (e != null))) {
txt = (txt != null ? txt : "");
out.println ((J.util.Logger.logLevel () ? "[" + J.util.Logger.getLevel (level) + "] " : "") + txt + (e != null ? ": " + e.toString () : ""));
if (e != null) {
var elements = e.getStackTrace ();
if (elements != null) {
for (var i = 0; i < elements.length; i++) {
out.println (elements[i].getClassName () + " - " + elements[i].getLineNumber () + " - " + elements[i].getMethodName ());
}
}}}if (out === System.err) System.err.flush ();
}, "java.io.PrintStream,~N,~S,Throwable");
$_V(c$, "debug", 
function (txt) {
this.log (System.out, 5, txt, null);
}, "~S");
$_V(c$, "info", 
function (txt) {
this.log (System.out, 4, txt, null);
}, "~S");
$_V(c$, "warn", 
function (txt) {
this.log (System.out, 3, txt, null);
}, "~S");
$_V(c$, "warnEx", 
function (txt, e) {
this.log (System.out, 3, txt, e);
}, "~S,Throwable");
$_V(c$, "error", 
function (txt) {
this.log (System.err, 2, txt, null);
}, "~S");
$_V(c$, "errorEx", 
function (txt, e) {
this.log (System.err, 2, txt, e);
}, "~S,Throwable");
$_V(c$, "fatal", 
function (txt) {
this.log (System.err, 1, txt, null);
}, "~S");
$_V(c$, "fatalEx", 
function (txt, e) {
this.log (System.err, 1, txt, e);
}, "~S,Throwable");
});
Clazz_declarePackage ("J.util");
Clazz_load (["java.util.Hashtable", "J.util.DefaultLogger"], "J.util.Logger", ["java.lang.Long"], function () {
c$ = Clazz_declareType (J.util, "Logger");
c$.getProperty = $_M(c$, "getProperty", 
function (level, defaultValue) {
try {
var property = System.getProperty ("jmol.logger." + level, null);
if (property != null) {
return (property.equalsIgnoreCase ("true"));
}} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
return defaultValue;
}, "~S,~B");
c$.setLogger = $_M(c$, "setLogger", 
function (logger) {
($t$ = J.util.Logger._logger = logger, J.util.Logger.prototype._logger = J.util.Logger._logger, $t$);
($t$ = J.util.Logger.debugging = J.util.Logger.isActiveLevel (5) || J.util.Logger.isActiveLevel (6), J.util.Logger.prototype.debugging = J.util.Logger.debugging, $t$);
($t$ = J.util.Logger.debuggingHigh = (J.util.Logger.debugging && J.util.Logger._activeLevels[6]), J.util.Logger.prototype.debuggingHigh = J.util.Logger.debuggingHigh, $t$);
}, "J.util.LoggerInterface");
c$.isActiveLevel = $_M(c$, "isActiveLevel", 
function (level) {
return J.util.Logger._logger != null && level >= 0 && level < 7 && J.util.Logger._activeLevels[level];
}, "~N");
c$.setActiveLevel = $_M(c$, "setActiveLevel", 
function (level, active) {
if (level < 0) level = 0;
if (level >= 7) level = 6;
J.util.Logger._activeLevels[level] = active;
($t$ = J.util.Logger.debugging = J.util.Logger.isActiveLevel (5) || J.util.Logger.isActiveLevel (6), J.util.Logger.prototype.debugging = J.util.Logger.debugging, $t$);
($t$ = J.util.Logger.debuggingHigh = (J.util.Logger.debugging && J.util.Logger._activeLevels[6]), J.util.Logger.prototype.debuggingHigh = J.util.Logger.debuggingHigh, $t$);
}, "~N,~B");
c$.setLogLevel = $_M(c$, "setLogLevel", 
function (level) {
for (var i = 7; --i >= 0; ) J.util.Logger.setActiveLevel (i, i <= level);

}, "~N");
c$.getLevel = $_M(c$, "getLevel", 
function (level) {
switch (level) {
case 6:
return "DEBUGHIGH";
case 5:
return "DEBUG";
case 4:
return "INFO";
case 3:
return "WARN";
case 2:
return "ERROR";
case 1:
return "FATAL";
}
return "????";
}, "~N");
c$.logLevel = $_M(c$, "logLevel", 
function () {
return J.util.Logger._logLevel;
});
c$.doLogLevel = $_M(c$, "doLogLevel", 
function (log) {
($t$ = J.util.Logger._logLevel = log, J.util.Logger.prototype._logLevel = J.util.Logger._logLevel, $t$);
}, "~B");
c$.debug = $_M(c$, "debug", 
function (txt) {
if (!J.util.Logger.debugging) return;
try {
J.util.Logger._logger.debug (txt);
} catch (t) {
}
}, "~S");
c$.info = $_M(c$, "info", 
function (txt) {
try {
if (J.util.Logger.isActiveLevel (4)) {
J.util.Logger._logger.info (txt);
}} catch (t) {
}
}, "~S");
c$.warn = $_M(c$, "warn", 
function (txt) {
try {
if (J.util.Logger.isActiveLevel (3)) {
J.util.Logger._logger.warn (txt);
}} catch (t) {
}
}, "~S");
c$.warnEx = $_M(c$, "warnEx", 
function (txt, e) {
try {
if (J.util.Logger.isActiveLevel (3)) {
J.util.Logger._logger.warnEx (txt, e);
}} catch (t) {
}
}, "~S,Throwable");
c$.error = $_M(c$, "error", 
function (txt) {
try {
if (J.util.Logger.isActiveLevel (2)) {
J.util.Logger._logger.error (txt);
}} catch (t) {
}
}, "~S");
c$.errorEx = $_M(c$, "errorEx", 
function (txt, e) {
try {
if (J.util.Logger.isActiveLevel (2)) {
J.util.Logger._logger.errorEx (txt, e);
}} catch (t) {
}
}, "~S,Throwable");
c$.getLogLevel = $_M(c$, "getLogLevel", 
function () {
for (var i = 7; --i >= 0; ) if (J.util.Logger.isActiveLevel (i)) return i;

return 0;
});
c$.fatal = $_M(c$, "fatal", 
function (txt) {
try {
if (J.util.Logger.isActiveLevel (1)) {
J.util.Logger._logger.fatal (txt);
}} catch (t) {
}
}, "~S");
c$.fatalEx = $_M(c$, "fatalEx", 
function (txt, e) {
try {
if (J.util.Logger.isActiveLevel (1)) {
J.util.Logger._logger.fatalEx (txt, e);
}} catch (t) {
}
}, "~S,Throwable");
c$.startTimer = $_M(c$, "startTimer", 
function (msg) {
if (msg != null) J.util.Logger.htTiming.put (msg, Long.$valueOf (System.currentTimeMillis ()));
}, "~S");
c$.getTimerMsg = $_M(c$, "getTimerMsg", 
function (msg, time) {
if (time == 0) time = J.util.Logger.getTimeFrom (msg);
return "Time for " + msg + ": " + (time) + " ms";
}, "~S,~N");
c$.getTimeFrom = $_M(c$, "getTimeFrom", 
function (msg) {
var t;
return (msg == null || (t = J.util.Logger.htTiming.get (msg)) == null ? -1 : (System.currentTimeMillis () - t.longValue ()));
}, "~S");
c$.checkTimer = $_M(c$, "checkTimer", 
function (msg, andReset) {
var time = J.util.Logger.getTimeFrom (msg);
if (time >= 0 && !msg.startsWith ("(")) J.util.Logger.info (J.util.Logger.getTimerMsg (msg, time));
if (andReset) J.util.Logger.startTimer (msg);
return time;
}, "~S,~B");
c$.checkMemory = $_M(c$, "checkMemory", 
function () {
var bTotal = 0;
var bFree = 0;
var bMax = 0;
{
}J.util.Logger.info ("Memory: Total-Free=" + (bTotal - bFree) + "; Total=" + bTotal + "; Free=" + bFree + "; Max=" + bMax);
});
c$._logger = c$.prototype._logger =  new J.util.DefaultLogger ();
Clazz_defineStatics (c$,
"LEVEL_FATAL", 1,
"LEVEL_ERROR", 2,
"LEVEL_WARN", 3,
"LEVEL_INFO", 4,
"LEVEL_DEBUG", 5,
"LEVEL_DEBUGHIGH", 6,
"LEVEL_MAX", 7,
"_activeLevels",  Clazz_newBooleanArray (7, false),
"_logLevel", false,
"debugging", false,
"debuggingHigh", false);
{
J.util.Logger._activeLevels[6] = J.util.Logger.getProperty ("debugHigh", false);
J.util.Logger._activeLevels[5] = J.util.Logger.getProperty ("debug", false);
J.util.Logger._activeLevels[4] = J.util.Logger.getProperty ("info", true);
J.util.Logger._activeLevels[3] = J.util.Logger.getProperty ("warn", true);
J.util.Logger._activeLevels[2] = J.util.Logger.getProperty ("error", true);
J.util.Logger._activeLevels[1] = J.util.Logger.getProperty ("fatal", true);
($t$ = J.util.Logger._logLevel = J.util.Logger.getProperty ("logLevel", false), J.util.Logger.prototype._logLevel = J.util.Logger._logLevel, $t$);
($t$ = J.util.Logger.debugging = (J.util.Logger._logger != null && (J.util.Logger._activeLevels[5] || J.util.Logger._activeLevels[6])), J.util.Logger.prototype.debugging = J.util.Logger.debugging, $t$);
($t$ = J.util.Logger.debuggingHigh = (J.util.Logger.debugging && J.util.Logger._activeLevels[6]), J.util.Logger.prototype.debuggingHigh = J.util.Logger.debuggingHigh, $t$);
}c$.htTiming = c$.prototype.htTiming =  new java.util.Hashtable ();
});
Clazz_declarePackage ("J.i18n");
Clazz_load (null, "J.i18n.Resource", ["JU.PT"], function () {
c$ = Clazz_decorateAsClass (function () {
this.resource = null;
this.className = null;
Clazz_instantialize (this, arguments);
}, J.i18n, "Resource");
Clazz_makeConstructor (c$, 
function (resource, className) {
this.resource = resource;
this.className = className;
}, "~O,~S");
c$.getResource = $_M(c$, "getResource", 
function (className, name) {
var poData = null;
{
var base = ClazzLoader.fastGetJ2SLibBase(); var fname = base +
"/trans/" + name + ".po"; poData = Jmol._doAjax(fname, null,
null); if (!poData) return null;
poData = poData.toString();
}try {
return (poData == null ? null : J.i18n.Resource.getResourceFromPO (poData));
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return null;
} else {
throw e;
}
}
}, "~S,~S");
$_M(c$, "getString", 
function (string) {
{
return this.resource.get(string);
}}, "~S");
c$.getLanguage = $_M(c$, "getLanguage", 
function () {
var language = null;
{
language = Jmol.featureDetection.getDefaultLanguage().replace(/-/g,'_');
}return language;
});
c$.getResourceFromPO = $_M(c$, "getResourceFromPO", 
function (data) {
{
if (data == null || data.length == 0) return null;
var map = null; try {
var lines = J.util.TextFormat.split(data, '\n');
map = new java.util.Hashtable();
var mode = 0; var msgstr = ""; var msgid = "";
for (var i = 0; i < lines.length; i++) {
var line = lines[i];
if (line.length <= 2) {
if (mode == 2 && msgstr.length != 0 && msgid.length != 0) map.put(msgid, msgstr);
} else if (line.indexOf("msgid") == 0) {
mode = 1; msgid = J.i18n.Resource.fix(line);
} else if (line.indexOf("msgstr") == 0) {
mode = 2; msgstr = J.i18n.Resource.fix(line);
} else if (mode == 1) {
msgid += J.i18n.Resource.fix(line);
} else if (mode == 2) {
msgstr += J.i18n.Resource.fix(line);
}
}
} catch (e) { }
return (map == null || map.size() == 0 ? null : new J.i18n.Resource(map));
}}, "~S");
c$.fix = $_M(c$, "fix", 
function (line) {
return JU.PT.simpleReplace (line.substring (line.indexOf ("\"") + 1, line.lastIndexOf ("\"")), "\\n", "\n");
}, "~S");
});
Clazz_declarePackage ("J.i18n");
Clazz_load (null, "J.i18n.Language", ["J.i18n.GT"], function () {
c$ = Clazz_decorateAsClass (function () {
this.code = null;
this.language = null;
this.nativeLanguage = null;
this.display = false;
Clazz_instantialize (this, arguments);
}, J.i18n, "Language");
c$.getLanguageList = $_M(c$, "getLanguageList", 
function () {
return [ new J.i18n.Language ("ar", J.i18n.GT._ ("Arabic"), "العربية", false),  new J.i18n.Language ("ast", J.i18n.GT._ ("Asturian"), "Asturian", false),  new J.i18n.Language ("az", J.i18n.GT._ ("Azerbaijani"), "azərbaycan dili", false),  new J.i18n.Language ("bs", J.i18n.GT._ ("Bosnian"), "bosanski jezik", false),  new J.i18n.Language ("ca", J.i18n.GT._ ("Catalan"), "Català", true),  new J.i18n.Language ("cs", J.i18n.GT._ ("Czech"), "Čeština", true),  new J.i18n.Language ("da", J.i18n.GT._ ("Danish"), "Dansk", true),  new J.i18n.Language ("de", J.i18n.GT._ ("German"), "Deutsch", true),  new J.i18n.Language ("el", J.i18n.GT._ ("Greek"), "Ελληνικά", false),  new J.i18n.Language ("en_AU", J.i18n.GT._ ("Australian English"), "Australian English", false),  new J.i18n.Language ("en_GB", J.i18n.GT._ ("British English"), "British English", true),  new J.i18n.Language ("en_US", J.i18n.GT._ ("American English"), "American English", true),  new J.i18n.Language ("es", J.i18n.GT._ ("Spanish"), "Español", true),  new J.i18n.Language ("et", J.i18n.GT._ ("Estonian"), "Eesti", false),  new J.i18n.Language ("eu", J.i18n.GT._ ("Basque"), "Euskara", true),  new J.i18n.Language ("fi", J.i18n.GT._ ("Finnish"), "Suomi", true),  new J.i18n.Language ("fo", J.i18n.GT._ ("Faroese"), "Føroyskt", false),  new J.i18n.Language ("fr", J.i18n.GT._ ("French"), "Français", true),  new J.i18n.Language ("fy", J.i18n.GT._ ("Frisian"), "Frysk", false),  new J.i18n.Language ("gl", J.i18n.GT._ ("Galician"), "Galego", false),  new J.i18n.Language ("hr", J.i18n.GT._ ("Croatian"), "Hrvatski", false),  new J.i18n.Language ("hu", J.i18n.GT._ ("Hungarian"), "Magyar", true),  new J.i18n.Language ("hy", J.i18n.GT._ ("Armenian"), "Հայերեն", false),  new J.i18n.Language ("id", J.i18n.GT._ ("Indonesian"), "Indonesia", true),  new J.i18n.Language ("it", J.i18n.GT._ ("Italian"), "Italiano", true),  new J.i18n.Language ("ja", J.i18n.GT._ ("Japanese"), "日本語", true),  new J.i18n.Language ("jv", J.i18n.GT._ ("Javanese"), "Basa Jawa", false),  new J.i18n.Language ("ko", J.i18n.GT._ ("Korean"), "한국어", true),  new J.i18n.Language ("ms", J.i18n.GT._ ("Malay"), "Bahasa Melayu", true),  new J.i18n.Language ("nb", J.i18n.GT._ ("Norwegian Bokmal"), "Norsk Bokmål", false),  new J.i18n.Language ("nl", J.i18n.GT._ ("Dutch"), "Nederlands", true),  new J.i18n.Language ("oc", J.i18n.GT._ ("Occitan"), "Occitan", false),  new J.i18n.Language ("pl", J.i18n.GT._ ("Polish"), "Polski", false),  new J.i18n.Language ("pt", J.i18n.GT._ ("Portuguese"), "Português", false),  new J.i18n.Language ("pt_BR", J.i18n.GT._ ("Brazilian Portuguese"), "Português brasileiro", true),  new J.i18n.Language ("ru", J.i18n.GT._ ("Russian"), "Русский", false),  new J.i18n.Language ("sl", J.i18n.GT._ ("Slovenian"), "Slovenščina", false),  new J.i18n.Language ("sr", J.i18n.GT._ ("Serbian"), "српски језик", false),  new J.i18n.Language ("sv", J.i18n.GT._ ("Swedish"), "Svenska", true),  new J.i18n.Language ("ta", J.i18n.GT._ ("Tamil"), "தமிழ்", false),  new J.i18n.Language ("te", J.i18n.GT._ ("Telugu"), "తెలుగు", false),  new J.i18n.Language ("tr", J.i18n.GT._ ("Turkish"), "Türkçe", true),  new J.i18n.Language ("ug", J.i18n.GT._ ("Uyghur"), "Uyƣurqə", false),  new J.i18n.Language ("uk", J.i18n.GT._ ("Ukrainian"), "Українська", true),  new J.i18n.Language ("uz", J.i18n.GT._ ("Uzbek"), "O'zbek", false),  new J.i18n.Language ("zh_CN", J.i18n.GT._ ("Simplified Chinese"), "简体中文", true),  new J.i18n.Language ("zh_TW", J.i18n.GT._ ("Traditional Chinese"), "繁體中文", true)];
});
Clazz_makeConstructor (c$, 
function (code, language, nativeLanguage, display) {
this.code = code;
this.language = language;
this.nativeLanguage = nativeLanguage;
this.display = display;
}, "~S,~S,~S,~B");
c$.getSupported = $_M(c$, "getSupported", 
function (list, code) {
for (var i = list.length; --i >= 0; ) if (list[i].code.equalsIgnoreCase (code)) return list[i].code;

for (var i = list.length; --i >= 0; ) if (list[i].code.startsWith (code)) return list[i].code;

return null;
}, "~A,~S");
});
Clazz_declarePackage ("J.i18n");
Clazz_load (["java.util.Hashtable", "J.i18n.Language", "$.Resource"], "J.i18n.GT", ["java.text.MessageFormat", "J.util.Logger"], function () {
c$ = Clazz_decorateAsClass (function () {
this.resources = null;
this.resourceCount = 0;
this.doTranslate = true;
this.language = null;
Clazz_instantialize (this, arguments);
}, J.i18n, "GT");
Clazz_makeConstructor (c$, 
function () {
});
Clazz_makeConstructor (c$, 
function (langCode) {
{
}this.resources = null;
this.resourceCount = 0;
($t$ = J.i18n.GT.$getTextWrapper = this, J.i18n.GT.prototype.$getTextWrapper = J.i18n.GT.$getTextWrapper, $t$);
if (langCode != null && langCode.length == 0) langCode = "none";
if (langCode != null) this.language = langCode;
if ("none".equals (this.language)) this.language = null;
if (this.language == null) this.language = J.i18n.Resource.getLanguage ();
if (this.language == null) this.language = "en";
var la = this.language;
var la_co = null;
var la_co_va = null;
var i = this.language.indexOf ("_");
if (i >= 0) {
la = la.substring (0, i);
la_co = this.language;
if ((i = la_co.indexOf ("_", ++i)) >= 0) {
la_co = la_co.substring (0, i);
la_co_va = this.language;
}}if ((this.language = this.getSupported (la_co_va)) == null && (this.language = this.getSupported (la_co)) == null && (this.language = this.getSupported (la)) == null) {
this.language = "en";
System.out.println (this.language + " not supported -- using en");
return;
}la_co_va = null;
la_co = null;
switch (this.language.length) {
default:
la_co_va = this.language;
la_co = this.language.substring (0, 5);
la = this.language.substring (0, 2);
break;
case 5:
la_co = this.language;
la = this.language.substring (0, 2);
break;
case 2:
la = this.language;
break;
}
la_co = this.getSupported (la_co);
la = this.getSupported (la);
if (la === la_co || "en_US".equals (la)) la = null;
if (la_co === la_co_va) la_co = null;
if ("en_US".equals (la_co)) return;
if (J.i18n.GT.allowDebug && J.util.Logger.debugging) J.util.Logger.debug ("Instantiating gettext wrapper for " + this.language + " using files for language:" + la + " country:" + la_co + " variant:" + la_co_va);
if (!J.i18n.GT.$ignoreApplicationBundle) this.addBundles ("Jmol", la_co_va, la_co, la);
this.addBundles ("JmolApplet", la_co_va, la_co, la);
}, "~S");
c$.getLanguageList = $_M(c$, "getLanguageList", 
function (gt) {
if (J.i18n.GT.languageList == null) {
if (gt == null) gt = J.i18n.GT.getTextWrapper ();
gt.createLanguageList ();
}return J.i18n.GT.languageList;
}, "J.i18n.GT");
c$.getLanguage = $_M(c$, "getLanguage", 
function () {
return J.i18n.GT.getTextWrapper ().language;
});
c$.ignoreApplicationBundle = $_M(c$, "ignoreApplicationBundle", 
function () {
($t$ = J.i18n.GT.$ignoreApplicationBundle = true, J.i18n.GT.prototype.$ignoreApplicationBundle = J.i18n.GT.$ignoreApplicationBundle, $t$);
});
c$.setDoTranslate = $_M(c$, "setDoTranslate", 
function (TF) {
var b = J.i18n.GT.getDoTranslate ();
J.i18n.GT.getTextWrapper ().doTranslate = TF;
return b;
}, "~B");
c$.getDoTranslate = $_M(c$, "getDoTranslate", 
function () {
return J.i18n.GT.getTextWrapper ().doTranslate;
});
c$._ = $_M(c$, "_", 
function (string) {
return J.i18n.GT.getTextWrapper ().getString (string, null);
}, "~S");
c$._ = $_M(c$, "_", 
function (string, item) {
return J.i18n.GT.getTextWrapper ().getString (string, [item]);
}, "~S,~S");
c$._ = $_M(c$, "_", 
function (string, item) {
return J.i18n.GT.getTextWrapper ().getString (string, [Integer.$valueOf (item)]);
}, "~S,~N");
c$._ = $_M(c$, "_", 
function (string, objects) {
return J.i18n.GT.getTextWrapper ().getString (string, objects);
}, "~S,~A");
c$.escapeHTML = $_M(c$, "escapeHTML", 
function (msg) {
var ch;
for (var i = msg.length; --i >= 0; ) if (((ch = msg.charAt (i))).charCodeAt (0) > 0x7F) {
msg = msg.substring (0, i) + "&#" + ((ch).charCodeAt (0)) + ";" + msg.substring (i + 1);
}
return msg;
}, "~S");
c$.getTextWrapper = $_M(c$, "getTextWrapper", 
function () {
return (J.i18n.GT.$getTextWrapper == null ? ($t$ = J.i18n.GT.$getTextWrapper =  new J.i18n.GT (null), J.i18n.GT.prototype.$getTextWrapper = J.i18n.GT.$getTextWrapper, $t$) : J.i18n.GT.$getTextWrapper);
});
$_M(c$, "createLanguageList", 
function () {
var wasTranslating = this.doTranslate;
this.doTranslate = false;
($t$ = J.i18n.GT.languageList = J.i18n.Language.getLanguageList (), J.i18n.GT.prototype.languageList = J.i18n.GT.languageList, $t$);
this.doTranslate = wasTranslating;
});
$_M(c$, "getSupported", 
function (code) {
if (code == null) return null;
var s = J.i18n.GT.htLanguages.get (code);
if (s != null) return (s.length == 0 ? null : s);
s = J.i18n.Language.getSupported (J.i18n.GT.getLanguageList (this), code);
J.i18n.GT.htLanguages.put (code, (s == null ? "" : s));
return s;
}, "~S");
$_M(c$, "addBundles", 
function (type, la_co_va, la_co, la) {
try {
var className = "J.translation." + type + ".";
if (la_co_va != null) this.addBundle (className, la_co_va);
if (la_co != null) this.addBundle (className, la_co);
if (la != null) this.addBundle (className, la);
} catch (exception) {
if (Clazz_exceptionOf (exception, Exception)) {
if (J.i18n.GT.allowDebug) J.util.Logger.errorEx ("Some exception occurred!", exception);
this.resources = null;
this.resourceCount = 0;
} else {
throw exception;
}
}
}, "~S,~S,~S,~S");
$_M(c$, "addBundle", 
function (className, name) {
var resource = J.i18n.Resource.getResource (className, name);
if (resource != null) {
if (this.resources == null) {
this.resources =  new Array (8);
this.resourceCount = 0;
}this.resources[this.resourceCount] = resource;
this.resourceCount++;
if (J.i18n.GT.allowDebug) J.util.Logger.debug ("GT adding " + className);
}}, "~S,~S");
$_M(c$, "getString", 
function (string, objects) {
var trans = null;
if (this.doTranslate) {
for (var bundle = this.resourceCount; --bundle >= 0; ) {
trans = this.resources[bundle].getString (string);
if (trans != null) {
string = trans;
break;
}}
if (this.resourceCount > 0 && trans == null && J.i18n.GT.allowDebug && J.util.Logger.debugging) J.util.Logger.debug ("No trans, using default: " + string);
}if (trans == null) {
if (string.startsWith ("[")) string = string.substring (string.indexOf ("]") + 1);
 else if (string.endsWith ("]")) string = string.substring (0, string.indexOf ("["));
}return (objects == null ? string : java.text.MessageFormat.format (string, objects));
}, "~S,~A");
Clazz_defineStatics (c$,
"$ignoreApplicationBundle", false,
"$getTextWrapper", null,
"languageList", null,
"allowDebug", false);
c$.htLanguages = c$.prototype.htLanguages =  new java.util.Hashtable ();
});
Clazz_declarePackage ("J.api");
Clazz_declareInterface (J.api, "JmolCallbackListener");
Clazz_declarePackage ("J.api");
Clazz_load (["J.api.JmolCallbackListener"], "J.api.JmolStatusListener", null, function () {
Clazz_declareInterface (J.api, "JmolStatusListener", J.api.JmolCallbackListener);
});
Clazz_declarePackage ("J.api");
Clazz_declareInterface (J.api, "JmolSyncInterface");
Clazz_declarePackage ("J.appletjs");
Clazz_load (["J.api.JmolStatusListener", "$.JmolSyncInterface", "java.util.Hashtable"], "J.appletjs.Jmol", ["java.lang.Boolean", "java.net.URL", "javajs.awt.Dimension", "JU.List", "$.PT", "$.SB", "J.appletjs.JmolAppletRegistry", "J.constant.EnumCallback", "J.i18n.GT", "J.util.Escape", "$.Logger", "$.Parser", "J.viewer.JC", "$.Viewer"], function () {
c$ = Clazz_decorateAsClass (function () {
this.language = null;
this.doTranslate = true;
this.haveDocumentAccess = false;
this.isStereoSlave = false;
this.loading = false;
this.mayScript = true;
this.htmlName = null;
this.fullName = null;
this.syncId = null;
this.outputBuffer = null;
this.gRight = null;
this.viewer = null;
this.b$ = null;
this.viewerOptions = null;
this.htParams = null;
this.jmol = null;
this.haveNotifiedError = false;
if (!Clazz_isClassDefined ("J.appletjs.Jmol.MyStatusListener")) {
J.appletjs.Jmol.$Jmol$MyStatusListener$ ();
}
Clazz_instantialize (this, arguments);
}, J.appletjs, "Jmol", null, J.api.JmolSyncInterface);
Clazz_prepareFields (c$, function () {
this.b$ =  new java.util.Hashtable ();
this.htParams =  new java.util.Hashtable ();
});
Clazz_makeConstructor (c$, 
function (viewerOptions) {
if (viewerOptions == null) viewerOptions =  new java.util.Hashtable ();
this.viewerOptions = viewerOptions;
for (var entry, $entry = viewerOptions.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) this.htParams.put (entry.getKey ().toLowerCase (), entry.getValue ());

this.init ();
}, "java.util.Map");
$_M(c$, "jmolReady", 
function () {
System.out.println ("Jmol applet " + this.fullName + " ready");
this.viewer.getBooleanProperty ("__appletReady");
});
$_M(c$, "destroy", 
function () {
this.gRight = null;
J.appletjs.JmolAppletRegistry.checkOut (this.fullName);
this.viewer.setModeMouse (-1);
this.viewer.getBooleanProperty ("__appletDestroyed");
this.viewer = null;
System.out.println ("Jmol applet " + this.fullName + " destroyed");
});
$_M(c$, "setStereoGraphics", 
function (isStereo) {
{
}return null;
}, "~B");
$_M(c$, "init", 
function () {
this.jmol = this;
this.htmlName = this.getParameter ("name");
this.syncId = this.getParameter ("syncId");
this.fullName = this.htmlName + "__" + this.syncId + "__";
System.out.println ("Jmol JavaScript applet " + this.fullName + " initializing");
this.setLogging ();
J.i18n.GT.ignoreApplicationBundle ();
this.viewerOptions.remove ("debug");
this.viewerOptions.put ("fullName", this.fullName);
this.haveDocumentAccess = "true".equalsIgnoreCase ("" + this.getValue ("allowjavascript", "true"));
J.appletjs.JmolAppletRegistry.checkIn (this.fullName, this);
this.initWindows ();
this.initApplication ();
});
$_M(c$, "initWindows", 
function () {
this.viewerOptions.put ("applet", Boolean.TRUE);
if (this.getParameter ("statusListener") == null) this.viewerOptions.put ("statusListener", Clazz_innerTypeInstance (J.appletjs.Jmol.MyStatusListener, this, null));
this.viewer =  new J.viewer.Viewer (this.viewerOptions);
this.mayScript = true;
});
$_M(c$, "initApplication", 
function () {
this.viewer.pushHoldRepaint ();
var emulate = this.getValueLowerCase ("emulate", "jmol");
this.setStringProperty ("defaults", emulate.equals ("chime") ? "RasMol" : "Jmol");
this.setStringProperty ("backgroundColor", this.getValue ("bgcolor", this.getValue ("boxbgcolor", "black")));
this.loading = true;
for (var item, $item = 0, $$item = J.constant.EnumCallback.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) {
this.setValue (item.name () + "Callback", null);
}
this.loading = false;
this.language = this.getParameter ("language");
if (this.language != null) {
System.out.println ("requested language=" + this.language);
 new J.i18n.GT (this.language);
}this.doTranslate = (!"none".equals (this.language) && this.getBooleanValue ("doTranslate", true));
this.language = J.i18n.GT.getLanguage ();
System.out.println ("language=" + this.language);
if (this.b$.get (J.constant.EnumCallback.SCRIPT) == null && this.b$.get (J.constant.EnumCallback.ERROR) == null) if (this.b$.get (J.constant.EnumCallback.MESSAGE) != null) {
if (this.doTranslate && (this.getValue ("doTranslate", null) == null)) {
this.doTranslate = false;
J.util.Logger.warn ("Note -- Presence of message callback disables translation; to enable message translation use jmolSetTranslation(true) prior to jmolApplet()");
}if (this.doTranslate) J.util.Logger.warn ("Note -- Automatic language translation may affect parsing of message callbacks messages; use scriptCallback or errorCallback to process errors");
}if (!this.doTranslate) {
J.i18n.GT.setDoTranslate (false);
J.util.Logger.warn ("Note -- language translation disabled");
}if (!this.getBooleanValue ("popupMenu", true)) this.viewer.getProperty ("DATA_API", "disablePopupMenu", null);
var scriptParam = this.getValue ("script", "");
this.viewer.popHoldRepaint ("applet init");
if (scriptParam.length > 0) this.scriptProcessor (scriptParam, null, 1);
this.jmolReady ();
});
$_M(c$, "setLogging", 
function () {
var iLevel = (this.getValue ("logLevel", (this.getBooleanValue ("debug", false) ? "5" : "4"))).charCodeAt (0) - 48;
if (iLevel != 4) System.out.println ("setting logLevel=" + iLevel + " -- To change, use script \"set logLevel [0-5]\"");
J.util.Logger.setLogLevel (iLevel);
});
$_M(c$, "getParameter", 
function (paramName) {
var o = this.htParams.get (paramName.toLowerCase ());
return (o == null ? null :  String.instantialize (o.toString ()));
}, "~S");
$_M(c$, "getBooleanValue", 
function (propertyName, defaultValue) {
var value = this.getValue (propertyName, defaultValue ? "true" : "");
return (value.equalsIgnoreCase ("true") || value.equalsIgnoreCase ("on") || value.equalsIgnoreCase ("yes"));
}, "~S,~B");
$_M(c$, "getValue", 
function (propertyName, defaultValue) {
var stringValue = this.getParameter (propertyName);
System.out.println ("getValue " + propertyName + " = " + stringValue);
if (stringValue != null) return stringValue;
return defaultValue;
}, "~S,~S");
$_M(c$, "getValueLowerCase", 
function (paramName, defaultValue) {
var value = this.getValue (paramName, defaultValue);
if (value != null) {
value = value.trim ().toLowerCase ();
if (value.length == 0) value = null;
}return value;
}, "~S,~S");
$_M(c$, "setValue", 
function (name, defaultValue) {
this.setStringProperty (name, this.getValue (name, defaultValue));
}, "~S,~S");
$_M(c$, "setStringProperty", 
function (name, value) {
if (value == null) return;
J.util.Logger.info (name + " = \"" + value + "\"");
this.viewer.setStringProperty (name, value);
}, "~S,~S");
$_M(c$, "sendJsTextStatus", 
function (message) {
System.out.println (message);
}, "~S");
$_M(c$, "sendJsTextareaStatus", 
function (message) {
System.out.println (message);
}, "~S");
$_M(c$, "handleEvent", 
function (e) {
if (this.viewer == null) return false;
return this.viewer.processMouseEvent (e.id, e.x, e.y, e.modifiers, e.when);
}, "java.awt.Event");
$_M(c$, "scriptProcessor", 
function (script, statusParams, processType) {
if (script == null || script.length == 0) return "";
switch (processType) {
case 0:
var err = this.viewer.scriptCheck (script);
return (Clazz_instanceOf (err, String) ? err : "");
case 1:
if (statusParams != null) return this.viewer.scriptWaitStatus (script, statusParams).toString ();
return this.viewer.scriptWait (script);
case 2:
default:
return this.viewer.script (script);
}
}, "~S,~S,~N");
$_M(c$, "script", 
function (script) {
this.scriptNoWait (script);
}, "~S");
$_M(c$, "scriptNoWait", 
function (script) {
if (script == null || script.length == 0) return "";
return this.scriptProcessor (script, null, 2);
}, "~S");
$_M(c$, "scriptCheck", 
function (script) {
if (script == null || script.length == 0) return "";
return this.scriptProcessor (script, null, 0);
}, "~S");
$_M(c$, "scriptWait", 
function (script) {
return this.scriptWait (script, null);
}, "~S");
$_M(c$, "scriptWait", 
function (script, statusParams) {
if (script == null || script.length == 0) return "";
this.outputBuffer = null;
return this.scriptProcessor (script, statusParams, 1);
}, "~S,~S");
$_M(c$, "scriptWaitOutput", 
function (script) {
if (script == null || script.length == 0) return "";
this.outputBuffer =  new JU.SB ();
this.viewer.scriptWaitStatus (script, "");
var str = (this.outputBuffer == null ? "" : this.outputBuffer.toString ());
this.outputBuffer = null;
return str;
}, "~S");
$_M(c$, "syncScript", 
function (script) {
this.viewer.syncScript (script, "~", 0);
}, "~S");
$_M(c$, "getAppletInfo", 
function () {
return J.i18n.GT._ ("Jmol Applet version {0} {1}.\n\nAn OpenScience project.\n\nSee http://www.jmol.org for more information", [J.viewer.JC.version, J.viewer.JC.date]) + "\nhtmlName = " + J.util.Escape.eS (this.htmlName) + "\nsyncId = " + J.util.Escape.eS (this.syncId) + "\ndocumentBase = " + J.util.Escape.eS ("" + this.getProperty ("documentBase")) + "\ncodeBase = " + J.util.Escape.eS ("" + this.getProperty ("codeBase"));
});
$_V(c$, "getProperty", 
function (infoType, paramInfo) {
{
paramInfo || (paramInfo = "");
}return this.viewer.getProperty (null, infoType, paramInfo);
}, "~S,~S");
$_V(c$, "getPropertyAsString", 
function (infoType, paramInfo) {
{
paramInfo || (paramInfo = "");
}return this.viewer.getProperty ("readable", infoType, paramInfo).toString ();
}, "~S,~S");
$_V(c$, "getPropertyAsJSON", 
function (infoType, paramInfo) {
{
paramInfo || (paramInfo = "");
}return this.viewer.getProperty ("JSON", infoType, paramInfo).toString ();
}, "~S,~S");
$_M(c$, "loadInlineString", 
function (strModel, script, isAppend) {
var errMsg = this.viewer.loadInlineAppend (strModel, isAppend);
if (errMsg == null) this.script (script);
return errMsg;
}, "~S,~S,~B");
$_M(c$, "loadInlineArray", 
function (strModels, script, isAppend) {
if (strModels == null || strModels.length == 0) return null;
var errMsg = this.viewer.loadInline (strModels, isAppend);
if (errMsg == null) this.script (script);
return errMsg;
}, "~A,~S,~B");
$_V(c$, "register", 
function (id, jsi) {
J.appletjs.JmolAppletRegistry.checkIn (id, jsi);
}, "~S,J.api.JmolSyncInterface");
$_M(c$, "doNotifySync", 
function (info, appletName) {
var syncCallback = this.b$.get (J.constant.EnumCallback.SYNC);
if (!this.mayScript || syncCallback == null || !this.haveDocumentAccess && !syncCallback.startsWith ("Jmol.")) return info;
J.util.Logger.info ("Jmol.notifySync " + appletName + " >> " + info);
try {
{
if (syncCallback=="Jmol._mySyncCallback")
return Jmol._mySyncCallback(this.htmlName, info, appletName);
var f = eval(syncCallback);
return f(this.htmlName, info, appletName);
}} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
if (!this.haveNotifiedError) if (J.util.Logger.debugging) {
J.util.Logger.debug ("syncCallback call error to " + syncCallback + ": " + e);
}this.haveNotifiedError = true;
} else {
throw e;
}
}
return info;
}, "~S,~S");
$_M(c$, "doEval", 
function (strEval) {
try {
{
return "" + eval(strEval);
}} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
J.util.Logger.error ("# error evaluating " + strEval + ":" + e.toString ());
} else {
throw e;
}
}
return "";
}, "~S");
$_M(c$, "doFunctionXY", 
function (functionName, nX, nY) {
var fxy =  Clazz_newFloatArray (Math.abs (nX), Math.abs (nY), 0);
if (!this.mayScript || !this.haveDocumentAccess || nX == 0 || nY == 0) return fxy;
try {
if (nX > 0 && nY > 0) {
for (var i = 0; i < nX; i++) for (var j = 0; j < nY; j++) {
{
fxy[i][j] = eval(functionName)(this.htmlName, i, j);
}}

} else if (nY > 0) {
var data;
{
data = eval(functionName)(this.htmlName, nX, nY);
}nX = Math.abs (nX);
var fdata =  Clazz_newFloatArray (nX * nY, 0);
J.util.Parser.parseStringInfestedFloatArray (data, null, fdata);
for (var i = 0, ipt = 0; i < nX; i++) {
for (var j = 0; j < nY; j++, ipt++) {
fxy[i][j] = fdata[ipt];
}
}
} else {
{
data = eval(functionName)(htmlName, nX, nY, fxy);
}}} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
J.util.Logger.error ("Exception " + e + " with nX, nY: " + nX + " " + nY);
} else {
throw e;
}
}
return fxy;
}, "~S,~N,~N");
$_M(c$, "doFunctionXYZ", 
function (functionName, nX, nY, nZ) {
var fxyz =  Clazz_newFloatArray (Math.abs (nX), Math.abs (nY), Math.abs (nZ), 0);
if (!this.mayScript || !this.haveDocumentAccess || nX == 0 || nY == 0 || nZ == 0) return fxyz;
try {
{
eval(functionName)(this.htmlName, nX, nY, nZ, fxyz);
}} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
J.util.Logger.error ("Exception " + e + " for " + functionName + " with nX, nY, nZ: " + nX + " " + nY + " " + nZ);
} else {
throw e;
}
}
return fxyz;
}, "~S,~N,~N,~N");
$_M(c$, "doShowUrl", 
function (urlString) {
if (J.util.Logger.debugging) {
J.util.Logger.debug ("showUrl(" + urlString + ")");
}if (urlString != null && urlString.length > 0) {
try {
var url =  new java.net.URL (Clazz_castNullAs ("java.net.URL"), urlString, null);
{
window.open(url);
}} catch (mue) {
if (Clazz_exceptionOf (mue, java.net.MalformedURLException)) {
return false;
} else {
throw mue;
}
}
}return true;
}, "~S");
c$.doSendCallback = $_M(c$, "doSendCallback", 
function (strInfo, callback, data) {
if (callback == null || callback.length == 0) {
} else if (callback.equals ("alert")) {
{
alert(strInfo); return "";
}} else {
var tokens = JU.PT.split (callback, ".");
{
try{
var o = window[tokens[0]];
for (i = 1; i < tokens.length; i++){
o = o[tokens[i]]
}
return o(data[0],data[1],data[2],data[3],data[4],data[5],data[6],data[7]);
} catch (e) {
System.out.println(callback + " failed " + e);
}
}}return "";
}, "~S,~S,~A");
c$.$Jmol$MyStatusListener$ = function () {
Clazz_pu$h ();
c$ = Clazz_decorateAsClass (function () {
Clazz_prepareCallback (this, arguments);
Clazz_instantialize (this, arguments);
}, J.appletjs.Jmol, "MyStatusListener", null, J.api.JmolStatusListener);
$_V(c$, "getRegistryInfo", 
function () {
J.appletjs.JmolAppletRegistry.checkIn (null, null);
return J.appletjs.JmolAppletRegistry.htRegistry;
});
$_V(c$, "resizeInnerPanel", 
function (a) {
return  new javajs.awt.Dimension (0, 0);
}, "~S");
$_V(c$, "notifyEnabled", 
function (a) {
switch (a) {
case J.constant.EnumCallback.ANIMFRAME:
case J.constant.EnumCallback.ECHO:
case J.constant.EnumCallback.ERROR:
case J.constant.EnumCallback.EVAL:
case J.constant.EnumCallback.LOADSTRUCT:
case J.constant.EnumCallback.MEASURE:
case J.constant.EnumCallback.MESSAGE:
case J.constant.EnumCallback.PICK:
case J.constant.EnumCallback.STRUCTUREMODIFIED:
case J.constant.EnumCallback.SYNC:
case J.constant.EnumCallback.SCRIPT:
return true;
case J.constant.EnumCallback.APPLETREADY:
case J.constant.EnumCallback.ATOMMOVED:
case J.constant.EnumCallback.CLICK:
case J.constant.EnumCallback.HOVER:
case J.constant.EnumCallback.MINIMIZATION:
case J.constant.EnumCallback.RESIZE:
break;
}
return (this.b$["J.appletjs.Jmol"].b$.get (a) != null);
}, "J.constant.EnumCallback");
$_M(c$, "notifyCallback", 
function (a, b) {
var c = this.b$["J.appletjs.Jmol"].b$.get (a);
var d = (c != null && (b == null || b[0] == null));
var e = false;
if (b != null) b[0] = this.b$["J.appletjs.Jmol"].htmlName;
var f = (b == null || b[1] == null ? null : b[1].toString ());
switch (a) {
case J.constant.EnumCallback.APPLETREADY:
b[3] = this.b$["J.appletjs.Jmol"].jmol;
break;
case J.constant.EnumCallback.ERROR:
case J.constant.EnumCallback.EVAL:
case J.constant.EnumCallback.HOVER:
case J.constant.EnumCallback.MINIMIZATION:
case J.constant.EnumCallback.RESIZE:
break;
case J.constant.EnumCallback.CLICK:
if ("alert".equals (c)) f = "x=" + b[1] + " y=" + b[2] + " action=" + b[3] + " clickCount=" + b[4];
break;
case J.constant.EnumCallback.ANIMFRAME:
var g = b[1];
var h = g[0];
var i = g[1];
var j = g[2];
var k = g[3];
var l = g[4];
var m = (h <= -2);
var n = (k < 0 ? -1 : 1);
var o = (l < 0 ? -1 : 1);
if (d) {
b = [this.b$["J.appletjs.Jmol"].htmlName, Integer.$valueOf (Math.max (h, -2 - h)), Integer.$valueOf (i), Integer.$valueOf (j), Integer.$valueOf (Math.abs (k)), Integer.$valueOf (Math.abs (l)), Integer.$valueOf (m ? 1 : 0), Integer.$valueOf (n), Integer.$valueOf (o)];
}break;
case J.constant.EnumCallback.ECHO:
var p = (b.length == 2);
var q = (p || (b[2]).intValue () == 1);
if (!d) {
if (q) e = true;
d = (!p && (c = this.b$["J.appletjs.Jmol"].b$.get ((a = J.constant.EnumCallback.MESSAGE))) != null);
}if (!e) this.output (f);
break;
case J.constant.EnumCallback.LOADSTRUCT:
var r = b[4];
if (r != null) {
r = (r.indexOf ("NOTE:") >= 0 ? "" : J.i18n.GT._ ("File Error:")) + r;
this.showStatus (r);
this.notifyCallback (J.constant.EnumCallback.MESSAGE, ["", r]);
return;
}break;
case J.constant.EnumCallback.MEASURE:
if (!d) d = ((c = this.b$["J.appletjs.Jmol"].b$.get ((a = J.constant.EnumCallback.MESSAGE))) != null);
var s = b[3];
if (s.indexOf ("Picked") >= 0 || s.indexOf ("Sequence") >= 0) {
this.showStatus (f);
e = true;
} else if (s.indexOf ("Completed") >= 0) {
f = s + ": " + f;
e = true;
}break;
case J.constant.EnumCallback.MESSAGE:
e = !d;
d = new Boolean (d & (f != null)).valueOf ();
if (!e) this.output (f);
break;
case J.constant.EnumCallback.PICK:
this.showStatus (f);
e = true;
break;
case J.constant.EnumCallback.SCRIPT:
var t = (b[3]).intValue ();
if (t > 0) {
this.notifyScriptTermination ();
} else if (!d) {
d = ((c = this.b$["J.appletjs.Jmol"].b$.get ((a = J.constant.EnumCallback.MESSAGE))) != null);
}this.output (f);
this.showStatus (f);
break;
case J.constant.EnumCallback.STRUCTUREMODIFIED:
this.notifyStructureModified ((b[1]).intValue (), (b[2]).intValue ());
break;
case J.constant.EnumCallback.SYNC:
this.sendScript (f, b[2], true, d);
return;
}
if (e) {
var u = this.b$["J.appletjs.Jmol"].viewer.getProperty ("DATA_API", "getAppConsole", null);
if (u != null) {
u.notifyCallback (a, b);
this.output (f);
this.b$["J.appletjs.Jmol"].sendJsTextareaStatus (f);
}}if (!d || !this.b$["J.appletjs.Jmol"].mayScript || c == null || !this.b$["J.appletjs.Jmol"].haveDocumentAccess && !c.startsWith ("Jmol.")) return;
try {
J.appletjs.Jmol.doSendCallback (f, c, b);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
if (!this.b$["J.appletjs.Jmol"].haveNotifiedError) if (J.util.Logger.debugging) {
J.util.Logger.debug (a.name () + "Callback call error to " + c + ": " + e);
}this.b$["J.appletjs.Jmol"].haveNotifiedError = true;
} else {
throw e;
}
}
}, "J.constant.EnumCallback,~A");
$_M(c$, "notifyStructureModified", 
function (a, b) {
}, "~N,~N");
$_M(c$, "output", 
function (a) {
if (this.b$["J.appletjs.Jmol"].outputBuffer != null && a != null) this.b$["J.appletjs.Jmol"].outputBuffer.append (a).appendC ('\n');
}, "~S");
$_M(c$, "notifyScriptTermination", 
function () {
});
$_V(c$, "setCallbackFunction", 
function (a, b) {
if (a.equalsIgnoreCase ("modelkit")) return;
if (a.equalsIgnoreCase ("language")) {
this.consoleMessage ("");
this.consoleMessage (null);
return;
}var c = J.constant.EnumCallback.getCallback (a);
if (c != null && (this.b$["J.appletjs.Jmol"].loading || c !== J.constant.EnumCallback.EVAL)) {
if (b == null) this.b$["J.appletjs.Jmol"].b$.remove (c);
 else this.b$["J.appletjs.Jmol"].b$.put (c, b);
return;
}this.consoleMessage ("Available callbacks include: " + J.constant.EnumCallback.getNameList ().$replace (';', ' ').trim ());
}, "~S,~S");
$_V(c$, "eval", 
function (a) {
var b = a.indexOf ("\1");
if (b >= 0) return this.sendScript (a.substring (b + 1), a.substring (0, b), false, false);
if (!this.b$["J.appletjs.Jmol"].haveDocumentAccess) return "NO EVAL ALLOWED";
if (this.b$["J.appletjs.Jmol"].b$.get (J.constant.EnumCallback.EVAL) != null) {
this.notifyCallback (J.constant.EnumCallback.EVAL, [null, a]);
return "";
}return this.b$["J.appletjs.Jmol"].doEval (a);
}, "~S");
$_V(c$, "createImage", 
function (a, b, c, d) {
return null;
}, "~S,~S,~O,~N");
$_V(c$, "functionXY", 
function (a, b, c) {
return this.b$["J.appletjs.Jmol"].doFunctionXY (a, b, c);
}, "~S,~N,~N");
$_V(c$, "functionXYZ", 
function (a, b, c, d) {
return this.b$["J.appletjs.Jmol"].doFunctionXYZ (a, b, c, d);
}, "~S,~N,~N,~N");
$_V(c$, "showUrl", 
function (a) {
if (!this.b$["J.appletjs.Jmol"].doShowUrl (a)) this.consoleMessage ("Malformed URL:" + a);
}, "~S");
$_M(c$, "finalize", 
function () {
if (J.util.Logger.debugging) J.util.Logger.debug ("MyStatusListener finalize " + this);
Clazz_superCall (this, J.appletjs.Jmol.MyStatusListener, "finalize", []);
});
$_M(c$, "showStatus", 
function (a) {
try {
System.out.println (a);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
}, "~S");
$_M(c$, "consoleMessage", 
function (a) {
this.notifyCallback (J.constant.EnumCallback.ECHO, ["", a]);
}, "~S");
$_M(c$, "sendScript", 
function (a, b, c, d) {
if (d) {
a = this.b$["J.appletjs.Jmol"].doNotifySync (a, b);
if (a == null || a.length == 0 || a.equals ("0")) return "";
}var e =  new JU.List ();
J.appletjs.JmolAppletRegistry.findApplets (b, this.b$["J.appletjs.Jmol"].syncId, this.b$["J.appletjs.Jmol"].fullName, e);
var f = e.size ();
if (f == 0) {
if (!d && !b.equals ("*")) J.util.Logger.error (this.b$["J.appletjs.Jmol"].fullName + " couldn't find applet " + b);
return "";
}var g = (c ? null :  new JU.SB ());
var h = (c && a.equals ("GET_GRAPHICS"));
var i = (c && a.equals ("SET_GRAPHICS_OFF"));
if (h) this.b$["J.appletjs.Jmol"].gRight = null;
for (var j = 0; j < f; j++) {
var k = e.get (j);
var l = J.appletjs.JmolAppletRegistry.htRegistry.get (k);
var m = true;
if (J.util.Logger.debugging) J.util.Logger.debug (this.b$["J.appletjs.Jmol"].fullName + " sending to " + k + ": " + a);
try {
if (m && (h || i)) {
this.b$["J.appletjs.Jmol"].gRight = (l).setStereoGraphics (h);
return "";
}if (c) l.syncScript (a);
 else if (m) g.append ((l).scriptWait (a, "output")).append ("\n");
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
var n = this.b$["J.appletjs.Jmol"].htmlName + " couldn't send to " + k + ": " + a + ": " + e;
J.util.Logger.error (n);
if (!c) g.append (n);
} else {
throw e;
}
}
}
return (c ? "" : g.toString ());
}, "~S,~S,~B,~B");
$_V(c$, "getProperty", 
function (a) {
return null;
}, "~S");
c$ = Clazz_p0p ();
};
Clazz_defineStatics (c$,
"SCRIPT_CHECK", 0,
"SCRIPT_WAIT", 1,
"SCRIPT_NOWAIT", 2);
});
Clazz_declarePackage ("J.appletjs");
Clazz_load (["java.util.Hashtable"], "J.appletjs.JmolAppletRegistry", ["JU.PT", "J.util.Logger"], function () {
c$ = Clazz_declareType (J.appletjs, "JmolAppletRegistry");
c$.checkIn = $_M(c$, "checkIn", 
function (name, applet) {
{
if (Jmol._htRegistry) {J.appletjs.JmolAppletRegistry.htRegistry = Jmol._htRegistry} else {Jmol._htRegistry = J.appletjs.JmolAppletRegistry.htRegistry};
}J.appletjs.JmolAppletRegistry.cleanRegistry ();
if (name != null) {
J.util.Logger.info ("AppletRegistry.checkIn(" + name + ")");
J.appletjs.JmolAppletRegistry.htRegistry.put (name, applet);
}if (J.util.Logger.debugging) {
for (var entry, $entry = J.appletjs.JmolAppletRegistry.htRegistry.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) {
var theApplet = entry.getKey ();
J.util.Logger.debug (theApplet + " " + entry.getValue ());
}
}}, "~S,J.api.JmolSyncInterface");
c$.checkOut = $_M(c$, "checkOut", 
function (name) {
J.appletjs.JmolAppletRegistry.htRegistry.remove (name);
}, "~S");
c$.findApplets = $_M(c$, "findApplets", 
function (appletName, mySyncId, excludeName, apps) {
if (appletName != null && appletName.indexOf (",") >= 0) {
var names = JU.PT.split (appletName, ",");
for (var i = 0; i < names.length; i++) J.appletjs.JmolAppletRegistry.findApplets (names[i], mySyncId, excludeName, apps);

return;
}var ext = "__" + mySyncId + "__";
if (appletName == null || appletName.equals ("*") || appletName.equals (">")) {
for (var appletName2, $appletName2 = J.appletjs.JmolAppletRegistry.htRegistry.keySet ().iterator (); $appletName2.hasNext () && ((appletName2 = $appletName2.next ()) || true);) {
if (!appletName2.equals (excludeName)) {
apps.addLast (appletName2);
}}
return;
}if (appletName.indexOf ("__") < 0) appletName += ext;
if (!J.appletjs.JmolAppletRegistry.htRegistry.containsKey (appletName)) appletName = "jmolApplet" + appletName;
if (!appletName.equals (excludeName) && J.appletjs.JmolAppletRegistry.htRegistry.containsKey (appletName)) {
apps.addLast (appletName);
}}, "~S,~S,~S,JU.List");
c$.cleanRegistry = $_M(c$, "cleanRegistry", 
function () {
});
c$.htRegistry = c$.prototype.htRegistry =  new java.util.Hashtable ();
});
$_L(null,"java.lang.Enum",["java.lang.CloneNotSupportedException","$.IllegalArgumentException","$.NullPointerException","java.security.AccessController","$.PrivilegedExceptionAction"],function(){
c$=$_C(function(){
this.$name=null;
this.$ordinal=0;
$_Z(this,arguments);
},java.lang,"Enum",null,[java.io.Serializable,Comparable]);
$_K(c$,
function(name,ordinal){
this.$name=name;
this.$ordinal=ordinal;
},"~S,~N");
$_M(c$,"name",
function(){
return this.$name;
});
$_M(c$,"ordinal",
function(){
return this.$ordinal;
});
$_V(c$,"toString",
function(){
return this.$name;
});
$_V(c$,"equals",
function(other){
return this===other;
},"~O");
$_V(c$,"hashCode",
function(){
return this.$ordinal+(this.$name==null?0:this.$name.hashCode());
});
$_V(c$,"clone",
function(){
throw new CloneNotSupportedException(("KA004"));
});
$_V(c$,"compareTo",
function(o){
return this.$ordinal-o.$ordinal;
},"~O");
$_M(c$,"getDeclaringClass",
function(){
var myClass=this.getClass();
var mySuperClass=myClass.getSuperclass();
if(Enum===mySuperClass){
return myClass;
}return mySuperClass;
});
c$.$valueOf=$_M(c$,"$valueOf",
function(enumType,name){
if((enumType==null)||(name==null)){
throw new NullPointerException(("KA001"));
}var values=Enum.getValues(enumType);
if(values==null){
throw new IllegalArgumentException(("KA005"));
}for(var enumConst,$enumConst=0,$$enumConst=values;$enumConst<$$enumConst.length&&((enumConst=$$enumConst[$enumConst])||true);$enumConst++){
if(enumConst.$name.equals(name)){
return enumConst;
}}
throw new IllegalArgumentException(("KA006"));
},"Class,~S");
c$.getValues=$_M(c$,"getValues",
function(enumType){
try{
var values=java.security.AccessController.doPrivileged((($_D("Enum$1")?0:java.lang.Enum.$Enum$1$()),$_N(Enum$1,this,$_F("enumType",enumType))));
return values.invoke(enumType,Clazz_castNullAs("Array"));
}catch(e){
if($_O(e,Exception)){
return null;
}else{
throw e;
}
}
},"Class");
c$.$Enum$1$=function(){
$_H();
c$=$_W(null,"Enum$1",null,java.security.PrivilegedExceptionAction);
$_V(c$,"run",
function(){
var valsMethod=this.f$.enumType.getMethod("values",null);
valsMethod.setAccessible(true);
return valsMethod;
});
c$=$_P();
};
});
Clazz_declarePackage ("J.constant");
Clazz_load (["java.lang.Enum"], "J.constant.EnumCallback", ["JU.SB"], function () {
c$ = Clazz_declareType (J.constant, "EnumCallback", Enum);
c$.getCallback = $_M(c$, "getCallback", 
function (name) {
name = name.toUpperCase ();
name = name.substring (0, Math.max (name.indexOf ("CALLBACK"), 0));
for (var item, $item = 0, $$item = J.constant.EnumCallback.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (item.name ().equalsIgnoreCase (name)) return item;

return null;
}, "~S");
c$.getNameList = $_M(c$, "getNameList", 
function () {
if (J.constant.EnumCallback.nameList == null) {
var names =  new JU.SB ();
for (var item, $item = 0, $$item = J.constant.EnumCallback.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) names.append (item.name ().toLowerCase ()).append ("Callback;");

($t$ = J.constant.EnumCallback.nameList = names.toString (), J.constant.EnumCallback.prototype.nameList = J.constant.EnumCallback.nameList, $t$);
}return J.constant.EnumCallback.nameList;
});
c$.nameList = null;
Clazz_defineEnumConstant (c$, "ANIMFRAME", 0, []);
Clazz_defineEnumConstant (c$, "APPLETREADY", 1, []);
Clazz_defineEnumConstant (c$, "ATOMMOVED", 2, []);
Clazz_defineEnumConstant (c$, "CLICK", 3, []);
Clazz_defineEnumConstant (c$, "ECHO", 4, []);
Clazz_defineEnumConstant (c$, "ERROR", 5, []);
Clazz_defineEnumConstant (c$, "EVAL", 6, []);
Clazz_defineEnumConstant (c$, "HOVER", 7, []);
Clazz_defineEnumConstant (c$, "LOADSTRUCT", 8, []);
Clazz_defineEnumConstant (c$, "MEASURE", 9, []);
Clazz_defineEnumConstant (c$, "MESSAGE", 10, []);
Clazz_defineEnumConstant (c$, "MINIMIZATION", 11, []);
Clazz_defineEnumConstant (c$, "PICK", 12, []);
Clazz_defineEnumConstant (c$, "RESIZE", 13, []);
Clazz_defineEnumConstant (c$, "SCRIPT", 14, []);
Clazz_defineEnumConstant (c$, "SYNC", 15, []);
Clazz_defineEnumConstant (c$, "STRUCTUREMODIFIED", 16, []);
});
Clazz_declarePackage ("J.util");
Clazz_load (null, "J.util.Escape", ["java.lang.Character", "$.Float", "JU.List", "$.M3", "$.M4", "$.P3", "$.P4", "$.PT", "$.SB", "J.script.SV", "J.util.BSUtil"], function () {
c$ = Clazz_declareType (J.util, "Escape");
c$.escapeColor = $_M(c$, "escapeColor", 
function (argb) {
return (argb == 0 ? null : "[x" + J.util.Escape.getHexColorFromRGB (argb) + "]");
}, "~N");
c$.getHexColorFromRGB = $_M(c$, "getHexColorFromRGB", 
function (argb) {
if (argb == 0) return null;
var r = "00" + Integer.toHexString ((argb >> 16) & 0xFF);
r = r.substring (r.length - 2);
var g = "00" + Integer.toHexString ((argb >> 8) & 0xFF);
g = g.substring (g.length - 2);
var b = "00" + Integer.toHexString (argb & 0xFF);
b = b.substring (b.length - 2);
return r + g + b;
}, "~N");
c$.eP = $_M(c$, "eP", 
function (xyz) {
if (xyz == null) return "null";
return "{" + xyz.x + " " + xyz.y + " " + xyz.z + "}";
}, "JU.T3");
c$.matrixToScript = $_M(c$, "matrixToScript", 
function (m) {
return JU.PT.replaceAllCharacters (m.toString (), "\n\r ", "").$replace ('\t', ' ');
}, "~O");
c$.eP4 = $_M(c$, "eP4", 
function (x) {
return "{" + x.x + " " + x.y + " " + x.z + " " + x.w + "}";
}, "JU.P4");
c$.e = $_M(c$, "e", 
function (x) {
if (x == null) return "null";
if (Clazz_instanceOf (x, String)) return J.util.Escape.eS (x);
if (Clazz_instanceOf (x, JU.List)) return J.util.Escape.eV (x);
if (Clazz_instanceOf (x, JU.BS)) return J.util.Escape.eBS (x);
if (Clazz_instanceOf (x, JU.T3)) return J.util.Escape.eP (x);
if (Clazz_instanceOf (x, JU.P4)) return J.util.Escape.eP4 (x);
if (JU.PT.isAS (x)) return J.util.Escape.eAS (x, true);
if (JU.PT.isAI (x)) return J.util.Escape.eAI (x);
if (JU.PT.isAF (x)) return J.util.Escape.eAF (x);
if (JU.PT.isAD (x)) return J.util.Escape.eAD (x);
if (JU.PT.isAP (x)) return J.util.Escape.eAP (x);
if (Clazz_instanceOf (x, JU.M3)) return JU.PT.simpleReplace ((x).toString (), "\t", ",\t");
if (Clazz_instanceOf (x, JU.M4)) return JU.PT.simpleReplace ((x).toString (), "\t", ",\t");
if (Clazz_instanceOf (x, JU.A4)) {
var a = x;
return "{" + a.x + " " + a.y + " " + a.z + " " + (a.angle * 180 / 3.141592653589793) + "}";
}if (Clazz_instanceOf (x, java.util.Map)) return J.util.Escape.escapeMap (x);
if (JU.PT.isAII (x) || JU.PT.isAFF (x) || JU.PT.isAFFF (x)) return JU.PT.toJSON (null, x);
return x.toString ();
}, "~O");
c$.eS = $_M(c$, "eS", 
function (str) {
if (str == null || str.length == 0) return "\"\"";
var haveEscape = false;
var i = 0;
for (; i < "\\\\\tt\rr\nn\"\"".length; i += 2) if (str.indexOf ("\\\\\tt\rr\nn\"\"".charAt (i)) >= 0) {
haveEscape = true;
break;
}
if (haveEscape) while (i < "\\\\\tt\rr\nn\"\"".length) {
var pt = -1;
var ch = "\\\\\tt\rr\nn\"\"".charAt (i++);
var ch2 = "\\\\\tt\rr\nn\"\"".charAt (i++);
var sb =  new JU.SB ();
var pt0 = 0;
while ((pt = str.indexOf (ch, pt + 1)) >= 0) {
sb.append (str.substring (pt0, pt)).appendC ('\\').appendC (ch2);
pt0 = pt + 1;
}
sb.append (str.substring (pt0, str.length));
str = sb.toString ();
}
for (i = str.length; --i >= 0; ) if (str.charCodeAt (i) > 0x7F) str = str.substring (0, i) + J.util.Escape.unicode (str.charAt (i)) + str.substring (i + 1);

return "\"" + str + "\"";
}, "~S");
c$.unicode = $_M(c$, "unicode", 
function (c) {
var s = "0000" + Integer.toHexString (c.charCodeAt (0));
return "\\u" + s.substring (s.length - 4);
}, "~S");
c$.eV = $_M(c$, "eV", 
function (list) {
if (list == null) return J.util.Escape.eS ("");
var s =  new JU.SB ();
s.append ("[");
for (var i = 0; i < list.size (); i++) {
if (i > 0) s.append (", ");
s.append (J.util.Escape.escapeNice (list.get (i).asString ()));
}
s.append ("]");
return s.toString ();
}, "JU.List");
c$.escapeMap = $_M(c$, "escapeMap", 
function (ht) {
var sb =  new JU.SB ();
sb.append ("{ ");
var sep = "";
for (var entry, $entry = ht.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) {
var key = entry.getKey ();
sb.append (sep).append (J.util.Escape.eS (key)).appendC (':');
var val = entry.getValue ();
if (!(Clazz_instanceOf (val, J.script.SV))) val = J.script.SV.getVariable (val);
sb.append ((val).escape ());
sep = ",";
}
sb.append (" }");
return sb.toString ();
}, "java.util.Map");
c$.escapeFloatA = $_M(c$, "escapeFloatA", 
function (f, asArray) {
if (asArray) return JU.PT.toJSON (null, f);
var sb =  new JU.SB ();
for (var i = 0; i < f.length; i++) {
if (i > 0) sb.appendC ('\n');
sb.appendF (f[i]);
}
return sb.toString ();
}, "~A,~B");
c$.escapeFloatAA = $_M(c$, "escapeFloatAA", 
function (f, addSemi) {
var sb =  new JU.SB ();
var eol = (addSemi ? ";\n" : "\n");
for (var i = 0; i < f.length; i++) if (f[i] != null) {
if (i > 0) sb.append (eol);
for (var j = 0; j < f[i].length; j++) sb.appendF (f[i][j]).appendC ('\t');

}
return sb.toString ();
}, "~A,~B");
c$.escapeFloatAAA = $_M(c$, "escapeFloatAAA", 
function (f, addSemi) {
var sb =  new JU.SB ();
var eol = (addSemi ? ";\n" : "\n");
if (f[0] == null || f[0][0] == null) return "0 0 0" + eol;
sb.appendI (f.length).append (" ").appendI (f[0].length).append (" ").appendI (f[0][0].length);
for (var i = 0; i < f.length; i++) if (f[i] != null) {
sb.append (eol);
for (var j = 0; j < f[i].length; j++) if (f[i][j] != null) {
sb.append (eol);
for (var k = 0; k < f[i][j].length; k++) sb.appendF (f[i][j][k]).appendC ('\t');

}
}
return sb.toString ();
}, "~A,~B");
c$.eAS = $_M(c$, "eAS", 
function (list, nicely) {
if (list == null) return J.util.Escape.eS ("");
var s =  new JU.SB ();
s.append ("[");
for (var i = 0; i < list.length; i++) {
if (i > 0) s.append (", ");
s.append (nicely ? J.util.Escape.escapeNice (list[i]) : J.util.Escape.eS (list[i]));
}
s.append ("]");
return s.toString ();
}, "~A,~B");
c$.eAI = $_M(c$, "eAI", 
function (ilist) {
if (ilist == null) return J.util.Escape.eS ("");
var s =  new JU.SB ();
s.append ("[");
for (var i = 0; i < ilist.length; i++) {
if (i > 0) s.append (", ");
s.appendI (ilist[i]);
}
return s.append ("]").toString ();
}, "~A");
c$.eAD = $_M(c$, "eAD", 
function (dlist) {
if (dlist == null) return J.util.Escape.eS ("");
var s =  new JU.SB ();
s.append ("[");
for (var i = 0; i < dlist.length; i++) {
if (i > 0) s.append (", ");
s.appendD (dlist[i]);
}
return s.append ("]").toString ();
}, "~A");
c$.eAF = $_M(c$, "eAF", 
function (flist) {
if (flist == null) return J.util.Escape.eS ("");
var s =  new JU.SB ();
s.append ("[");
for (var i = 0; i < flist.length; i++) {
if (i > 0) s.append (", ");
s.appendF (flist[i]);
}
return s.append ("]").toString ();
}, "~A");
c$.eAP = $_M(c$, "eAP", 
function (plist) {
if (plist == null) return J.util.Escape.eS ("");
var s =  new JU.SB ();
s.append ("[");
for (var i = 0; i < plist.length; i++) {
if (i > 0) s.append (", ");
s.append (J.util.Escape.eP (plist[i]));
}
return s.append ("]").toString ();
}, "~A");
c$.escapeNice = $_M(c$, "escapeNice", 
function (s) {
if (s == null) return "null";
var f = JU.PT.parseFloatStrict (s);
return (Float.isNaN (f) ? J.util.Escape.eS (s) : s);
}, "~S");
c$.uABsM = $_M(c$, "uABsM", 
function (s) {
if (s.charAt (0) == '{') return J.util.Escape.uP (s);
if ((J.util.Escape.isStringArray (s) || s.startsWith ("[{") && s.indexOf ("[{") == s.lastIndexOf ("[{")) && s.indexOf (',') < 0 && s.indexOf ('.') < 0 && s.indexOf ('-') < 0) return J.util.Escape.uB (s);
if (s.startsWith ("[[")) return J.util.Escape.unescapeMatrix (s);
return s;
}, "~S");
c$.isStringArray = $_M(c$, "isStringArray", 
function (s) {
return s.startsWith ("({") && s.lastIndexOf ("({") == 0 && s.indexOf ("})") == s.length - 2;
}, "~S");
c$.uP = $_M(c$, "uP", 
function (strPoint) {
if (strPoint == null || strPoint.length == 0) return strPoint;
var str = strPoint.$replace ('\n', ' ').trim ();
if (str.charAt (0) != '{' || str.charAt (str.length - 1) != '}') return strPoint;
var points =  Clazz_newFloatArray (5, 0);
var nPoints = 0;
str = str.substring (1, str.length - 1);
var next =  Clazz_newIntArray (1, 0);
for (; nPoints < 5; nPoints++) {
points[nPoints] = JU.PT.parseFloatNext (str, next);
if (Float.isNaN (points[nPoints])) {
if (next[0] >= str.length || str.charAt (next[0]) != ',') break;
next[0]++;
nPoints--;
}}
if (nPoints == 3) return JU.P3.new3 (points[0], points[1], points[2]);
if (nPoints == 4) return JU.P4.new4 (points[0], points[1], points[2], points[3]);
return strPoint;
}, "~S");
c$.uB = $_M(c$, "uB", 
function (str) {
var ch;
var len;
if (str == null || (len = (str = str.trim ()).length) < 4 || str.equalsIgnoreCase ("({null})") || (ch = str.charAt (0)) != '(' && ch != '[' || str.charAt (len - 1) != (ch == '(' ? ')' : ']') || str.charAt (1) != '{' || str.indexOf ('}') != len - 2) return null;
len -= 2;
for (var i = len; --i >= 2; ) if (!Character.isDigit (ch = str.charAt (i)) && ch != ' ' && ch != '\t' && ch != ':') return null;

var lastN = len;
while (Character.isDigit (str.charAt (--lastN))) {
}
if (++lastN == len) lastN = 0;
 else try {
lastN = Integer.parseInt (str.substring (lastN, len));
} catch (e) {
if (Clazz_exceptionOf (e, NumberFormatException)) {
return null;
} else {
throw e;
}
}
var bs = J.util.BSUtil.newBitSet (lastN);
lastN = -1;
var iPrev = -1;
var iThis = -2;
for (var i = 2; i <= len; i++) {
switch (ch = str.charAt (i)) {
case '\t':
case ' ':
case '}':
if (iThis < 0) break;
if (iThis < lastN) return null;
lastN = iThis;
if (iPrev < 0) iPrev = iThis;
bs.setBits (iPrev, iThis + 1);
iPrev = -1;
iThis = -2;
break;
case ':':
iPrev = lastN = iThis;
iThis = -2;
break;
default:
if (Character.isDigit (ch)) {
if (iThis < 0) iThis = 0;
iThis = (iThis * 10) + (ch.charCodeAt (0) - 48);
}}
}
return (iPrev >= 0 ? null : bs);
}, "~S");
c$.unescapeMatrix = $_M(c$, "unescapeMatrix", 
function (strMatrix) {
if (strMatrix == null || strMatrix.length == 0) return strMatrix;
var str = strMatrix.$replace ('\n', ' ').trim ();
if (str.lastIndexOf ("[[") != 0 || str.indexOf ("]]") != str.length - 2) return strMatrix;
var points =  Clazz_newFloatArray (16, 0);
str = str.substring (2, str.length - 2).$replace ('[', ' ').$replace (']', ' ').$replace (',', ' ');
var next =  Clazz_newIntArray (1, 0);
var nPoints = 0;
for (; nPoints < 16; nPoints++) {
points[nPoints] = JU.PT.parseFloatNext (str, next);
if (Float.isNaN (points[nPoints])) {
break;
}}
if (!Float.isNaN (JU.PT.parseFloatNext (str, next))) return strMatrix;
if (nPoints == 9) return JU.M3.newA (points);
if (nPoints == 16) return JU.M4.newA (points);
return strMatrix;
}, "~S");
c$.eBS = $_M(c$, "eBS", 
function (bs) {
return J.util.Escape.eB (bs, '(', ')');
}, "JU.BS");
c$.eBond = $_M(c$, "eBond", 
function (bs) {
return J.util.Escape.eB (bs, '[', ']');
}, "JU.BS");
c$.eB = $_M(c$, "eB", 
function (bs, chOpen, chClose) {
if (bs == null) return chOpen + "{}" + chClose;
var s =  new JU.SB ();
s.append (chOpen + "{");
var imax = bs.length ();
var iLast = -1;
var iFirst = -2;
var i = -1;
while (++i <= imax) {
var isSet = bs.get (i);
if (i == imax || iLast >= 0 && !isSet) {
if (iLast >= 0 && iFirst != iLast) s.append ((iFirst == iLast - 1 ? " " : ":") + iLast);
if (i == imax) break;
iLast = -1;
}if (bs.get (i)) {
if (iLast < 0) {
s.append ((iFirst == -2 ? "" : " ") + i);
iFirst = i;
}iLast = i;
}}
s.append ("}").appendC (chClose);
return s.toString ();
}, "JU.BS,~S,~S");
c$.toReadable = $_M(c$, "toReadable", 
function (name, info) {
var sb =  new JU.SB ();
var sep = "";
if (info == null) return "null";
if (Clazz_instanceOf (info, String)) return J.util.Escape.packageReadable (name, null, J.util.Escape.eS (info));
if (JU.PT.isAS (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).append (J.util.Escape.eS ((info)[i]));
sep = ",";
}
sb.append ("]");
return J.util.Escape.packageReadableSb (name, "String[" + imax + "]", sb);
}if (JU.PT.isAI (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).appendI ((info)[i]);
sep = ",";
}
sb.append ("]");
return J.util.Escape.packageReadableSb (name, "int[" + imax + "]", sb);
}if (JU.PT.isAF (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).appendF ((info)[i]);
sep = ",";
}
sb.append ("]");
return J.util.Escape.packageReadableSb (name, "float[" + imax + "]", sb);
}if (JU.PT.isAD (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).appendD ((info)[i]);
sep = ",";
}
sb.append ("]");
return J.util.Escape.packageReadableSb (name, "double[" + imax + "]", sb);
}if (JU.PT.isAP (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).append (J.util.Escape.eP ((info)[i]));
sep = ",";
}
sb.append ("]");
return J.util.Escape.packageReadableSb (name, "point3f[" + imax + "]", sb);
}if (JU.PT.isASS (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).append (J.util.Escape.toReadable (null, (info)[i]));
sep = ",\n";
}
sb.append ("]");
return J.util.Escape.packageReadableSb (name, "String[" + imax + "][]", sb);
}if (JU.PT.isAII (info)) {
sb.append ("[");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).append (J.util.Escape.toReadable (null, (info)[i]));
sep = ",";
}
sb.append ("]");
return J.util.Escape.packageReadableSb (name, "int[" + imax + "][]", sb);
}if (JU.PT.isAFF (info)) {
sb.append ("[\n");
var imax = (info).length;
for (var i = 0; i < imax; i++) {
sb.append (sep).append (J.util.Escape.toReadable (null, (info)[i]));
sep = ",\n";
}
sb.append ("]");
return J.util.Escape.packageReadableSb (name, "float[][]", sb);
}if (Clazz_instanceOf (info, JU.List)) {
var imax = (info).size ();
for (var i = 0; i < imax; i++) {
sb.append (J.util.Escape.toReadable (name + "[" + (i + 1) + "]", (info).get (i)));
}
return J.util.Escape.packageReadableSb (name, "List[" + imax + "]", sb);
}if (Clazz_instanceOf (info, JU.M3) || Clazz_instanceOf (info, JU.T3) || Clazz_instanceOf (info, JU.P4) || Clazz_instanceOf (info, JU.A4)) {
sb.append (J.util.Escape.e (info));
return J.util.Escape.packageReadableSb (name, null, sb);
}if (Clazz_instanceOf (info, java.util.Map)) {
var e = (info).keySet ().iterator ();
while (e.hasNext ()) {
var key = e.next ();
sb.append (J.util.Escape.toReadable ((name == null ? "" : name + ".") + key, (info).get (key)));
}
return sb.toString ();
}return J.util.Escape.packageReadable (name, null, info.toString ());
}, "~S,~O");
c$.packageReadableSb = $_M(c$, "packageReadableSb", 
function (infoName, infoType, sb) {
return J.util.Escape.packageReadable (infoName, infoType, sb.toString ());
}, "~S,~S,JU.SB");
c$.packageReadable = $_M(c$, "packageReadable", 
function (infoName, infoType, info) {
var s = (infoType == null ? "" : infoType + "\t");
if (infoName == null) return s + info;
return "\n" + infoName + "\t" + (infoType == null ? "" : "*" + infoType + "\t") + info;
}, "~S,~S,~S");
c$.escapeModelFileNumber = $_M(c$, "escapeModelFileNumber", 
function (iv) {
return "" + (Clazz_doubleToInt (iv / 1000000)) + "." + (iv % 1000000);
}, "~N");
c$.encapsulateData = $_M(c$, "encapsulateData", 
function (name, data, depth) {
return "  DATA \"" + name + "\"\n" + (depth == 2 ? J.util.Escape.escapeFloatAA (data, true) + ";\n" : depth == 3 ? J.util.Escape.escapeFloatAAA (data, true) + ";\n" : data) + "    END \"" + name + "\";\n";
}, "~S,~O,~N");
c$.unescapeUnicode = $_M(c$, "unescapeUnicode", 
function (s) {
var ichMax = s.length;
var sb = JU.SB.newN (ichMax);
var ich = 0;
while (ich < ichMax) {
var ch = s.charAt (ich++);
if (ch == '\\' && ich < ichMax) {
ch = s.charAt (ich++);
switch (ch) {
case 'u':
if (ich < ichMax) {
var unicode = 0;
for (var k = 4; --k >= 0 && ich < ichMax; ) {
var chT = s.charAt (ich);
var hexit = J.util.Escape.getHexitValue (chT);
if (hexit < 0) break;
unicode <<= 4;
unicode += hexit;
++ich;
}
ch = String.fromCharCode (unicode);
}}
}sb.appendC (ch);
}
return sb.toString ();
}, "~S");
c$.getHexitValue = $_M(c$, "getHexitValue", 
function (ch) {
if (ch.charCodeAt (0) >= 48 && ch.charCodeAt (0) <= 57) return ch.charCodeAt (0) - 48;
 else if (ch.charCodeAt (0) >= 97 && ch.charCodeAt (0) <= 102) return 10 + ch.charCodeAt (0) - 97;
 else if (ch.charCodeAt (0) >= 65 && ch.charCodeAt (0) <= 70) return 10 + ch.charCodeAt (0) - 65;
 else return -1;
}, "~S");
c$.unescapeStringArray = $_M(c$, "unescapeStringArray", 
function (data) {
if (data == null || !data.startsWith ("[") || !data.endsWith ("]")) return null;
var v =  new JU.List ();
var next =  Clazz_newIntArray (1, 0);
next[0] = 1;
while (next[0] < data.length) {
var s = JU.PT.getQuotedStringNext (data, next);
if (s == null) return null;
v.addLast (JU.PT.simpleReplace (s, "\\\"", "\""));
while (next[0] < data.length && data.charAt (next[0]) != '"') next[0]++;

}
return v.toArray ( new Array (v.size ()));
}, "~S");
c$.isAV = $_M(c$, "isAV", 
function (x) {
{
return Clazz_instanceOf(x[0], J.scriSV);
}}, "~O");
Clazz_defineStatics (c$,
"escapable", "\\\\\tt\rr\nn\"\"");
});
Clazz_declarePackage ("J.util");
Clazz_load (null, "J.util.Parser", ["java.lang.Float", "JU.AU", "$.PT"], function () {
c$ = Clazz_declareType (J.util, "Parser");
c$.parseStringInfestedFloatArray = $_M(c$, "parseStringInfestedFloatArray", 
function (str, bs, data) {
return J.util.Parser.parseFloatArrayBsData (JU.PT.getTokens (str), bs, data);
}, "~S,JU.BS,~A");
c$.parseFloatArrayBsData = $_M(c$, "parseFloatArrayBsData", 
function (tokens, bs, data) {
var len = data.length;
var nTokens = tokens.length;
var n = 0;
var max = 0;
var haveBitSet = (bs != null);
for (var i = (haveBitSet ? bs.nextSetBit (0) : 0); i >= 0 && i < len && n < nTokens; i = (haveBitSet ? bs.nextSetBit (i + 1) : i + 1)) {
var f;
while (Float.isNaN (f = JU.PT.parseFloat (tokens[n++])) && n < nTokens) {
}
if (!Float.isNaN (f)) data[(max = i)] = f;
if (n == nTokens) break;
}
return max + 1;
}, "~A,JU.BS,~A");
c$.parseFloatArrayFromMatchAndField = $_M(c$, "parseFloatArrayFromMatchAndField", 
function (str, bs, fieldMatch, fieldMatchColumnCount, matchData, field, fieldColumnCount, data, firstLine) {
var f;
var i = -1;
var isMatch = (matchData != null);
var lines = J.util.Parser.markLines (str, (str.indexOf ('\n') >= 0 ? '\n' : ';'));
var iLine = (firstLine <= 1 || firstLine >= lines.length ? 0 : firstLine - 1);
var pt = (iLine == 0 ? 0 : lines[iLine - 1]);
var nLines = lines.length;
if (data == null) data =  Clazz_newFloatArray (nLines - iLine, 0);
var len = data.length;
var minLen = (fieldColumnCount <= 0 ? Math.max (field, fieldMatch) : Math.max (field + fieldColumnCount, fieldMatch + fieldMatchColumnCount) - 1);
var haveBitSet = (bs != null);
for (; iLine < nLines; iLine++) {
var line = str.substring (pt, lines[iLine]).trim ();
pt = lines[iLine];
var tokens = (fieldColumnCount <= 0 ? JU.PT.getTokens (line) : null);
if (fieldColumnCount <= 0) {
if (tokens.length < minLen || Float.isNaN (f = JU.PT.parseFloat (tokens[field - 1]))) continue;
} else {
if (line.length < minLen || Float.isNaN (f = JU.PT.parseFloat (line.substring (field - 1, field + fieldColumnCount - 1)))) continue;
}var iData;
if (isMatch) {
iData = JU.PT.parseInt (tokens == null ? line.substring (fieldMatch - 1, fieldMatch + fieldMatchColumnCount - 1) : tokens[fieldMatch - 1]);
if (iData == -2147483648 || iData < 0 || iData >= len || (iData = matchData[iData]) < 0) continue;
if (haveBitSet) bs.set (iData);
} else {
if (haveBitSet) i = bs.nextSetBit (i + 1);
 else i++;
if (i < 0 || i >= len) return data;
iData = i;
}data[iData] = f;
}
return data;
}, "~S,JU.BS,~N,~N,~A,~N,~N,~A,~N");
c$.fixDataString = $_M(c$, "fixDataString", 
function (str) {
str = str.$replace (';', str.indexOf ('\n') < 0 ? '\n' : ' ');
str = JU.PT.trim (str, "\n \t");
str = JU.PT.simpleReplace (str, "\n ", "\n");
str = JU.PT.simpleReplace (str, "\n\n", "\n");
return str;
}, "~S");
c$.parseFloatArray2d = $_M(c$, "parseFloatArray2d", 
function (str) {
str = J.util.Parser.fixDataString (str);
var lines = J.util.Parser.markLines (str, '\n');
var nLines = lines.length;
var data = JU.AU.newFloat2 (nLines);
for (var iLine = 0, pt = 0; iLine < nLines; pt = lines[iLine++]) {
var tokens = JU.PT.getTokens (str.substring (pt, lines[iLine]));
JU.PT.parseFloatArrayData (tokens, data[iLine] =  Clazz_newFloatArray (tokens.length, 0));
}
return data;
}, "~S");
c$.parseFloatArray3d = $_M(c$, "parseFloatArray3d", 
function (str) {
str = J.util.Parser.fixDataString (str);
var lines = J.util.Parser.markLines (str, '\n');
var nLines = lines.length;
var tokens = JU.PT.getTokens (str.substring (0, lines[0]));
if (tokens.length != 3) return  Clazz_newFloatArray (0, 0, 0, 0);
var nX = JU.PT.parseInt (tokens[0]);
var nY = JU.PT.parseInt (tokens[1]);
var nZ = JU.PT.parseInt (tokens[2]);
if (nX < 1 || nY < 1 || nZ < 1) return  Clazz_newFloatArray (1, 1, 1, 0);
var data = JU.AU.newFloat3 (nX, nY);
var iX = 0;
var iY = 0;
for (var iLine = 1, pt = lines[0]; iLine < nLines && iX < nX; pt = lines[iLine++]) {
tokens = JU.PT.getTokens (str.substring (pt, lines[iLine]));
if (tokens.length < nZ) continue;
JU.PT.parseFloatArrayData (tokens, data[iX][iY] =  Clazz_newFloatArray (tokens.length, 0));
if (++iY == nY) {
iX++;
iY = 0;
}}
if (iX != nX) {
System.out.println ("Error reading 3D data -- nX = " + nX + ", but only " + iX + " blocks read");
return  Clazz_newFloatArray (1, 1, 1, 0);
}return data;
}, "~S");
c$.markLines = $_M(c$, "markLines", 
function (data, eol) {
var nLines = 0;
for (var i = data.length; --i >= 0; ) if (data.charAt (i) == eol) nLines++;

var lines =  Clazz_newIntArray (nLines + 1, 0);
nLines = 0;
var pt = 0;
while ((pt = data.indexOf (eol, pt)) >= 0) lines[nLines++] = ++pt;

lines[nLines] = data.length;
return lines;
}, "~S,~S");
});
Clazz_declarePackage ("J.util");
Clazz_load (null, "J.util.Txt", ["java.lang.Character", "$.Double", "$.Float", "JU.PT", "$.SB"], function () {
c$ = Clazz_declareType (J.util, "Txt");
c$.formatStringS = $_M(c$, "formatStringS", 
function (strFormat, key, strT) {
return J.util.Txt.formatString (strFormat, key, strT, NaN, NaN, false);
}, "~S,~S,~S");
c$.formatStringF = $_M(c$, "formatStringF", 
function (strFormat, key, floatT) {
return J.util.Txt.formatString (strFormat, key, null, floatT, NaN, false);
}, "~S,~S,~N");
c$.formatStringI = $_M(c$, "formatStringI", 
function (strFormat, key, intT) {
return J.util.Txt.formatString (strFormat, key, "" + intT, NaN, NaN, false);
}, "~S,~S,~N");
c$.sprintf = $_M(c$, "sprintf", 
function (strFormat, list, values) {
if (values == null) return strFormat;
var n = list.length;
if (n == values.length) try {
for (var o = 0; o < n; o++) {
if (values[o] == null) continue;
switch (list.charAt (o)) {
case 's':
strFormat = J.util.Txt.formatString (strFormat, "s", values[o], NaN, NaN, true);
break;
case 'f':
strFormat = J.util.Txt.formatString (strFormat, "f", null, (values[o]).floatValue (), NaN, true);
break;
case 'i':
strFormat = J.util.Txt.formatString (strFormat, "d", "" + values[o], NaN, NaN, true);
strFormat = J.util.Txt.formatString (strFormat, "i", "" + values[o], NaN, NaN, true);
break;
case 'd':
strFormat = J.util.Txt.formatString (strFormat, "e", null, NaN, (values[o]).doubleValue (), true);
break;
case 'p':
var pVal = values[o];
strFormat = J.util.Txt.formatString (strFormat, "p", null, pVal.x, NaN, true);
strFormat = J.util.Txt.formatString (strFormat, "p", null, pVal.y, NaN, true);
strFormat = J.util.Txt.formatString (strFormat, "p", null, pVal.z, NaN, true);
break;
case 'q':
var qVal = values[o];
strFormat = J.util.Txt.formatString (strFormat, "q", null, qVal.x, NaN, true);
strFormat = J.util.Txt.formatString (strFormat, "q", null, qVal.y, NaN, true);
strFormat = J.util.Txt.formatString (strFormat, "q", null, qVal.z, NaN, true);
strFormat = J.util.Txt.formatString (strFormat, "q", null, qVal.w, NaN, true);
break;
case 'S':
var sVal = values[o];
for (var i = 0; i < sVal.length; i++) strFormat = J.util.Txt.formatString (strFormat, "s", sVal[i], NaN, NaN, true);

break;
case 'F':
var fVal = values[o];
for (var i = 0; i < fVal.length; i++) strFormat = J.util.Txt.formatString (strFormat, "f", null, fVal[i], NaN, true);

break;
case 'I':
var iVal = values[o];
for (var i = 0; i < iVal.length; i++) strFormat = J.util.Txt.formatString (strFormat, "d", "" + iVal[i], NaN, NaN, true);

for (var i = 0; i < iVal.length; i++) strFormat = J.util.Txt.formatString (strFormat, "i", "" + iVal[i], NaN, NaN, true);

break;
case 'D':
var dVal = values[o];
for (var i = 0; i < dVal.length; i++) strFormat = J.util.Txt.formatString (strFormat, "e", null, NaN, dVal[i], true);

}
}
return JU.PT.simpleReplace (strFormat, "%%", "%");
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
System.out.println ("TextFormat.sprintf error " + list + " " + strFormat);
return JU.PT.simpleReplace (strFormat, "%", "?");
}, "~S,~S,~A");
c$.formatString = $_M(c$, "formatString", 
function (strFormat, key, strT, floatT, doubleT, doOne) {
if (strFormat == null) return null;
if ("".equals (strFormat)) return "";
var len = key.length;
if (strFormat.indexOf ("%") < 0 || len == 0 || strFormat.indexOf (key) < 0) return strFormat;
var strLabel = "";
var ich;
var ichPercent;
var ichKey;
for (ich = 0; (ichPercent = strFormat.indexOf ('%', ich)) >= 0 && (ichKey = strFormat.indexOf (key, ichPercent + 1)) >= 0; ) {
if (ich != ichPercent) strLabel += strFormat.substring (ich, ichPercent);
ich = ichPercent + 1;
if (ichKey > ichPercent + 6) {
strLabel += '%';
continue;
}try {
var alignLeft = false;
if (strFormat.charAt (ich) == '-') {
alignLeft = true;
++ich;
}var zeroPad = false;
if (strFormat.charAt (ich) == '0') {
zeroPad = true;
++ich;
}var ch;
var width = 0;
while ((ch = strFormat.charAt (ich)) >= '0' && (ch <= '9')) {
width = (10 * width) + (ch.charCodeAt (0) - 48);
++ich;
}
var precision = 2147483647;
var isExponential = false;
if (strFormat.charAt (ich) == '.') {
++ich;
if ((ch = strFormat.charAt (ich)) == '-') {
isExponential = true;
++ich;
}if ((ch = strFormat.charAt (ich)) >= '0' && ch <= '9') {
precision = ch.charCodeAt (0) - 48;
++ich;
}if (isExponential) precision = -precision - (strT == null ? 1 : 0);
}var st = strFormat.substring (ich, ich + len);
if (!st.equals (key)) {
ich = ichPercent + 1;
strLabel += '%';
continue;
}ich += len;
if (!Float.isNaN (floatT)) strLabel += JU.PT.formatF (floatT, width, precision, alignLeft, zeroPad);
 else if (strT != null) strLabel += JU.PT.formatS (strT, width, precision, alignLeft, zeroPad);
 else if (!Double.isNaN (doubleT)) strLabel += JU.PT.formatD (doubleT, width, precision, alignLeft, zeroPad, true);
if (doOne) break;
} catch (ioobe) {
if (Clazz_exceptionOf (ioobe, IndexOutOfBoundsException)) {
ich = ichPercent;
break;
} else {
throw ioobe;
}
}
}
strLabel += strFormat.substring (ich);
return strLabel;
}, "~S,~S,~S,~N,~N,~B");
c$.formatCheck = $_M(c$, "formatCheck", 
function (strFormat) {
if (strFormat == null || strFormat.indexOf ('p') < 0 && strFormat.indexOf ('q') < 0) return strFormat;
strFormat = JU.PT.simpleReplace (strFormat, "%%", "\1");
strFormat = JU.PT.simpleReplace (strFormat, "%p", "%6.2p");
strFormat = JU.PT.simpleReplace (strFormat, "%q", "%6.2q");
var format = JU.PT.split (strFormat, "%");
var sb =  new JU.SB ();
sb.append (format[0]);
for (var i = 1; i < format.length; i++) {
var f = "%" + format[i];
var pt;
if (f.length >= 3) {
if ((pt = f.indexOf ('p')) >= 0) f = J.util.Txt.fdup (f, pt, 3);
if ((pt = f.indexOf ('q')) >= 0) f = J.util.Txt.fdup (f, pt, 4);
}sb.append (f);
}
return sb.toString ().$replace ('\1', '%');
}, "~S");
c$.fdup = $_M(c$, "fdup", 
function (f, pt, n) {
var ch;
var count = 0;
for (var i = pt; --i >= 1; ) {
if (Character.isDigit (ch = f.charAt (i))) continue;
switch (ch) {
case '.':
if (count++ != 0) return f;
continue;
case '-':
if (i != 1) return f;
continue;
default:
return f;
}
}
var s = f.substring (0, pt + 1);
var sb =  new JU.SB ();
for (var i = 0; i < n; i++) sb.append (s);

sb.append (f.substring (pt + 1));
return sb.toString ();
}, "~S,~N,~N");
c$.leftJustify = $_M(c$, "leftJustify", 
function (s, s1, s2) {
s.append (s2);
var n = s1.length - s2.length;
if (n > 0) s.append (s1.substring (0, n));
}, "JU.SB,~S,~S");
c$.rightJustify = $_M(c$, "rightJustify", 
function (s, s1, s2) {
var n = s1.length - s2.length;
if (n > 0) s.append (s1.substring (0, n));
s.append (s2);
}, "JU.SB,~S,~S");
c$.safeTruncate = $_M(c$, "safeTruncate", 
function (f, n) {
if (f > -0.001 && f < 0.001) f = 0;
return (f + "         ").substring (0, n);
}, "~N,~N");
c$.isWild = $_M(c$, "isWild", 
function (s) {
return s != null && (s.indexOf ("*") >= 0 || s.indexOf ("?") >= 0);
}, "~S");
c$.isMatch = $_M(c$, "isMatch", 
function (s, strWildcard, checkStar, allowInitialStar) {
var ich = 0;
var cchWildcard = strWildcard.length;
var cchs = s.length;
if (cchs == 0 || cchWildcard == 0) return (cchs == cchWildcard || cchWildcard == 1 && strWildcard.charAt (0) == '*');
var isStar0 = (checkStar && allowInitialStar ? strWildcard.charAt (0) == '*' : false);
if (isStar0 && strWildcard.charAt (cchWildcard - 1) == '*') return (cchWildcard < 3 || s.indexOf (strWildcard.substring (1, cchWildcard - 1)) >= 0);
var qqq = "????";
while (qqq.length < s.length) qqq += qqq;

if (checkStar) {
if (allowInitialStar && isStar0) strWildcard = qqq + strWildcard.substring (1);
if (strWildcard.charAt (ich = strWildcard.length - 1) == '*') strWildcard = strWildcard.substring (0, ich) + qqq;
cchWildcard = strWildcard.length;
}if (cchWildcard < cchs) return false;
ich = 0;
while (cchWildcard > cchs) {
if (allowInitialStar && strWildcard.charAt (ich) == '?') {
++ich;
} else if (strWildcard.charAt (ich + cchWildcard - 1) != '?') {
return false;
}--cchWildcard;
}
for (var i = cchs; --i >= 0; ) {
var charWild = strWildcard.charAt (ich + i);
if (charWild == '?') continue;
if (charWild != s.charAt (i) && (charWild != '\1' || s.charAt (i) != '?')) return false;
}
return true;
}, "~S,~S,~B,~B");
c$.join = $_M(c$, "join", 
function (s, c, i0) {
if (s.length < i0) return null;
var sb =  new JU.SB ();
sb.append (s[i0++]);
for (var i = i0; i < s.length; i++) sb.appendC (c).append (s[i]);

return sb.toString ();
}, "~A,~S,~N");
c$.replaceQuotedStrings = $_M(c$, "replaceQuotedStrings", 
function (s, list, newList) {
var n = list.size ();
for (var i = 0; i < n; i++) {
var name = list.get (i);
var newName = newList.get (i);
if (!newName.equals (name)) s = JU.PT.simpleReplace (s, "\"" + name + "\"", "\"" + newName + "\"");
}
return s;
}, "~S,java.util.List,java.util.List");
c$.replaceStrings = $_M(c$, "replaceStrings", 
function (s, list, newList) {
var n = list.size ();
for (var i = 0; i < n; i++) {
var name = list.get (i);
var newName = newList.get (i);
if (!newName.equals (name)) s = JU.PT.simpleReplace (s, name, newName);
}
return s;
}, "~S,java.util.List,java.util.List");
c$.ichMathTerminator = $_M(c$, "ichMathTerminator", 
function (script, ichT, len) {
var nP = 1;
var chFirst = '\u0000';
var chLast = '\u0000';
while (nP > 0 && ++ichT < len) {
var ch = script.charAt (ichT);
if (chFirst != '\0') {
if (chLast == '\\') {
ch = '\0';
} else if (ch == chFirst) {
chFirst = '\0';
}chLast = ch;
continue;
}switch (ch) {
case '\'':
case '"':
chFirst = ch;
break;
case '{':
nP++;
break;
case '}':
nP--;
break;
}
}
return ichT;
}, "~S,~N,~N");
});
Clazz_declarePackage ("J.script");
Clazz_load (["java.util.Hashtable"], "J.script.T", ["java.lang.Boolean", "java.util.Arrays", "JU.AU", "$.List", "J.util.Logger"], function () {
c$ = Clazz_decorateAsClass (function () {
this.tok = 0;
this.value = null;
this.intValue = 2147483647;
Clazz_instantialize (this, arguments);
}, J.script, "T");
c$.t = $_M(c$, "t", 
function (tok) {
var token =  new J.script.T ();
token.tok = tok;
return token;
}, "~N");
c$.tv = $_M(c$, "tv", 
function (tok, intValue, value) {
var token = J.script.T.t (tok);
token.intValue = intValue;
token.value = value;
return token;
}, "~N,~N,~O");
c$.o = $_M(c$, "o", 
function (tok, value) {
var token = J.script.T.t (tok);
token.value = value;
return token;
}, "~N,~O");
c$.n = $_M(c$, "n", 
function (tok, intValue) {
var token = J.script.T.t (tok);
token.intValue = intValue;
return token;
}, "~N,~N");
c$.i = $_M(c$, "i", 
function (intValue) {
var token = J.script.T.t (2);
token.intValue = intValue;
return token;
}, "~N");
c$.tokAttr = $_M(c$, "tokAttr", 
function (a, b) {
return (a & b) == (b & b);
}, "~N,~N");
c$.tokAttrOr = $_M(c$, "tokAttrOr", 
function (a, b1, b2) {
return (a & b1) == (b1 & b1) || (a & b2) == (b2 & b2);
}, "~N,~N,~N");
c$.getPrecedence = $_M(c$, "getPrecedence", 
function (tokOperator) {
return ((tokOperator >> 4) & 0xF);
}, "~N");
c$.getMaxMathParams = $_M(c$, "getMaxMathParams", 
function (tokCommand) {
return ((tokCommand >> 9) & 0x7);
}, "~N");
c$.addToken = $_M(c$, "addToken", 
function (ident, token) {
J.script.T.tokenMap.put (ident, token);
}, "~S,J.script.T");
c$.getTokenFromName = $_M(c$, "getTokenFromName", 
function (name) {
return J.script.T.tokenMap.get (name);
}, "~S");
c$.getTokFromName = $_M(c$, "getTokFromName", 
function (name) {
var token = J.script.T.getTokenFromName (name.toLowerCase ());
return (token == null ? 0 : token.tok);
}, "~S");
c$.nameOf = $_M(c$, "nameOf", 
function (tok) {
for (var token, $token = J.script.T.tokenMap.values ().iterator (); $token.hasNext () && ((token = $token.next ()) || true);) {
if (token.tok == tok) return "" + token.value;
}
return "0x" + Integer.toHexString (tok);
}, "~N");
$_V(c$, "toString", 
function () {
return this.toString2 ();
});
$_M(c$, "toString2", 
function () {
return "Token[" + J.script.T.astrType[this.tok < 14 ? this.tok : 14] + "(" + (this.tok % (512)) + "/0x" + Integer.toHexString (this.tok) + ")" + ((this.intValue == 2147483647) ? "" : " intValue=" + this.intValue + "(0x" + Integer.toHexString (this.intValue) + ")") + ((this.value == null) ? "" : Clazz_instanceOf (this.value, String) ? " value=\"" + this.value + "\"" : " value=" + this.value) + "]";
});
c$.getCommandSet = $_M(c$, "getCommandSet", 
function (strBegin) {
var cmds = "";
var htSet =  new java.util.Hashtable ();
var nCmds = 0;
var s = (strBegin == null || strBegin.length == 0 ? null : strBegin.toLowerCase ());
var isMultiCharacter = (s != null && s.length > 1);
for (var entry, $entry = J.script.T.tokenMap.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) {
var name = entry.getKey ();
var token = entry.getValue ();
if ((token.tok & 4096) != 0 && (s == null || name.indexOf (s) == 0) && (isMultiCharacter || (token.value).equals (name))) htSet.put (name, Boolean.TRUE);
}
for (var entry, $entry = htSet.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) {
var name = entry.getKey ();
if (name.charAt (name.length - 1) != 's' || !htSet.containsKey (name.substring (0, name.length - 1))) cmds += (nCmds++ == 0 ? "" : ";") + name;
}
return cmds;
}, "~S");
c$.getAtomPropertiesLike = $_M(c$, "getAtomPropertiesLike", 
function (type) {
type = type.toLowerCase ();
var v =  new JU.List ();
var isAll = (type.length == 0);
for (var entry, $entry = J.script.T.tokenMap.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) {
var name = entry.getKey ();
if (name.charAt (0) == '_') continue;
var token = entry.getValue ();
if (J.script.T.tokAttr (token.tok, 1078984704) && (isAll || name.toLowerCase ().startsWith (type))) {
if (isAll || !(token.value).toLowerCase ().startsWith (type)) token = J.script.T.o (token.tok, name);
v.addLast (token);
}}
return (v.size () == 0 ? null : v);
}, "~S");
c$.getTokensLike = $_M(c$, "getTokensLike", 
function (type) {
var attr = (type.equals ("setparam") ? 536870912 : type.equals ("misc") ? 1073741824 : type.equals ("mathfunc") ? 135266304 : 4096);
var notattr = (attr == 536870912 ? 1610612736 : 0);
var v =  new JU.List ();
for (var entry, $entry = J.script.T.tokenMap.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) {
var name = entry.getKey ();
var token = entry.getValue ();
if (J.script.T.tokAttr (token.tok, attr) && (notattr == 0 || !J.script.T.tokAttr (token.tok, notattr))) v.addLast (name);
}
var a = v.toArray ( new Array (v.size ()));
java.util.Arrays.sort (a);
return a;
}, "~S");
c$.getSettableTokFromString = $_M(c$, "getSettableTokFromString", 
function (s) {
var tok = J.script.T.getTokFromName (s);
return (tok != 0 && J.script.T.tokAttr (tok, 2048) && !J.script.T.tokAttr (tok, 1141899264) ? tok : 0);
}, "~S");
c$.completeCommand = $_M(c$, "completeCommand", 
function (map, isSet, asCommand, str, n) {
if (map == null) map = J.script.T.tokenMap;
 else asCommand = false;
var v =  new JU.List ();
str = str.toLowerCase ();
for (var name, $name = map.keySet ().iterator (); $name.hasNext () && ((name = $name.next ()) || true);) {
if (!name.startsWith (str)) continue;
var tok = J.script.T.getTokFromName (name);
if (asCommand ? J.script.T.tokAttr (tok, 4096) : isSet ? J.script.T.tokAttr (tok, 536870912) && !J.script.T.tokAttr (tok, 1610612736) : true) v.addLast (name);
}
return JU.AU.sortedItem (v, n);
}, "java.util.Map,~B,~B,~S,~N");
c$.getParamType = $_M(c$, "getParamType", 
function (tok) {
if (!J.script.T.tokAttr (tok, 536870912)) return 0;
return tok & 662700032;
}, "~N");
c$.getTokensType = $_M(c$, "getTokensType", 
function (map, attr) {
for (var e, $e = J.script.T.tokenMap.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var t = e.getValue ();
if (J.script.T.tokAttr (t.tok, attr)) map.put (e.getKey (), e.getValue ());
}
}, "java.util.Map,~N");
c$.isIDcmd = $_M(c$, "isIDcmd", 
function (cmdtok) {
switch (cmdtok) {
case 135180:
case 135176:
case 135174:
case 135188:
case 135402505:
return true;
default:
return false;
}
}, "~N");
Clazz_defineStatics (c$,
"nada", 0,
"integer", 2,
"decimal", 3,
"string", 4,
"seqcode", 5,
"hash", 6,
"varray", 7,
"point3f", 8,
"point4f", 9,
"bitset", 10,
"matrix3f", 11,
"matrix4f", 12,
"listf", 13,
"keyword", 14,
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J.script.T.t (603979796), "autobond", J.script.T.t (603979798), "autoFPS", J.script.T.t (603979800), "axesMolecular", J.script.T.t (603979804), "axesOrientationRasmol", J.script.T.t (603979806), "axesUnitCell", J.script.T.t (603979808), "axesWindow", J.script.T.t (603979810), "bondModeOr", J.script.T.t (603979812), "bondPicking", J.script.T.t (603979814), "bonds", J.script.T.t (1678770178), "bond", null, "cartoonBaseEdges", J.script.T.t (603979817), "cartoonsFancy", J.script.T.t (603979819), "cartoonFancy", null, "cartoonLadders", J.script.T.t (603979820), "cartoonRockets", J.script.T.t (603979818), "chainCaseSensitive", J.script.T.t (603979822), "colorRasmol", J.script.T.t (603979823), "debugScript", J.script.T.t (603979824), "defaultStructureDssp", J.script.T.t (603979825), "disablePopupMenu", J.script.T.t (603979826), "displayCellParameters", J.script.T.t (603979828), "dotsSelectedOnly", J.script.T.t (603979829), "dotSurface", J.script.T.t (603979830), "dragSelected", J.script.T.t (603979831), "drawHover", J.script.T.t (603979832), "drawPicking", J.script.T.t (603979833), "dsspCalculateHydrogenAlways", J.script.T.t (603979834), "dynamicMeasurements", J.script.T.t (603979835), "ellipsoidArcs", J.script.T.t (603979836), "ellipsoidArrows", J.script.T.t (603979837), "ellipsoidAxes", J.script.T.t (603979838), "ellipsoidBall", J.script.T.t (603979839), "ellipsoidDots", J.script.T.t (603979840), "ellipsoidFill", J.script.T.t (603979841), "fileCaching", J.script.T.t (603979842), "fontCaching", J.script.T.t (603979844), "fontScaling", J.script.T.t (603979845), "forceAutoBond", J.script.T.t (603979846), "fractionalRelative", J.script.T.t (603979848), "greyscaleRendering", J.script.T.t (603979850), "hbondsBackbone", J.script.T.t (603979852), "hbondsRasmol", J.script.T.t (603979853), "hbondsSolid", J.script.T.t (603979854), "hetero", J.script.T.t (1613758470), "hideNameInPopup", J.script.T.t (603979858), "hideNavigationPoint", J.script.T.t (603979860), "hideNotSelected", J.script.T.t (603979862), "highResolution", J.script.T.t (603979864), "hydrogen", J.script.T.t (1613758476), "hydrogens", null, "imageState", J.script.T.t (603979868), "isKiosk", J.script.T.t (603979869), "isosurfaceKey", J.script.T.t (603979870), "isosurfacePropertySmoothing", J.script.T.t (603979871), "isosurfacePropertySmoothingPower", J.script.T.t (553648149), "justifyMeasurements", J.script.T.t (603979872), "languageTranslation", J.script.T.t (603979873), "legacyAutoBonding", J.script.T.t (603979874), "legacyHAddition", J.script.T.t (603979875), "logCommands", J.script.T.t (603979876), "logGestures", J.script.T.t (603979877), "measureAllModels", J.script.T.t (603979878), "measurementLabels", J.script.T.t (603979879), "measurementNumbers", J.script.T.t (1610612739), "messageStyleChime", J.script.T.t (603979880), "minimizationRefresh", J.script.T.t (603979881), "minimizationSilent", J.script.T.t (603979882), "modelkitMode", J.script.T.t (603979883), "monitorEnergy", J.script.T.t (603979884), "multipleBondRadiusFactor", J.script.T.t (570425368), "multipleBondSpacing", J.script.T.t (570425369), "multiProcessor", J.script.T.t (603979885), "navigateSurface", J.script.T.t (603979886), "navigationMode", J.script.T.t (603979887), "navigationPeriodic", J.script.T.t (603979888), "partialDots", J.script.T.t (603979889), "pdbAddHydrogens", J.script.T.t (603979890), "pdbGetHeader", J.script.T.t (603979891), "pdbSequential", J.script.T.t (603979892), "perspectiveDepth", J.script.T.t (603979893), "preserveState", J.script.T.t (603979894), "rangeSelected", J.script.T.t (603979895), "redoMove", J.script.T.t (4139), "refreshing", J.script.T.t (603979896), "ribbonBorder", J.script.T.t (603979898), "rocketBarrels", J.script.T.t (603979900), "saveProteinStructureState", J.script.T.t (603979902), "scriptQueue", J.script.T.t (603979904), "selectAllModels", J.script.T.t (603979906), "selectHetero", J.script.T.t (603979908), "selectHydrogen", J.script.T.t (603979910), "showAxes", J.script.T.t (603979914), "showBoundBox", J.script.T.t (603979916), "showBoundingBox", null, "showFrank", J.script.T.t (603979918), "showHiddenSelectionHalos", J.script.T.t (603979920), "showHydrogens", J.script.T.t (603979922), "showKeyStrokes", J.script.T.t (603979924), "showMeasurements", J.script.T.t (603979926), "showMultipleBonds", J.script.T.t (603979928), "showNavigationPointAlways", J.script.T.t (603979930), "showTiming", J.script.T.t (603979934), "showUnitcell", J.script.T.t (603979936), "slabByAtom", J.script.T.t (603979938), "slabByMolecule", J.script.T.t (603979940), "slabEnabled", J.script.T.t (603979942), "smartAromatic", J.script.T.t (603979944), "solvent", J.script.T.t (1613758488), "solventProbe", J.script.T.t (603979948), "ssBondsBackbone", J.script.T.t (603979952), "statusReporting", J.script.T.t (603979954), "strutsMultiple", J.script.T.t (603979955), "syncMouse", J.script.T.t (603979956), "syncScript", J.script.T.t (603979958), "testFlag1", J.script.T.t (603979960), "testFlag2", J.script.T.t (603979962), "testFlag3", J.script.T.t (603979964), "testFlag4", J.script.T.t (603979965), "traceAlpha", J.script.T.t (603979966), "twistedSheets", J.script.T.t (603979968), "undo", J.script.T.t (536870928), "undoMove", J.script.T.t (4165), "useArcBall", J.script.T.t (603979969), "useMinimizationThread", J.script.T.t (603979970), "useNumberLocalization", J.script.T.t (603979972), "waitForMoveTo", J.script.T.t (603979974), "windowCentered", J.script.T.t (603979975), "wireframeRotation", J.script.T.t (603979976), "zeroBasedXyzRasmol", J.script.T.t (603979978), "zoomEnabled", J.script.T.t (603979980), "zoomHeight", J.script.T.t (603979982), "zoomLarge", J.script.T.t (603979983), "zShade", J.script.T.t (603979984)];
var tokenLast = null;
var stringThis;
var tokenThis;
var lcase;
for (var i = 0; i + 1 < arrayPairs.length; i += 2) {
stringThis = arrayPairs[i];
lcase = stringThis.toLowerCase ();
tokenThis = arrayPairs[i + 1];
if (tokenThis == null) tokenThis = tokenLast;
if (tokenThis.value == null) tokenThis.value = stringThis;
if (J.script.T.tokenMap.get (lcase) != null) J.util.Logger.error ("duplicate token definition:" + lcase);
J.script.T.tokenMap.put (lcase, tokenThis);
tokenLast = tokenThis;
}
arrayPairs = null;
}});
Clazz_declarePackage ("J.util");
Clazz_load (["JU.BS"], "J.util.BSUtil", null, function () {
c$ = Clazz_declareType (J.util, "BSUtil");
c$.newAndSetBit = $_M(c$, "newAndSetBit", 
function (i) {
var bs = J.util.BSUtil.newBitSet (i + 1);
bs.set (i);
return bs;
}, "~N");
c$.areEqual = $_M(c$, "areEqual", 
function (a, b) {
return (a == null || b == null ? a == null && b == null : a.equals (b));
}, "JU.BS,JU.BS");
c$.haveCommon = $_M(c$, "haveCommon", 
function (a, b) {
return (a == null || b == null ? false : a.intersects (b));
}, "JU.BS,JU.BS");
c$.cardinalityOf = $_M(c$, "cardinalityOf", 
function (bs) {
return (bs == null ? 0 : bs.cardinality ());
}, "JU.BS");
c$.newBitSet2 = $_M(c$, "newBitSet2", 
function (i0, i1) {
var bs = J.util.BSUtil.newBitSet (i1);
bs.setBits (i0, i1);
return bs;
}, "~N,~N");
c$.setAll = $_M(c$, "setAll", 
function (n) {
var bs = J.util.BSUtil.newBitSet (n);
bs.setBits (0, n);
return bs;
}, "~N");
c$.andNot = $_M(c$, "andNot", 
function (a, b) {
if (b != null && a != null) a.andNot (b);
return a;
}, "JU.BS,JU.BS");
c$.copy = $_M(c$, "copy", 
function (bs) {
return bs == null ? null : bs.clone ();
}, "JU.BS");
c$.copy2 = $_M(c$, "copy2", 
function (a, b) {
if (a == null || b == null) return null;
b.clearAll ();
b.or (a);
return b;
}, "JU.BS,JU.BS");
c$.copyInvert = $_M(c$, "copyInvert", 
function (bs, n) {
return (bs == null ? null : J.util.BSUtil.andNot (J.util.BSUtil.setAll (n), bs));
}, "JU.BS,~N");
c$.invertInPlace = $_M(c$, "invertInPlace", 
function (bs, n) {
return J.util.BSUtil.copy2 (J.util.BSUtil.copyInvert (bs, n), bs);
}, "JU.BS,~N");
c$.toggleInPlace = $_M(c$, "toggleInPlace", 
function (a, b) {
if (a.equals (b)) {
a.clearAll ();
} else if (J.util.BSUtil.andNot (J.util.BSUtil.copy (b), a).length () == 0) {
J.util.BSUtil.andNot (a, b);
} else {
a.or (b);
}return a;
}, "JU.BS,JU.BS");
c$.deleteBits = $_M(c$, "deleteBits", 
function (bs, bsDelete) {
if (bs == null || bsDelete == null) return bs;
var ipt = bsDelete.nextSetBit (0);
if (ipt < 0) return bs;
var len = bs.length ();
var lend = Math.min (len, bsDelete.length ());
var i;
for (i = bsDelete.nextClearBit (ipt); i < lend && i >= 0; i = bsDelete.nextClearBit (i + 1)) bs.setBitTo (ipt++, bs.get (i));

for (i = lend; i < len; i++) bs.setBitTo (ipt++, bs.get (i));

if (ipt < len) bs.clearBits (ipt, len);
return bs;
}, "JU.BS,JU.BS");
c$.newBitSet = $_M(c$, "newBitSet", 
function (nFree) {
return JU.BS.newN (nFree);
}, "~N");
c$.offset = $_M(c$, "offset", 
function (bs0, pos, offset) {
if (bs0 == null) return;
var bsTemp = JU.BS.newN (bs0.length () + offset);
for (var i = bs0.nextSetBit (0); i >= pos; i = bs0.nextSetBit (i + 1)) bsTemp.set (i + offset);

J.util.BSUtil.copy2 (bsTemp, bs0);
}, "JU.BS,~N,~N");
c$.setMapBitSet = $_M(c$, "setMapBitSet", 
function (ht, i1, i2, key) {
var bs;
if (ht.containsKey (key)) bs = ht.get (key);
 else ht.put (key, bs =  new JU.BS ());
bs.setBits (i1, i2 + 1);
}, "java.util.Map,~N,~N,~S");
c$.emptySet = c$.prototype.emptySet =  new JU.BS ();
});
Clazz_declarePackage ("J.util");
Clazz_load (["java.lang.Enum"], "J.util.JmolEdge", null, function () {
c$ = Clazz_decorateAsClass (function () {
this.index = -1;
this.order = 0;
Clazz_instantialize (this, arguments);
}, J.util, "JmolEdge");
c$.getArgbHbondType = $_M(c$, "getArgbHbondType", 
function (order) {
var argbIndex = ((order & 30720) >> 11);
return J.util.JmolEdge.argbsHbondType[argbIndex];
}, "~N");
c$.getBondOrderNumberFromOrder = $_M(c$, "getBondOrderNumberFromOrder", 
function (order) {
order &= -131073;
if (order == 131071 || order == 65535) return "0";
if (J.modelset.Bond.isOrderH (order) || (order & 256) != 0) return J.util.JmolEdge.EnumBondOrder.SINGLE.number;
if ((order & 224) != 0) return (order >> 5) + "." + (order & 0x1F);
return J.util.JmolEdge.EnumBondOrder.getNumberFromCode (order);
}, "~N");
c$.getCmlBondOrder = $_M(c$, "getCmlBondOrder", 
function (order) {
var sname = J.util.JmolEdge.getBondOrderNameFromOrder (order);
switch (sname.charAt (0)) {
case 's':
case 'd':
case 't':
return "" + sname.toUpperCase ().charAt (0);
case 'a':
if (sname.indexOf ("Double") >= 0) return "D";
 else if (sname.indexOf ("Single") >= 0) return "S";
return "aromatic";
case 'p':
if (sname.indexOf (" ") >= 0) return sname.substring (sname.indexOf (" ") + 1);
return "partial12";
}
return null;
}, "~N");
c$.getBondOrderNameFromOrder = $_M(c$, "getBondOrderNameFromOrder", 
function (order) {
order &= -131073;
switch (order) {
case 65535:
case 131071:
return "";
case 32768:
return J.util.JmolEdge.EnumBondOrder.STRUT.$$name;
case 1:
return J.util.JmolEdge.EnumBondOrder.SINGLE.$$name;
case 2:
return J.util.JmolEdge.EnumBondOrder.DOUBLE.$$name;
}
if ((order & 224) != 0) return "partial " + J.util.JmolEdge.getBondOrderNumberFromOrder (order);
if (J.modelset.Bond.isOrderH (order)) return J.util.JmolEdge.EnumBondOrder.H_REGULAR.$$name;
if ((order & 256) != 0) return J.util.JmolEdge.EnumBondOrder.SINGLE.$$name;
return J.util.JmolEdge.EnumBondOrder.getNameFromCode (order);
}, "~N");
c$.getPartialBondDotted = $_M(c$, "getPartialBondDotted", 
function (order) {
return (order & 0x1F);
}, "~N");
c$.getPartialBondOrder = $_M(c$, "getPartialBondOrder", 
function (order) {
return ((order & -131073) >> 5);
}, "~N");
c$.getCovalentBondOrder = $_M(c$, "getCovalentBondOrder", 
function (order) {
if ((order & 1023) == 0) return 0;
order &= -131073;
if ((order & 224) != 0) return J.util.JmolEdge.getPartialBondOrder (order);
if ((order & 256) != 0) order &= -257;
if ((order & 0xF8) != 0) order = 1;
return order & 7;
}, "~N");
c$.getBondOrderFromFloat = $_M(c$, "getBondOrderFromFloat", 
function (fOrder) {
switch (Clazz_floatToInt (fOrder * 10)) {
case 10:
return 1;
case 5:
case -10:
return 33;
case 15:
return 515;
case -15:
return 66;
case 20:
return 2;
case 25:
return 97;
case -25:
return 100;
case 30:
return 3;
case 40:
return 4;
}
return 131071;
}, "~N");
c$.getBondOrderFromString = $_M(c$, "getBondOrderFromString", 
function (name) {
return J.util.JmolEdge.EnumBondOrder.getCodeFromName (name);
}, "~S");
Clazz_pu$h ();
c$ = Clazz_decorateAsClass (function () {
this.code = 0;
this.number = null;
this.$$name = null;
Clazz_instantialize (this, arguments);
}, J.util.JmolEdge, "EnumBondOrder", Enum);
Clazz_makeConstructor (c$, 
function (a, b, c) {
this.code = a;
this.number = b;
this.$$name = c;
}, "~N,~S,~S");
c$.getCodeFromName = $_M(c$, "getCodeFromName", 
function (a) {
for (var item, $item = 0, $$item = J.util.JmolEdge.EnumBondOrder.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (item.$$name.equalsIgnoreCase (a)) return item.code;

return 131071;
}, "~S");
c$.getNameFromCode = $_M(c$, "getNameFromCode", 
function (a) {
for (var item, $item = 0, $$item = J.util.JmolEdge.EnumBondOrder.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (item.code == a) return item.$$name;

return "?";
}, "~N");
c$.getNumberFromCode = $_M(c$, "getNumberFromCode", 
function (a) {
for (var item, $item = 0, $$item = J.util.JmolEdge.EnumBondOrder.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (item.code == a) return item.number;

return "?";
}, "~N");
Clazz_defineEnumConstant (c$, "SINGLE", 0, [1, "1", "single"]);
Clazz_defineEnumConstant (c$, "DOUBLE", 1, [2, "2", "double"]);
Clazz_defineEnumConstant (c$, "TRIPLE", 2, [3, "3", "triple"]);
Clazz_defineEnumConstant (c$, "QUADRUPLE", 3, [4, "4", "quadruple"]);
Clazz_defineEnumConstant (c$, "AROMATIC", 4, [515, "1.5", "aromatic"]);
Clazz_defineEnumConstant (c$, "STRUT", 5, [32768, "1", "struts"]);
Clazz_defineEnumConstant (c$, "H_REGULAR", 6, [2048, "1", "hbond"]);
Clazz_defineEnumConstant (c$, "PARTIAL01", 7, [33, "0.5", "partial"]);
Clazz_defineEnumConstant (c$, "PARTIAL12", 8, [66, "1.5", "partialDouble"]);
Clazz_defineEnumConstant (c$, "PARTIAL23", 9, [97, "2.5", "partialTriple"]);
Clazz_defineEnumConstant (c$, "PARTIAL32", 10, [100, "2.5", "partialTriple2"]);
Clazz_defineEnumConstant (c$, "AROMATIC_SINGLE", 11, [513, "1", "aromaticSingle"]);
Clazz_defineEnumConstant (c$, "AROMATIC_DOUBLE", 12, [514, "2", "aromaticDouble"]);
Clazz_defineEnumConstant (c$, "UNSPECIFIED", 13, [17, "1", "unspecified"]);
c$ = Clazz_p0p ();
Clazz_defineStatics (c$,
"BOND_STEREO_MASK", 0x400,
"BOND_STEREO_NEAR", 0x401,
"BOND_STEREO_FAR", 0x411,
"BOND_AROMATIC_MASK", 0x200,
"BOND_AROMATIC_SINGLE", 0x201,
"BOND_AROMATIC_DOUBLE", 0x202,
"BOND_AROMATIC", 0x203,
"BOND_SULFUR_MASK", 0x100,
"BOND_PARTIAL_MASK", 0xE0,
"BOND_PARTIAL01", 0x21,
"BOND_PARTIAL12", 0x42,
"BOND_PARTIAL23", 0x61,
"BOND_PARTIAL32", 0x64,
"BOND_COVALENT_MASK", 0x3FF,
"BOND_COVALENT_SINGLE", 1,
"BOND_COVALENT_DOUBLE", 2,
"BOND_COVALENT_TRIPLE", 3,
"BOND_COVALENT_QUADRUPLE", 4,
"BOND_ORDER_UNSPECIFIED", 0x11,
"BOND_ORDER_ANY", 0x0FFFF,
"BOND_ORDER_NULL", 0x1FFFF,
"BOND_STRUT", 0x08000,
"BOND_AS_SINGLE", 0x10000,
"BOND_NEW", 0x20000,
"BOND_HBOND_SHIFT", 11,
"BOND_HYDROGEN_MASK", 30720,
"BOND_H_REGULAR", 2048,
"BOND_H_CALC_MASK", 28672,
"BOND_H_CALC", 4096,
"BOND_H_PLUS_2", 6144,
"BOND_H_PLUS_3", 8192,
"BOND_H_PLUS_4", 10240,
"BOND_H_PLUS_5", 12288,
"BOND_H_MINUS_3", 14336,
"BOND_H_MINUS_4", 16384,
"BOND_H_NUCLEOTIDE", 18432,
"argbsHbondType", [0xFFFF69B4, 0xFFFFFF00, 0xFFFFFF00, 0xFFFFFFFF, 0xFFFF00FF, 0xFFFF0000, 0xFFFFA500, 0xFF00FFFF, 0xFF00FF00, 0xFFFF8080],
"FLAG_AROMATIC_DOUBLE", 16,
"FLAG_AROMATIC_DEFINED", 8,
"FLAG_AROMATIC_STRICT", 4,
"FLAG_IGNORE_STEREOCHEMISTRY", 2,
"FLAG_NO_AROMATIC", 1);
});
Clazz_declarePackage ("J.modelset");
Clazz_load (["JU.BS", "J.util.JmolEdge", "J.viewer.JC"], "J.modelset.Bond", ["J.util.BSUtil", "$.C"], function () {
c$ = Clazz_decorateAsClass (function () {
this.atom1 = null;
this.atom2 = null;
this.mad = 0;
this.colix = 0;
this.shapeVisibilityFlags = 0;
Clazz_instantialize (this, arguments);
}, J.modelset, "Bond", J.util.JmolEdge);
Clazz_makeConstructor (c$, 
function (atom1, atom2, order, mad, colix) {
Clazz_superConstructor (this, J.modelset.Bond, []);
this.atom1 = atom1;
this.atom2 = atom2;
this.colix = colix;
this.setOrder (order);
this.setMad (mad);
}, "J.modelset.Atom,J.modelset.Atom,~N,~N,~N");
$_M(c$, "setMad", 
function (mad) {
this.mad = mad;
this.setShapeVisibility (mad != 0);
}, "~N");
$_M(c$, "setShapeVisibilityFlags", 
function (shapeVisibilityFlags) {
this.shapeVisibilityFlags = shapeVisibilityFlags;
}, "~N");
$_M(c$, "getShapeVisibilityFlags", 
function () {
return this.shapeVisibilityFlags;
});
$_M(c$, "setShapeVisibility", 
function (isVisible) {
var wasVisible = ((this.shapeVisibilityFlags & J.modelset.Bond.myVisibilityFlag) != 0);
if (wasVisible == isVisible) return;
this.atom1.addDisplayedBond (J.modelset.Bond.myVisibilityFlag, isVisible);
this.atom2.addDisplayedBond (J.modelset.Bond.myVisibilityFlag, isVisible);
if (isVisible) this.shapeVisibilityFlags |= J.modelset.Bond.myVisibilityFlag;
 else this.shapeVisibilityFlags &= ~J.modelset.Bond.myVisibilityFlag;
}, "~B");
$_M(c$, "getIdentity", 
function () {
return (this.index + 1) + " " + this.getOrderNumberAsString () + " " + this.atom1.getInfo () + " -- " + this.atom2.getInfo () + " " + this.atom1.distance (this.atom2);
});
$_V(c$, "isCovalent", 
function () {
return (this.order & 1023) != 0;
});
$_V(c$, "isHydrogen", 
function () {
return J.modelset.Bond.isOrderH (this.order);
});
c$.isOrderH = $_M(c$, "isOrderH", 
function (order) {
return (order & 30720) != 0;
}, "~N");
$_M(c$, "isStereo", 
function () {
return (this.order & 1024) != 0;
});
$_M(c$, "isPartial", 
function () {
return (this.order & 224) != 0;
});
$_M(c$, "isAromatic", 
function () {
return (this.order & 512) != 0;
});
$_M(c$, "setPaletteID", 
function (pid) {
}, "~N");
$_M(c$, "getEnergy", 
function () {
return 0;
});
$_M(c$, "getValence", 
function () {
return (!this.isCovalent () ? 0 : this.isPartial () || this.is (515) ? 1 : this.order & 7);
});
$_M(c$, "deleteAtomReferences", 
function () {
if (this.atom1 != null) this.atom1.deleteBond (this);
if (this.atom2 != null) this.atom2.deleteBond (this);
this.atom1 = this.atom2 = null;
});
$_M(c$, "setColix", 
function (colix) {
this.colix = colix;
}, "~N");
$_M(c$, "setTranslucent", 
function (isTranslucent, translucentLevel) {
this.colix = J.util.C.getColixTranslucent3 (this.colix, isTranslucent, translucentLevel);
}, "~B,~N");
$_M(c$, "setOrder", 
function (order) {
if (this.atom1.getElementNumber () == 16 && this.atom2.getElementNumber () == 16) order |= 256;
if (order == 512) order = 515;
this.order = order | (this.order & 131072);
}, "~N");
$_M(c$, "getAtom1", 
function () {
return this.atom1;
});
$_M(c$, "getAtom2", 
function () {
return this.atom2;
});
$_V(c$, "getAtomIndex1", 
function () {
return this.atom1.index;
});
$_V(c$, "getAtomIndex2", 
function () {
return this.atom2.index;
});
$_M(c$, "getRadius", 
function () {
return this.mad / 2000;
});
$_V(c$, "getCovalentOrder", 
function () {
return J.util.JmolEdge.getCovalentBondOrder (this.order);
});
$_M(c$, "getOrderName", 
function () {
return J.util.JmolEdge.getBondOrderNameFromOrder (this.order);
});
$_M(c$, "getOrderNumberAsString", 
function () {
return J.util.JmolEdge.getBondOrderNumberFromOrder (this.order);
});
$_M(c$, "getColix1", 
function () {
return J.util.C.getColixInherited (this.colix, this.atom1.colixAtom);
});
$_M(c$, "getColix2", 
function () {
return J.util.C.getColixInherited (this.colix, this.atom2.colixAtom);
});
$_M(c$, "getOtherAtom", 
function (thisAtom) {
return (this.atom1 === thisAtom ? this.atom2 : this.atom2 === thisAtom ? this.atom1 : null);
}, "J.modelset.Atom");
$_M(c$, "setIndex", 
function (i) {
this.index = i;
}, "~N");
$_M(c$, "is", 
function (bondType) {
return (this.order & -131073) == bondType;
}, "~N");
$_V(c$, "getOtherAtomNode", 
function (thisAtom) {
return (this.atom1 === thisAtom ? this.atom2 : this.atom2 === thisAtom ? this.atom1 : null);
}, "J.util.JmolNode");
$_V(c$, "toString", 
function () {
return this.atom1 + " - " + this.atom2;
});
Clazz_pu$h ();
c$ = Clazz_decorateAsClass (function () {
this.associatedAtoms = null;
Clazz_instantialize (this, arguments);
}, J.modelset.Bond, "BondSet", JU.BS);
Clazz_makeConstructor (c$, 
function () {
Clazz_superConstructor (this, J.modelset.Bond.BondSet, []);
});
$_M(c$, "getAssociatedAtoms", 
function () {
return this.associatedAtoms;
});
Clazz_makeConstructor (c$, 
function (a) {
Clazz_superConstructor (this, J.modelset.Bond.BondSet, []);
J.util.BSUtil.copy2 (a, this);
}, "JU.BS");
Clazz_makeConstructor (c$, 
function (a, b) {
this.construct (a);
this.associatedAtoms = b;
}, "JU.BS,~A");
c$ = Clazz_p0p ();
c$.myVisibilityFlag = c$.prototype.myVisibilityFlag = J.viewer.JC.getShapeVisibilityFlag (1);
});
Clazz_declarePackage ("J.util");
Clazz_load (null, "J.util.Measure", ["java.lang.Float", "JU.List", "$.P3", "$.P4", "$.V3", "J.api.Interface", "J.util.Escape", "$.Logger", "$.Quaternion", "J.viewer.JC"], function () {
c$ = Clazz_declareType (J.util, "Measure");
c$.computeAngle = $_M(c$, "computeAngle", 
function (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees) {
vectorBA.sub2 (pointA, pointB);
vectorBC.sub2 (pointC, pointB);
var angle = vectorBA.angle (vectorBC);
return (asDegrees ? angle / 0.017453292 : angle);
}, "JU.T3,JU.T3,JU.T3,JU.V3,JU.V3,~B");
c$.computeAngleABC = $_M(c$, "computeAngleABC", 
function (pointA, pointB, pointC, asDegrees) {
var vectorBA =  new JU.V3 ();
var vectorBC =  new JU.V3 ();
return J.util.Measure.computeAngle (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees);
}, "JU.T3,JU.T3,JU.T3,~B");
c$.computeTorsion = $_M(c$, "computeTorsion", 
function (p1, p2, p3, p4, asDegrees) {
var ijx = p1.x - p2.x;
var ijy = p1.y - p2.y;
var ijz = p1.z - p2.z;
var kjx = p3.x - p2.x;
var kjy = p3.y - p2.y;
var kjz = p3.z - p2.z;
var klx = p3.x - p4.x;
var kly = p3.y - p4.y;
var klz = p3.z - p4.z;
var ax = ijy * kjz - ijz * kjy;
var ay = ijz * kjx - ijx * kjz;
var az = ijx * kjy - ijy * kjx;
var cx = kjy * klz - kjz * kly;
var cy = kjz * klx - kjx * klz;
var cz = kjx * kly - kjy * klx;
var ai2 = 1 / (ax * ax + ay * ay + az * az);
var ci2 = 1 / (cx * cx + cy * cy + cz * cz);
var ai = Math.sqrt (ai2);
var ci = Math.sqrt (ci2);
var denom = ai * ci;
var cross = ax * cx + ay * cy + az * cz;
var cosang = cross * denom;
if (cosang > 1) {
cosang = 1;
}if (cosang < -1) {
cosang = -1;
}var torsion = Math.acos (cosang);
var dot = ijx * cx + ijy * cy + ijz * cz;
var absDot = Math.abs (dot);
torsion = (dot / absDot > 0) ? torsion : -torsion;
return (asDegrees ? torsion / 0.017453292 : torsion);
}, "JU.T3,JU.T3,JU.T3,JU.T3,~B");
c$.computeHelicalAxis = $_M(c$, "computeHelicalAxis", 
function (id, tokType, a, b, dq) {
var vab =  new JU.V3 ();
vab.sub2 (b, a);
var theta = dq.getTheta ();
var n = dq.getNormal ();
var v_dot_n = vab.dot (n);
if (Math.abs (v_dot_n) < 0.0001) v_dot_n = 0;
if (tokType == 1073741854) {
if (v_dot_n != 0) n.scale (v_dot_n);
return n;
}var va_prime_d =  new JU.V3 ();
va_prime_d.cross (vab, n);
if (va_prime_d.dot (va_prime_d) != 0) va_prime_d.normalize ();
var vda =  new JU.V3 ();
var vcb = JU.V3.newV (n);
if (v_dot_n == 0) v_dot_n = 1.4E-45;
vcb.scale (v_dot_n);
vda.sub2 (vcb, vab);
vda.scale (0.5);
va_prime_d.scale (theta == 0 ? 0 : (vda.length () / Math.tan (theta / 2 / 180 * 3.141592653589793)));
var r = JU.V3.newV (va_prime_d);
if (theta != 0) r.add (vda);
if (tokType == 1666189314) return r;
var pt_a_prime = JU.P3.newP (a);
pt_a_prime.sub (r);
if (tokType == 135266320) {
return pt_a_prime;
}if (v_dot_n != 1.4E-45) n.scale (v_dot_n);
var pt_b_prime = JU.P3.newP (pt_a_prime);
pt_b_prime.add (n);
theta = J.util.Measure.computeTorsion (a, pt_a_prime, pt_b_prime, b, true);
if (Float.isNaN (theta) || r.length () < 0.0001) theta = dq.getThetaDirectedV (n);
if (tokType == 135266305) return Float.$valueOf (theta);
if (tokType == 135176) return "draw ID \"" + id + "\" VECTOR " + J.util.Escape.eP (pt_a_prime) + " " + J.util.Escape.eP (n) + " color " + (theta < 0 ? "{255.0 200.0 0.0}" : "{255.0 0.0 128.0}");
if (tokType == 1746538509) return "measure " + J.util.Escape.eP (a) + J.util.Escape.eP (pt_a_prime) + J.util.Escape.eP (pt_b_prime) + J.util.Escape.eP (b);
var residuesPerTurn = Math.abs (theta == 0 ? 0 : 360 / theta);
var pitch = Math.abs (v_dot_n == 1.4E-45 ? 0 : n.length () * (theta == 0 ? 1 : 360 / theta));
switch (tokType) {
case 135266306:
return [pt_a_prime, n, r, JU.P3.new3 (theta, pitch, residuesPerTurn)];
case 1073742001:
return [J.util.Escape.eP (pt_a_prime), J.util.Escape.eP (n), J.util.Escape.eP (r), J.util.Escape.eP (JU.P3.new3 (theta, pitch, residuesPerTurn))];
default:
return null;
}
}, "~S,~N,JU.P3,JU.P3,J.util.Quaternion");
c$.getPlaneThroughPoints = $_M(c$, "getPlaneThroughPoints", 
function (pointA, pointB, pointC, vNorm, vAB, vAC, plane) {
var w = J.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB, vAC);
plane.set (vNorm.x, vNorm.y, vNorm.z, w);
}, "JU.P3,JU.P3,JU.P3,JU.V3,JU.V3,JU.V3,JU.P4");
c$.getPlaneThroughPoint = $_M(c$, "getPlaneThroughPoint", 
function (pt, normal, plane) {
plane.set (normal.x, normal.y, normal.z, -normal.dot (pt));
}, "JU.P3,JU.V3,JU.P4");
c$.distanceToPlane = $_M(c$, "distanceToPlane", 
function (plane, pt) {
return (plane == null ? NaN : (plane.x * pt.x + plane.y * pt.y + plane.z * pt.z + plane.w) / Math.sqrt (plane.x * plane.x + plane.y * plane.y + plane.z * plane.z));
}, "JU.P4,JU.P3");
c$.distanceToPlaneD = $_M(c$, "distanceToPlaneD", 
function (plane, d, pt) {
return (plane == null ? NaN : (plane.x * pt.x + plane.y * pt.y + plane.z * pt.z + plane.w) / d);
}, "JU.P4,~N,JU.P3");
c$.distanceToPlaneV = $_M(c$, "distanceToPlaneV", 
function (norm, w, pt) {
return (norm == null ? NaN : (norm.x * pt.x + norm.y * pt.y + norm.z * pt.z + w) / Math.sqrt (norm.x * norm.x + norm.y * norm.y + norm.z * norm.z));
}, "JU.V3,~N,JU.P3");
c$.calcNormalizedNormal = $_M(c$, "calcNormalizedNormal", 
function (pointA, pointB, pointC, vNormNorm, vAB, vAC) {
vAB.sub2 (pointB, pointA);
vAC.sub2 (pointC, pointA);
vNormNorm.cross (vAB, vAC);
vNormNorm.normalize ();
}, "JU.P3,JU.P3,JU.P3,JU.V3,JU.V3,JU.V3");
c$.getDirectedNormalThroughPoints = $_M(c$, "getDirectedNormalThroughPoints", 
function (pointA, pointB, pointC, ptRef, vNorm, vAB, vAC) {
var nd = J.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB, vAC);
if (ptRef != null) {
var pt0 = JU.P3.newP (pointA);
pt0.add (vNorm);
var d = pt0.distance (ptRef);
pt0.setT (pointA);
pt0.sub (vNorm);
if (d > pt0.distance (ptRef)) {
vNorm.scale (-1);
nd = -nd;
}}return nd;
}, "JU.P3,JU.P3,JU.P3,JU.P3,JU.V3,JU.V3,JU.V3");
c$.getNormalThroughPoints = $_M(c$, "getNormalThroughPoints", 
function (pointA, pointB, pointC, vNorm, vAB, vAC) {
J.util.Measure.calcNormalizedNormal (pointA, pointB, pointC, vNorm, vAB, vAC);
vAB.setT (pointA);
return -vAB.dot (vNorm);
}, "JU.P3,JU.P3,JU.P3,JU.V3,JU.V3,JU.V3");
c$.getPlaneProjection = $_M(c$, "getPlaneProjection", 
function (pt, plane, ptProj, vNorm) {
var dist = J.util.Measure.distanceToPlane (plane, pt);
vNorm.set (plane.x, plane.y, plane.z);
vNorm.normalize ();
vNorm.scale (-dist);
ptProj.setT (pt);
ptProj.add (vNorm);
}, "JU.P3,JU.P4,JU.P3,JU.V3");
c$.getNormalFromCenter = $_M(c$, "getNormalFromCenter", 
function (ptCenter, ptA, ptB, ptC, isOutward, normal) {
var vAB =  new JU.V3 ();
var vAC =  new JU.V3 ();
var d = J.util.Measure.getNormalThroughPoints (ptA, ptB, ptC, normal, vAB, vAC);
var isReversed = (J.util.Measure.distanceToPlaneV (normal, d, ptCenter) > 0);
if (isReversed == isOutward) normal.scale (-1.0);
return !isReversed;
}, "JU.P3,JU.P3,JU.P3,JU.P3,~B,JU.V3");
c$.getNormalToLine = $_M(c$, "getNormalToLine", 
function (pointA, pointB, vNormNorm) {
vNormNorm.sub2 (pointA, pointB);
vNormNorm.cross (vNormNorm, J.viewer.JC.axisY);
vNormNorm.normalize ();
if (Float.isNaN (vNormNorm.x)) vNormNorm.set (1, 0, 0);
}, "JU.P3,JU.P3,JU.V3");
c$.getBisectingPlane = $_M(c$, "getBisectingPlane", 
function (pointA, vAB, ptTemp, vTemp, plane) {
ptTemp.scaleAdd2 (0.5, vAB, pointA);
vTemp.setT (vAB);
vTemp.normalize ();
J.util.Measure.getPlaneThroughPoint (ptTemp, vTemp, plane);
}, "JU.P3,JU.V3,JU.P3,JU.V3,JU.P4");
c$.projectOntoAxis = $_M(c$, "projectOntoAxis", 
function (point, axisA, axisUnitVector, vectorProjection) {
vectorProjection.sub2 (point, axisA);
var projectedLength = vectorProjection.dot (axisUnitVector);
point.setT (axisUnitVector);
point.scaleAdd (projectedLength, axisA);
vectorProjection.sub2 (point, axisA);
}, "JU.P3,JU.P3,JU.V3,JU.V3");
c$.calcBestAxisThroughPoints = $_M(c$, "calcBestAxisThroughPoints", 
function (points, axisA, axisUnitVector, vectorProjection, nTriesMax) {
var nPoints = points.length;
axisA.setT (points[0]);
axisUnitVector.sub2 (points[nPoints - 1], axisA);
axisUnitVector.normalize ();
J.util.Measure.calcAveragePointN (points, nPoints, axisA);
var nTries = 0;
while (nTries++ < nTriesMax && J.util.Measure.findAxis (points, nPoints, axisA, axisUnitVector, vectorProjection) > 0.001) {
}
var tempA = JU.P3.newP (points[0]);
J.util.Measure.projectOntoAxis (tempA, axisA, axisUnitVector, vectorProjection);
axisA.setT (tempA);
}, "~A,JU.P3,JU.V3,JU.V3,~N");
c$.findAxis = $_M(c$, "findAxis", 
function (points, nPoints, axisA, axisUnitVector, vectorProjection) {
var sumXiYi =  new JU.V3 ();
var vTemp =  new JU.V3 ();
var pt =  new JU.P3 ();
var ptProj =  new JU.P3 ();
var a = JU.V3.newV (axisUnitVector);
var sum_Xi2 = 0;
var sum_Yi2 = 0;
for (var i = nPoints; --i >= 0; ) {
pt.setT (points[i]);
ptProj.setT (pt);
J.util.Measure.projectOntoAxis (ptProj, axisA, axisUnitVector, vectorProjection);
vTemp.sub2 (pt, ptProj);
sum_Yi2 += vTemp.lengthSquared ();
vTemp.cross (vectorProjection, vTemp);
sumXiYi.add (vTemp);
sum_Xi2 += vectorProjection.lengthSquared ();
}
var m = JU.V3.newV (sumXiYi);
m.scale (1 / sum_Xi2);
vTemp.cross (m, axisUnitVector);
axisUnitVector.add (vTemp);
axisUnitVector.normalize ();
vTemp.setT (axisUnitVector);
vTemp.sub (a);
return vTemp.length ();
}, "~A,~N,JU.P3,JU.V3,JU.V3");
c$.calcAveragePoint = $_M(c$, "calcAveragePoint", 
function (pointA, pointB, pointC) {
pointC.set ((pointA.x + pointB.x) / 2, (pointA.y + pointB.y) / 2, (pointA.z + pointB.z) / 2);
}, "JU.P3,JU.P3,JU.P3");
c$.calcAveragePointN = $_M(c$, "calcAveragePointN", 
function (points, nPoints, averagePoint) {
averagePoint.setT (points[0]);
for (var i = 1; i < nPoints; i++) averagePoint.add (points[i]);

averagePoint.scale (1 / nPoints);
}, "~A,~N,JU.P3");
c$.getCenterAndPoints = $_M(c$, "getCenterAndPoints", 
function (vPts) {
var n = vPts.size ();
var pts =  new Array (n + 1);
pts[0] =  new JU.P3 ();
if (n > 0) {
for (var i = 0; i < n; i++) {
pts[0].add (pts[i + 1] = vPts.get (i));
}
pts[0].scale (1 / n);
}return pts;
}, "JU.List");
c$.getTransformMatrix4 = $_M(c$, "getTransformMatrix4", 
function (ptsA, ptsB, m, centerA) {
var cptsA = J.util.Measure.getCenterAndPoints (ptsA);
var cptsB = J.util.Measure.getCenterAndPoints (ptsB);
var retStddev =  Clazz_newFloatArray (2, 0);
var q = J.util.Measure.calculateQuaternionRotation ([cptsA, cptsB], retStddev, true);
var v = JU.V3.newV (cptsB[0]);
v.sub (cptsA[0]);
m.setMV (q.getMatrix (), v);
if (centerA != null) centerA.setT (cptsA[0]);
return retStddev[1];
}, "JU.List,JU.List,JU.M4,JU.P3");
c$.calculateQuaternionRotation = $_M(c$, "calculateQuaternionRotation", 
function (centerAndPoints, retStddev, doReport) {
retStddev[1] = NaN;
var q =  new J.util.Quaternion ();
if (centerAndPoints[0].length == 1 || centerAndPoints[0].length != centerAndPoints[1].length) return q;
var n = centerAndPoints[0].length - 1;
if (doReport) for (var i = 1; i <= n; i++) {
var aij = centerAndPoints[0][i];
var bij = centerAndPoints[1][i];
if (Clazz_instanceOf (aij, J.modelset.Atom) && Clazz_instanceOf (bij, J.modelset.Atom)) J.util.Logger.info (" atom 1 " + (aij).getInfo () + "\tatom 2 " + (bij).getInfo ());
 else break;
}
if (n < 2) return q;
var Sxx = 0;
var Sxy = 0;
var Sxz = 0;
var Syx = 0;
var Syy = 0;
var Syz = 0;
var Szx = 0;
var Szy = 0;
var Szz = 0;
var ptA =  new JU.P3 ();
var ptB =  new JU.P3 ();
for (var i = n + 1; --i >= 1; ) {
var aij = centerAndPoints[0][i];
var bij = centerAndPoints[1][i];
ptA.setT (aij);
ptA.sub (centerAndPoints[0][0]);
ptB.setT (bij);
ptB.sub (centerAndPoints[0][1]);
Sxx += ptA.x * ptB.x;
Sxy += ptA.x * ptB.y;
Sxz += ptA.x * ptB.z;
Syx += ptA.y * ptB.x;
Syy += ptA.y * ptB.y;
Syz += ptA.y * ptB.z;
Szx += ptA.z * ptB.x;
Szy += ptA.z * ptB.y;
Szz += ptA.z * ptB.z;
}
retStddev[0] = J.util.Measure.getRmsd (centerAndPoints, q);
var N =  Clazz_newDoubleArray (4, 4, 0);
N[0][0] = Sxx + Syy + Szz;
N[0][1] = N[1][0] = Syz - Szy;
N[0][2] = N[2][0] = Szx - Sxz;
N[0][3] = N[3][0] = Sxy - Syx;
N[1][1] = Sxx - Syy - Szz;
N[1][2] = N[2][1] = Sxy + Syx;
N[1][3] = N[3][1] = Szx + Sxz;
N[2][2] = -Sxx + Syy - Szz;
N[2][3] = N[3][2] = Syz + Szy;
N[3][3] = -Sxx - Syy + Szz;
var eigen = (J.api.Interface.getOptionInterface ("util.Eigen")).newM (N);
var v = eigen.getEigenvectorsFloatTransposed ()[3];
q = J.util.Quaternion.newP4 (JU.P4.new4 (v[1], v[2], v[3], v[0]));
retStddev[1] = J.util.Measure.getRmsd (centerAndPoints, q);
return q;
}, "~A,~A,~B");
c$.getRmsd = $_M(c$, "getRmsd", 
function (centerAndPoints, q) {
var sum2 = 0;
var ptsA = centerAndPoints[0];
var ptsB = centerAndPoints[1];
var cA = ptsA[0];
var cB = ptsB[0];
var n = ptsA.length - 1;
var ptAnew =  new JU.P3 ();
for (var i = n + 1; --i >= 1; ) {
ptAnew.setT (ptsA[i]);
ptAnew.sub (cA);
q.transformP2 (ptAnew, ptAnew).add (cB);
sum2 += ptAnew.distanceSquared (ptsB[i]);
}
return Math.sqrt (sum2 / n);
}, "~A,J.util.Quaternion");
c$.transformPoints = $_M(c$, "transformPoints", 
function (vPts, m4, center) {
var v =  new JU.List ();
for (var i = 0; i < vPts.size (); i++) {
var pt = JU.P3.newP (vPts.get (i));
pt.sub (center);
m4.transform2 (pt, pt);
pt.add (center);
v.addLast (pt);
}
return v;
}, "JU.List,JU.M4,JU.P3");
c$.isInTetrahedron = $_M(c$, "isInTetrahedron", 
function (pt, ptA, ptB, ptC, ptD, plane, vTemp, vTemp2, vTemp3, fullyEnclosed) {
J.util.Measure.getPlaneThroughPoints (ptC, ptD, ptA, vTemp, vTemp2, vTemp3, plane);
var b = (J.util.Measure.distanceToPlane (plane, pt) >= 0);
J.util.Measure.getPlaneThroughPoints (ptA, ptD, ptB, vTemp, vTemp2, vTemp3, plane);
if (b != (J.util.Measure.distanceToPlane (plane, pt) >= 0)) return false;
J.util.Measure.getPlaneThroughPoints (ptB, ptD, ptC, vTemp, vTemp2, vTemp3, plane);
if (b != (J.util.Measure.distanceToPlane (plane, pt) >= 0)) return false;
J.util.Measure.getPlaneThroughPoints (ptA, ptB, ptC, vTemp, vTemp2, vTemp3, plane);
var d = J.util.Measure.distanceToPlane (plane, pt);
if (fullyEnclosed) return (b == (d >= 0));
var d1 = J.util.Measure.distanceToPlane (plane, ptD);
return d1 * d <= 0 || Math.abs (d1) > Math.abs (d);
}, "JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P4,JU.V3,JU.V3,JU.V3,~B");
c$.getIntersectionPP = $_M(c$, "getIntersectionPP", 
function (plane1, plane2) {
var a1 = plane1.x;
var b1 = plane1.y;
var c1 = plane1.z;
var d1 = plane1.w;
var a2 = plane2.x;
var b2 = plane2.y;
var c2 = plane2.z;
var d2 = plane2.w;
var norm1 = JU.V3.new3 (a1, b1, c1);
var norm2 = JU.V3.new3 (a2, b2, c2);
var nxn =  new JU.V3 ();
nxn.cross (norm1, norm2);
var ax = Math.abs (nxn.x);
var ay = Math.abs (nxn.y);
var az = Math.abs (nxn.z);
var x;
var y;
var z;
var diff;
var type = (ax > ay ? (ax > az ? 1 : 3) : ay > az ? 2 : 3);
switch (type) {
case 1:
x = 0;
diff = (b1 * c2 - b2 * c1);
if (Math.abs (diff) < 0.01) return null;
y = (c1 * d2 - c2 * d1) / diff;
z = (b2 * d1 - d2 * b1) / diff;
break;
case 2:
diff = (a1 * c2 - a2 * c1);
if (Math.abs (diff) < 0.01) return null;
x = (c1 * d2 - c2 * d1) / diff;
y = 0;
z = (a2 * d1 - d2 * a1) / diff;
break;
case 3:
default:
diff = (a1 * b2 - a2 * b1);
if (Math.abs (diff) < 0.01) return null;
x = (b1 * d2 - b2 * d1) / diff;
y = (a2 * d1 - d2 * a1) / diff;
z = 0;
}
var list =  new JU.List ();
list.addLast (JU.P3.new3 (x, y, z));
nxn.normalize ();
list.addLast (nxn);
return list;
}, "JU.P4,JU.P4");
c$.getIntersection = $_M(c$, "getIntersection", 
function (pt1, v, plane, ptRet, tempNorm, vTemp) {
J.util.Measure.getPlaneProjection (pt1, plane, ptRet, tempNorm);
tempNorm.set (plane.x, plane.y, plane.z);
tempNorm.normalize ();
if (v == null) v = JU.V3.newV (tempNorm);
var l_dot_n = v.dot (tempNorm);
if (Math.abs (l_dot_n) < 0.01) return null;
vTemp.setT (ptRet);
vTemp.sub (pt1);
ptRet.scaleAdd2 (vTemp.dot (tempNorm) / l_dot_n, v, pt1);
return ptRet;
}, "JU.P3,JU.V3,JU.P4,JU.P3,JU.V3,JU.V3");
Clazz_defineStatics (c$,
"radiansPerDegree", (0.017453292519943295));
});
Clazz_declarePackage ("J.script");
Clazz_load (["J.script.T", "JU.P3"], "J.script.SV", ["java.lang.Boolean", "$.Float", "java.util.Arrays", "$.Collections", "$.Hashtable", "JU.BS", "$.List", "$.PT", "$.SB", "J.modelset.Bond", "J.util.BSUtil", "$.Escape", "$.Measure", "$.Txt"], function () {
c$ = Clazz_decorateAsClass (function () {
this.index = 2147483647;
this.flags = 2;
this.myName = null;
if (!Clazz_isClassDefined ("J.script.SV.Sort")) {
J.script.SV.$SV$Sort$ ();
}
Clazz_instantialize (this, arguments);
}, J.script, "SV", J.script.T);
c$.newVariable = $_M(c$, "newVariable", 
function (tok, value) {
var sv =  new J.script.SV ();
sv.tok = tok;
sv.value = value;
return sv;
}, "~N,~O");
c$.newScriptVariableInt = $_M(c$, "newScriptVariableInt", 
function (i) {
var sv =  new J.script.SV ();
sv.tok = 2;
sv.intValue = i;
return sv;
}, "~N");
c$.newScriptVariableBs = $_M(c$, "newScriptVariableBs", 
function (bs, index) {
var sv = J.script.SV.newVariable (10, bs);
if (index >= 0) sv.index = index;
return sv;
}, "JU.BS,~N");
c$.newScriptVariableToken = $_M(c$, "newScriptVariableToken", 
function (x) {
return J.script.SV.newScriptVariableIntValue (x.tok, x.intValue, x.value);
}, "J.script.T");
c$.newScriptVariableIntValue = $_M(c$, "newScriptVariableIntValue", 
function (tok, intValue, value) {
var sv = J.script.SV.newVariable (tok, value);
sv.intValue = intValue;
return sv;
}, "~N,~N,~O");
c$.sizeOf = $_M(c$, "sizeOf", 
function (x) {
switch (x == null ? 0 : x.tok) {
case 10:
return J.util.BSUtil.cardinalityOf (J.script.SV.bsSelectToken (x));
case 1048589:
case 1048588:
return -1;
case 2:
return -2;
case 3:
return -4;
case 8:
return -8;
case 9:
return -16;
case 11:
return -32;
case 12:
return -64;
case 4:
return (x.value).length;
case 7:
return x.intValue == 2147483647 ? (x).getList ().size () : J.script.SV.sizeOf (J.script.SV.selectItemTok (x));
case 6:
return (x.value).size ();
default:
return 0;
}
}, "J.script.T");
c$.isVariableType = $_M(c$, "isVariableType", 
function (x) {
return (Clazz_instanceOf (x, J.script.SV) || Clazz_instanceOf (x, JU.BS) || Clazz_instanceOf (x, Boolean) || Clazz_instanceOf (x, Float) || Clazz_instanceOf (x, Integer) || Clazz_instanceOf (x, String) || Clazz_instanceOf (x, JU.P3) || Clazz_instanceOf (x, JU.V3) || Clazz_instanceOf (x, JU.P4) || Clazz_instanceOf (x, J.util.Quaternion) || Clazz_instanceOf (x, java.util.Map) || J.script.SV.isArray (x));
}, "~O");
c$.getVariable = $_M(c$, "getVariable", 
function (x) {
if (x == null) return J.script.SV.newVariable (4, "");
if (Clazz_instanceOf (x, J.script.SV)) return x;
if (Clazz_instanceOf (x, Boolean)) return J.script.SV.getBoolean ((x).booleanValue ());
if (Clazz_instanceOf (x, Integer)) return J.script.SV.newScriptVariableInt ((x).intValue ());
if (Clazz_instanceOf (x, Float)) return J.script.SV.newVariable (3, x);
if (Clazz_instanceOf (x, String)) {
x = J.script.SV.unescapePointOrBitsetAsVariable (x);
if (Clazz_instanceOf (x, J.script.SV)) return x;
return J.script.SV.newVariable (4, x);
}if (Clazz_instanceOf (x, JU.P3)) return J.script.SV.newVariable (8, x);
if (Clazz_instanceOf (x, JU.V3)) return J.script.SV.newVariable (8, JU.P3.newP (x));
if (Clazz_instanceOf (x, JU.BS)) return J.script.SV.newVariable (10, x);
if (Clazz_instanceOf (x, JU.P4)) return J.script.SV.newVariable (9, x);
if (Clazz_instanceOf (x, J.util.Quaternion)) return J.script.SV.newVariable (9, (x).toPoint4f ());
if (Clazz_instanceOf (x, JU.M3)) return J.script.SV.newVariable (11, x);
if (Clazz_instanceOf (x, JU.M4)) return J.script.SV.newVariable (12, x);
if (Clazz_instanceOf (x, java.util.Map)) return J.script.SV.getVariableMap (x);
if (Clazz_instanceOf (x, JU.List)) return J.script.SV.getVariableList (x);
if (J.util.Escape.isAV (x)) return J.script.SV.getVariableAV (x);
if (JU.PT.isAI (x)) return J.script.SV.getVariableAI (x);
if (JU.PT.isAB (x)) return J.script.SV.getVariableAB (x);
if (JU.PT.isAF (x)) return J.script.SV.getVariableAF (x);
if (JU.PT.isAD (x)) return J.script.SV.getVariableAD (x);
if (JU.PT.isAS (x)) return J.script.SV.getVariableAS (x);
if (JU.PT.isAP (x)) return J.script.SV.getVariableAP (x);
if (JU.PT.isAII (x)) return J.script.SV.getVariableAII (x);
if (JU.PT.isAFF (x)) return J.script.SV.getVariableAFF (x);
if (JU.PT.isAFloat (x)) return J.script.SV.newVariable (13, x);
return J.script.SV.newVariable (4, J.util.Escape.toReadable (null, x));
}, "~O");
c$.isArray = $_M(c$, "isArray", 
function (x) {
{
return Clazz_instanceOf(x, Array);
}}, "~O");
c$.getVariableMap = $_M(c$, "getVariableMap", 
function (x) {
var ht = x;
var o = null;
for (var oo, $oo = ht.values ().iterator (); $oo.hasNext () && ((oo = $oo.next ()) || true);) {
o = oo;
break;
}
if (!(Clazz_instanceOf (o, J.script.SV))) {
var x2 =  new java.util.Hashtable ();
for (var entry, $entry = ht.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) {
var key = entry.getKey ();
o = entry.getValue ();
x2.put (key, J.script.SV.isVariableType (o) ? J.script.SV.getVariable (o) : J.script.SV.newVariable (4, J.util.Escape.toReadable (null, o)));
}
x = x2;
}return J.script.SV.newVariable (6, x);
}, "java.util.Map");
c$.getVariableList = $_M(c$, "getVariableList", 
function (v) {
var len = v.size ();
if (len > 0 && Clazz_instanceOf (v.get (0), J.script.SV)) return J.script.SV.newVariable (7, v);
var objects =  new JU.List ();
for (var i = 0; i < len; i++) objects.addLast (J.script.SV.getVariable (v.get (i)));

return J.script.SV.newVariable (7, objects);
}, "JU.List");
c$.getVariableAV = $_M(c$, "getVariableAV", 
function (v) {
var objects =  new JU.List ();
for (var i = 0; i < v.length; i++) objects.addLast (v[i]);

return J.script.SV.newVariable (7, objects);
}, "~A");
c$.getVariableAD = $_M(c$, "getVariableAD", 
function (f) {
var objects =  new JU.List ();
for (var i = 0; i < f.length; i++) objects.addLast (J.script.SV.newVariable (3, Float.$valueOf (f[i])));

return J.script.SV.newVariable (7, objects);
}, "~A");
c$.getVariableAS = $_M(c$, "getVariableAS", 
function (s) {
var objects =  new JU.List ();
for (var i = 0; i < s.length; i++) objects.addLast (J.script.SV.newVariable (4, s[i]));

return J.script.SV.newVariable (7, objects);
}, "~A");
c$.getVariableAP = $_M(c$, "getVariableAP", 
function (p) {
var objects =  new JU.List ();
for (var i = 0; i < p.length; i++) objects.addLast (J.script.SV.newVariable (8, p[i]));

return J.script.SV.newVariable (7, objects);
}, "~A");
c$.getVariableAFF = $_M(c$, "getVariableAFF", 
function (fx) {
var objects =  new JU.List ();
for (var i = 0; i < fx.length; i++) objects.addLast (J.script.SV.getVariableAF (fx[i]));

return J.script.SV.newVariable (7, objects);
}, "~A");
c$.getVariableAII = $_M(c$, "getVariableAII", 
function (ix) {
var objects =  new JU.List ();
for (var i = 0; i < ix.length; i++) objects.addLast (J.script.SV.getVariableAI (ix[i]));

return J.script.SV.newVariable (7, objects);
}, "~A");
c$.getVariableAF = $_M(c$, "getVariableAF", 
function (f) {
var objects =  new JU.List ();
for (var i = 0; i < f.length; i++) objects.addLast (J.script.SV.newVariable (3, Float.$valueOf (f[i])));

return J.script.SV.newVariable (7, objects);
}, "~A");
c$.getVariableAI = $_M(c$, "getVariableAI", 
function (ix) {
var objects =  new JU.List ();
for (var i = 0; i < ix.length; i++) objects.addLast (J.script.SV.newScriptVariableInt (ix[i]));

return J.script.SV.newVariable (7, objects);
}, "~A");
c$.getVariableAB = $_M(c$, "getVariableAB", 
function (ix) {
var objects =  new JU.List ();
for (var i = 0; i < ix.length; i++) objects.addLast (J.script.SV.newScriptVariableInt (ix[i]));

return J.script.SV.newVariable (7, objects);
}, "~A");
$_M(c$, "setv", 
function (v, asCopy) {
this.index = v.index;
this.intValue = v.intValue;
this.tok = v.tok;
this.value = v.value;
if (asCopy) {
switch (this.tok) {
case 6:
this.value =  new java.util.Hashtable (v.value);
break;
case 7:
var o2 =  new JU.List ();
var o1 = v.getList ();
for (var i = 0; i < o1.size (); i++) o2.addLast (o1.get (i));

this.value = o2;
break;
}
}return this;
}, "J.script.SV,~B");
$_M(c$, "setName", 
function (name) {
this.myName = name;
this.flags |= 1;
return this;
}, "~S");
$_M(c$, "setGlobal", 
function () {
this.flags &= -3;
return this;
});
$_M(c$, "canIncrement", 
function () {
return J.script.T.tokAttr (this.flags, 1);
});
$_M(c$, "increment", 
function (n) {
if (!this.canIncrement ()) return false;
switch (this.tok) {
case 2:
this.intValue += n;
break;
case 3:
this.value = Float.$valueOf ((this.value).floatValue () + n);
break;
default:
this.value = J.script.SV.nValue (this);
if (Clazz_instanceOf (this.value, Integer)) {
this.tok = 2;
this.intValue = (this.value).intValue ();
} else {
this.tok = 3;
}}
return true;
}, "~N");
$_M(c$, "asBoolean", 
function () {
return J.script.SV.bValue (this);
});
$_M(c$, "asInt", 
function () {
return J.script.SV.iValue (this);
});
$_M(c$, "asFloat", 
function () {
return J.script.SV.fValue (this);
});
$_M(c$, "asString", 
function () {
return J.script.SV.sValue (this);
});
c$.oValue = $_M(c$, "oValue", 
function (x) {
switch (x == null ? 0 : x.tok) {
case 1048589:
return Boolean.TRUE;
case 0:
case 1048588:
return Boolean.FALSE;
case 2:
return Integer.$valueOf (x.intValue);
case 10:
case 135266306:
return J.script.SV.selectItemVar (x).value;
default:
return x.value;
}
}, "J.script.SV");
c$.nValue = $_M(c$, "nValue", 
function (x) {
var iValue;
switch (x == null ? 0 : x.tok) {
case 3:
return x.value;
case 2:
iValue = x.intValue;
break;
case 4:
if ((x.value).indexOf (".") >= 0) return Float.$valueOf (J.script.SV.toFloat (x.value));
iValue = Clazz_floatToInt (J.script.SV.toFloat (x.value));
break;
default:
iValue = 0;
}
return Integer.$valueOf (iValue);
}, "J.script.T");
c$.bValue = $_M(c$, "bValue", 
function (x) {
switch (x == null ? 0 : x.tok) {
case 1048589:
case 6:
return true;
case 1048588:
return false;
case 2:
return x.intValue != 0;
case 3:
case 4:
case 7:
return J.script.SV.fValue (x) != 0;
case 10:
return J.script.SV.iValue (x) != 0;
case 8:
case 9:
case 11:
case 12:
return Math.abs (J.script.SV.fValue (x)) > 0.0001;
default:
return false;
}
}, "J.script.T");
c$.iValue = $_M(c$, "iValue", 
function (x) {
switch (x == null ? 0 : x.tok) {
case 1048589:
return 1;
case 1048588:
return 0;
case 2:
return x.intValue;
case 3:
case 7:
case 4:
case 8:
case 9:
case 11:
case 12:
return Clazz_floatToInt (J.script.SV.fValue (x));
case 10:
return J.util.BSUtil.cardinalityOf (J.script.SV.bsSelectToken (x));
default:
return 0;
}
}, "J.script.T");
c$.fValue = $_M(c$, "fValue", 
function (x) {
switch (x == null ? 0 : x.tok) {
case 1048589:
return 1;
case 1048588:
return 0;
case 2:
return x.intValue;
case 3:
return (x.value).floatValue ();
case 7:
var i = x.intValue;
if (i == 2147483647) return (x).getList ().size ();
case 4:
return J.script.SV.toFloat (J.script.SV.sValue (x));
case 10:
return J.script.SV.iValue (x);
case 8:
return (x.value).length ();
case 9:
return J.util.Measure.distanceToPlane (x.value, J.script.SV.pt0);
case 11:
var pt =  new JU.P3 ();
(x.value).transform (pt);
return pt.length ();
case 12:
var pt1 =  new JU.P3 ();
(x.value).transform (pt1);
return pt1.length ();
default:
return 0;
}
}, "J.script.T");
c$.sValue = $_M(c$, "sValue", 
function (x) {
if (x == null) return "";
var i;
var sb;
var map;
switch (x.tok) {
case 1048589:
return "true";
case 1048588:
return "false";
case 2:
return "" + x.intValue;
case 10:
var bs = J.script.SV.bsSelectToken (x);
return (Clazz_instanceOf (x.value, J.modelset.Bond.BondSet) ? J.util.Escape.eBond (bs) : J.util.Escape.eBS (bs));
case 7:
var sv = (x).getList ();
i = x.intValue;
if (i <= 0) i = sv.size () - i;
if (i != 2147483647) return (i < 1 || i > sv.size () ? "" : J.script.SV.sValue (sv.get (i - 1)));
case 6:
sb =  new JU.SB ();
map =  new java.util.Hashtable ();
J.script.SV.sValueArray (sb, x, map, 0, false);
return sb.toString ();
case 4:
var s = x.value;
i = x.intValue;
if (i <= 0) i = s.length - i;
if (i == 2147483647) return s;
if (i < 1 || i > s.length) return "";
return "" + s.charAt (i - 1);
case 8:
return J.util.Escape.eP (x.value);
case 9:
return J.util.Escape.eP4 (x.value);
case 11:
case 12:
return J.util.Escape.e (x.value);
default:
return x.value.toString ();
}
}, "J.script.T");
c$.sValueArray = $_M(c$, "sValueArray", 
function (sb, vx, map, level, isEscaped) {
switch (vx.tok) {
case 6:
if (map.containsKey (vx)) {
sb.append (isEscaped ? "{}" : vx.myName == null ? "<circular reference>" : "<" + vx.myName + ">");
break;
}map.put (vx, Boolean.TRUE);
var ht = vx.value;
var keyset = ht.keySet ();
var keys = ht.keySet ().toArray ( new Array (keyset.size ()));
java.util.Arrays.sort (keys);
if (isEscaped) {
sb.append ("{ ");
var sep = "";
for (var i = 0; i < keys.length; i++) {
var key = keys[i];
sb.append (sep).append (J.util.Escape.eS (key)).appendC (':');
J.script.SV.sValueArray (sb, ht.get (key), map, level + 1, true);
sep = ", ";
}
sb.append (" }");
break;
}for (var i = 0; i < keys.length; i++) {
sb.append (keys[i]).append ("\t:");
var v = ht.get (keys[i]);
var sb2 =  new JU.SB ();
J.script.SV.sValueArray (sb2, v, map, level + 1, isEscaped);
var value = sb2.toString ();
sb.append (value.indexOf ("\n") >= 0 ? "\n" : "\t");
sb.append (value).append ("\n");
}
break;
case 7:
if (map.containsKey (vx)) {
sb.append (isEscaped ? "[]" : vx.myName == null ? "<circular reference>" : "<" + vx.myName + ">");
break;
}map.put (vx, Boolean.TRUE);
if (isEscaped) sb.append ("[");
var sx = vx.getList ();
for (var i = 0; i < sx.size (); i++) {
if (isEscaped && i > 0) sb.append (",");
var sv = sx.get (i);
J.script.SV.sValueArray (sb, sv, map, level + 1, isEscaped);
if (!isEscaped) sb.append ("\n");
}
if (isEscaped) sb.append ("]");
break;
default:
if (!isEscaped) for (var j = 0; j < level - 1; j++) sb.append ("\t");

sb.append (isEscaped ? vx.escape () : J.script.SV.sValue (vx));
}
}, "JU.SB,J.script.SV,java.util.Map,~N,~B");
c$.ptValue = $_M(c$, "ptValue", 
function (x) {
switch (x.tok) {
case 8:
return x.value;
case 4:
var o = J.util.Escape.uP (x.value);
if (Clazz_instanceOf (o, JU.P3)) return o;
}
return null;
}, "J.script.SV");
c$.pt4Value = $_M(c$, "pt4Value", 
function (x) {
switch (x.tok) {
case 9:
return x.value;
case 4:
var o = J.util.Escape.uP (x.value);
if (!(Clazz_instanceOf (o, JU.P4))) break;
return o;
}
return null;
}, "J.script.SV");
c$.toFloat = $_M(c$, "toFloat", 
function (s) {
if (s.equalsIgnoreCase ("true")) return 1;
if (s.equalsIgnoreCase ("false") || s.length == 0) return 0;
return JU.PT.parseFloatStrict (s);
}, "~S");
c$.concatList = $_M(c$, "concatList", 
function (x1, x2, asNew) {
var v1 = x1.getList ();
var v2 = x2.getList ();
if (!asNew) {
if (v2 == null) v1.addLast (J.script.SV.newScriptVariableToken (x2));
 else for (var i = 0; i < v2.size (); i++) v1.addLast (v2.get (i));

return x1;
}var vlist =  new JU.List ();
if (v1 == null) vlist.addLast (x1);
 else for (var i = 0; i < v1.size (); i++) vlist.addLast (v1.get (i));

if (v2 == null) vlist.addLast (x2);
 else for (var i = 0; i < v2.size (); i++) vlist.addLast (v2.get (i));

return J.script.SV.getVariableList (vlist);
}, "J.script.SV,J.script.SV,~B");
c$.bsSelectToken = $_M(c$, "bsSelectToken", 
function (x) {
x = J.script.SV.selectItemTok2 (x, -2147483648);
return x.value;
}, "J.script.T");
c$.bsSelectVar = $_M(c$, "bsSelectVar", 
function ($var) {
if ($var.index == 2147483647) $var = J.script.SV.selectItemVar ($var);
return $var.value;
}, "J.script.SV");
c$.bsSelectRange = $_M(c$, "bsSelectRange", 
function (x, n) {
x = J.script.SV.selectItemTok (x);
x = J.script.SV.selectItemTok2 (x, (n <= 0 ? n : 1));
x = J.script.SV.selectItemTok2 (x, (n <= 0 ? 2147483646 : n));
return x.value;
}, "J.script.T,~N");
c$.selectItemVar = $_M(c$, "selectItemVar", 
function ($var) {
if ($var.index != 2147483647 || $var.tok == 7 && $var.intValue == 2147483647) return $var;
return J.script.SV.selectItemVar2 ($var, -2147483648);
}, "J.script.SV");
c$.selectItemTok = $_M(c$, "selectItemTok", 
function ($var) {
return J.script.SV.selectItemTok2 ($var, -2147483648);
}, "J.script.T");
c$.selectItemVar2 = $_M(c$, "selectItemVar2", 
function ($var, i2) {
return J.script.SV.selectItemTok2 ($var, i2);
}, "J.script.SV,~N");
c$.selectItemTok2 = $_M(c$, "selectItemTok2", 
function (tokenIn, i2) {
switch (tokenIn.tok) {
case 11:
case 12:
case 10:
case 7:
case 4:
break;
default:
return tokenIn;
}
var bs = null;
var s = null;
var i1 = tokenIn.intValue;
if (i1 == 2147483647) {
if (i2 == -2147483648) i2 = i1;
var v = J.script.SV.newScriptVariableIntValue (tokenIn.tok, i2, tokenIn.value);
return v;
}var len = 0;
var isInputSelected = (Clazz_instanceOf (tokenIn, J.script.SV) && (tokenIn).index != 2147483647);
var tokenOut = J.script.SV.newScriptVariableIntValue (tokenIn.tok, 2147483647, null);
switch (tokenIn.tok) {
case 10:
if (Clazz_instanceOf (tokenIn.value, J.modelset.Bond.BondSet)) {
bs =  new J.modelset.Bond.BondSet (tokenIn.value, (tokenIn.value).getAssociatedAtoms ());
len = J.util.BSUtil.cardinalityOf (bs);
} else {
bs = J.util.BSUtil.copy (tokenIn.value);
len = (isInputSelected ? 1 : J.util.BSUtil.cardinalityOf (bs));
}break;
case 7:
len = (tokenIn).getList ().size ();
break;
case 4:
s = tokenIn.value;
len = s.length;
break;
case 11:
len = -3;
break;
case 12:
len = -4;
break;
}
if (len < 0) {
len = -len;
if (i1 > 0 && Math.abs (i1) > len) {
var col = i1 % 10;
var row = Clazz_doubleToInt ((i1 - col) / 10);
if (col > 0 && col <= len && row <= len) {
if (tokenIn.tok == 11) return J.script.SV.newVariable (3, Float.$valueOf ((tokenIn.value).getElement (row - 1, col - 1)));
return J.script.SV.newVariable (3, Float.$valueOf ((tokenIn.value).getElement (row - 1, col - 1)));
}return J.script.SV.newVariable (4, "");
}if (Math.abs (i1) > len) return J.script.SV.newVariable (4, "");
var data =  Clazz_newFloatArray (len, 0);
if (len == 3) {
if (i1 < 0) (tokenIn.value).getColumn (-1 - i1, data);
 else (tokenIn.value).getRow (i1 - 1, data);
} else {
if (i1 < 0) (tokenIn.value).getColumn (-1 - i1, data);
 else (tokenIn.value).getRow (i1 - 1, data);
}if (i2 == -2147483648) return J.script.SV.getVariableAF (data);
if (i2 < 1 || i2 > len) return J.script.SV.newVariable (4, "");
return J.script.SV.newVariable (3, Float.$valueOf (data[i2 - 1]));
}if (i1 <= 0) i1 = len + i1;
if (i1 < 1) i1 = 1;
if (i2 == 0) i2 = len;
 else if (i2 < 0) i2 = len + i2;
if (i2 > len) i2 = len;
 else if (i2 < i1) i2 = i1;
switch (tokenIn.tok) {
case 10:
tokenOut.value = bs;
if (isInputSelected) {
if (i1 > 1) bs.clearAll ();
break;
}var n = 0;
for (var j = bs.nextSetBit (0); j >= 0; j = bs.nextSetBit (j + 1)) if (++n < i1 || n > i2) bs.clear (j);

break;
case 4:
if (i1 < 1 || i1 > len) tokenOut.value = "";
 else tokenOut.value = s.substring (i1 - 1, i2);
break;
case 7:
if (i1 < 1 || i1 > len || i2 > len) return J.script.SV.newVariable (4, "");
if (i2 == i1) return (tokenIn).getList ().get (i1 - 1);
var o2 =  new JU.List ();
var o1 = (tokenIn).getList ();
n = i2 - i1 + 1;
for (var i = 0; i < n; i++) o2.addLast (J.script.SV.newScriptVariableToken (o1.get (i + i1 - 1)));

tokenOut.value = o2;
break;
}
return tokenOut;
}, "J.script.T,~N");
$_M(c$, "setSelectedValue", 
function (selector, $var) {
if (selector == 2147483647) return false;
var len;
switch (this.tok) {
case 11:
case 12:
len = (this.tok == 11 ? 3 : 4);
if (selector > 10) {
var col = selector % 10;
var row = Clazz_doubleToInt ((selector - col) / 10);
if (col > 0 && col <= len && row <= len) {
if (this.tok == 11) (this.value).setElement (row - 1, col - 1, J.script.SV.fValue ($var));
 else (this.value).setElement (row - 1, col - 1, J.script.SV.fValue ($var));
return true;
}}if (selector != 0 && Math.abs (selector) <= len && $var.tok == 7) {
var sv = $var.getList ();
if (sv.size () == len) {
var data =  Clazz_newFloatArray (len, 0);
for (var i = 0; i < len; i++) data[i] = J.script.SV.fValue (sv.get (i));

if (selector > 0) {
if (this.tok == 11) (this.value).setRowA (selector - 1, data);
 else (this.value).setRow (selector - 1, data);
} else {
if (this.tok == 11) (this.value).setColumnA (-1 - selector, data);
 else (this.value).setColumn (-1 - selector, data);
}return true;
}}return false;
case 4:
var str = this.value;
var pt = str.length;
if (selector <= 0) selector = pt + selector;
if (--selector < 0) selector = 0;
while (selector >= str.length) str += " ";

this.value = str.substring (0, selector) + J.script.SV.sValue ($var) + str.substring (selector + 1);
return true;
case 7:
len = this.getList ().size ();
if (selector <= 0) selector = len + selector;
if (--selector < 0) selector = 0;
if (len <= selector) {
for (var i = len; i <= selector; i++) this.getList ().addLast (J.script.SV.newVariable (4, ""));

}this.getList ().set (selector, $var);
return true;
}
return false;
}, "~N,J.script.SV");
$_M(c$, "escape", 
function () {
switch (this.tok) {
case 4:
return J.util.Escape.eS (this.value);
case 7:
case 6:
var sb =  new JU.SB ();
var map =  new java.util.Hashtable ();
J.script.SV.sValueArray (sb, this, map, 0, true);
return sb.toString ();
default:
return J.script.SV.sValue (this);
}
});
c$.unescapePointOrBitsetAsVariable = $_M(c$, "unescapePointOrBitsetAsVariable", 
function (o) {
if (o == null) return o;
var v = null;
var s = null;
if (Clazz_instanceOf (o, J.script.SV)) {
var sv = o;
switch (sv.tok) {
case 8:
case 9:
case 11:
case 12:
case 10:
v = sv.value;
break;
case 4:
s = sv.value;
break;
default:
s = J.script.SV.sValue (sv);
break;
}
} else if (Clazz_instanceOf (o, String)) {
s = o;
}if (s != null && s.length == 0) return s;
if (v == null) v = J.util.Escape.uABsM (s);
if (Clazz_instanceOf (v, JU.P3)) return (J.script.SV.newVariable (8, v));
if (Clazz_instanceOf (v, JU.P4)) return J.script.SV.newVariable (9, v);
if (Clazz_instanceOf (v, JU.BS)) {
if (s != null && s.indexOf ("[{") == 0) v =  new J.modelset.Bond.BondSet (v);
return J.script.SV.newVariable (10, v);
}if (Clazz_instanceOf (v, JU.M3)) return (J.script.SV.newVariable (11, v));
if (Clazz_instanceOf (v, JU.M4)) return J.script.SV.newVariable (12, v);
return o;
}, "~O");
c$.getBoolean = $_M(c$, "getBoolean", 
function (value) {
return J.script.SV.newScriptVariableToken (value ? J.script.SV.vT : J.script.SV.vF);
}, "~B");
c$.sprintf = $_M(c$, "sprintf", 
function (strFormat, $var) {
if ($var == null) return strFormat;
var vd = (strFormat.indexOf ("d") >= 0 || strFormat.indexOf ("i") >= 0 ?  Clazz_newIntArray (1, 0) : null);
var vf = (strFormat.indexOf ("f") >= 0 ?  Clazz_newFloatArray (1, 0) : null);
var ve = (strFormat.indexOf ("e") >= 0 ?  Clazz_newDoubleArray (1, 0) : null);
var getS = (strFormat.indexOf ("s") >= 0);
var getP = (strFormat.indexOf ("p") >= 0 && $var.tok == 8);
var getQ = (strFormat.indexOf ("q") >= 0 && $var.tok == 9);
var of = [vd, vf, ve, null, null, null];
if ($var.tok != 7) return J.script.SV.sprintf (strFormat, $var, of, vd, vf, ve, getS, getP, getQ);
var sv = $var.getList ();
var list2 =  new Array (sv.size ());
for (var i = 0; i < list2.length; i++) list2[i] = J.script.SV.sprintf (strFormat, sv.get (i), of, vd, vf, ve, getS, getP, getQ);

return list2;
}, "~S,J.script.SV");
c$.sprintf = $_M(c$, "sprintf", 
function (strFormat, $var, of, vd, vf, ve, getS, getP, getQ) {
if (vd != null) vd[0] = J.script.SV.iValue ($var);
if (vf != null) vf[0] = J.script.SV.fValue ($var);
if (ve != null) ve[0] = J.script.SV.fValue ($var);
if (getS) of[3] = J.script.SV.sValue ($var);
if (getP) of[4] = $var.value;
if (getQ) of[5] = $var.value;
return J.util.Txt.sprintf (strFormat, "IFDspq", of);
}, "~S,J.script.SV,~A,~A,~A,~A,~B,~B,~B");
c$.sprintfArray = $_M(c$, "sprintfArray", 
function (args) {
switch (args.length) {
case 0:
return "";
case 1:
return J.script.SV.sValue (args[0]);
}
var format = JU.PT.split (JU.PT.simpleReplace (J.script.SV.sValue (args[0]), "%%", "\1"), "%");
var sb =  new JU.SB ();
sb.append (format[0]);
for (var i = 1; i < format.length; i++) {
var ret = J.script.SV.sprintf (J.util.Txt.formatCheck ("%" + format[i]), (i < args.length ? args[i] : null));
if (JU.PT.isAS (ret)) {
var list = ret;
for (var j = 0; j < list.length; j++) sb.append (list[j]).append ("\n");

continue;
}sb.append (ret);
}
return sb.toString ();
}, "~A");
$_V(c$, "toString", 
function () {
return this.toString2 () + "[" + this.myName + " index =" + this.index + " intValue=" + this.intValue + "]";
});
c$.getBitSet = $_M(c$, "getBitSet", 
function (x, allowNull) {
switch (x.tok) {
case 10:
return J.script.SV.bsSelectVar (x);
case 7:
var bs =  new JU.BS ();
var sv = x.value;
for (var i = 0; i < sv.size (); i++) if (!sv.get (i).unEscapeBitSetArray (bs) && allowNull) return null;

return bs;
}
return (allowNull ? null :  new JU.BS ());
}, "J.script.SV,~B");
c$.areEqual = $_M(c$, "areEqual", 
function (x1, x2) {
if (x1 == null || x2 == null) return false;
if (x1.tok == 4 && x2.tok == 4) return J.script.SV.sValue (x1).equalsIgnoreCase (J.script.SV.sValue (x2));
if (x1.tok == 8 && x2.tok == 8) return ((x1.value).distance (x2.value) < 0.000001);
if (x1.tok == 9 && x2.tok == 9) return ((x1.value).distance (x2.value) < 0.000001);
return (Math.abs (J.script.SV.fValue (x1) - J.script.SV.fValue (x2)) < 0.000001);
}, "J.script.SV,J.script.SV");
$_M(c$, "sortOrReverse", 
function (arrayPt) {
var x = this.getList ();
if (x == null || x.size () < 2) return this;
if (arrayPt == -2147483648) {
var n = x.size ();
for (var i = 0; i < n; i++) {
var v = x.get (i);
x.set (i, x.get (--n));
x.set (n, v);
}
} else {
java.util.Collections.sort (this.getList (), Clazz_innerTypeInstance (J.script.SV.Sort, this, null, --arrayPt));
}return this;
}, "~N");
$_M(c$, "unEscapeBitSetArray", 
function (bs) {
switch (this.tok) {
case 4:
var bs1 = J.util.Escape.uB (this.value);
if (bs1 == null) return false;
bs.or (bs1);
return true;
case 10:
bs.or (this.value);
return true;
}
return false;
}, "JU.BS");
c$.unEscapeBitSetArray = $_M(c$, "unEscapeBitSetArray", 
function (x, allowNull) {
var bs =  new JU.BS ();
for (var i = 0; i < x.size (); i++) if (!x.get (i).unEscapeBitSetArray (bs) && allowNull) return null;

return bs;
}, "java.util.ArrayList,~B");
c$.listValue = $_M(c$, "listValue", 
function (x) {
if (x.tok != 7) return [J.script.SV.sValue (x)];
var sv = (x).getList ();
var list =  new Array (sv.size ());
for (var i = sv.size (); --i >= 0; ) list[i] = J.script.SV.sValue (sv.get (i));

return list;
}, "J.script.T");
c$.listAny = $_M(c$, "listAny", 
function (x) {
var list =  new JU.List ();
var l = x.getList ();
for (var i = 0; i < l.size (); i++) {
var v = l.get (i);
var l2 = v.getList ();
if (l2 == null) {
list.addLast (v.value);
} else {
var o =  new JU.List ();
for (var j = 0; j < l2.size (); j++) {
v = l2.get (j);
}
list.addLast (o);
}}
return list;
}, "J.script.SV");
c$.flistValue = $_M(c$, "flistValue", 
function (x, nMin) {
if (x.tok != 7) return [J.script.SV.fValue (x)];
var sv = (x).getList ();
var list;
list =  Clazz_newFloatArray (Math.max (nMin, sv.size ()), 0);
if (nMin == 0) nMin = list.length;
for (var i = Math.min (sv.size (), nMin); --i >= 0; ) list[i] = J.script.SV.fValue (sv.get (i));

return list;
}, "J.script.T,~N");
$_M(c$, "toArray", 
function () {
var dim;
var m3 = null;
var m4 = null;
switch (this.tok) {
case 11:
m3 = this.value;
dim = 3;
break;
case 12:
m4 = this.value;
dim = 4;
break;
default:
return;
}
this.tok = 7;
var o2 =  new JU.List ();
for (var i = 0; i < dim; i++) {
var a =  Clazz_newFloatArray (dim, 0);
if (m3 == null) m4.getRow (i, a);
 else m3.getRow (i, a);
o2.set (i, J.script.SV.getVariableAF (a));
}
this.value = o2;
});
$_M(c$, "mapValue", 
function (key) {
return (this.tok == 6 ? (this.value).get (key) : null);
}, "~S");
$_M(c$, "getList", 
function () {
return (this.tok == 7 ? this.value : null);
});
c$.$SV$Sort$ = function () {
Clazz_pu$h ();
c$ = Clazz_decorateAsClass (function () {
Clazz_prepareCallback (this, arguments);
this.arrayPt = 0;
Clazz_instantialize (this, arguments);
}, J.script.SV, "Sort", null, java.util.Comparator);
Clazz_makeConstructor (c$, 
function (a) {
this.arrayPt = a;
}, "~N");
$_V(c$, "compare", 
function (a, b) {
if (a.tok != b.tok) {
if (a.tok == 3 || a.tok == 2 || b.tok == 3 || b.tok == 2) {
var c = J.script.SV.fValue (a);
var d = J.script.SV.fValue (b);
return (c < d ? -1 : c > d ? 1 : 0);
}if (a.tok == 4 || b.tok == 4) return J.script.SV.sValue (a).compareTo (J.script.SV.sValue (b));
}switch (a.tok) {
case 4:
return J.script.SV.sValue (a).compareTo (J.script.SV.sValue (b));
case 7:
var c = a.getList ();
var d = b.getList ();
if (c.size () != d.size ()) return (c.size () < d.size () ? -1 : 1);
var e = this.arrayPt;
if (e < 0) e += c.size ();
if (e < 0 || e >= c.size ()) return 0;
return this.compare (c.get (e), d.get (e));
default:
var f = J.script.SV.fValue (a);
var g = J.script.SV.fValue (b);
return (f < g ? -1 : f > g ? 1 : 0);
}
}, "J.script.SV,J.script.SV");
c$ = Clazz_p0p ();
};
c$.vT = c$.prototype.vT = J.script.SV.newScriptVariableIntValue (1048589, 1, "true");
c$.vF = c$.prototype.vF = J.script.SV.newScriptVariableIntValue (1048588, 0, "false");
Clazz_defineStatics (c$,
"FLAG_CANINCREMENT", 1,
"FLAG_LOCALVAR", 2);
c$.pt0 = c$.prototype.pt0 =  new JU.P3 ();
});
Clazz_declarePackage ("JU");
Clazz_load (["java.lang.Enum"], "JU.Encoding", null, function () {
c$ = Clazz_declareType (JU, "Encoding", Enum);
Clazz_defineEnumConstant (c$, "NONE", 0, []);
Clazz_defineEnumConstant (c$, "UTF8", 1, []);
Clazz_defineEnumConstant (c$, "UTF_16BE", 2, []);
Clazz_defineEnumConstant (c$, "UTF_16LE", 3, []);
Clazz_defineEnumConstant (c$, "UTF_32BE", 4, []);
Clazz_defineEnumConstant (c$, "UTF_32LE", 5, []);
});
$_L(["java.util.Hashtable"],"java.util.Properties",["java.lang.NullPointerException","$.StringBuffer"],function(){
c$=$_C(function(){
this.builder=null;
this.defaults=null;
$_Z(this,arguments);
},java.util,"Properties",java.util.Hashtable);

$_K(c$,
function(properties){
$_R(this,java.util.Properties,[]);
this.defaults=properties;
},"java.util.Properties");
$_M(c$,"dumpString",
($fz=function(buffer,string,key){
var i=0;
if(!key&&i<string.length&&(string.charAt(i)).charCodeAt(0)==(' ').charCodeAt(0)){
buffer.append("\\ ");
i++;
}for(;i<string.length;i++){
var ch=string.charAt(i);
switch(ch){
case'\t':
buffer.append("\\t");
break;
case'\n':
buffer.append("\\n");
break;
case'\f':
buffer.append("\\f");
break;
case'\r':
buffer.append("\\r");
break;
default:
if("\\#!=:".indexOf(ch)>=0||(key&&(ch).charCodeAt(0)==(' ').charCodeAt(0))){
buffer.append('\\');
}if((ch).charCodeAt(0)>=(' ').charCodeAt (0) && (ch).charCodeAt (0) <= ('~').charCodeAt(0)){
buffer.append(ch);
}else{
var hex=Integer.toHexString(ch.charCodeAt(0));
buffer.append("\\u");
for(var j=0;j<4-hex.length;j++){
buffer.append("0");
}
buffer.append(hex);
}}
}
},$fz.isPrivate=true,$fz),"StringBuilder,~S,~B");
$_M(c$,"getProperty",
function(name){
var result=this.get(name);
var property=$_O(result,String)?result:null;
if(property==null&&this.defaults!=null){
property=this.defaults.getProperty(name);
}return property;
},"~S");
$_M(c$,"getProperty",
function(name,defaultValue){
var result=this.get(name);
var property=$_O(result,String)?result:null;
if(property==null&&this.defaults!=null){
property=this.defaults.getProperty(name);
}if(property==null){
return defaultValue;
}return property;
},"~S,~S");
$_M(c$,"list",
function(out){
if(out==null){
throw new NullPointerException();
}var buffer=new StringBuffer(80);
var keys=this.propertyNames();
while(keys.hasMoreElements()){
var key=keys.nextElement();
buffer.append(key);
buffer.append('=');
var property=this.get(key);
var def=this.defaults;
while(property==null){
property=def.get(key);
def=def.defaults;
}
if(property.length>40){
buffer.append(property.substring(0,37));
buffer.append("...");
}else{
buffer.append(property);
}out.println(buffer.toString());
buffer.setLength(0);
}
},"java.io.PrintStream");
$_M(c$,"list",
function(writer){
if(writer==null){
throw new NullPointerException();
}var buffer=new StringBuffer(80);
var keys=this.propertyNames();
while(keys.hasMoreElements()){
var key=keys.nextElement();
buffer.append(key);
buffer.append('=');
var property=this.get(key);
var def=this.defaults;
while(property==null){
property=def.get(key);
def=def.defaults;
}
if(property.length>40){
buffer.append(property.substring(0,37));
buffer.append("...");
}else{
buffer.append(property);
}writer.println(buffer.toString());
buffer.setLength(0);
}
},"java.io.PrintWriter");
$_M(c$,"load",
function($in){

},"java.io.InputStream");
$_M(c$,"propertyNames",
function(){
if(this.defaults==null){
return this.keys();
}var set=new java.util.Hashtable(this.defaults.size()+this.size());
var keys=this.defaults.propertyNames();
while(keys.hasMoreElements()){
set.put(keys.nextElement(),set);
}
keys=this.keys();
while(keys.hasMoreElements()){
set.put(keys.nextElement(),set);
}
return set.keys();
});
$_M(c$,"save",
function(out,comment){
try{
this.store(out,comment);
}catch(e){
if($_O(e,java.io.IOException)){
}else{
throw e;
}
}
},"java.io.OutputStream,~S");
$_M(c$,"setProperty",
function(name,value){
return this.put(name,value);
},"~S,~S");
$_M(c$,"store",
function(out,comment){

},"java.io.OutputStream,~S");
$_M(c$,"loadFromXML",
function($in){

},"java.io.InputStream");
$_M(c$,"storeToXML",
function(os,comment){

},"java.io.OutputStream,~S");
$_M(c$,"storeToXML",
function(os,comment,encoding){

},"java.io.OutputStream,~S,~S");
$_M(c$,"substitutePredefinedEntries",
($fz=function(s){
return s.replaceAll("&","&amp;").replaceAll("<","&lt;").replaceAll(">","&gt;").replaceAll("\u0027","&apos;").replaceAll("\"","&quot;");
},$fz.isPrivate=true,$fz),"~S");
$_S(c$,
"PROP_DTD_NAME","http://java.sun.com/dtd/properties.dtd",
"PROP_DTD","<?xml version=\"1.0\" encoding=\"UTF-8\"?>    <!ELEMENT properties (comment?, entry*) >    <!ATTLIST properties version CDATA #FIXED \"1.0\" >    <!ELEMENT comment (#PCDATA) >    <!ELEMENT entry (#PCDATA) >    <!ATTLIST entry key CDATA #REQUIRED >",
"NONE",0,
"SLASH",1,
"UNICODE",2,
"CONTINUE",3,
"KEY_DONE",4,
"IGNORE",5,
"lineSeparator",null);

});
Clazz_declarePackage ("J.util");
Clazz_load (["JU.BS"], "J.util.Elements", ["java.lang.Character", "java.util.Hashtable", "JU.PT", "J.util.Logger"], function () {
c$ = Clazz_declareType (J.util, "Elements");
c$.getAtomicMass = $_M(c$, "getAtomicMass", 
function (i) {
return (i < 1 || i >= J.util.Elements.atomicMass.length ? 0 : J.util.Elements.atomicMass[i]);
}, "~N");
c$.elementNumberFromSymbol = $_M(c$, "elementNumberFromSymbol", 
function (elementSymbol, isSilent) {
if (J.util.Elements.htElementMap == null) {
var map =  new java.util.Hashtable ();
for (var elementNumber = J.util.Elements.elementNumberMax; --elementNumber >= 0; ) {
var symbol = J.util.Elements.elementSymbols[elementNumber];
var boxed = Integer.$valueOf (elementNumber);
map.put (symbol, boxed);
if (symbol.length == 2) map.put (symbol.toUpperCase (), boxed);
}
for (var i = J.util.Elements.altElementMax; --i >= 4; ) {
var symbol = J.util.Elements.altElementSymbols[i];
var boxed = Integer.$valueOf (J.util.Elements.altElementNumbers[i]);
map.put (symbol, boxed);
if (symbol.length == 2) map.put (symbol.toUpperCase (), boxed);
}
($t$ = J.util.Elements.htElementMap = map, J.util.Elements.prototype.htElementMap = J.util.Elements.htElementMap, $t$);
}if (elementSymbol == null) return 0;
var boxedAtomicNumber = J.util.Elements.htElementMap.get (elementSymbol);
if (boxedAtomicNumber != null) return boxedAtomicNumber.intValue ();
if (Character.isDigit (elementSymbol.charAt (0))) {
var pt = elementSymbol.length - 2;
if (pt >= 0 && Character.isDigit (elementSymbol.charAt (pt))) pt++;
var isotope = (pt > 0 ? JU.PT.parseInt (elementSymbol.substring (0, pt)) : 0);
if (isotope > 0) {
var n = J.util.Elements.elementNumberFromSymbol (elementSymbol.substring (pt), true);
if (n > 0) {
isotope = J.util.Elements.getAtomicAndIsotopeNumber (n, isotope);
J.util.Elements.htElementMap.put (elementSymbol.toUpperCase (), Integer.$valueOf (isotope));
return isotope;
}}}if (!isSilent) J.util.Logger.error ("'" + elementSymbol + "' is not a recognized symbol");
return 0;
}, "~S,~B");
c$.elementSymbolFromNumber = $_M(c$, "elementSymbolFromNumber", 
function (elemNo) {
var isoNumber = 0;
if (elemNo >= J.util.Elements.elementNumberMax) {
for (var j = J.util.Elements.altElementMax; --j >= 0; ) if (elemNo == J.util.Elements.altElementNumbers[j]) return J.util.Elements.altElementSymbols[j];

isoNumber = J.util.Elements.getIsotopeNumber (elemNo);
elemNo %= 128;
return "" + isoNumber + J.util.Elements.getElementSymbol (elemNo);
}return J.util.Elements.getElementSymbol (elemNo);
}, "~N");
c$.getElementSymbol = $_M(c$, "getElementSymbol", 
function (elemNo) {
if (elemNo < 0 || elemNo >= J.util.Elements.elementNumberMax) elemNo = 0;
return J.util.Elements.elementSymbols[elemNo];
}, "~N");
c$.elementNameFromNumber = $_M(c$, "elementNameFromNumber", 
function (elementNumber) {
if (elementNumber >= J.util.Elements.elementNumberMax) {
for (var j = J.util.Elements.altElementMax; --j >= 0; ) if (elementNumber == J.util.Elements.altElementNumbers[j]) return J.util.Elements.altElementNames[j];

elementNumber %= 128;
}if (elementNumber < 0 || elementNumber >= J.util.Elements.elementNumberMax) elementNumber = 0;
return J.util.Elements.elementNames[elementNumber];
}, "~N");
c$.altElementNameFromIndex = $_M(c$, "altElementNameFromIndex", 
function (i) {
return J.util.Elements.altElementNames[i];
}, "~N");
c$.altElementNumberFromIndex = $_M(c$, "altElementNumberFromIndex", 
function (i) {
return J.util.Elements.altElementNumbers[i];
}, "~N");
c$.altElementSymbolFromIndex = $_M(c$, "altElementSymbolFromIndex", 
function (i) {
return J.util.Elements.altElementSymbols[i];
}, "~N");
c$.altIsotopeSymbolFromIndex = $_M(c$, "altIsotopeSymbolFromIndex", 
function (i) {
var code = J.util.Elements.altElementNumbers[i];
return (code >> 7) + J.util.Elements.elementSymbolFromNumber (code & 127);
}, "~N");
c$.altIsotopeSymbolFromIndex2 = $_M(c$, "altIsotopeSymbolFromIndex2", 
function (i) {
var code = J.util.Elements.altElementNumbers[i];
return J.util.Elements.elementSymbolFromNumber (code & 127) + (code >> 7);
}, "~N");
c$.getElementNumber = $_M(c$, "getElementNumber", 
function (atomicAndIsotopeNumber) {
return atomicAndIsotopeNumber & 127;
}, "~N");
c$.getIsotopeNumber = $_M(c$, "getIsotopeNumber", 
function (atomicAndIsotopeNumber) {
return atomicAndIsotopeNumber >> 7;
}, "~N");
c$.getAtomicAndIsotopeNumber = $_M(c$, "getAtomicAndIsotopeNumber", 
function (n, mass) {
return ((n < 0 ? 0 : n) + (mass <= 0 ? 0 : mass << 7));
}, "~N,~N");
c$.altElementIndexFromNumber = $_M(c$, "altElementIndexFromNumber", 
function (atomicAndIsotopeNumber) {
for (var i = 0; i < J.util.Elements.altElementMax; i++) if (J.util.Elements.altElementNumbers[i] == atomicAndIsotopeNumber) return i;

return 0;
}, "~N");
c$.getNaturalIsotope = $_M(c$, "getNaturalIsotope", 
function (elementNumber) {
for (var i = 0; i < J.util.Elements.naturalIsotopeMasses.length; i += 2) if (J.util.Elements.naturalIsotopeMasses[i] == elementNumber) return J.util.Elements.naturalIsotopeMasses[++i];

return 0;
}, "~N");
c$.isNaturalIsotope = $_M(c$, "isNaturalIsotope", 
function (isotopeSymbol) {
return ("1H,12C,14N,".indexOf (isotopeSymbol + ",") >= 0);
}, "~S");
c$.getBondingRadiusFloat = $_M(c$, "getBondingRadiusFloat", 
function (atomicNumberAndIsotope, charge) {
var atomicNumber = atomicNumberAndIsotope & 127;
if (charge > 0 && J.util.Elements.bsCations.get (atomicNumber)) return J.util.Elements.getBondingRadFromTable (atomicNumber, charge, J.util.Elements.cationLookupTable);
if (charge < 0 && J.util.Elements.bsAnions.get (atomicNumber)) return J.util.Elements.getBondingRadFromTable (atomicNumber, charge, J.util.Elements.anionLookupTable);
return J.util.Elements.covalentMars[atomicNumber] / 1000;
}, "~N,~N");
c$.getBondingRadFromTable = $_M(c$, "getBondingRadFromTable", 
function (atomicNumber, charge, table) {
var ionic = (atomicNumber << 4) + (charge + 4);
var iVal = 0;
var iMid = 0;
var iMin = 0;
var iMax = Clazz_doubleToInt (table.length / 2);
while (iMin != iMax) {
iMid = Clazz_doubleToInt ((iMin + iMax) / 2);
iVal = table[iMid << 1];
if (iVal > ionic) iMax = iMid;
 else if (iVal < ionic) iMin = iMid + 1;
 else return table[(iMid << 1) + 1] / 1000;
}
if (iVal > ionic) iMid--;
iVal = table[iMid << 1];
if (atomicNumber != (iVal >> 4)) iMid++;
return table[(iMid << 1) + 1] / 1000;
}, "~N,~N,~A");
c$.getVanderwaalsMar = $_M(c$, "getVanderwaalsMar", 
function (atomicAndIsotopeNumber, type) {
return J.util.Elements.vanderwaalsMars[((atomicAndIsotopeNumber & 127) << 2) + (type.pt % 4)];
}, "~N,J.constant.EnumVdw");
c$.getHydrophobicity = $_M(c$, "getHydrophobicity", 
function (i) {
return (i < 1 || i >= J.util.Elements.hydrophobicities.length ? 0 : J.util.Elements.hydrophobicities[i]);
}, "~N");
c$.getAllredRochowElectroNeg = $_M(c$, "getAllredRochowElectroNeg", 
function (elemno) {
return (elemno > 0 && elemno < J.util.Elements.electroNegativities.length ? J.util.Elements.electroNegativities[elemno] : 0);
}, "~N");
c$.isElement = $_M(c$, "isElement", 
function (atomicAndIsotopeNumber, elemNo) {
return ((atomicAndIsotopeNumber & 127) == elemNo);
}, "~N,~N");
Clazz_defineStatics (c$,
"elementSymbols", ["Xx", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt"],
"atomicMass", [0, 1.008, 4.003, 6.941, 9.012, 10.81, 12.011, 14.007, 15.999, 18.998, 20.18, 22.99, 24.305, 26.981, 28.086, 30.974, 32.07, 35.453, 39.948, 39.1, 40.08, 44.956, 47.88, 50.941, 52, 54.938, 55.847, 58.93, 58.69, 63.55, 65.39, 69.72, 72.61, 74.92, 78.96, 79.9, 83.8, 85.47, 87.62, 88.91, 91.22, 92.91, 95.94, 98.91, 101.07, 102.91, 106.42, 107.87, 112.41, 114.82, 118.71, 121.75, 127.6, 126.91, 131.29, 132.91, 137.33, 138.91, 140.12, 140.91, 144.24, 144.9, 150.36, 151.96, 157.25, 158.93, 162.5, 164.93, 167.26, 168.93, 173.04, 174.97, 178.49, 180.95, 183.85, 186.21, 190.2, 192.22, 195.08, 196.97, 200.59, 204.38, 207.2, 208.98, 210, 210, 222, 223, 226.03, 227.03, 232.04, 231.04, 238.03, 237.05, 239.1, 243.1, 247.1, 247.1, 252.1, 252.1, 257.1, 256.1, 259.1, 260.1, 261, 262, 263, 262, 265, 268]);
c$.elementNumberMax = c$.prototype.elementNumberMax = J.util.Elements.elementSymbols.length;
Clazz_defineStatics (c$,
"htElementMap", null,
"elementNames", ["unknown", "hydrogen", "helium", "lithium", "beryllium", "boron", "carbon", "nitrogen", "oxygen", "fluorine", "neon", "sodium", "magnesium", "aluminum", "silicon", "phosphorus", "sulfur", "chlorine", "argon", "potassium", "calcium", "scandium", "titanium", "vanadium", "chromium", "manganese", "iron", "cobalt", "nickel", "copper", "zinc", "gallium", "germanium", "arsenic", "selenium", "bromine", "krypton", "rubidium", "strontium", "yttrium", "zirconium", "niobium", "molybdenum", "technetium", "ruthenium", "rhodium", "palladium", "silver", "cadmium", "indium", "tin", "antimony", "tellurium", "iodine", "xenon", "cesium", "barium", "lanthanum", "cerium", "praseodymium", "neodymium", "promethium", "samarium", "europium", "gadolinium", "terbium", "dysprosium", "holmium", "erbium", "thulium", "ytterbium", "lutetium", "hafnium", "tantalum", "tungsten", "rhenium", "osmium", "iridium", "platinum", "gold", "mercury", "thallium", "lead", "bismuth", "polonium", "astatine", "radon", "francium", "radium", "actinium", "thorium", "protactinium", "uranium", "neptunium", "plutonium", "americium", "curium", "berkelium", "californium", "einsteinium", "fermium", "mendelevium", "nobelium", "lawrencium", "rutherfordium", "dubnium", "seaborgium", "bohrium", "hassium", "meitnerium"],
"naturalIsotopeMasses", [1, 1, 6, 12, 7, 14, 8, 16],
"naturalIsotopes", "1H,12C,14N,",
"firstIsotope", 4,
"altElementNumbers", [0, 13, 16, 55, 257, 385, 1414, 1670, 1798, 1927]);
c$.altElementMax = c$.prototype.altElementMax = J.util.Elements.altElementNumbers.length;
Clazz_defineStatics (c$,
"altElementSymbols", ["Xx", "Al", "S", "Cs", "D", "T", "11C", "13C", "14C", "15N"],
"altElementNames", ["dummy", "aluminium", "sulphur", "caesium", "deuterium", "tritium", "", "", "", ""],
"VdwPROBE", "#VDW radii for PROBE;{_H}.vdw = 1.0;{_H and connected(_C) and not connected(within(smiles,\'[a]\'))}.vdw = 1.17;{_C}.vdw = 1.75;{_C and connected(3) and connected(_O)}.vdw = 1.65;{_N}.vdw = 1.55;{_O}.vdw = 1.4;{_P}.vdw = 1.8;{_S}.vdw = 1.8;message VDW radii for H, C, N, O, P, and S set according to Word, et al., J. Mol. Biol. (1999) 285, 1711-1733",
"vanderwaalsMars", [1000, 1000, 1000, 1000, 1200, 1100, 1100, 1200, 1400, 1400, 2200, 1400, 1820, 1810, 1220, 2200, 1700, 1530, 628, 1900, 2080, 1920, 1548, 1800, 1950, 1700, 1548, 1700, 1850, 1550, 1400, 1600, 1700, 1520, 1348, 1550, 1730, 1470, 1300, 1500, 1540, 1540, 2020, 1540, 2270, 2270, 2200, 2400, 1730, 1730, 1500, 2200, 2050, 1840, 1500, 2100, 2100, 2100, 2200, 2100, 2080, 1800, 1880, 1950, 2000, 1800, 1808, 1800, 1970, 1750, 1748, 1800, 1880, 1880, 2768, 1880, 2750, 2750, 2388, 2800, 1973, 2310, 1948, 2400, 1700, 2300, 1320, 2300, 1700, 2150, 1948, 2150, 1700, 2050, 1060, 2050, 1700, 2050, 1128, 2050, 1700, 2050, 1188, 2050, 1700, 2050, 1948, 2050, 1700, 2000, 1128, 2000, 1630, 2000, 1240, 2000, 1400, 2000, 1148, 2000, 1390, 2100, 1148, 2100, 1870, 1870, 1548, 2100, 1700, 2110, 3996, 2100, 1850, 1850, 828, 2050, 1900, 1900, 900, 1900, 2100, 1830, 1748, 1900, 2020, 2020, 1900, 2020, 1700, 3030, 2648, 2900, 1700, 2490, 2020, 2550, 1700, 2400, 1608, 2400, 1700, 2300, 1420, 2300, 1700, 2150, 1328, 2150, 1700, 2100, 1748, 2100, 1700, 2050, 1800, 2050, 1700, 2050, 1200, 2050, 1700, 2000, 1220, 2000, 1630, 2050, 1440, 2050, 1720, 2100, 1548, 2100, 1580, 2200, 1748, 2200, 1930, 2200, 1448, 2200, 2170, 1930, 1668, 2250, 2200, 2170, 1120, 2200, 2060, 2060, 1260, 2100, 2150, 1980, 1748, 2100, 2160, 2160, 2100, 2160, 1700, 3430, 3008, 3000, 1700, 2680, 2408, 2700, 1700, 2500, 1828, 2500, 1700, 2480, 1860, 2480, 1700, 2470, 1620, 2470, 1700, 2450, 1788, 2450, 1700, 2430, 1760, 2430, 1700, 2420, 1740, 2420, 1700, 2400, 1960, 2400, 1700, 2380, 1688, 2380, 1700, 2370, 1660, 2370, 1700, 2350, 1628, 2350, 1700, 2330, 1608, 2330, 1700, 2320, 1588, 2320, 1700, 2300, 1568, 2300, 1700, 2280, 1540, 2280, 1700, 2270, 1528, 2270, 1700, 2250, 1400, 2250, 1700, 2200, 1220, 2200, 1700, 2100, 1260, 2100, 1700, 2050, 1300, 2050, 1700, 2000, 1580, 2000, 1700, 2000, 1220, 2000, 1720, 2050, 1548, 2050, 1660, 2100, 1448, 2100, 1550, 2050, 1980, 2050, 1960, 1960, 1708, 2200, 2020, 2020, 2160, 2300, 1700, 2070, 1728, 2300, 1700, 1970, 1208, 2000, 1700, 2020, 1120, 2000, 1700, 2200, 2300, 2000, 1700, 3480, 3240, 2000, 1700, 2830, 2568, 2000, 1700, 2000, 2120, 2000, 1700, 2400, 1840, 2400, 1700, 2000, 1600, 2000, 1860, 2300, 1748, 2300, 1700, 2000, 1708, 2000, 1700, 2000, 1668, 2000, 1700, 2000, 1660, 2000, 1700, 2000, 1648, 2000, 1700, 2000, 1640, 2000, 1700, 2000, 1628, 2000, 1700, 2000, 1620, 2000, 1700, 2000, 1608, 2000, 1700, 2000, 1600, 2000, 1700, 2000, 1588, 2000, 1700, 2000, 1580, 2000, 1700, 2000, 1600, 2000, 1700, 2000, 1600, 2000, 1700, 2000, 1600, 2000, 1700, 2000, 1600, 2000, 1700, 2000, 1600, 2000, 1700, 2000, 1600, 2000],
"covalentMars", [0, 230, 930, 680, 350, 830, 680, 680, 680, 640, 1120, 970, 1100, 1350, 1200, 750, 1020, 990, 1570, 1330, 990, 1440, 1470, 1330, 1350, 1350, 1340, 1330, 1500, 1520, 1450, 1220, 1170, 1210, 1220, 1210, 1910, 1470, 1120, 1780, 1560, 1480, 1470, 1350, 1400, 1450, 1500, 1590, 1690, 1630, 1460, 1460, 1470, 1400, 1980, 1670, 1340, 1870, 1830, 1820, 1810, 1800, 1800, 1990, 1790, 1760, 1750, 1740, 1730, 1720, 1940, 1720, 1570, 1430, 1370, 1350, 1370, 1320, 1500, 1500, 1700, 1550, 1540, 1540, 1680, 1700, 2400, 2000, 1900, 1880, 1790, 1610, 1580, 1550, 1530, 1510, 1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500, 1600, 1600, 1600, 1600, 1600, 1600],
"FORMAL_CHARGE_MIN", -4,
"FORMAL_CHARGE_MAX", 7,
"cationLookupTable", [53, 680, 69, 440, 70, 350, 85, 350, 87, 230, 104, 160, 117, 680, 119, 160, 121, 130, 133, 220, 138, 90, 155, 80, 165, 1120, 181, 970, 197, 820, 198, 660, 215, 510, 229, 650, 232, 420, 247, 440, 249, 350, 262, 2190, 264, 370, 266, 300, 281, 340, 283, 270, 293, 1540, 309, 1330, 325, 1180, 326, 990, 343, 732, 357, 960, 358, 940, 359, 760, 360, 680, 374, 880, 375, 740, 376, 630, 377, 590, 389, 810, 390, 890, 391, 630, 394, 520, 406, 800, 407, 660, 408, 600, 411, 460, 422, 740, 423, 640, 438, 720, 439, 630, 454, 690, 469, 960, 470, 720, 485, 880, 486, 740, 501, 810, 503, 620, 518, 730, 520, 530, 535, 580, 537, 460, 549, 660, 552, 500, 554, 420, 569, 470, 571, 390, 597, 1470, 614, 1120, 631, 893, 645, 1090, 648, 790, 661, 1000, 664, 740, 665, 690, 677, 930, 680, 700, 682, 620, 699, 979, 712, 670, 727, 680, 742, 800, 744, 650, 757, 1260, 758, 890, 773, 1140, 774, 970, 791, 810, 806, 930, 808, 710, 823, 760, 825, 620, 837, 820, 840, 700, 842, 560, 857, 620, 859, 500, 885, 1670, 901, 1530, 902, 1340, 917, 1390, 919, 1016, 933, 1270, 935, 1034, 936, 920, 951, 1013, 952, 900, 967, 995, 983, 979, 999, 964, 1014, 1090, 1015, 950, 1031, 938, 1047, 923, 1048, 840, 1063, 908, 1079, 894, 1095, 881, 1111, 870, 1126, 930, 1127, 858, 1143, 850, 1160, 780, 1177, 680, 1192, 700, 1194, 620, 1208, 720, 1211, 560, 1224, 880, 1226, 690, 1240, 680, 1254, 800, 1256, 650, 1269, 1370, 1271, 850, 1285, 1270, 1286, 1100, 1301, 1470, 1303, 950, 1318, 1200, 1320, 840, 1333, 980, 1335, 960, 1337, 740, 1354, 670, 1371, 620, 1397, 1800, 1414, 1430, 1431, 1180, 1448, 1020, 1463, 1130, 1464, 980, 1465, 890, 1480, 970, 1482, 800, 1495, 1100, 1496, 950, 1499, 710, 1511, 1080, 1512, 930, 1527, 1070, 1528, 920],
"anionLookupTable", [19, 1540, 96, 2600, 113, 1710, 130, 1360, 131, 680, 147, 1330, 241, 2120, 258, 1840, 275, 1810, 512, 2720, 529, 2220, 546, 1980, 563, 1960, 800, 2940, 803, 3700, 817, 2450, 834, 2110, 835, 2500, 851, 2200]);
c$.bsCations = c$.prototype.bsCations =  new JU.BS ();
c$.bsAnions = c$.prototype.bsAnions =  new JU.BS ();
{
for (var i = 0; i < J.util.Elements.anionLookupTable.length; i += 2) J.util.Elements.bsAnions.set (J.util.Elements.anionLookupTable[i] >> 4);

for (var i = 0; i < J.util.Elements.cationLookupTable.length; i += 2) J.util.Elements.bsCations.set (J.util.Elements.cationLookupTable[i] >> 4);

}Clazz_defineStatics (c$,
"hydrophobicities", [0, 0.62, -2.53, -0.78, -0.9, 0.29, -0.85, -0.74, 0.48, -0.4, 1.38, 1.06, -1.5, 0.64, 1.19, 0.12, -0.18, -0.05, 0.81, 0.26, 1.08]);
{
if ((J.util.Elements.elementNames.length != J.util.Elements.elementNumberMax) || (Clazz_doubleToInt (J.util.Elements.vanderwaalsMars.length / 4) != J.util.Elements.elementNumberMax) || (J.util.Elements.covalentMars.length != J.util.Elements.elementNumberMax)) {
J.util.Logger.error ("ERROR!!! Element table length mismatch:\n elementSymbols.length=" + J.util.Elements.elementSymbols.length + "\n elementNames.length=" + J.util.Elements.elementNames.length + "\n vanderwaalsMars.length=" + J.util.Elements.vanderwaalsMars.length + "\n covalentMars.length=" + J.util.Elements.covalentMars.length);
}}Clazz_defineStatics (c$,
"electroNegativities", [0, 2.2, 0, 0.97, 1.47, 2.01, 2.5, 3.07, 3.5, 4.1, 0, 1.01, 1.23, 1.47, 1.74, 2.06, 2.44, 2.83, 0, 0.91, 1.04, 1.2, 1.32, 1.45, 1.56, 1.6, 1.64, 1.7, 1.75, 1.75, 1.66, 1.82, 2.02, 2.2, 2.48, 2.74, 0, 0.89, 0.99, 1.11, 1.22, 1.23, 1.3, 1.36, 1.42, 1.45, 1.35, 1.42, 1.46, 1.49, 1.72, 1.82, 2.01, 2.21]);
});
Clazz_declarePackage ("J.util");
Clazz_load (["JU.V3"], "J.util.Vibration", null, function () {
c$ = Clazz_declareType (J.util, "Vibration", JU.V3);
$_M(c$, "setTempPoint", 
function (pt, t, scale) {
pt.scaleAdd2 ((Math.cos (t * 6.283185307179586) * scale), this, pt);
}, "JU.P3,~N,~N");
Clazz_defineStatics (c$,
"twoPI", 6.283185307179586);
});
Clazz_declarePackage ("J.viewer");
Clazz_load (["JU.SB", "$.V3", "J.util.Elements", "$.Txt"], "J.viewer.JC", ["java.lang.NullPointerException", "java.util.Hashtable", "JU.PT", "J.util.Logger"], function () {
c$ = Clazz_declareType (J.viewer, "JC");
c$.embedScript = $_M(c$, "embedScript", 
function (s) {
return "\n/**" + "**** Jmol Embedded Script ****" + " \n" + s + "\n**/";
}, "~S");
c$.getSpecialAtomName = $_M(c$, "getSpecialAtomName", 
function (atomID) {
return J.viewer.JC.specialAtomNames[atomID];
}, "~N");
c$.getSpecialAtomNames = $_M(c$, "getSpecialAtomNames", 
function () {
($t$ = J.viewer.JC.htSpecialAtoms =  new java.util.Hashtable (), J.viewer.JC.prototype.htSpecialAtoms = J.viewer.JC.htSpecialAtoms, $t$);
for (var i = J.viewer.JC.specialAtomNames.length; --i >= 0; ) {
var specialAtomName = J.viewer.JC.specialAtomNames[i];
if (specialAtomName != null) J.viewer.JC.htSpecialAtoms.put (specialAtomName, Integer.$valueOf (i));
}
});
c$.lookupSpecialAtomID = $_M(c$, "lookupSpecialAtomID", 
function (atomName) {
if (J.viewer.JC.htSpecialAtoms == null) J.viewer.JC.getSpecialAtomNames ();
var boxedAtomID = J.viewer.JC.htSpecialAtoms.get (atomName);
if (boxedAtomID != null) return (boxedAtomID.intValue ());
return 0;
}, "~S");
c$.getAminoAcidValenceAndCharge = $_M(c$, "getAminoAcidValenceAndCharge", 
function (res, name, ret) {
if (res == null || res.length == 0 || res.length > 3 || name.equals ("CA") || name.equals ("CB")) return false;
var ch0 = name.charAt (0);
var ch1 = (name.length == 1 ? '\0' : name.charAt (1));
var isSp2 = false;
var bondCount = ret[3];
switch (res.length) {
case 3:
if (name.length == 1) {
switch (ch0) {
case 'N':
if (bondCount > 1) return false;
ret[1] = 1;
break;
case 'O':
isSp2 = ("HOH;DOD;WAT".indexOf (res) < 0);
break;
default:
isSp2 = true;
}
} else {
var id = res + ch0;
isSp2 = ("ARGN;ASNN;ASNO;ASPO;GLNN;GLNO;GLUO;HISN;HISC;PHECTRPC;TRPN;TYRC".indexOf (id) >= 0);
if ("LYSN".indexOf (id) >= 0) {
ret[1] = 1;
} else if (ch0 == 'O' && ch1 == 'X') {
ret[1] = -1;
}}break;
case 1:
case 2:
if (name.length > 2 && name.charAt (2) == '\'') return false;
switch (ch0) {
case 'C':
if (ch1 == '7') return false;
break;
case 'N':
switch (ch1) {
case '1':
case '3':
if ("A3;A1;C3;G3;I3".indexOf ("" + res.charAt (res.length - 1) + ch1) >= 0) ret[0]--;
break;
case '7':
ret[0]--;
break;
}
break;
}
isSp2 = true;
}
if (isSp2) {
switch (ch0) {
case 'N':
ret[2] = 2;
break;
case 'C':
ret[2] = 2;
ret[0]--;
break;
case 'O':
ret[0]--;
break;
}
}return true;
}, "~S,~S,~A");
c$.getStandardPdbHydrogenCount = $_M(c$, "getStandardPdbHydrogenCount", 
function (pt) {
return (pt < 0 || pt >= J.viewer.JC.pdbHydrogenCount.length ? -1 : J.viewer.JC.pdbHydrogenCount[pt]);
}, "~N");
c$.getPdbBondInfo = $_M(c$, "getPdbBondInfo", 
function (pt, isLegacy) {
if (pt < 0 || pt > J.viewer.JC.pdbBondInfo.length) return null;
var s = J.viewer.JC.pdbBondInfo[pt];
if (isLegacy && (pt = s.indexOf ("O3'")) >= 0) s = s.substring (0, pt);
var temp = JU.PT.getTokens (s);
var info =  new Array (Clazz_doubleToInt (temp.length / 2));
for (var i = 0, p = 0; i < info.length; i++) {
var source = temp[p++];
var target = temp[p++];
if (target.length == 1) switch (target.charAt (0)) {
case 'N':
target = "H@H2";
break;
case 'B':
target = "HB3@HB2";
break;
case 'D':
target = "HD2@HD3";
break;
case 'G':
target = "HG3@HG2";
break;
case '2':
target = "H2''@H2'";
break;
case '5':
target = "H5''@H5'";
break;
}
if (target.charAt (0) != 'H' && source.compareTo (target) > 0) {
s = target;
target = source;
source = s;
}info[i] = [source, target, (target.startsWith ("H") ? "1" : "2")];
}
return info;
}, "~N,~B");
c$.checkCarbohydrate = $_M(c$, "checkCarbohydrate", 
function (group3) {
return (group3 != null && ",[AHR],[ALL],[AMU],[ARA],[ARB],[BDF],[BDR],[BGC],[BMA],[FCA],[FCB],[FRU],[FUC],[FUL],[GAL],[GLA],[GLC],[GXL],[GUP],[LXC],[MAN],[RAM],[RIB],[RIP],[XYP],[XYS],[CBI],[CT3],[CTR],[CTT],[LAT],[MAB],[MAL],[MLR],[MTT],[SUC],[TRE],[GCU],[MTL],[NAG],[NDG],[RHA],[SOR],[SOL],[SOE],[XYL],[A2G],[LBT],[NGA],[SIA],[SLB],[AFL],[AGC],[GLB],[NAN],[RAA]".indexOf ("[" + group3.toUpperCase () + "]") >= 0);
}, "~S");
c$.getGroup3List = $_M(c$, "getGroup3List", 
function () {
if (J.viewer.JC.group3List != null) return J.viewer.JC.group3List;
var s =  new JU.SB ();
for (var i = 1; i < 42; i++) s.append (",[").append ((J.viewer.JC.predefinedGroup3Names[i] + "   ").substring (0, 3) + "]");

s.append (",[AHR],[ALL],[AMU],[ARA],[ARB],[BDF],[BDR],[BGC],[BMA],[FCA],[FCB],[FRU],[FUC],[FUL],[GAL],[GLA],[GLC],[GXL],[GUP],[LXC],[MAN],[RAM],[RIB],[RIP],[XYP],[XYS],[CBI],[CT3],[CTR],[CTT],[LAT],[MAB],[MAL],[MLR],[MTT],[SUC],[TRE],[GCU],[MTL],[NAG],[NDG],[RHA],[SOR],[SOL],[SOE],[XYL],[A2G],[LBT],[NGA],[SIA],[SLB],[AFL],[AGC],[GLB],[NAN],[RAA]");
($t$ = J.viewer.JC.group3Count = Clazz_doubleToInt (s.length () / 6), J.viewer.JC.prototype.group3Count = J.viewer.JC.group3Count, $t$);
return ($t$ = J.viewer.JC.group3List = s.toString (), J.viewer.JC.prototype.group3List = J.viewer.JC.group3List, $t$);
});
c$.isHetero = $_M(c$, "isHetero", 
function (group3) {
return J.viewer.JC.getGroup3Pt (group3) >= 42;
}, "~S");
c$.getGroup3Pt = $_M(c$, "getGroup3Pt", 
function (group3) {
J.viewer.JC.getGroup3List ();
var sb =  new JU.SB ().append ("[");
sb.append (group3);
switch (group3.length) {
case 1:
sb.append ("  ");
break;
case 2:
sb.append (" ");
break;
}
var pt = J.viewer.JC.group3List.indexOf (sb.toString ());
return (pt < 0 ? 2147483647 : Clazz_doubleToInt (pt / 6) + 1);
}, "~S");
c$.getGroup3Count = $_M(c$, "getGroup3Count", 
function () {
if (J.viewer.JC.group3Count > 0) return J.viewer.JC.group3Count;
J.viewer.JC.getGroup3List ();
return ($t$ = J.viewer.JC.group3Count = Clazz_doubleToInt (J.viewer.JC.group3List.length / 6), J.viewer.JC.prototype.group3Count = J.viewer.JC.group3Count, $t$);
});
c$.isShapeSecondary = $_M(c$, "isShapeSecondary", 
function (i) {
return i >= 9 && i < 16;
}, "~N");
c$.shapeTokenIndex = $_M(c$, "shapeTokenIndex", 
function (tok) {
switch (tok) {
case 1141899265:
case 1073741860:
return 0;
case 1678770178:
case 659488:
return 1;
case 1612189718:
return 2;
case 1611141176:
return 3;
case 1708058:
return 4;
case 1826248715:
return 5;
case 1746538509:
case 537006096:
return 6;
case 1113200652:
return 7;
case 1113200646:
return 8;
case 1115297793:
return 9;
case 1113200654:
return 10;
case 1113200642:
return 11;
case 1650071565:
return 12;
case 1113200647:
return 13;
case 1113200649:
return 14;
case 1113200650:
return 15;
case 1113198595:
return 16;
case 135175:
return 17;
case 135198:
return 18;
case 1113198597:
return 19;
case 1113198596:
return 20;
case 135192:
return 21;
case 135174:
return 23;
case 135176:
return 22;
case 135180:
return 24;
case 135402505:
return 25;
case 135182:
return 26;
case 1183762:
return 27;
case 135188:
return 28;
case 135190:
return 29;
case 537022465:
return 30;
case 1611272194:
return 31;
case 1679429641:
return 32;
case 1614417948:
return 33;
case 544771:
return 34;
case 1611272202:
return 35;
}
return -1;
}, "~N");
c$.getShapeClassName = $_M(c$, "getShapeClassName", 
function (shapeID, isRenderer) {
if (shapeID < 0) return J.viewer.JC.shapeClassBases[~shapeID];
return "J." + (isRenderer ? "render" : "shape") + (shapeID >= 9 && shapeID < 16 ? "bio." : shapeID >= 16 && shapeID < 23 ? "special." : shapeID >= 24 && shapeID < 29 ? "surface." : shapeID == 23 ? "cgo." : ".") + J.viewer.JC.shapeClassBases[shapeID];
}, "~N,~B");
c$.getShapeVisibilityFlag = $_M(c$, "getShapeVisibilityFlag", 
function (shapeID) {
return (4 << shapeID);
}, "~N");
c$.getOffset = $_M(c$, "getOffset", 
function (xOffset, yOffset) {
xOffset = Math.min (Math.max (xOffset, -127), 127);
yOffset = Math.min (Math.max (yOffset, -127), 127);
return ((xOffset & 0xFF) << 8) | (yOffset & 0xFF);
}, "~N,~N");
c$.getXOffset = $_M(c$, "getXOffset", 
function (offset) {
switch (offset) {
case 0:
return 4;
case 32767:
return 0;
default:
return ((offset << 48) >> 56);
}
}, "~N");
c$.getYOffset = $_M(c$, "getYOffset", 
function (offset) {
switch (offset) {
case 0:
return -4;
case 32767:
return 0;
default:
return -((offset << 56) >> 56);
}
}, "~N");
c$.getAlignmentName = $_M(c$, "getAlignmentName", 
function (align) {
return J.viewer.JC.hAlignNames[align & 3];
}, "~N");
c$.getPointer = $_M(c$, "getPointer", 
function (pointer) {
return ((pointer & 1) == 0 ? "" : (pointer & 2) > 0 ? "background" : "on");
}, "~N");
Clazz_defineStatics (c$,
"copyright", "(C) 2012 Jmol Development",
"version", null,
"date", null);
{
var tmpVersion = null;
var tmpDate = null;
{
tmpVersion = ___JmolVersion; tmpDate = ___JmolDate;
}if (tmpDate != null) {
tmpDate = tmpDate.substring (7, 24);
}($t$ = J.viewer.JC.version = (tmpVersion != null ? tmpVersion : "(Unknown version)"), J.viewer.JC.prototype.version = J.viewer.JC.version, $t$);
($t$ = J.viewer.JC.date = (tmpDate != null ? tmpDate : "(Unknown date)"), J.viewer.JC.prototype.date = J.viewer.JC.date, $t$);
}Clazz_defineStatics (c$,
"officialRelease", false,
"DEFAULT_HELP_PATH", "http://chemapps.stolaf.edu/jmol/docs/index.htm",
"STATE_VERSION_STAMP", "# Jmol state version ",
"EMBEDDED_SCRIPT_TAG", "**** Jmol Embedded Script ****",
"NOTE_SCRIPT_FILE", "NOTE: file recognized as a script file: ",
"SCRIPT_EDITOR_IGNORE", "\1## EDITOR_IGNORE ##",
"REPAINT_IGNORE", "\1## REPAINT_IGNORE ##",
"LOAD_ATOM_DATA_TYPES", ";xyz;vxyz;vibration;temperature;occupancy;partialcharge;",
"radiansPerDegree", (0.017453292519943295),
"allowedQuaternionFrames", "RC;RP;a;b;c;n;p;q;x;",
"EXPORT_DRIVER_LIST", "Idtf;Maya;Povray;Vrml;X3d;Tachyon;Obj");
c$.center = c$.prototype.center = JU.V3.new3 (0, 0, 0);
c$.axisX = c$.prototype.axisX = JU.V3.new3 (1, 0, 0);
c$.axisY = c$.prototype.axisY = JU.V3.new3 (0, 1, 0);
c$.axisZ = c$.prototype.axisZ = JU.V3.new3 (0, 0, 1);
c$.axisNX = c$.prototype.axisNX = JU.V3.new3 (-1, 0, 0);
c$.axisNY = c$.prototype.axisNY = JU.V3.new3 (0, -1, 0);
c$.axisNZ = c$.prototype.axisNZ = JU.V3.new3 (0, 0, -1);
c$.unitAxisVectors = c$.prototype.unitAxisVectors = [J.viewer.JC.axisX, J.viewer.JC.axisY, J.viewer.JC.axisZ, J.viewer.JC.axisNX, J.viewer.JC.axisNY, J.viewer.JC.axisNZ];
Clazz_defineStatics (c$,
"XY_ZTOP", 100,
"DEFAULT_PERCENT_VDW_ATOM", 23,
"DEFAULT_BOND_RADIUS", 0.15,
"DEFAULT_BOND_MILLIANGSTROM_RADIUS", Clazz_floatToShort (150.0),
"DEFAULT_STRUT_RADIUS", 0.3,
"DEFAULT_BOND_TOLERANCE", 0.45,
"DEFAULT_MIN_BOND_DISTANCE", 0.4,
"DEFAULT_MAX_CONNECT_DISTANCE", 100000000,
"DEFAULT_MIN_CONNECT_DISTANCE", 0.1,
"MINIMIZATION_ATOM_MAX", 200,
"MINIMIZE_FIXED_RANGE", 5.0,
"ENC_CALC_MAX_DIST", 3,
"ENV_CALC_MAX_LEVEL", 3,
"LABEL_FRONT_FLAG", 0x20,
"LABEL_GROUP_FLAG", 0x10,
"LABEL_POINTER_FLAGS", 0x03,
"LABEL_ALIGN_FLAGS", 0x0C,
"LABEL_ZPOS_FLAGS", 0x30,
"LABEL_SCALE_FLAG", 0x40,
"LABEL_EXACT_OFFSET_FLAG", 0x80,
"LABEL_FLAGS", 0xFF,
"LABEL_FLAG_OFFSET", 8,
"MOUSE_NONE", -1,
"MULTIBOND_NEVER", 0,
"MULTIBOND_WIREFRAME", 1,
"MULTIBOND_NOTSMALL", 2,
"MULTIBOND_ALWAYS", 3,
"MAXIMUM_AUTO_BOND_COUNT", 20,
"madMultipleBondSmallMaximum", 500,
"ANGSTROMS_PER_BOHR", 0.5291772,
"altArgbsCpk", [0xFFFF1493, 0xFFBFA6A6, 0xFFFFFF30, 0xFF57178F, 0xFFFFFFC0, 0xFFFFFFA0, 0xFFD8D8D8, 0xFF505050, 0xFF404040, 0xFF105050],
"argbsAmino", [0xFFBEA06E, 0xFFC8C8C8, 0xFF145AFF, 0xFF00DCDC, 0xFFE60A0A, 0xFFE6E600, 0xFF00DCDC, 0xFFE60A0A, 0xFFEBEBEB, 0xFF8282D2, 0xFF0F820F, 0xFF0F820F, 0xFF145AFF, 0xFFE6E600, 0xFF3232AA, 0xFFDC9682, 0xFFFA9600, 0xFFFA9600, 0xFFB45AB4, 0xFF3232AA, 0xFF0F820F, 0xFFFF69B4, 0xFFFF69B4, 0xFFBEA06E],
"argbShapelyBackbone", 0xFFB8B8B8,
"argbShapelySpecial", 0xFF5E005E,
"argbShapelyDefault", 0xFFFF00FF,
"argbsChainAtom", [0xFFffffff, 0xFFC0D0FF, 0xFFB0FFB0, 0xFFFFC0C8, 0xFFFFFF80, 0xFFFFC0FF, 0xFFB0F0F0, 0xFFFFD070, 0xFFF08080, 0xFFF5DEB3, 0xFF00BFFF, 0xFFCD5C5C, 0xFF66CDAA, 0xFF9ACD32, 0xFFEE82EE, 0xFF00CED1, 0xFF00FF7F, 0xFF3CB371, 0xFF00008B, 0xFFBDB76B, 0xFF006400, 0xFF800000, 0xFF808000, 0xFF800080, 0xFF008080, 0xFFB8860B, 0xFFB22222],
"argbsChainHetero", [0xFFffffff, -7298865, -8335464, -3174224, -3158160, -3174193, -8339264, -3170208, -4173712, -3821949, -16734257, -4895668, -11094638, -7686870, -4296002, -16730463, -16724113, -13329567, -16777029, -5922981, -16739328, -5242880, -5197824, -5242704, -16731984, -1526253, -4050382],
"argbsFormalCharge", [0xFFFF0000, 0xFFFF4040, 0xFFFF8080, 0xFFFFC0C0, 0xFFFFFFFF, 0xFFD8D8FF, 0xFFB4B4FF, 0xFF9090FF, 0xFF6C6CFF, 0xFF4848FF, 0xFF2424FF, 0xFF0000FF],
"argbsRwbScale", [0xFFFF0000, 0xFFFF1010, 0xFFFF2020, 0xFFFF3030, 0xFFFF4040, 0xFFFF5050, 0xFFFF6060, 0xFFFF7070, 0xFFFF8080, 0xFFFF9090, 0xFFFFA0A0, 0xFFFFB0B0, 0xFFFFC0C0, 0xFFFFD0D0, 0xFFFFE0E0, 0xFFFFFFFF, 0xFFE0E0FF, 0xFFD0D0FF, 0xFFC0C0FF, 0xFFB0B0FF, 0xFFA0A0FF, 0xFF9090FF, 0xFF8080FF, 0xFF7070FF, 0xFF6060FF, 0xFF5050FF, 0xFF4040FF, 0xFF3030FF, 0xFF2020FF, 0xFF1010FF, 0xFF0000FF]);
c$.FORMAL_CHARGE_COLIX_RED = c$.prototype.FORMAL_CHARGE_COLIX_RED = J.util.Elements.elementSymbols.length;
c$.PARTIAL_CHARGE_COLIX_RED = c$.prototype.PARTIAL_CHARGE_COLIX_RED = J.util.Elements.elementSymbols.length + J.viewer.JC.argbsFormalCharge.length;
c$.PARTIAL_CHARGE_RANGE_SIZE = c$.prototype.PARTIAL_CHARGE_RANGE_SIZE = J.viewer.JC.argbsRwbScale.length;
Clazz_defineStatics (c$,
"argbsRoygbScale", [0xFFFF0000, 0xFFFF2000, 0xFFFF4000, 0xFFFF6000, 0xFFFF8000, 0xFFFFA000, 0xFFFFC000, 0xFFFFE000, 0xFFFFF000, 0xFFFFFF00, 0xFFF0F000, 0xFFE0FF00, 0xFFC0FF00, 0xFFA0FF00, 0xFF80FF00, 0xFF60FF00, 0xFF40FF00, 0xFF20FF00, 0xFF00FF00, 0xFF00FF20, 0xFF00FF40, 0xFF00FF60, 0xFF00FF80, 0xFF00FFA0, 0xFF00FFC0, 0xFF00FFE0, 0xFF00FFFF, 0xFF00E0FF, 0xFF00C0FF, 0xFF00A0FF, 0xFF0080FF, 0xFF0060FF, 0xFF0040FF, 0xFF0020FF, 0xFF0000FF],
"argbsIsosurfacePositive", 0xFF5020A0,
"argbsIsosurfaceNegative", 0xFFA02050,
"specialAtomNames", [null, "N", "CA", "C", "O", "O1", "O5'", "C5'", "C4'", "C3'", "O3'", "C2'", "C1'", "P", "OD1", "OD2", "OE1", "OE2", "SG", null, null, null, null, null, null, null, null, null, null, null, null, null, "N1", "C2", "N3", "C4", "C5", "C6", "O2", "N7", "C8", "N9", "N4", "N2", "N6", "C5M", "O6", "O4", "S4", "C7", "H1", "H2", "H3", null, null, null, null, null, null, null, null, null, null, null, "OXT", "H", "1H", "2H", "3H", "HA", "1HA", "2HA", "H5T", "O5T", "O1P", "OP1", "O2P", "OP2", "O4'", "O2'", "1H5'", "2H5'", "H4'", "H3'", "1H2'", "2H2'", "2HO'", "H1'", "H3T", "HO3'", "HO5'", "HA2", "HA3", "HA2", "H5'", "H5''", "H2'", "H2''", "HO2'", "O3P", "OP3"]);
c$.ATOMID_MAX = c$.prototype.ATOMID_MAX = J.viewer.JC.specialAtomNames.length;
Clazz_defineStatics (c$,
"ATOMID_AMINO_NITROGEN", 1,
"ATOMID_ALPHA_CARBON", 2,
"ATOMID_CARBONYL_CARBON", 3,
"ATOMID_CARBONYL_OXYGEN", 4,
"ATOMID_O1", 5,
"ATOMID_ALPHA_ONLY_MASK", 4,
"ATOMID_PROTEIN_MASK", 14,
"ATOMID_O5_PRIME", 6,
"ATOMID_C4_PRIME", 8,
"ATOMID_C3_PRIME", 9,
"ATOMID_O3_PRIME", 10,
"ATOMID_C1_PRIME", 12,
"ATOMID_NUCLEIC_MASK", 8128,
"ATOMID_NUCLEIC_PHOSPHORUS", 13,
"ATOMID_PHOSPHORUS_ONLY_MASK", 8192,
"ATOMID_DISTINGUISHING_ATOM_MAX", 14,
"ATOMID_CARBONYL_OD1", 14,
"ATOMID_CARBONYL_OD2", 15,
"ATOMID_CARBONYL_OE1", 16,
"ATOMID_CARBONYL_OE2", 17,
"ATOMID_SG", 18,
"ATOMID_N1", 32,
"ATOMID_C2", 33,
"ATOMID_N3", 34,
"ATOMID_C4", 35,
"ATOMID_C5", 36,
"ATOMID_C6", 37,
"ATOMID_O2", 38,
"ATOMID_N7", 39,
"ATOMID_C8", 40,
"ATOMID_N9", 41,
"ATOMID_N4", 42,
"ATOMID_N2", 43,
"ATOMID_N6", 44,
"ATOMID_C5M", 45,
"ATOMID_O6", 46,
"ATOMID_O4", 47,
"ATOMID_S4", 48,
"ATOMID_C7", 49,
"ATOMID_TERMINATING_OXT", 64,
"ATOMID_H5T_TERMINUS", 72,
"ATOMID_O5T_TERMINUS", 73,
"ATOMID_O1P", 74,
"ATOMID_OP1", 75,
"ATOMID_O2P", 76,
"ATOMID_OP2", 77,
"ATOMID_O2_PRIME", 79,
"ATOMID_H3T_TERMINUS", 88,
"ATOMID_HO3_PRIME", 89,
"ATOMID_HO5_PRIME", 90,
"htSpecialAtoms", null,
"GROUPID_ARGININE", 2,
"GROUPID_ASPARAGINE", 3,
"GROUPID_ASPARTATE", 4,
"GROUPID_CYSTEINE", 5,
"GROUPID_GLUTAMINE", 6,
"GROUPID_GLUTAMATE", 7,
"GROUPID_HISTIDINE", 9,
"GROUPID_LYSINE", 12,
"GROUPID_PROLINE", 15,
"GROUPID_TRYPTOPHAN", 19,
"GROUPID_AMINO_MAX", 24,
"GROUPID_NUCLEIC_MAX", 42,
"GROUPID_WATER", 42,
"GROUPID_SOLVENT_MIN", 45,
"GROUPID_ION_MIN", 46,
"GROUPID_ION_MAX", 48,
"predefinedGroup3Names", ["", "ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "GLY", "HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL", "ASX", "GLX", "UNK", "G", "C", "A", "T", "U", "I", "DG", "DC", "DA", "DT", "DU", "DI", "+G", "+C", "+A", "+T", "+U", "+I", "HOH", "DOD", "WAT", "UREA", "PO4", "SO4", "UNL"],
"naNoH", "A3;A1;C3;G3;I3",
"aaSp2", "ARGN;ASNN;ASNO;ASPO;GLNN;GLNO;GLUO;HISN;HISC;PHECTRPC;TRPN;TYRC",
"aaPlus", "LYSN",
"pdbBondInfo", ["", "N N CA HA C O CB HB?", "N N CA HA C O CB HB2@HB3 CG HG2@HG3 CD D NE HE CZ NH1 NH1 HH11@HH12 NH2 HH21@HH22", "N N CA HA C O CB B CG OD1 ND2 HD21@HD22", "N N CA HA C O CB B CG OD1", "N N CA HA C O CB B SG HG", "N N CA HA C O CB B CG G CD OE1 NE2 HE21@HE22", "N N CA HA C O CB B CG G CD OE1", "N N CA HA2@HA3 C O", "N N CA HA C O CB B CG CD2 ND1 CE1 ND1 HD1 CD2 HD2 CE1 HE1 NE2 HE2", "N N CA HA C O CB HB CG1 HG12@HG13 CG2 HG2? CD1 HD1?", "N N CA HA C O CB HB2@HB3 CG HG CD1 HD1? CD2 HD2?", "N N CA HA C O CB B CG G CD HD2@HD3 CE HE3@HE2 NZ HZ?", "N N CA HA C O CB HB2@HB3 CG HG2@HG3 CE HE?", "N N CA HA C O CB B CG CD1 CD1 HD1 CD2 CE2 CD2 HD2 CE1 CZ CE1 HE1 CE2 HE2 CZ HZ", "N H CA HA C O CB B CG G CD HD2@HD3", "N N CA HA C O CB B OG HG", "N N CA HA C O CB HB OG1 HG1 CG2 HG2?", "N N CA HA C O CB B CG CD1 CD1 HD1 CD2 CE2 NE1 HE1 CE3 CZ3 CE3 HE3 CZ2 CH2 CZ2 HZ2 CZ3 HZ3 CH2 HH2", "N N CA HA C O CB B CG CD1 CD1 HD1 CD2 CE2 CD2 HD2 CE1 CZ CE1 HE1 CE2 HE2 OH HH", "N N CA HA C O CB HB CG1 HG1? CG2 HG2?", "CA HA C O CB HB2@HB1 C H", "CA HA C O CB HB1 CB HB2 CG HG1 CG HG2", "", "P OP1 C5' 5 C4' H4' C3' H3' C2' H2' O2' HO2' C1' H1' C8 N7 C8 H8 C5 C4 C6 O6 N1 H1 C2 N3 N2 H21@H22 O3' HO3' O5' HO5'", "P OP1 C5' 5 C4' H4' C3' H3' C2' H2' O2' HO2' C1' H1' C2 O2 N3 C4 N4 H41@H42 C5 C6 C5 H5 C6 H6 O3' HO3' O5' HO5'", "P OP1 C5' 5 C4' H4' C3' H3' C2' H2' O2' HO2' C1' H1' C8 N7 C8 H8 C5 C4 C6 N1 N6 H61@H62 C2 N3 C2 H2 O3' HO3' O5' HO5'", "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C2 O2 N3 H3 C4 O4 C5 C6 C7 H7? C6 H6 O3' HO3' O5' HO5'", "P OP1 C5' 5 C4' H4' C3' H3' C2' H2' O2' HO2' C1' H1' C2 O2 N3 H3 C4 O4 C5 C6 C5 H5 C6 H6 O3' HO3' O5' HO5'", "P OP1 C5' 5 C4' H4' C3' H3' C2' H2' O2' HO2' C1' H1' C8 N7 C8 H8 C5 C4 C6 O6 N1 H1 C2 N3 C2 H2 O3' HO3' O5' HO5'", "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C8 N7 C8 H8 C5 C4 C6 O6 N1 H1 C2 N3 N2 H21@H22 O3' HO3' O5' HO5'", "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C2 O2 N3 C4 N4 H41@H42 C5 C6 C5 H5 C6 H6 O3' HO3' O5' HO5'", "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C8 N7 C8 H8 C5 C4 C6 N1 N6 H61@H62 C2 N3 C2 H2 O3' HO3' O5' HO5'", "P OP1 C5' H5'@H5'' C4' H4' C3' H3' C2' H2'@H2'' C1' H1' C2 O2 N3 H3 C4 O4 C5 C6 C7 H7? C6 H6 O3' HO3' O5' HO5'", "P OP1 C5' 5 C4' H4' C3' H3' C2' H2'@H2'' C1' H1' C2 O2 N3 H3 C4 O4 C5 C6 C5 H5 C6 H6 O3' HO3' O5' HO5'", "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C8 N7 C8 H8 C5 C4 C6 O6 N1 H1 C2 N3 C2 H2 O3' HO3' O5' HO5'"],
"pdbHydrogenCount", [0, 6, 16, 7, 6, 6, 9, 8, 4, 9, 12, 12, 14, 10, 10, 8, 6, 8, 11, 10, 10, 3, 5, 0, 13, 13, 13, -1, 12, 12, 13, 13, 13, 14, 12, 12],
"argbsShapely", [0xFFFF00FF, 0xFF00007C, 0xFFFF7C70, 0xFF8CFF8C, 0xFFA00042, 0xFFFFFF70, 0xFFFF4C4C, 0xFF660000, 0xFFFFFFFF, 0xFF7070FF, 0xFF004C00, 0xFF455E45, 0xFF4747B8, 0xFF534C52, 0xFFB8A042, 0xFF525252, 0xFFFF7042, 0xFFB84C00, 0xFF4F4600, 0xFF8C704C, 0xFFFF8CFF, 0xFFFF00FF, 0xFFFF00FF, 0xFFFF00FF, 0xFFFF7070, 0xFFFF8C4B, 0xFFA0A0FF, 0xFFA0FFA0, 0xFFFF8080, 0xFF80FFFF, 0xFFFF7070, 0xFFFF8C4B, 0xFFA0A0FF, 0xFFA0FFA0, 0xFFFF8080, 0xFF80FFFF, 0xFFFF7070, 0xFFFF8C4B, 0xFFA0A0FF, 0xFFA0FFA0, 0xFFFF8080, 0xFF80FFFF],
"allCarbohydrates", ",[AHR],[ALL],[AMU],[ARA],[ARB],[BDF],[BDR],[BGC],[BMA],[FCA],[FCB],[FRU],[FUC],[FUL],[GAL],[GLA],[GLC],[GXL],[GUP],[LXC],[MAN],[RAM],[RIB],[RIP],[XYP],[XYS],[CBI],[CT3],[CTR],[CTT],[LAT],[MAB],[MAL],[MLR],[MTT],[SUC],[TRE],[GCU],[MTL],[NAG],[NDG],[RHA],[SOR],[SOL],[SOE],[XYL],[A2G],[LBT],[NGA],[SIA],[SLB],[AFL],[AGC],[GLB],[NAN],[RAA]",
"group3List", null,
"group3Count", 0,
"predefinedGroup1Names", ['\0', 'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', 'A', 'G', '?', 'G', 'C', 'A', 'T', 'U', 'I', 'G', 'C', 'A', 'T', 'U', 'I', 'G', 'C', 'A', 'T', 'U', 'I', 'I'],
"predefinedVariable", ["@_1H _H & !(_2H,_3H)", "@_12C _C & !(_13C,_14C)", "@_14N _N & !(_15N)", "@water _g>=42 & _g<45, oxygen & connected(2) & connected(2, hydrogen), (hydrogen) & connected(oxygen & connected(2) & connected(2, hydrogen))", "@solvent water, (_g>=45 & _g<48)", "@ligand _g=0|!(_g<46,protein,nucleic,water)", "@turn structure=1", "@sheet structure=2", "@helix structure=3", "@helix310 substructure=7", "@helixalpha substructure=8", "@helixpi substructure=9", "@bonded bondcount>0"],
"predefinedStatic", ["@amino _g>0 & _g<=23", "@acidic asp,glu", "@basic arg,his,lys", "@charged acidic,basic", "@negative acidic", "@positive basic", "@neutral amino&!(acidic,basic)", "@polar amino&!hydrophobic", "@cyclic his,phe,pro,trp,tyr", "@acyclic amino&!cyclic", "@aliphatic ala,gly,ile,leu,val", "@aromatic his,phe,trp,tyr", "@cystine within(group, (cys.sg or cyx.sg) and connected(cys.sg or cyx.sg))", "@buried ala,cys,ile,leu,met,phe,trp,val", "@surface amino&!buried", "@hydrophobic ala,gly,ile,leu,met,phe,pro,trp,tyr,val", "@mainchain backbone", "@small ala,gly,ser", "@medium asn,asp,cys,pro,thr,val", "@large arg,glu,gln,his,ile,leu,lys,met,phe,trp,tyr", "@c nucleic & ([C] or [DC] or within(group,_a=42))", "@g nucleic & ([G] or [DG] or within(group,_a=43))", "@cg c,g", "@a nucleic & ([A] or [DA] or within(group,_a=44))", "@t nucleic & ([T] or [DT] or within(group,_a=45 | _a=49))", "@at a,t", "@i nucleic & ([I] or [DI] or within(group,_a=46) & !g)", "@u nucleic & ([U] or [DU] or within(group,_a=47) & !t)", "@tu nucleic & within(group,_a=48)", "@ions _g>=46&_g<48", "@alpha _a=2", "@backbone protein&(_a>=1&_a<6|_a>=64&_a<72)|nucleic&(_a>=6&_a<14|_a>=72)", "@spine protein&_a>=1&_a<4|nucleic&_a>=6&_a<14&_a!=12", "@sidechain (protein,nucleic) & !backbone", "@base nucleic & !backbone", "@dynamic_flatring search('[a]')"],
"databases", ["ligand", "http://www.rcsb.org/pdb/files/ligand/%FILE.cif", "mp", "http://www.materialsproject.org/materials/%FILE/cif", "nci", "http://cactus.nci.nih.gov/chemical/structure/%FILE", "nmr", "http://www.nmrdb.org/predictor?POST?molfile=", "nmrdb", "http://www.nmrdb.org/service/predictor?POST?molfile=", "pdb", "http://www.rcsb.org/pdb/files/%FILE.pdb.gz", "pubchem", "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d"],
"MODELKIT_ZAP_STRING", "5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63",
"MODELKIT_ZAP_TITLE", "Jmol Model Kit",
"ADD_HYDROGEN_TITLE", "Viewer.AddHydrogens",
"DEFAULT_FONTFACE", "SansSerif",
"DEFAULT_FONTSTYLE", "Plain",
"LABEL_MINIMUM_FONTSIZE", 6,
"LABEL_MAXIMUM_FONTSIZE", 63,
"LABEL_DEFAULT_FONTSIZE", 13,
"LABEL_DEFAULT_X_OFFSET", 4,
"LABEL_DEFAULT_Y_OFFSET", 4,
"MEASURE_DEFAULT_FONTSIZE", 15,
"AXES_DEFAULT_FONTSIZE", 14,
"SHAPE_BALLS", 0,
"SHAPE_STICKS", 1,
"SHAPE_HSTICKS", 2,
"SHAPE_SSSTICKS", 3,
"SHAPE_STRUTS", 4,
"SHAPE_LABELS", 5,
"SHAPE_MEASURES", 6,
"SHAPE_STARS", 7,
"SHAPE_HALOS", 8,
"SHAPE_MIN_SECONDARY", 9,
"SHAPE_BACKBONE", 9,
"SHAPE_TRACE", 10,
"SHAPE_CARTOON", 11,
"SHAPE_STRANDS", 12,
"SHAPE_MESHRIBBON", 13,
"SHAPE_RIBBONS", 14,
"SHAPE_ROCKETS", 15,
"SHAPE_MAX_SECONDARY", 16,
"SHAPE_MIN_SPECIAL", 16,
"SHAPE_DOTS", 16,
"SHAPE_DIPOLES", 17,
"SHAPE_VECTORS", 18,
"SHAPE_GEOSURFACE", 19,
"SHAPE_ELLIPSOIDS", 20,
"SHAPE_MAX_SIZE_ZERO_ON_RESTRICT", 21,
"SHAPE_POLYHEDRA", 21,
"SHAPE_MIN_HAS_ID", 22,
"SHAPE_MIN_MESH_COLLECTION", 22,
"SHAPE_DRAW", 22,
"SHAPE_MAX_SPECIAL", 23,
"SHAPE_CGO", 23,
"SHAPE_MIN_SURFACE", 24,
"SHAPE_ISOSURFACE", 24,
"SHAPE_CONTACT", 25,
"SHAPE_LCAOCARTOON", 26,
"SHAPE_MO", 27,
"SHAPE_PMESH", 28,
"SHAPE_PLOT3D", 29,
"SHAPE_MAX_SURFACE", 29,
"SHAPE_MAX_MESH_COLLECTION", 29,
"SHAPE_ECHO", 30,
"SHAPE_MAX_HAS_ID", 31,
"SHAPE_AXES", 31,
"SHAPE_BBCAGE", 32,
"SHAPE_UCCAGE", 33,
"SHAPE_HOVER", 34,
"SHAPE_FRANK", 35,
"SHAPE_MAX", 36,
"shapeClassBases", ["Balls", "Sticks", "Hsticks", "Sssticks", "Struts", "Labels", "Measures", "Stars", "Halos", "Backbone", "Trace", "Cartoon", "Strands", "MeshRibbon", "Ribbons", "Rockets", "Dots", "Dipoles", "Vectors", "GeoSurface", "Ellipsoids", "Polyhedra", "Draw", "CGO", "Isosurface", "Contact", "LcaoCartoon", "MolecularOrbital", "Pmesh", "Plot3D", "Echo", "Axes", "Bbcage", "Uccage", "Hover", "Frank"],
"ATOM_IN_FRAME", 1,
"ATOM_SLABBED", 2,
"binaryExtensions", ";pse=PyMOL;",
"SCRIPT_COMPLETED", "Script completed",
"JPEG_EXTENSIONS", ";jpg;jpeg;jpg64;jpeg64;");
c$.IMAGE_TYPES = c$.prototype.IMAGE_TYPES = ";jpg;jpeg;jpg64;jpeg64;gif;pdf;ppm;png;pngj;pngt;";
c$.IMAGE_OR_SCENE = c$.prototype.IMAGE_OR_SCENE = ";jpg;jpeg;jpg64;jpeg64;gif;pdf;ppm;png;pngj;pngt;scene;";
{
if (J.viewer.JC.argbsFormalCharge.length != 12) {
J.util.Logger.error ("formal charge color table length");
throw  new NullPointerException ();
}if (J.viewer.JC.shapeClassBases.length != 36) {
J.util.Logger.error ("shapeClassBases wrong length");
throw  new NullPointerException ();
}if (J.viewer.JC.argbsAmino.length != 24) {
J.util.Logger.error ("argbsAmino wrong length");
throw  new NullPointerException ();
}if (J.viewer.JC.argbsShapely.length != 42) {
J.util.Logger.error ("argbsShapely wrong length");
throw  new NullPointerException ();
}if (J.viewer.JC.argbsChainHetero.length != J.viewer.JC.argbsChainAtom.length) {
J.util.Logger.error ("argbsChainHetero wrong length");
throw  new NullPointerException ();
}if (J.viewer.JC.shapeClassBases.length != 36) {
J.util.Logger.error ("the shapeClassBases array has the wrong length");
throw  new NullPointerException ();
}}Clazz_defineStatics (c$,
"hAlignNames", ["", "left", "center", "right", ""],
"vAlignNames", ["xy", "top", "bottom", "middle"],
"POINTER_NONE", 0,
"POINTER_ON", 1,
"POINTER_BACKGROUND", 2,
"VALIGN_XY", 0,
"VALIGN_TOP", 1,
"VALIGN_BOTTOM", 2,
"VALIGN_MIDDLE", 3,
"VALIGN_XYZ", 4,
"ALIGN_NONE", 0,
"ALIGN_LEFT", 1,
"ALIGN_CENTER", 2,
"ALIGN_RIGHT", 3);
});
Clazz_declarePackage ("J.util");
c$ = Clazz_decorateAsClass (function () {
this.entryCount = 0;
this.entries = null;
Clazz_instantialize (this, arguments);
}, J.util, "Int2IntHash");
Clazz_makeConstructor (c$, 
function (initialCapacity) {
this.entries =  new Array (initialCapacity);
}, "~N");
$_M(c$, "get", 
function (key) {
var entries = this.entries;
var hash = (key & 0x7FFFFFFF) % entries.length;
for (var e = entries[hash]; e != null; e = e.next) if (e.key == key) return e.value;

return -2147483648;
}, "~N");
$_M(c$, "put", 
function (key, value) {
var entries = this.entries;
var hash = (key & 0x7FFFFFFF) % entries.length;
for (var e = entries[hash]; e != null; e = e.next) if (e.key == key) {
e.value = value;
return;
}
if (this.entryCount > entries.length) this.rehash ();
entries = this.entries;
hash = (key & 0x7FFFFFFF) % entries.length;
entries[hash] =  new J.util.Int2IntHash.Entry (key, value, entries[hash]);
++this.entryCount;
}, "~N,~N");
$_M(c$, "rehash", 
function () {
var oldEntries = this.entries;
var oldSize = oldEntries.length;
var newSize = oldSize * 2 + 1;
var newEntries =  new Array (newSize);
for (var i = oldSize; --i >= 0; ) {
for (var e = oldEntries[i]; e != null; ) {
var t = e;
e = e.next;
var hash = (t.key & 0x7FFFFFFF) % newSize;
t.next = newEntries[hash];
newEntries[hash] = t;
}
}
this.entries = newEntries;
});
Clazz_pu$h ();
c$ = Clazz_decorateAsClass (function () {
this.key = 0;
this.value = 0;
this.next = null;
Clazz_instantialize (this, arguments);
}, J.util.Int2IntHash, "Entry");
Clazz_makeConstructor (c$, 
function (a, b, c) {
this.key = a;
this.value = b;
this.next = c;
}, "~N,~N,J.util.Int2IntHash.Entry");
c$ = Clazz_p0p ();
Clazz_declarePackage ("J.util");
Clazz_load (["J.util.Int2IntHash"], "J.util.C", ["java.lang.Float", "JU.AU", "$.CU", "$.PT", "$.SB", "J.constant.EnumPalette", "J.util.Escape", "$.Logger"], function () {
c$ = Clazz_declareType (J.util, "C");
Clazz_makeConstructor (c$, 
function () {
});
c$.getColix = $_M(c$, "getColix", 
function (argb) {
if (argb == 0) return 0;
var translucentFlag = 0;
if ((argb & 0xFF000000) != (-16777216)) {
translucentFlag = J.util.C.getTranslucentFlag ((argb >> 24) & 0xFF);
argb |= 0xFF000000;
}var c = J.util.C.colixHash.get (argb);
if ((c & 3) == 3) translucentFlag = 0;
return ((c > 0 ? c : J.util.C.allocateColix (argb)) | translucentFlag);
}, "~N");
c$.allocateColix = $_M(c$, "allocateColix", 
function (argb) {
for (var i = J.util.C.colixMax; --i >= 4; ) if ((argb & 0xFFFFFF) == (J.util.C.argbs[i] & 0xFFFFFF)) return i;

if (J.util.C.colixMax == J.util.C.argbs.length) {
var oldSize = J.util.C.colixMax;
var newSize = oldSize * 2;
if (newSize > 2048) newSize = 2048;
($t$ = J.util.C.argbs = JU.AU.arrayCopyI (J.util.C.argbs, newSize), J.util.C.prototype.argbs = J.util.C.argbs, $t$);
if (J.util.C.argbsGreyscale != null) ($t$ = J.util.C.argbsGreyscale = JU.AU.arrayCopyI (J.util.C.argbsGreyscale, newSize), J.util.C.prototype.argbsGreyscale = J.util.C.argbsGreyscale, $t$);
}J.util.C.argbs[J.util.C.colixMax] = argb;
if (J.util.C.argbsGreyscale != null) J.util.C.argbsGreyscale[J.util.C.colixMax] = JU.CU.toFFGGGfromRGB (argb);
J.util.C.colixHash.put (argb, J.util.C.colixMax);
return (J.util.C.colixMax < 2047 ? ($t$ = J.util.C.colixMax ++, J.util.C.prototype.colixMax = J.util.C.colixMax, $t$) : J.util.C.colixMax);
}, "~N");
c$.setLastGrey = $_M(c$, "setLastGrey", 
function (argb) {
J.util.C.calcArgbsGreyscale ();
J.util.C.argbsGreyscale[2047] = JU.CU.toFFGGGfromRGB (argb);
}, "~N");
c$.calcArgbsGreyscale = $_M(c$, "calcArgbsGreyscale", 
function () {
if (J.util.C.argbsGreyscale != null) return;
var a =  Clazz_newIntArray (J.util.C.argbs.length, 0);
for (var i = J.util.C.argbs.length; --i >= 4; ) a[i] = JU.CU.toFFGGGfromRGB (J.util.C.argbs[i]);

($t$ = J.util.C.argbsGreyscale = a, J.util.C.prototype.argbsGreyscale = J.util.C.argbsGreyscale, $t$);
});
c$.getArgbGreyscale = $_M(c$, "getArgbGreyscale", 
function (colix) {
if (J.util.C.argbsGreyscale == null) J.util.C.calcArgbsGreyscale ();
return J.util.C.argbsGreyscale[colix & -30721];
}, "~N");
c$.getColixO = $_M(c$, "getColixO", 
function (obj) {
if (obj == null) return 0;
if (Clazz_instanceOf (obj, J.constant.EnumPalette)) return ((obj) === J.constant.EnumPalette.NONE ? 0 : 2);
if (Clazz_instanceOf (obj, Integer)) return J.util.C.getColix ((obj).intValue ());
if (Clazz_instanceOf (obj, String)) return J.util.C.getColixS (obj);
if (Clazz_instanceOf (obj, Byte)) return ((obj).byteValue () == 0 ? 0 : 2);
if (J.util.Logger.debugging) {
J.util.Logger.debug ("?? getColix(" + obj + ")");
}return 22;
}, "~O");
c$.getTranslucentFlag = $_M(c$, "getTranslucentFlag", 
function (translucentLevel) {
if (translucentLevel == 0) return 0;
if (translucentLevel < 0) return 30720;
if (Float.isNaN (translucentLevel) || translucentLevel >= 255 || translucentLevel == 1.0) return 16384;
var iLevel = Clazz_doubleToInt (Math.floor (translucentLevel < 1 ? translucentLevel * 256 : translucentLevel <= 9 ? (Clazz_doubleToInt (Math.floor (translucentLevel - 1))) << 5 : translucentLevel < 15 ? 256 : translucentLevel));
return (((iLevel >> 5) & 0xF) << 11);
}, "~N");
c$.isColixLastAvailable = $_M(c$, "isColixLastAvailable", 
function (colix) {
return (colix > 0 && (colix & 2047) == 2047);
}, "~N");
c$.getArgb = $_M(c$, "getArgb", 
function (colix) {
return J.util.C.argbs[colix & -30721];
}, "~N");
c$.isColixColorInherited = $_M(c$, "isColixColorInherited", 
function (colix) {
switch (colix) {
case 0:
case 1:
return true;
default:
return (colix & -30721) == 1;
}
}, "~N");
c$.getColixInherited = $_M(c$, "getColixInherited", 
function (myColix, parentColix) {
switch (myColix) {
case 0:
return parentColix;
case 1:
return (parentColix & -30721);
default:
return ((myColix & -30721) == 1 ? (parentColix & -30721 | myColix & 30720) : myColix);
}
}, "~N,~N");
c$.isColixTranslucent = $_M(c$, "isColixTranslucent", 
function (colix) {
return ((colix & 30720) != 0);
}, "~N");
c$.getChangeableColixIndex = $_M(c$, "getChangeableColixIndex", 
function (colix) {
return (colix >= 0 ? -1 : (colix & 2047));
}, "~N");
c$.getColixTranslucent3 = $_M(c$, "getColixTranslucent3", 
function (colix, isTranslucent, translucentLevel) {
colix &= -30721;
if (colix == 0) colix = 1;
return (isTranslucent ? (colix | J.util.C.getTranslucentFlag (translucentLevel)) : colix);
}, "~N,~B,~N");
c$.copyColixTranslucency = $_M(c$, "copyColixTranslucency", 
function (colixFrom, colixTo) {
return J.util.C.getColixTranslucent3 (colixTo, J.util.C.isColixTranslucent (colixFrom), J.util.C.getColixTranslucencyLevel (colixFrom));
}, "~N,~N");
c$.getColixTranslucencyFractional = $_M(c$, "getColixTranslucencyFractional", 
function (colix) {
var translevel = J.util.C.getColixTranslucencyLevel (colix);
return (translevel == -1 ? 0.5 : translevel == 0 ? 0 : translevel == 255 ? 1 : translevel / 256);
}, "~N");
c$.getColixTranslucencyLevel = $_M(c$, "getColixTranslucencyLevel", 
function (colix) {
var logAlpha = (colix >> 11) & 0xF;
switch (logAlpha) {
case 0:
return 0;
case 1:
case 2:
case 3:
case 4:
case 5:
case 6:
case 7:
return logAlpha << 5;
case 15:
return -1;
default:
return 255;
}
}, "~N");
c$.getColixS = $_M(c$, "getColixS", 
function (colorName) {
var argb = JU.CU.getArgbFromString (colorName);
if (argb != 0) return J.util.C.getColix (argb);
if ("none".equalsIgnoreCase (colorName)) return 0;
if ("opaque".equalsIgnoreCase (colorName)) return 1;
return 2;
}, "~S");
c$.getColixArray = $_M(c$, "getColixArray", 
function (colorNames) {
if (colorNames == null || colorNames.length == 0) return null;
var colors = JU.PT.getTokens (colorNames);
var colixes =  Clazz_newShortArray (colors.length, 0);
for (var j = 0; j < colors.length; j++) {
colixes[j] = J.util.C.getColix (JU.CU.getArgbFromString (colors[j]));
if (colixes[j] == 0) return null;
}
return colixes;
}, "~S");
c$.getHexCode = $_M(c$, "getHexCode", 
function (colix) {
return J.util.Escape.escapeColor (J.util.C.getArgb (colix));
}, "~N");
c$.getHexCodes = $_M(c$, "getHexCodes", 
function (colixes) {
if (colixes == null) return null;
var s =  new JU.SB ();
for (var i = 0; i < colixes.length; i++) s.append (i == 0 ? "" : " ").append (J.util.C.getHexCode (colixes[i]));

return s.toString ();
}, "~A");
c$.getColixTranslucent = $_M(c$, "getColixTranslucent", 
function (argb) {
var a = (argb >> 24) & 0xFF;
return (a == 0xFF ? J.util.C.getColix (argb) : J.util.C.getColixTranslucent3 (J.util.C.getColix (argb), true, a / 255));
}, "~N");
c$.getBgContrast = $_M(c$, "getBgContrast", 
function (argb) {
return ((JU.CU.toFFGGGfromRGB (argb) & 0xFF) < 128 ? 8 : 4);
}, "~N");
Clazz_defineStatics (c$,
"INHERIT_ALL", 0,
"INHERIT_COLOR", 1,
"USE_PALETTE", 2,
"RAW_RGB", 3,
"SPECIAL_COLIX_MAX", 4,
"colixMax", 4,
"argbs",  Clazz_newIntArray (128, 0),
"argbsGreyscale", null);
c$.colixHash = c$.prototype.colixHash =  new J.util.Int2IntHash (256);
Clazz_defineStatics (c$,
"RAW_RGB_INT", 3,
"UNMASK_CHANGEABLE_TRANSLUCENT", 0x07FF,
"CHANGEABLE_MASK", 0x8000,
"LAST_AVAILABLE_COLIX", 2047,
"TRANSLUCENT_SHIFT", 11,
"ALPHA_SHIFT", 13,
"TRANSLUCENT_MASK", 30720,
"TRANSLUCENT_SCREENED", 30720,
"TRANSPARENT", 16384,
"OPAQUE_MASK", -30721,
"BLACK", 4,
"ORANGE", 5,
"PINK", 6,
"BLUE", 7,
"WHITE", 8,
"CYAN", 9,
"RED", 10,
"GREEN", 11,
"GRAY", 12,
"SILVER", 13,
"LIME", 14,
"MAROON", 15,
"NAVY", 16,
"OLIVE", 17,
"PURPLE", 18,
"TEAL", 19,
"MAGENTA", 20,
"YELLOW", 21,
"HOTPINK", 22,
"GOLD", 23,
"predefinedArgbs", [0xFF000000, 0xFFFFA500, 0xFFFFC0CB, 0xFF0000FF, 0xFFFFFFFF, 0xFF00FFFF, 0xFFFF0000, 0xFF008000, 0xFF808080, 0xFFC0C0C0, 0xFF00FF00, 0xFF800000, 0xFF000080, 0xFF808000, 0xFF800080, 0xFF008080, 0xFFFF00FF, 0xFFFFFF00, 0xFFFF69B4, 0xFFFFD700]);
{
for (var i = 0; i < J.util.C.predefinedArgbs.length; ++i) J.util.C.getColix (J.util.C.predefinedArgbs[i]);

}});
Clazz_declarePackage ("J.util");
Clazz_load (["JU.P4"], "J.util.Quaternion", ["java.lang.Float", "JU.A4", "$.M3", "$.P3", "$.V3", "J.util.Escape", "$.Logger", "$.Txt"], function () {
c$ = Clazz_decorateAsClass (function () {
this.q0 = 0;
this.q1 = 0;
this.q2 = 0;
this.q3 = 0;
this.mat = null;
Clazz_instantialize (this, arguments);
}, J.util, "Quaternion");
Clazz_makeConstructor (c$, 
function () {
this.q0 = 1;
});
c$.newQ = $_M(c$, "newQ", 
function (q) {
var q1 =  new J.util.Quaternion ();
q1.set (q);
return q1;
}, "J.util.Quaternion");
c$.newVA = $_M(c$, "newVA", 
function (pt, theta) {
var q =  new J.util.Quaternion ();
q.setTA (pt, theta);
return q;
}, "JU.T3,~N");
c$.newM = $_M(c$, "newM", 
function (mat) {
var q =  new J.util.Quaternion ();
q.setM (mat);
return q;
}, "JU.M3");
c$.newAA = $_M(c$, "newAA", 
function (a) {
var q =  new J.util.Quaternion ();
q.setAA (a);
return q;
}, "JU.A4");
c$.newP4 = $_M(c$, "newP4", 
function (pt) {
var q =  new J.util.Quaternion ();
q.setP4 (pt);
return q;
}, "JU.P4");
c$.new4 = $_M(c$, "new4", 
function (q0, q1, q2, q3) {
var q =  new J.util.Quaternion ();
if (q0 < -1) {
q.q0 = -1;
return q;
}if (q0 > 1) {
q.q0 = 1;
return q;
}q.q0 = q0;
q.q1 = q1;
q.q2 = q2;
q.q3 = q3;
return q;
}, "~N,~N,~N,~N");
$_M(c$, "set", 
function (q) {
this.q0 = q.q0;
this.q1 = q.q1;
this.q2 = q.q2;
this.q3 = q.q3;
}, "J.util.Quaternion");
$_M(c$, "setP4", 
function (pt) {
var factor = (pt == null ? 0 : pt.distance (J.util.Quaternion.qZero));
if (factor == 0) {
this.q0 = 1;
return;
}this.q0 = pt.w / factor;
this.q1 = pt.x / factor;
this.q2 = pt.y / factor;
this.q3 = pt.z / factor;
}, "JU.P4");
$_M(c$, "setTA", 
function (pt, theta) {
if (pt.x == 0 && pt.y == 0 && pt.z == 0) {
this.q0 = 1;
return;
}var fact = (Math.sin (theta / 2 * 0.017453292519943295) / Math.sqrt (pt.x * pt.x + pt.y * pt.y + pt.z * pt.z));
this.q0 = (Math.cos (theta / 2 * 0.017453292519943295));
this.q1 = (pt.x * fact);
this.q2 = (pt.y * fact);
this.q3 = (pt.z * fact);
}, "JU.T3,~N");
$_M(c$, "setAA", 
function (a) {
var aa = JU.A4.newAA (a);
if (aa.angle == 0) aa.y = 1;
var m3 =  new JU.M3 ();
m3.setAA (aa);
this.setM (m3);
}, "JU.A4");
$_M(c$, "setM", 
function (mat) {
this.mat = mat;
var trace = mat.m00 + mat.m11 + mat.m22;
var temp;
var w;
var x;
var y;
var z;
if (trace >= 0.5) {
w = Math.sqrt (1.0 + trace);
x = (mat.m21 - mat.m12) / w;
y = (mat.m02 - mat.m20) / w;
z = (mat.m10 - mat.m01) / w;
} else if ((temp = mat.m00 + mat.m00 - trace) >= 0.5) {
x = Math.sqrt (1.0 + temp);
w = (mat.m21 - mat.m12) / x;
y = (mat.m10 + mat.m01) / x;
z = (mat.m20 + mat.m02) / x;
} else if ((temp = mat.m11 + mat.m11 - trace) >= 0.5 || mat.m11 > mat.m22) {
y = Math.sqrt (1.0 + temp);
w = (mat.m02 - mat.m20) / y;
x = (mat.m10 + mat.m01) / y;
z = (mat.m21 + mat.m12) / y;
} else {
z = Math.sqrt (1.0 + mat.m22 + mat.m22 - trace);
w = (mat.m10 - mat.m01) / z;
x = (mat.m20 + mat.m02) / z;
y = (mat.m21 + mat.m12) / z;
}this.q0 = (w * 0.5);
this.q1 = (x * 0.5);
this.q2 = (y * 0.5);
this.q3 = (z * 0.5);
}, "JU.M3");
$_M(c$, "setRef", 
function (qref) {
if (qref == null) {
this.mul (this.getFixFactor ());
return;
}if (this.dot (qref) >= 0) return;
this.q0 *= -1;
this.q1 *= -1;
this.q2 *= -1;
this.q3 *= -1;
}, "J.util.Quaternion");
c$.getQuaternionFrame = $_M(c$, "getQuaternionFrame", 
function (center, x, xy) {
var vA = JU.V3.newV (x);
var vB = JU.V3.newV (xy);
if (center != null) {
vA.sub (center);
vB.sub (center);
}return J.util.Quaternion.getQuaternionFrameV (vA, vB, null, false);
}, "JU.P3,JU.T3,JU.T3");
c$.getQuaternionFrameV = $_M(c$, "getQuaternionFrameV", 
function (vA, vB, vC, yBased) {
if (vC == null) {
vC =  new JU.V3 ();
vC.cross (vA, vB);
if (yBased) vA.cross (vB, vC);
}var vBprime =  new JU.V3 ();
vBprime.cross (vC, vA);
vA.normalize ();
vBprime.normalize ();
vC.normalize ();
var mat =  new JU.M3 ();
mat.setColumnV (0, vA);
mat.setColumnV (1, vBprime);
mat.setColumnV (2, vC);
var q = J.util.Quaternion.newM (mat);
return q;
}, "JU.V3,JU.V3,JU.V3,~B");
$_M(c$, "getMatrix", 
function () {
if (this.mat == null) this.setMatrix ();
return this.mat;
});
$_M(c$, "setMatrix", 
function () {
this.mat =  new JU.M3 ();
this.mat.m00 = this.q0 * this.q0 + this.q1 * this.q1 - this.q2 * this.q2 - this.q3 * this.q3;
this.mat.m01 = 2 * this.q1 * this.q2 - 2 * this.q0 * this.q3;
this.mat.m02 = 2 * this.q1 * this.q3 + 2 * this.q0 * this.q2;
this.mat.m10 = 2 * this.q1 * this.q2 + 2 * this.q0 * this.q3;
this.mat.m11 = this.q0 * this.q0 - this.q1 * this.q1 + this.q2 * this.q2 - this.q3 * this.q3;
this.mat.m12 = 2 * this.q2 * this.q3 - 2 * this.q0 * this.q1;
this.mat.m20 = 2 * this.q1 * this.q3 - 2 * this.q0 * this.q2;
this.mat.m21 = 2 * this.q2 * this.q3 + 2 * this.q0 * this.q1;
this.mat.m22 = this.q0 * this.q0 - this.q1 * this.q1 - this.q2 * this.q2 + this.q3 * this.q3;
});
$_M(c$, "add", 
function (x) {
return J.util.Quaternion.newVA (this.getNormal (), this.getTheta () + x);
}, "~N");
$_M(c$, "mul", 
function (x) {
return (x == 1 ? J.util.Quaternion.new4 (this.q0, this.q1, this.q2, this.q3) : J.util.Quaternion.newVA (this.getNormal (), this.getTheta () * x));
}, "~N");
$_M(c$, "mulQ", 
function (p) {
return J.util.Quaternion.new4 (this.q0 * p.q0 - this.q1 * p.q1 - this.q2 * p.q2 - this.q3 * p.q3, this.q0 * p.q1 + this.q1 * p.q0 + this.q2 * p.q3 - this.q3 * p.q2, this.q0 * p.q2 + this.q2 * p.q0 + this.q3 * p.q1 - this.q1 * p.q3, this.q0 * p.q3 + this.q3 * p.q0 + this.q1 * p.q2 - this.q2 * p.q1);
}, "J.util.Quaternion");
$_M(c$, "div", 
function (p) {
return this.mulQ (p.inv ());
}, "J.util.Quaternion");
$_M(c$, "divLeft", 
function (p) {
return this.inv ().mulQ (p);
}, "J.util.Quaternion");
$_M(c$, "dot", 
function (q) {
return this.q0 * q.q0 + this.q1 * q.q1 + this.q2 * q.q2 + this.q3 * q.q3;
}, "J.util.Quaternion");
$_M(c$, "inv", 
function () {
return J.util.Quaternion.new4 (this.q0, -this.q1, -this.q2, -this.q3);
});
$_M(c$, "negate", 
function () {
return J.util.Quaternion.new4 (-this.q0, -this.q1, -this.q2, -this.q3);
});
$_M(c$, "getFixFactor", 
function () {
return (this.q0 < 0 || this.q0 == 0 && (this.q1 < 0 || this.q1 == 0 && (this.q2 < 0 || this.q2 == 0 && this.q3 < 0)) ? -1 : 1);
});
$_M(c$, "getVector", 
function (i) {
return this.getVectorS (i, 1);
}, "~N");
$_M(c$, "getVectorS", 
function (i, scale) {
if (i == -1) {
scale *= this.getFixFactor ();
return JU.V3.new3 (this.q1 * scale, this.q2 * scale, this.q3 * scale);
}if (this.mat == null) this.setMatrix ();
var v =  new JU.V3 ();
this.mat.getColumnV (i, v);
if (scale != 1) v.scale (scale);
return v;
}, "~N,~N");
$_M(c$, "getNormal", 
function () {
var v = J.util.Quaternion.getRawNormal (this);
v.scale (this.getFixFactor ());
return v;
});
c$.getRawNormal = $_M(c$, "getRawNormal", 
function (q) {
var v = JU.V3.new3 (q.q1, q.q2, q.q3);
if (v.length () == 0) return JU.V3.new3 (0, 0, 1);
v.normalize ();
return v;
}, "J.util.Quaternion");
$_M(c$, "getTheta", 
function () {
return (Math.acos (Math.abs (this.q0)) * 2 * 180 / 3.141592653589793);
});
$_M(c$, "getThetaRadians", 
function () {
return (Math.acos (Math.abs (this.q0)) * 2);
});
$_M(c$, "getNormalDirected", 
function (v0) {
var v = this.getNormal ();
if (v.x * v0.x + v.y * v0.y + v.z * v0.z < 0) {
v.scale (-1);
}return v;
}, "JU.V3");
$_M(c$, "get3dProjection", 
function (v3d) {
v3d.set (this.q1, this.q2, this.q3);
return v3d;
}, "JU.V3");
$_M(c$, "getThetaDirected", 
function (axisAngle) {
var theta = this.getTheta ();
var v = this.getNormal ();
if (axisAngle.x * this.q1 + axisAngle.y * this.q2 + axisAngle.z * this.q3 < 0) {
v.scale (-1);
theta = -theta;
}axisAngle.set (v.x, v.y, v.z, theta);
return axisAngle;
}, "JU.P4");
$_M(c$, "getThetaDirectedV", 
function (vector) {
var theta = this.getTheta ();
var v = this.getNormal ();
if (vector.x * this.q1 + vector.y * this.q2 + vector.z * this.q3 < 0) {
v.scale (-1);
theta = -theta;
}return theta;
}, "JU.V3");
$_M(c$, "toPoint4f", 
function () {
return JU.P4.new4 (this.q1, this.q2, this.q3, this.q0);
});
$_M(c$, "toAxisAngle4f", 
function () {
var theta = 2 * Math.acos (Math.abs (this.q0));
var sinTheta2 = Math.sin (theta / 2);
var v = this.getNormal ();
if (sinTheta2 < 0) {
v.scale (-1);
theta = 3.141592653589793 - theta;
}return JU.A4.newVA (v, theta);
});
$_M(c$, "transformPt", 
function (pt) {
if (this.mat == null) this.setMatrix ();
var ptNew = JU.P3.newP (pt);
this.mat.transform (ptNew);
return ptNew;
}, "JU.P3");
$_M(c$, "transformP2", 
function (pt, ptNew) {
if (this.mat == null) this.setMatrix ();
this.mat.transform2 (pt, ptNew);
return ptNew;
}, "JU.T3,JU.T3");
$_M(c$, "transform", 
function (v) {
if (this.mat == null) this.setMatrix ();
var vNew = JU.V3.newV (v);
this.mat.transform (vNew);
return vNew;
}, "JU.V3");
$_M(c$, "leftDifference", 
function (q2) {
var q2adjusted = (this.dot (q2) < 0 ? q2.negate () : q2);
return this.inv ().mulQ (q2adjusted);
}, "J.util.Quaternion");
$_M(c$, "rightDifference", 
function (q2) {
var q2adjusted = (this.dot (q2) < 0 ? q2.negate () : q2);
return this.mulQ (q2adjusted.inv ());
}, "J.util.Quaternion");
$_M(c$, "getInfo", 
function () {
var axis = this.toAxisAngle4f ();
return J.util.Txt.sprintf ("%10.6f%10.6f%10.6f%10.6f  %6.2f  %10.5f %10.5f %10.5f", "F", [[this.q0, this.q1, this.q2, this.q3, (axis.angle * 180 / 3.141592653589793), axis.x, axis.y, axis.z]]);
});
$_M(c$, "draw", 
function (prefix, id, ptCenter, scale) {
var strV = " VECTOR " + J.util.Escape.eP (ptCenter) + " ";
if (scale == 0) scale = 1;
return "draw " + prefix + "x" + id + strV + J.util.Escape.eP (this.getVectorS (0, scale)) + " color red\n" + "draw " + prefix + "y" + id + strV + J.util.Escape.eP (this.getVectorS (1, scale)) + " color green\n" + "draw " + prefix + "z" + id + strV + J.util.Escape.eP (this.getVectorS (2, scale)) + " color blue\n";
}, "~S,~S,JU.P3,~N");
$_V(c$, "toString", 
function () {
return "{" + this.q1 + " " + this.q2 + " " + this.q3 + " " + this.q0 + "}";
});
c$.div = $_M(c$, "div", 
function (data1, data2, nMax, isRelative) {
var n;
if (data1 == null || data2 == null || (n = Math.min (data1.length, data2.length)) == 0) return null;
if (nMax > 0 && n > nMax) n = nMax;
var dqs =  new Array (n);
for (var i = 0; i < n; i++) {
if (data1[i] == null || data2[i] == null) return null;
dqs[i] = (isRelative ? data1[i].divLeft (data2[i]) : data1[i].div (data2[i]));
}
return dqs;
}, "~A,~A,~N,~B");
c$.sphereMean = $_M(c$, "sphereMean", 
function (data, retStddev, criterion) {
if (data == null || data.length == 0) return  new J.util.Quaternion ();
if (retStddev == null) retStddev =  Clazz_newFloatArray (1, 0);
if (data.length == 1) {
retStddev[0] = 0;
return J.util.Quaternion.newQ (data[0]);
}var diff = 3.4028235E38;
var lastStddev = 3.4028235E38;
var qMean = J.util.Quaternion.simpleAverage (data);
var maxIter = 100;
var iter = 0;
while (diff > criterion && lastStddev != 0 && iter < maxIter) {
qMean = J.util.Quaternion.newMean (data, qMean);
retStddev[0] = J.util.Quaternion.stdDev (data, qMean);
diff = Math.abs (retStddev[0] - lastStddev);
lastStddev = retStddev[0];
J.util.Logger.info (++iter + " sphereMean " + qMean + " stddev=" + lastStddev + " diff=" + diff);
}
return qMean;
}, "~A,~A,~N");
c$.simpleAverage = $_M(c$, "simpleAverage", 
function (ndata) {
var mean = JU.V3.new3 (0, 0, 1);
var v = ndata[0].getNormal ();
mean.add (v);
for (var i = ndata.length; --i >= 0; ) mean.add (ndata[i].getNormalDirected (mean));

mean.sub (v);
mean.normalize ();
var f = 0;
for (var i = ndata.length; --i >= 0; ) f += Math.abs (ndata[i].get3dProjection (v).dot (mean));

if (f != 0) mean.scale (f / ndata.length);
f = Math.sqrt (1 - mean.lengthSquared ());
if (Float.isNaN (f)) f = 0;
return J.util.Quaternion.newP4 (JU.P4.new4 (mean.x, mean.y, mean.z, f));
}, "~A");
c$.newMean = $_M(c$, "newMean", 
function (data, mean) {
var sum =  new JU.V3 ();
var v;
var q;
var dq;
for (var i = data.length; --i >= 0; ) {
q = data[i];
dq = q.div (mean);
v = dq.getNormal ();
v.scale (dq.getTheta ());
sum.add (v);
}
sum.scale (1 / data.length);
var dqMean = J.util.Quaternion.newVA (sum, sum.length ());
return dqMean.mulQ (mean);
}, "~A,J.util.Quaternion");
c$.stdDev = $_M(c$, "stdDev", 
function (data, mean) {
var sum = 0;
var sum2 = 0;
var n = data.length;
for (var i = n; --i >= 0; ) {
var dq = data[i].div (mean);
var theta = dq.getTheta ();
sum += theta;
sum2 += theta * theta;
}
sum2 = sum2 - sum * sum / n;
if (sum2 < 0) sum2 = 0;
return Math.sqrt (sum2 / (n - 1));
}, "~A,J.util.Quaternion");
$_M(c$, "getEulerZYZ", 
function () {
var rA;
var rB;
var rG;
rA = Math.atan2 (2 * (this.q2 * this.q3 - this.q0 * this.q1), 2 * (this.q1 * this.q3 + this.q0 * this.q2));
rB = Math.acos (this.q3 * this.q3 - this.q2 * this.q2 - this.q1 * this.q1 + this.q0 * this.q0);
rG = Math.atan2 (2 * (this.q2 * this.q3 + this.q0 * this.q1), 2 * (this.q0 * this.q2 - this.q1 * this.q3));
return [(rA / 0.017453292519943295), (rB / 0.017453292519943295), (rG / 0.017453292519943295)];
});
$_M(c$, "getEulerZXZ", 
function () {
var rA;
var rB;
var rG;
rA = Math.atan2 (2 * (this.q1 * this.q3 + this.q0 * this.q2), 2 * (this.q0 * this.q1 - this.q2 * this.q3));
rB = Math.acos (this.q3 * this.q3 - this.q2 * this.q2 - this.q1 * this.q1 + this.q0 * this.q0);
rG = Math.atan2 (2 * (this.q1 * this.q3 - this.q0 * this.q2), 2 * (this.q2 * this.q3 + this.q0 * this.q1));
return [(rA / 0.017453292519943295), (rB / 0.017453292519943295), (rG / 0.017453292519943295)];
});
c$.qZero = c$.prototype.qZero =  new JU.P4 ();
Clazz_defineStatics (c$,
"RAD_PER_DEG", 0.017453292519943295);
});
Clazz_declarePackage ("J.constant");
Clazz_load (["java.lang.Enum"], "J.constant.EnumPalette", null, function () {
c$ = Clazz_decorateAsClass (function () {
this.$$name = null;
this.id = 0;
Clazz_instantialize (this, arguments);
}, J.constant, "EnumPalette", Enum);
Clazz_makeConstructor (c$, 
function (name, id) {
this.$$name = name;
this.id = id;
}, "~S,~N");
c$.pidOf = $_M(c$, "pidOf", 
function (value) {
return (Clazz_instanceOf (value, J.constant.EnumPalette) ? (value).id : Clazz_instanceOf (value, Byte) ? (value).byteValue () : J.constant.EnumPalette.UNKNOWN.id);
}, "~O");
c$.isPaletteVariable = $_M(c$, "isPaletteVariable", 
function (pid) {
return ((pid & 64) != 0);
}, "~N");
c$.getPalette = $_M(c$, "getPalette", 
function (paletteName) {
if (paletteName.indexOf ('_') < 0) for (var item, $item = 0, $$item = J.constant.EnumPalette.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (paletteName.equalsIgnoreCase (item.$$name)) return item;

return (paletteName.indexOf ("property_") == 0 ? J.constant.EnumPalette.PROPERTY : J.constant.EnumPalette.UNKNOWN);
}, "~S");
c$.getPaletteID = $_M(c$, "getPaletteID", 
function (paletteName) {
if (paletteName.indexOf ('_') < 0) for (var item, $item = 0, $$item = J.constant.EnumPalette.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (paletteName.equalsIgnoreCase (item.$$name)) return item.id;

return (paletteName.indexOf ("property_") == 0 ? J.constant.EnumPalette.PROPERTY.id : J.constant.EnumPalette.UNKNOWN.id);
}, "~S");
c$.getPaletteName = $_M(c$, "getPaletteName", 
function (pid) {
for (var item, $item = 0, $$item = J.constant.EnumPalette.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (item.id == pid) return item.$$name;

return null;
}, "~N");
c$.argbsCpkRasmol = [16716947, 33554431, 50315467, 62005794, 83951360, 113821896, 126849023, 149946368, 165324064, 184549631, 203590434, 226525328, 249210144, 268412160, 285198386, 285277952, 343965840, 377520272, 411074704, 427851920, 452961536, 480586282, 497363498, 514140714, 598026794, 796950672, 899686640, 956278016, 1339729184];
c$.argbsCpk = [0xFFFF1493, 0xFFFFFFFF, 0xFFD9FFFF, 0xFFCC80FF, 0xFFC2FF00, 0xFFFFB5B5, 0xFF909090, 0xFF3050F8, 0xFFFF0D0D, 0xFF90E050, 0xFFB3E3F5, 0xFFAB5CF2, 0xFF8AFF00, 0xFFBFA6A6, 0xFFF0C8A0, 0xFFFF8000, 0xFFFFFF30, 0xFF1FF01F, 0xFF80D1E3, 0xFF8F40D4, 0xFF3DFF00, 0xFFE6E6E6, 0xFFBFC2C7, 0xFFA6A6AB, 0xFF8A99C7, 0xFF9C7AC7, 0xFFE06633, 0xFFF090A0, 0xFF50D050, 0xFFC88033, 0xFF7D80B0, 0xFFC28F8F, 0xFF668F8F, 0xFFBD80E3, 0xFFFFA100, 0xFFA62929, 0xFF5CB8D1, 0xFF702EB0, 0xFF00FF00, 0xFF94FFFF, 0xFF94E0E0, 0xFF73C2C9, 0xFF54B5B5, 0xFF3B9E9E, 0xFF248F8F, 0xFF0A7D8C, 0xFF006985, 0xFFC0C0C0, 0xFFFFD98F, 0xFFA67573, 0xFF668080, 0xFF9E63B5, 0xFFD47A00, 0xFF940094, 0xFF429EB0, 0xFF57178F, 0xFF00C900, 0xFF70D4FF, 0xFFFFFFC7, 0xFFD9FFC7, 0xFFC7FFC7, 0xFFA3FFC7, 0xFF8FFFC7, 0xFF61FFC7, 0xFF45FFC7, 0xFF30FFC7, 0xFF1FFFC7, 0xFF00FF9C, 0xFF00E675, 0xFF00D452, 0xFF00BF38, 0xFF00AB24, 0xFF4DC2FF, 0xFF4DA6FF, 0xFF2194D6, 0xFF267DAB, 0xFF266696, 0xFF175487, 0xFFD0D0E0, 0xFFFFD123, 0xFFB8B8D0, 0xFFA6544D, 0xFF575961, 0xFF9E4FB5, 0xFFAB5C00, 0xFF754F45, 0xFF428296, 0xFF420066, 0xFF007D00, 0xFF70ABFA, 0xFF00BAFF, 0xFF00A1FF, 0xFF008FFF, 0xFF0080FF, 0xFF006BFF, 0xFF545CF2, 0xFF785CE3, 0xFF8A4FE3, 0xFFA136D4, 0xFFB31FD4, 0xFFB31FBA, 0xFFB30DA6, 0xFFBD0D87, 0xFFC70066, 0xFFCC0059, 0xFFD1004F, 0xFFD90045, 0xFFE00038, 0xFFE6002E, 0xFFEB0026];
Clazz_defineEnumConstant (c$, "UNKNOWN", 0, [null, 0xFF]);
Clazz_defineEnumConstant (c$, "NONE", 1, ["none", 0]);
Clazz_defineEnumConstant (c$, "CPK", 2, ["cpk", 1]);
Clazz_defineEnumConstant (c$, "PARTIAL_CHARGE", 3, ["partialcharge", 2]);
Clazz_defineEnumConstant (c$, "FORMAL_CHARGE", 4, ["formalcharge", 3]);
Clazz_defineEnumConstant (c$, "TEMP", 5, ["temperature", 68]);
Clazz_defineEnumConstant (c$, "FIXEDTEMP", 6, ["fixedtemperature", 5]);
Clazz_defineEnumConstant (c$, "SURFACE", 7, ["surfacedistance", 70]);
Clazz_defineEnumConstant (c$, "STRUCTURE", 8, ["structure", 7]);
Clazz_defineEnumConstant (c$, "AMINO", 9, ["amino", 8]);
Clazz_defineEnumConstant (c$, "SHAPELY", 10, ["shapely", 9]);
Clazz_defineEnumConstant (c$, "CHAIN", 11, ["chain", 10]);
Clazz_defineEnumConstant (c$, "GROUP", 12, ["group", 75]);
Clazz_defineEnumConstant (c$, "MONOMER", 13, ["monomer", 76]);
Clazz_defineEnumConstant (c$, "MOLECULE", 14, ["molecule", 77]);
Clazz_defineEnumConstant (c$, "ALTLOC", 15, ["altloc", 14]);
Clazz_defineEnumConstant (c$, "INSERTION", 16, ["insertion", 15]);
Clazz_defineEnumConstant (c$, "JMOL", 17, ["jmol", 16]);
Clazz_defineEnumConstant (c$, "RASMOL", 18, ["rasmol", 17]);
Clazz_defineEnumConstant (c$, "TYPE", 19, ["type", 18]);
Clazz_defineEnumConstant (c$, "ENERGY", 20, ["energy", 19]);
Clazz_defineEnumConstant (c$, "PROPERTY", 21, ["property", 84]);
Clazz_defineEnumConstant (c$, "VARIABLE", 22, ["variable", 85]);
Clazz_defineEnumConstant (c$, "STRAIGHTNESS", 23, ["straightness", 86]);
Clazz_defineEnumConstant (c$, "POLYMER", 24, ["polymer", 87]);
});
Clazz_declarePackage ("J.util");
Clazz_load (["JU.AU", "$.V3"], "J.util.Shader", ["JU.CU", "J.util.C"], function () {
c$ = Clazz_decorateAsClass (function () {
this.xLight = 0;
this.yLight = 0;
this.zLight = 0;
this.lightSource = null;
this.specularOn = true;
this.usePhongExponent = false;
this.ambientPercent = 45;
this.diffusePercent = 84;
this.specularExponent = 6;
this.specularPercent = 22;
this.specularPower = 40;
this.phongExponent = 64;
this.ambientFraction = 0;
this.diffuseFactor = 0;
this.intenseFraction = 0;
this.specularFactor = 0;
this.ashades = null;
this.ashadesGreyscale = null;
this.rgbContrast = 0;
this.sphereShadingCalculated = false;
this.sphereShadeIndexes = null;
this.seed = 0x12345679;
this.sphereShapeCache = null;
this.ellipsoidShades = null;
this.nOut = 0;
this.nIn = 0;
this.celOn = false;
Clazz_instantialize (this, arguments);
}, J.util, "Shader");
Clazz_prepareFields (c$, function () {
this.lightSource =  new JU.V3 ();
this.ambientFraction = this.ambientPercent / 100;
this.diffuseFactor = this.diffusePercent / 100;
this.intenseFraction = this.specularPower / 100;
this.specularFactor = this.specularPercent / 100;
this.ashades = JU.AU.newInt2 (128);
this.sphereShadeIndexes =  Clazz_newByteArray (65536, 0);
this.sphereShapeCache = JU.AU.newInt2 (128);
});
Clazz_makeConstructor (c$, 
function () {
this.setLightSource (-1.0, -1.0, 2.5);
});
$_M(c$, "setLightSource", 
function (x, y, z) {
this.lightSource.set (x, y, z);
this.lightSource.normalize ();
this.xLight = this.lightSource.x;
this.yLight = this.lightSource.y;
this.zLight = this.lightSource.z;
}, "~N,~N,~N");
$_M(c$, "setCel", 
function (celOn, argb) {
argb = J.util.C.getArgb (J.util.C.getBgContrast (argb));
if (argb == 0xFF000000) argb = 0xFF040404;
if (this.celOn == celOn && this.rgbContrast == argb) return;
this.celOn = celOn;
this.rgbContrast = argb;
this.flushCaches ();
}, "~B,~N");
$_M(c$, "flushCaches", 
function () {
this.flushShades ();
this.flushSphereCache ();
});
$_M(c$, "getCelOn", 
function () {
return this.celOn;
});
$_M(c$, "setLastColix", 
function (argb, asGrey) {
J.util.C.allocateColix (argb);
this.checkShades ();
if (asGrey) J.util.C.setLastGrey (argb);
this.ashades[2047] = this.getShades2 (argb, false);
}, "~N,~B");
$_M(c$, "getShades", 
function (colix) {
this.checkShades ();
colix &= -30721;
var shades = this.ashades[colix];
if (shades == null) shades = this.ashades[colix] = this.getShades2 (J.util.C.argbs[colix], false);
return shades;
}, "~N");
$_M(c$, "getShadesG", 
function (colix) {
this.checkShades ();
colix &= -30721;
if (this.ashadesGreyscale == null) this.ashadesGreyscale = JU.AU.newInt2 (this.ashades.length);
var shadesGreyscale = this.ashadesGreyscale[colix];
if (shadesGreyscale == null) shadesGreyscale = this.ashadesGreyscale[colix] = this.getShades2 (J.util.C.argbs[colix], true);
return shadesGreyscale;
}, "~N");
$_M(c$, "checkShades", 
function () {
if (this.ashades != null && this.ashades.length == J.util.C.colixMax) return;
this.ashades = JU.AU.arrayCopyII (this.ashades, J.util.C.colixMax);
if (this.ashadesGreyscale != null) this.ashadesGreyscale = JU.AU.arrayCopyII (this.ashadesGreyscale, J.util.C.colixMax);
});
$_M(c$, "flushShades", 
function () {
this.checkShades ();
for (var i = J.util.C.colixMax; --i >= 0; ) this.ashades[i] = null;

this.sphereShadingCalculated = false;
});
$_M(c$, "getShades2", 
function (rgb, greyScale) {
var shades =  Clazz_newIntArray (J.util.Shader.shadeIndexMax, 0);
if (rgb == 0) return shades;
var red0 = ((rgb >> 16) & 0xFF);
var grn0 = ((rgb >> 8) & 0xFF);
var blu0 = (rgb & 0xFF);
var red = 0;
var grn = 0;
var blu = 0;
var f = this.ambientFraction;
while (true) {
red = red0 * f + 0.5;
grn = grn0 * f + 0.5;
blu = blu0 * f + 0.5;
if (f > 0 && red < 4 && grn < 4 && blu < 4) {
red0++;
grn0++;
blu0++;
if (f < 0.1) f += 0.1;
rgb = JU.CU.rgb (Clazz_doubleToInt (Math.floor (red0)), Clazz_doubleToInt (Math.floor (grn0)), Clazz_doubleToInt (Math.floor (blu0)));
continue;
}break;
}
var i;
if (this.celOn) {
var max = Clazz_doubleToInt (J.util.Shader.shadeIndexMax / 2);
f = (1 - f) / J.util.Shader.shadeIndexNormal;
var redStep = red0 * f;
var grnStep = grn0 * f;
var bluStep = blu0 * f;
var _rgb = JU.CU.rgb (Clazz_doubleToInt (Math.floor (red)), Clazz_doubleToInt (Math.floor (grn)), Clazz_doubleToInt (Math.floor (blu)));
for (i = 0; i < max; ++i) shades[i] = _rgb;

red += redStep * max;
grn += grnStep * max;
blu += bluStep * max;
_rgb = JU.CU.rgb (Clazz_doubleToInt (Math.floor (red)), Clazz_doubleToInt (Math.floor (grn)), Clazz_doubleToInt (Math.floor (blu)));
for (; i < J.util.Shader.shadeIndexMax; i++) shades[i] = _rgb;

shades[0] = shades[1] = this.rgbContrast;
} else {
f = (1 - f) / J.util.Shader.shadeIndexNormal;
var redStep = red0 * f;
var grnStep = grn0 * f;
var bluStep = blu0 * f;
for (i = 0; i < J.util.Shader.shadeIndexNormal; ++i) {
shades[i] = JU.CU.rgb (Clazz_doubleToInt (Math.floor (red)), Clazz_doubleToInt (Math.floor (grn)), Clazz_doubleToInt (Math.floor (blu)));
red += redStep;
grn += grnStep;
blu += bluStep;
}
shades[i++] = rgb;
f = this.intenseFraction / (J.util.Shader.shadeIndexMax - i);
redStep = (255.5 - red) * f;
grnStep = (255.5 - grn) * f;
bluStep = (255.5 - blu) * f;
for (; i < J.util.Shader.shadeIndexMax; i++) {
red += redStep;
grn += grnStep;
blu += bluStep;
shades[i] = JU.CU.rgb (Clazz_doubleToInt (Math.floor (red)), Clazz_doubleToInt (Math.floor (grn)), Clazz_doubleToInt (Math.floor (blu)));
}
}if (greyScale) for (; --i >= 0; ) shades[i] = JU.CU.toFFGGGfromRGB (shades[i]);

return shades;
}, "~N,~B");
$_M(c$, "getShadeIndex", 
function (x, y, z) {
var magnitude = Math.sqrt (x * x + y * y + z * z);
return Math.round (this.getShadeF ((x / magnitude), (y / magnitude), (z / magnitude)) * J.util.Shader.shadeIndexLast);
}, "~N,~N,~N");
$_M(c$, "getShadeB", 
function (x, y, z) {
return Math.round (this.getShadeF (x, y, z) * J.util.Shader.shadeIndexLast);
}, "~N,~N,~N");
$_M(c$, "getShadeFp8", 
function (x, y, z) {
var magnitude = Math.sqrt (x * x + y * y + z * z);
return Clazz_doubleToInt (Math.floor (this.getShadeF ((x / magnitude), (y / magnitude), (z / magnitude)) * J.util.Shader.shadeIndexLast * (256)));
}, "~N,~N,~N");
$_M(c$, "getShadeF", 
function (x, y, z) {
var NdotL = x * this.xLight + y * this.yLight + z * this.zLight;
if (NdotL <= 0) return 0;
var intensity = NdotL * this.diffuseFactor;
if (this.specularOn) {
var k_specular = 2 * NdotL * z - this.zLight;
if (k_specular > 0) {
if (this.usePhongExponent) {
k_specular = Math.pow (k_specular, this.phongExponent);
} else {
for (var n = this.specularExponent; --n >= 0 && k_specular > .0001; ) k_specular *= k_specular;

}intensity += k_specular * this.specularFactor;
}}return (this.celOn && z < 0.5 ? 0 : intensity > 1 ? 1 : intensity);
}, "~N,~N,~N");
$_M(c$, "getShadeN", 
function (x, y, z, r) {
var fp8ShadeIndex = Clazz_doubleToInt (Math.floor (this.getShadeF (x / r, y / r, z / r) * J.util.Shader.shadeIndexLast * (256)));
var shadeIndex = fp8ShadeIndex >> 8;
if ((fp8ShadeIndex & 0xFF) > this.nextRandom8Bit ()) ++shadeIndex;
var random16bit = this.seed & 0xFFFF;
if (random16bit < 21845 && shadeIndex > 0) --shadeIndex;
 else if (random16bit > 43690 && shadeIndex < J.util.Shader.shadeIndexLast) ++shadeIndex;
return shadeIndex;
}, "~N,~N,~N,~N");
$_M(c$, "calcSphereShading", 
function () {
var xF = -127.5;
for (var i = 0; i < 256; ++xF, ++i) {
var yF = -127.5;
for (var j = 0; j < 256; ++yF, ++j) {
var shadeIndex = 0;
var z2 = 16900 - xF * xF - yF * yF;
if (z2 > 0) {
var z = Math.sqrt (z2);
shadeIndex = this.getShadeN (xF, yF, z, 130);
}this.sphereShadeIndexes[(j << 8) + i] = shadeIndex;
}
}
this.sphereShadingCalculated = true;
});
$_M(c$, "nextRandom8Bit", 
function () {
var t = this.seed;
this.seed = t = ((t << 16) + (t << 1) + t) & 0x7FFFFFFF;
return t >> 23;
});
$_M(c$, "getEllipsoidShade", 
function (x, y, z, radius, mDeriv) {
var tx = mDeriv.m00 * x + mDeriv.m01 * y + mDeriv.m02 * z + mDeriv.m03;
var ty = mDeriv.m10 * x + mDeriv.m11 * y + mDeriv.m12 * z + mDeriv.m13;
var tz = mDeriv.m20 * x + mDeriv.m21 * y + mDeriv.m22 * z + mDeriv.m23;
var f = Math.min (radius / 2, 45) / Math.sqrt (tx * tx + ty * ty + tz * tz);
var i = Clazz_floatToInt (-tx * f);
var j = Clazz_floatToInt (-ty * f);
var k = Clazz_floatToInt (tz * f);
var outside = i < -20 || i >= 20 || j < -20 || j >= 20 || k < 0 || k >= 40;
if (outside) {
while (i % 2 == 0 && j % 2 == 0 && k % 2 == 0 && i + j + k > 0) {
i >>= 1;
j >>= 1;
k >>= 1;
}
outside = i < -20 || i >= 20 || j < -20 || j >= 20 || k < 0 || k >= 40;
}if (outside) this.nOut++;
 else this.nIn++;
return (outside ? this.getShadeIndex (i, j, k) : this.ellipsoidShades[i + 20][j + 20][k]);
}, "~N,~N,~N,~N,JU.M4");
$_M(c$, "createEllipsoidShades", 
function () {
this.ellipsoidShades =  Clazz_newByteArray (40, 40, 40, 0);
for (var ii = 0; ii < 40; ii++) for (var jj = 0; jj < 40; jj++) for (var kk = 0; kk < 40; kk++) this.ellipsoidShades[ii][jj][kk] = this.getShadeIndex (ii - 20, jj - 20, kk);



});
$_M(c$, "flushSphereCache", 
function () {
for (var i = 128; --i >= 0; ) this.sphereShapeCache[i] = null;

this.ellipsoidShades = null;
});
Clazz_defineStatics (c$,
"shadeIndexMax", 64);
c$.shadeIndexLast = c$.prototype.shadeIndexLast = J.util.Shader.shadeIndexMax - 1;
Clazz_defineStatics (c$,
"shadeIndexNormal", 52,
"shadeIndexNoisyLimit", 56,
"SLIM", 20,
"SDIM", 40,
"maxSphereCache", 128);
});
Clazz_declarePackage ("J.api");
Clazz_load (["javajs.api.JSInterface"], "J.api.JmolViewer", ["java.util.Hashtable"], function () {
c$ = Clazz_decorateAsClass (function () {
this.menuStructure = null;
this.apiPlatform = null;
Clazz_instantialize (this, arguments);
}, J.api, "JmolViewer", null, javajs.api.JSInterface);
c$.allocateViewer = $_M(c$, "allocateViewer", 
function (display, modelAdapter, fullName, documentBase, codeBase, commandOptions, statusListener, implementedPlatform) {
var info =  new java.util.Hashtable ();
if (display != null) info.put ("display", display);
if (modelAdapter != null) info.put ("adapter", modelAdapter);
if (statusListener != null) info.put ("statuslistener", statusListener);
if (implementedPlatform != null) info.put ("platform", implementedPlatform);
if (commandOptions != null) info.put ("options", commandOptions);
if (fullName != null) info.put ("fullname", fullName);
if (documentBase != null) info.put ("documentbase", documentBase);
if (codeBase != null) info.put ("codebase", codeBase);
return  new J.viewer.Viewer (info);
}, "~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,javajs.api.GenericPlatform");
c$.allocateViewer = $_M(c$, "allocateViewer", 
function (container, jmolAdapter) {
return J.api.JmolViewer.allocateViewer (container, jmolAdapter, null, null, null, null, null, null);
}, "~O,J.api.JmolAdapter");
c$.allocateViewer = $_M(c$, "allocateViewer", 
function (display, modelAdapter, fullName, documentBase, codeBase, commandOptions, statusListener) {
return J.api.JmolViewer.allocateViewer (display, modelAdapter, fullName, documentBase, codeBase, commandOptions, statusListener, null);
}, "~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener");
$_M(c$, "setConsole", 
function (console) {
this.getProperty ("DATA_API", "getAppConsole", console);
}, "J.api.JmolAppConsoleInterface");
c$.getJmolVersion = $_M(c$, "getJmolVersion", 
function () {
return J.viewer.Viewer.getJmolVersion ();
});
c$.checkOption = $_M(c$, "checkOption", 
function (viewer, option) {
var testFlag = viewer.getParameter (option);
return (Clazz_instanceOf (testFlag, Boolean) && (testFlag).booleanValue () || Clazz_instanceOf (testFlag, Integer) && (testFlag).intValue () != 0);
}, "J.api.JmolViewer,~S");
$_M(c$, "openFileAsync", 
function (fileName) {
this.openFileAsyncSpecial (fileName, 0);
}, "~S");
$_M(c$, "mouseEvent", 
function (id, x, y, modifiers, when) {
this.processMouseEvent (id, x, y, modifiers, when);
}, "~N,~N,~N,~N,~N");
$_M(c$, "renderScreenImage", 
function (g, currentSize, rectClip) {
this.apiPlatform.renderScreenImage (g, currentSize);
}, "~O,~O,~O");
$_M(c$, "getJsObjectInfo", 
function (jsObject, method, args) {
return this.apiPlatform.getJsObjectInfo (jsObject, method, args);
}, "~A,~S,~A");
c$.getJmolValueAsString = $_M(c$, "getJmolValueAsString", 
function (jmolViewer, $var) {
return (jmolViewer == null ? "" : "" + jmolViewer.getParameter ($var));
}, "J.api.JmolViewer,~S");
});
Clazz_declarePackage ("J.atomdata");
Clazz_declareInterface (J.atomdata, "AtomDataServer");
Clazz_declarePackage ("J.constant");
Clazz_load (["java.lang.Enum"], "J.constant.EnumVdw", null, function () {
c$ = Clazz_decorateAsClass (function () {
this.pt = 0;
this.type = null;
this.type2 = null;
Clazz_instantialize (this, arguments);
}, J.constant, "EnumVdw", Enum);
Clazz_makeConstructor (c$, 
function (pt, type, type2) {
this.pt = pt;
this.type = type;
this.type2 = type2;
}, "~N,~S,~S");
$_M(c$, "getVdwLabel", 
function () {
return (this.type == null ? this.type2 : this.type);
});
c$.getVdwType = $_M(c$, "getVdwType", 
function (label) {
if (label != null) for (var item, $item = 0, $$item = J.constant.EnumVdw.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (label.equalsIgnoreCase (item.type)) return item;

return null;
}, "~S");
c$.getVdwType2 = $_M(c$, "getVdwType2", 
function (label) {
if (label != null) for (var item, $item = 0, $$item = J.constant.EnumVdw.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (label.equalsIgnoreCase (item.type2)) return item;

return null;
}, "~S");
Clazz_defineEnumConstant (c$, "JMOL", 0, [0, "Jmol", null]);
Clazz_defineEnumConstant (c$, "BABEL", 1, [1, "Babel", null]);
Clazz_defineEnumConstant (c$, "RASMOL", 2, [2, "RasMol", null]);
Clazz_defineEnumConstant (c$, "BABEL21", 3, [3, "Babel21", null]);
Clazz_defineEnumConstant (c$, "AUTO_JMOL", 4, [0, null, "Jmol"]);
Clazz_defineEnumConstant (c$, "AUTO_BABEL", 5, [1, null, "Babel"]);
Clazz_defineEnumConstant (c$, "AUTO_RASMOL", 6, [2, null, "RasMol"]);
Clazz_defineEnumConstant (c$, "AUTO", 7, [0, "Auto", null]);
Clazz_defineEnumConstant (c$, "USER", 8, [-1, "User", null]);
Clazz_defineEnumConstant (c$, "ADPMAX", 9, [-1, null, "adpmax"]);
Clazz_defineEnumConstant (c$, "ADPMIN", 10, [-1, null, "adpmin"]);
Clazz_defineEnumConstant (c$, "HYDRO", 11, [-1, null, "hydrophobic"]);
Clazz_defineEnumConstant (c$, "IONIC", 12, [-1, null, "ionic"]);
Clazz_defineEnumConstant (c$, "TEMP", 13, [-1, null, "temperature"]);
Clazz_defineEnumConstant (c$, "NOJMOL", 14, [-1, null, null]);
Clazz_defineEnumConstant (c$, "NADA", 15, [-1, null, null]);
});
Clazz_declarePackage ("J.atomdata");
Clazz_load (["java.lang.Enum", "J.constant.EnumVdw"], "J.atomdata.RadiusData", ["java.lang.Float", "JU.SB"], function () {
c$ = Clazz_decorateAsClass (function () {
this.info = null;
this.factorType = null;
this.vdwType = null;
this.value = NaN;
this.valueExtended = 0;
this.values = null;
Clazz_instantialize (this, arguments);
}, J.atomdata, "RadiusData");
Clazz_prepareFields (c$, function () {
this.factorType = J.atomdata.RadiusData.EnumType.ABSOLUTE;
this.vdwType = J.constant.EnumVdw.AUTO;
});
Clazz_makeConstructor (c$, 
function (values, value, factorType, vdwType) {
if (values != null) {
this.values = values;
this.value = 2147483647;
return;
}if (factorType == null) return;
this.factorType = factorType;
this.value = value;
if (vdwType != null) this.vdwType = vdwType;
}, "~A,~N,J.atomdata.RadiusData.EnumType,J.constant.EnumVdw");
$_V(c$, "toString", 
function () {
if (Float.isNaN (this.value)) return "";
var sb =  new JU.SB ();
switch (this.factorType) {
case J.atomdata.RadiusData.EnumType.ABSOLUTE:
sb.appendF (this.value);
break;
case J.atomdata.RadiusData.EnumType.OFFSET:
sb.append (this.value > 0 ? "+" : "").appendF (this.value);
break;
case J.atomdata.RadiusData.EnumType.FACTOR:
sb.appendI (Clazz_floatToInt (this.value * 100)).append ("%");
if (this.vdwType !== J.constant.EnumVdw.AUTO) sb.append (this.vdwType.getVdwLabel ());
break;
case J.atomdata.RadiusData.EnumType.SCREEN:
sb.appendI (Clazz_floatToInt (this.value));
}
return sb.toString ();
});
Clazz_pu$h ();
c$ = Clazz_declareType (J.atomdata.RadiusData, "EnumType", Enum);
Clazz_defineEnumConstant (c$, "ABSOLUTE", 0, []);
Clazz_defineEnumConstant (c$, "OFFSET", 1, []);
Clazz_defineEnumConstant (c$, "FACTOR", 2, []);
Clazz_defineEnumConstant (c$, "SCREEN", 3, []);
c$ = Clazz_p0p ();
});
Clazz_declarePackage ("J.util");
Clazz_load (null, "J.util.CommandHistory", ["JU.List"], function () {
c$ = Clazz_decorateAsClass (function () {
this.commandList = null;
this.maxSize = 100;
this.nextCommand = 0;
this.cursorPos = 0;
this.isOn = true;
Clazz_instantialize (this, arguments);
}, J.util, "CommandHistory");
Clazz_makeConstructor (c$, 
function () {
this.reset (100);
});
Clazz_makeConstructor (c$, 
function (maxSize) {
this.reset (maxSize);
}, "~N");
$_M(c$, "clear", 
function () {
this.reset (this.maxSize);
});
$_M(c$, "reset", 
function (maxSize) {
this.maxSize = maxSize;
this.commandList =  new JU.List ();
this.nextCommand = 0;
this.commandList.addLast ("");
this.cursorPos = 0;
}, "~N");
$_M(c$, "setMaxSize", 
function (maxSize) {
if (maxSize == this.maxSize) return;
if (maxSize < 2) maxSize = 2;
while (this.nextCommand > maxSize) {
this.commandList.remove (0);
this.nextCommand--;
}
if (this.nextCommand > maxSize) this.nextCommand = maxSize - 1;
this.cursorPos = this.nextCommand;
this.maxSize = maxSize;
}, "~N");
$_M(c$, "getCommandUp", 
function () {
if (this.cursorPos <= 0) return null;
this.cursorPos--;
var str = this.getCommand ();
if (str.endsWith ("#??")) this.removeCommand (this.cursorPos--);
if (this.cursorPos < 0) this.cursorPos = 0;
return str;
});
$_M(c$, "getCommandDown", 
function () {
if (this.cursorPos >= this.nextCommand) return null;
this.cursorPos++;
return this.getCommand ();
});
$_M(c$, "getCommand", 
function () {
return this.commandList.get (this.cursorPos);
});
$_M(c$, "addCommand", 
function (strCommand) {
if (!this.isOn && !strCommand.endsWith ("#??")) return;
if (strCommand.endsWith ("#----")) return;
var i;
while ((i = strCommand.indexOf ("\n")) >= 0) {
var str = strCommand.substring (0, i);
if (str.length > 0) this.addCommandLine (str);
strCommand = strCommand.substring (i + 1);
}
if (strCommand.length > 0) this.addCommandLine (strCommand);
}, "~S");
$_M(c$, "getSetHistory", 
function (n) {
this.isOn = (n == -2 ? this.isOn : true);
switch (n) {
case 0:
this.isOn = false;
this.clear ();
return "";
case -2147483648:
case -2:
this.clear ();
return "";
case -1:
return this.getCommandUp ();
case 1:
return this.getCommandDown ();
default:
if (n < 0) {
this.setMaxSize (-2 - n);
return "";
}n = Math.max (this.nextCommand - n, 0);
}
var str = "";
for (var i = n; i < this.nextCommand; i++) if (!this.commandList.get (i).toUpperCase ().startsWith ("WRITE HISTORY")) str += this.commandList.get (i) + "\n";

return str;
}, "~N");
$_M(c$, "removeCommand", 
function () {
return this.removeCommand (this.nextCommand - 1);
});
$_M(c$, "removeCommand", 
function (n) {
if (n < 0 || n >= this.nextCommand) return "";
var str = this.commandList.remove (n);
this.nextCommand--;
return str;
}, "~N");
$_M(c$, "addCommandLine", 
function (command) {
if (command == null || command.length == 0) return;
if (command.endsWith ("#--")) return;
if (this.nextCommand >= this.maxSize) {
this.commandList.remove (0);
this.nextCommand = this.maxSize - 1;
}this.commandList.add (this.nextCommand, command);
this.nextCommand++;
this.cursorPos = this.nextCommand;
this.commandList.add (this.nextCommand, "");
}, "~S");
Clazz_defineStatics (c$,
"ERROR_FLAG", "#??",
"NOHISTORYLINE_FLAG", "#--",
"NOHISTORYATALL_FLAG", "#----",
"DEFAULT_MAX_SIZE", 100);
});
Clazz_declarePackage ("javajs.api");
Clazz_declareInterface (javajs.api, "JSInterface");
Clazz_declarePackage ("J.viewer");
Clazz_load (["java.lang.Enum", "javajs.api.PlatformViewer", "J.api.JmolViewer", "J.atomdata.AtomDataServer", "java.util.Hashtable", "javajs.awt.Dimension", "JU.List", "J.atomdata.RadiusData", "J.constant.EnumVdw", "J.i18n.GT", "J.util.CommandHistory"], "J.viewer.Viewer", ["java.io.BufferedReader", "$.StringReader", "java.lang.Boolean", "$.Character", "$.Float", "JU.AU", "$.BS", "$.CU", "$.DF", "$.P3", "$.P3i", "$.PT", "$.SB", "$.V3", "J.adapter.smarter.SmarterJmolAdapter", "J.api.Interface", "J.constant.EnumAnimationMode", "$.EnumAxesMode", "$.EnumFileStatus", "$.EnumStereoMode", "J.io.CifDataReader", "$.JmolBinary", "J.modelset.Group", "J.script.SV", "$.T", "J.thread.TimeoutThread", "J.util.BSUtil", "$.C", "$.Elements", "$.Escape", "$.GData", "$.JmolMolecule", "$.Logger", "$.Measure", "$.Parser", "$.TempArray", "$.Txt", "J.viewer.ActionManager", "$.AnimationManager", "$.ColorManager", "$.FileManager", "$.JC", "$.ModelManager", "$.SelectionManager", "$.ShapeManager", "$.StateManager", "$.StatusManager", "$.TransformManager", "J.viewer.binding.Binding"], function () {
c$ = Clazz_decorateAsClass (function () {
this.autoExit = false;
this.haveDisplay = false;
this.isJS = false;
this.isWebGL = false;
this.isSingleThreaded = false;
this.queueOnHold = false;
this.fullName = "";
this.appletDocumentBase = "";
this.appletCodeBase = "";
this.compiler = null;
this.definedAtomSets = null;
this.modelSet = null;
this.fileManager = null;
this.$isApplet = false;
this.isSyntaxAndFileCheck = false;
this.isSyntaxCheck = false;
this.listCommands = false;
this.mustRender = false;
this.htmlName = "";
this.insertedCommand = "";
this.gdata = null;
this.applet = null;
this.actionManager = null;
this.animationManager = null;
this.colorManager = null;
this.dataManager = null;
this.shapeManager = null;
this.selectionManager = null;
this.repaintManager = null;
this.global = null;
this.statusManager = null;
this.transformManager = null;
this.syncId = "";
this.logFilePath = "";
this.allowScripting = false;
this.isPrintOnly = false;
this.$isSignedApplet = false;
this.isSignedAppletLocal = false;
this.isSilent = false;
this.multiTouch = false;
this.$noGraphicsAllowed = false;
this.useCommandThread = false;
this.commandOptions = null;
this.viewerOptions = null;
this.display = null;
this.modelAdapter = null;
this.access = null;
this.commandHistory = null;
this.symmetry = null;
this.smilesMatcher = null;
this.modelManager = null;
this.stateManager = null;
this.scriptManager = null;
this.eval = null;
this.tempArray = null;
this.$isPreviewOnly = false;
this.mouse = null;
this.mouseEnabled = true;
this.noneSelected = false;
this.ligandModels = null;
this.ligandModelSet = null;
this.sc = null;
this.bsFrameOffsets = null;
this.frameOffsets = null;
this.motionEventNumber = 0;
this.inMotion = false;
this.refreshing = true;
this.axesAreTainted = false;
this.dimScreen = null;
this.maximumSize = 2147483647;
this.imageFontScaling = 1;
this.captureParams = null;
this.antialiasDisplay = false;
this.hoverAtomIndex = -1;
this.hoverText = null;
this.hoverEnabled = true;
this.currentCursor = 0;
this.prevFrame = -2147483648;
this.haveJDX = false;
this.jsv = null;
this.language = null;
this.rd = null;
this.frankOn = true;
this.scriptEditorVisible = false;
this.appConsole = null;
this.scriptEditor = null;
this.jmolpopup = null;
this.modelkitPopup = null;
this.headlessImageParams = null;
this.pm = null;
this.isTainted = true;
this.movingSelected = false;
this.showSelected = false;
this.rotateBondIndex = -1;
this.rotatePrev1 = -1;
this.rotatePrev2 = -1;
this.bsRotateBranch = null;
this.creatingImage = false;
this.outputManager = null;
this.bsUserVdws = null;
this.userVdws = null;
this.userVdwMars = null;
this.defaultVdw = null;
this.errorMessage = null;
this.errorMessageUntranslated = null;
this.currentShapeID = -1;
this.currentShapeState = null;
this.localFunctions = null;
this.privateKey = 0;
this.$isKiosk = false;
this.minimizer = null;
this.executor = null;
this.displayLoadErrors = true;
this.$isParallel = false;
this.actionStates = null;
this.actionStatesRedo = null;
this.stateScriptVersionInt = 0;
this.jsExporter3D = null;
this.htPdbBondInfo = null;
this.timeouts = null;
this.chainMap = null;
this.chainList = null;
this.nmrCalculation = null;
this.logFileName = null;
Clazz_instantialize (this, arguments);
}, J.viewer, "Viewer", J.api.JmolViewer, [J.atomdata.AtomDataServer, javajs.api.PlatformViewer]);
Clazz_prepareFields (c$, function () {
this.commandHistory =  new J.util.CommandHistory ();
this.dimScreen =  new javajs.awt.Dimension (0, 0);
this.language = J.i18n.GT.getLanguage ();
this.rd =  new J.atomdata.RadiusData (null, 0, null, null);
this.defaultVdw = J.constant.EnumVdw.JMOL;
this.localFunctions =  new java.util.Hashtable ();
this.privateKey = Math.random ();
this.actionStates =  new JU.List ();
this.actionStatesRedo =  new JU.List ();
this.chainMap =  new java.util.Hashtable ();
this.chainList =  new JU.List ();
});
$_M(c$, "finalize", 
function () {
if (J.util.Logger.debugging) J.util.Logger.debug ("viewer finalize " + this);
Clazz_superCall (this, J.viewer.Viewer, "finalize", []);
});
$_M(c$, "hasDisplay", 
function () {
return this.haveDisplay;
});
$_V(c$, "isApplet", 
function () {
return this.$isApplet;
});
$_M(c$, "setInsertedCommand", 
function (strScript) {
this.insertedCommand = strScript;
}, "~S");
$_M(c$, "getActionManager", 
function () {
return this.actionManager;
});
$_M(c$, "getLogFilePath", 
function () {
return this.logFilePath;
});
$_M(c$, "isSignedApplet", 
function () {
return this.$isSignedApplet;
});
c$.getJmolVersion = $_V(c$, "getJmolVersion", 
function () {
return (J.viewer.Viewer.version_date == null ? ($t$ = J.viewer.Viewer.version_date = J.viewer.JC.version + "  " + J.viewer.JC.date, J.viewer.Viewer.prototype.version_date = J.viewer.Viewer.version_date, $t$) : J.viewer.Viewer.version_date);
});
c$.allocateViewer = $_M(c$, "allocateViewer", 
function (display, modelAdapter, fullName, documentBase, codeBase, commandOptions, statusListener, implementedPlatform) {
var info =  new java.util.Hashtable ();
info.put ("display", display);
info.put ("adapter", modelAdapter);
info.put ("statusListener", statusListener);
info.put ("platform", implementedPlatform);
info.put ("options", commandOptions);
info.put ("fullName", fullName);
info.put ("documentBase", documentBase);
info.put ("codeBase", codeBase);
return  new J.viewer.Viewer (info);
}, "~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,javajs.api.GenericPlatform");
Clazz_makeConstructor (c$, 
function (info) {
Clazz_superConstructor (this, J.viewer.Viewer, []);
this.setOptions (info);
}, "java.util.Map");
$_M(c$, "getGlobalSettings", 
function () {
return this.global;
});
$_M(c$, "getStatusManager", 
function () {
return this.statusManager;
});
$_M(c$, "haveAccess", 
function (a) {
return this.access === a;
}, "J.viewer.Viewer.ACCESS");
$_V(c$, "getModelAdapter", 
function () {
if (this.modelAdapter == null) this.modelAdapter =  new J.adapter.smarter.SmarterJmolAdapter ();
return this.modelAdapter;
});
$_M(c$, "getSymmetry", 
function () {
if (this.symmetry == null) this.symmetry = J.api.Interface.getOptionInterface ("symmetry.Symmetry");
return this.symmetry;
});
$_M(c$, "getSymmetryInfo", 
function (bsAtoms, xyz, op, pt, pt2, id, type) {
return this.getPropertyManager ().getSymmetryInfo (bsAtoms, xyz, op, pt, pt2, id, type);
}, "JU.BS,~S,~N,JU.P3,JU.P3,~S,~N");
$_M(c$, "getSmilesMatcher", 
function () {
if (this.smilesMatcher == null) {
this.smilesMatcher = J.api.Interface.getOptionInterface ("smiles.SmilesMatcher");
}return this.smilesMatcher;
});
$_V(c$, "getSmartsMatch", 
function (smarts, bsSelected) {
if (bsSelected == null) bsSelected = this.getSelectionSet (false);
return this.getSmilesMatcher ().getSubstructureSet (smarts, this.modelSet.atoms, this.getAtomCount (), bsSelected, true, false);
}, "~S,JU.BS");
$_M(c$, "getViewerOptions", 
function () {
return this.viewerOptions;
});
$_M(c$, "setOptions", 
function (info) {
this.viewerOptions = info;
if (J.util.Logger.debugging) {
J.util.Logger.debug ("Viewer constructor " + this);
}this.modelAdapter = info.get ("adapter");
var statusListener = info.get ("statusListener");
this.fullName = info.get ("fullName");
if (this.fullName == null) this.fullName = "";
var o = info.get ("codeBase");
this.appletCodeBase = (o == null ? "" : o.toString ());
o = info.get ("documentBase");
this.appletDocumentBase = (o == null ? "" : o.toString ());
o = info.get ("options");
this.commandOptions = (o == null ? "" : o.toString ());
if (info.containsKey ("debug") || this.commandOptions.indexOf ("-debug") >= 0) J.util.Logger.setLogLevel (5);
this.$isSignedApplet = this.checkOption2 ("signedApplet", "-signed");
this.$isApplet = this.$isSignedApplet || this.checkOption2 ("applet", "-applet");
this.allowScripting = !this.checkOption2 ("noscripting", "-noscripting");
var i = this.fullName.indexOf ("__");
this.htmlName = (i < 0 ? this.fullName : this.fullName.substring (0, i));
this.syncId = (i < 0 ? "" : this.fullName.substring (i + 2, this.fullName.length - 2));
if (this.$isApplet) {
{
if(typeof Jmol != "undefined") this.applet =
Jmol._applets[this.htmlName.split("_object")[0]];
}if (info.containsKey ("maximumSize")) this.setMaximumSize ((info.get ("maximumSize")).intValue ());
}this.access = (this.checkOption2 ("access:READSPT", "-r") ? J.viewer.Viewer.ACCESS.READSPT : this.checkOption2 ("access:NONE", "-R") ? J.viewer.Viewer.ACCESS.NONE : J.viewer.Viewer.ACCESS.ALL);
this.$isPreviewOnly = info.containsKey ("previewOnly");
if (this.$isPreviewOnly) info.remove ("previewOnly");
this.isPrintOnly = this.checkOption2 ("printOnly", "-p");
o = info.get ("platform");
var platform = "unknown";
if (o == null) {
o = (this.commandOptions.contains ("platform=") ? this.commandOptions.substring (this.commandOptions.indexOf ("platform=") + 9) : "J.awt.Platform");
}if (Clazz_instanceOf (o, String)) {
platform = o;
this.isWebGL = (platform.indexOf (".awtjs.") >= 0);
this.isJS = this.isWebGL || (platform.indexOf (".awtjs2d.") >= 0);
o = J.api.Interface.getInterface (platform);
}this.apiPlatform = o;
this.display = info.get ("display");
this.isSingleThreaded = this.apiPlatform.isSingleThreaded ();
this.$noGraphicsAllowed = this.checkOption2 ("noGraphics", "-n");
this.haveDisplay = (this.isWebGL || this.display != null && !this.$noGraphicsAllowed && !this.isHeadless () && !this.checkOption2 ("isDataOnly", "\0"));
this.$noGraphicsAllowed = new Boolean (this.$noGraphicsAllowed & (this.display == null)).valueOf ();
if (this.haveDisplay) {
this.mustRender = true;
this.multiTouch = this.checkOption2 ("multiTouch", "-multitouch");
{
if (!this.isWebGL) this.display =
document.getElementById(this.display);
}} else {
this.display = null;
}this.apiPlatform.setViewer (this, this.display);
o = info.get ("graphicsAdapter");
if (o == null && !this.isWebGL) o = J.api.Interface.getInterface ("J.g3d.Graphics3D");
this.gdata = (o == null ?  new J.util.GData () : o);
this.gdata.initialize (this.apiPlatform);
this.stateManager =  new J.viewer.StateManager (this);
this.colorManager =  new J.viewer.ColorManager (this, this.gdata);
this.statusManager =  new J.viewer.StatusManager (this);
this.transformManager =  new J.viewer.TransformManager (this, 2147483647, 0);
this.selectionManager =  new J.viewer.SelectionManager (this);
if (this.haveDisplay) {
this.actionManager = (this.multiTouch ? J.api.Interface.getOptionInterface ("multitouch.ActionManagerMT") :  new J.viewer.ActionManager ());
this.actionManager.setViewer (this, this.commandOptions + "-multitouch-" + info.get ("multiTouch"));
this.mouse = this.apiPlatform.getMouseManager (this.privateKey, this.display);
if (this.multiTouch && !this.checkOption2 ("-simulated", "-simulated")) this.apiPlatform.setTransparentCursor (this.display);
}this.modelManager =  new J.viewer.ModelManager (this);
this.shapeManager =  new J.viewer.ShapeManager (this);
this.tempArray =  new J.util.TempArray ();
this.animationManager =  new J.viewer.AnimationManager (this);
o = info.get ("repaintManager");
if (o == null) o = (J.api.Interface.getOptionInterface ("render.RepaintManager"));
if (o != null && !o.equals ("")) (this.repaintManager = o).set (this, this.shapeManager);
this.initialize (true);
this.fileManager =  new J.viewer.FileManager (this);
this.definedAtomSets =  new java.util.Hashtable ();
this.setJmolStatusListener (statusListener);
if (this.$isApplet) {
J.util.Logger.info ("viewerOptions: \n" + J.util.Escape.escapeMap (this.viewerOptions));
var path = this.viewerOptions.get ("documentLocation");
if (!this.isJS && path != null && path.startsWith ("file:/")) {
path = path.substring (0, path.substring (0, (path + "?").indexOf ("?")).lastIndexOf ("/"));
J.util.Logger.info ("setting current directory to " + path);
this.cd (path);
}($t$ = J.viewer.Viewer.jsDocumentBase = this.appletDocumentBase, J.viewer.Viewer.prototype.jsDocumentBase = J.viewer.Viewer.jsDocumentBase, $t$);
i = J.viewer.Viewer.jsDocumentBase.indexOf ("#");
if (i >= 0) ($t$ = J.viewer.Viewer.jsDocumentBase = J.viewer.Viewer.jsDocumentBase.substring (0, i), J.viewer.Viewer.prototype.jsDocumentBase = J.viewer.Viewer.jsDocumentBase, $t$);
i = J.viewer.Viewer.jsDocumentBase.lastIndexOf ("?");
if (i >= 0) ($t$ = J.viewer.Viewer.jsDocumentBase = J.viewer.Viewer.jsDocumentBase.substring (0, i), J.viewer.Viewer.prototype.jsDocumentBase = J.viewer.Viewer.jsDocumentBase, $t$);
i = J.viewer.Viewer.jsDocumentBase.lastIndexOf ("/");
if (i >= 0) ($t$ = J.viewer.Viewer.jsDocumentBase = J.viewer.Viewer.jsDocumentBase.substring (0, i), J.viewer.Viewer.prototype.jsDocumentBase = J.viewer.Viewer.jsDocumentBase, $t$);
this.fileManager.setAppletContext (this.appletDocumentBase);
var appletProxy = info.get ("appletProxy");
if (appletProxy != null) this.setStringProperty ("appletProxy", appletProxy);
if (this.$isSignedApplet) {
this.logFilePath = JU.PT.simpleReplace (this.appletCodeBase, "file://", "");
this.logFilePath = JU.PT.simpleReplace (this.logFilePath, "file:/", "");
if (this.logFilePath.indexOf ("//") >= 0) this.logFilePath = null;
 else this.isSignedAppletLocal = true;
} else if (!this.isJS) {
this.logFilePath = null;
}} else {
this.gdata.setBackgroundTransparent (this.checkOption2 ("backgroundTransparent", "-b"));
this.isSilent = this.checkOption2 ("silent", "-i");
if (this.isSilent) J.util.Logger.setLogLevel (3);
this.isSyntaxAndFileCheck = this.checkOption2 ("checkLoad", "-C");
this.isSyntaxCheck = this.isSyntaxAndFileCheck || this.checkOption2 ("check", "-c");
this.listCommands = this.checkOption2 ("listCommands", "-l");
this.autoExit = this.checkOption2 ("exit", "-x");
this.cd (".");
if (this.isHeadless ()) {
this.headlessImageParams = info.get ("headlessImage");
o = info.get ("headlistMaxTimeMs");
if (o == null) o = Integer.$valueOf (60000);
this.setTimeout ("" + Math.random (), (o).intValue (), "exitJmol");
}}this.useCommandThread = !this.isHeadless () && this.checkOption2 ("useCommandThread", "-threaded");
this.setStartupBooleans ();
this.setIntProperty ("_nProcessors", J.viewer.Viewer.nProcessors);
o = info.get ("menuFile");
if (o != null) this.getProperty ("DATA_API", "setMenu", this.getFileAsString (o));
if (!this.isSilent) {
J.util.Logger.info ("(C) 2012 Jmol Development" + "\nJmol Version: " + J.viewer.Viewer.getJmolVersion () + "\njava.vendor: " + J.viewer.Viewer.strJavaVendor + "\njava.version: " + J.viewer.Viewer.strJavaVersion + "\nos.name: " + J.viewer.Viewer.strOSName + "\nAccess: " + this.access + "\nmemory: " + this.getParameter ("_memory") + "\nprocessors available: " + J.viewer.Viewer.nProcessors + "\nuseCommandThread: " + this.useCommandThread + (!this.$isApplet ? "" : "\nappletId:" + this.htmlName + (this.$isSignedApplet ? " (signed)" : "")));
}this.zap (false, true, false);
this.global.setS ("language", J.i18n.GT.getLanguage ());
this.stateManager.setJmolDefaults ();
}, "java.util.Map");
$_M(c$, "setDisplay", 
function (canvas) {
this.display = canvas;
this.apiPlatform.setViewer (this, canvas);
}, "~O");
$_M(c$, "getDataManager", 
function () {
return (this.dataManager == null ? (this.dataManager = (J.api.Interface.getOptionInterface ("viewer.DataManager")).set (this)) : this.dataManager);
});
$_M(c$, "getScriptManager", 
function () {
if (this.allowScripting && this.scriptManager == null) {
this.scriptManager = J.api.Interface.getOptionInterface ("script.ScriptManager");
this.scriptManager.setViewer (this);
this.eval = this.scriptManager.getEval ();
if (this.useCommandThread) this.scriptManager.startCommandWatcher (true);
}return this.scriptManager;
});
$_M(c$, "checkOption2", 
function (key1, key2) {
return (this.viewerOptions.containsKey (key1) || this.commandOptions.indexOf (key2) >= 0);
}, "~S,~S");
$_M(c$, "isPreviewOnly", 
function () {
return this.$isPreviewOnly;
});
$_M(c$, "isHeadless", 
function () {
return this.apiPlatform.isHeadless ();
});
$_M(c$, "setStartupBooleans", 
function () {
this.setBooleanProperty ("_applet", this.$isApplet);
this.setBooleanProperty ("_JSpecView".toLowerCase (), false);
this.setBooleanProperty ("_signedApplet", this.$isSignedApplet);
this.setBooleanProperty ("_headless", this.apiPlatform.isHeadless ());
this.setStringProperty ("_restrict", "\"" + this.access + "\"");
this.setBooleanProperty ("_useCommandThread", this.useCommandThread);
});
$_M(c$, "noGraphicsAllowed", 
function () {
return this.$noGraphicsAllowed;
});
$_M(c$, "getExportDriverList", 
function () {
return (this.haveAccess (J.viewer.Viewer.ACCESS.ALL) ? this.global.getParameter ("exportDrivers") : "");
});
$_M(c$, "getHtmlName", 
function () {
return this.htmlName;
});
$_V(c$, "getDisplay", 
function () {
return this.display;
});
$_M(c$, "clearMouse", 
function () {
this.mouse.clear ();
});
$_M(c$, "disposeMouse", 
function () {
this.actionManager.dispose ();
this.mouse.dispose ();
this.mouse = null;
});
$_V(c$, "processTwoPointGesture", 
function (touches) {
this.mouse.processTwoPointGesture (touches);
}, "~A");
$_V(c$, "processMouseEvent", 
function (id, x, y, modifiers, time) {
return this.mouse.processEvent (id, x, y, modifiers, time);
}, "~N,~N,~N,~N,~N");
$_M(c$, "reset", 
function (includingSpin) {
this.modelSet.calcBoundBoxDimensions (null, 1);
this.axesAreTainted = true;
this.transformManager.homePosition (includingSpin);
if (this.modelSet.setCrystallographicDefaults ()) this.stateManager.setCrystallographicDefaults ();
 else this.setAxesModeMolecular (false);
this.prevFrame = -2147483648;
if (!this.getSpinOn ()) this.refresh (-1, "Viewer:homePosition()");
}, "~B");
$_V(c$, "homePosition", 
function () {
this.evalString ("reset spin");
});
$_M(c$, "getAppletInfo", 
function () {
var info =  new java.util.Hashtable ();
info.put ("htmlName", this.htmlName);
info.put ("syncId", this.syncId);
info.put ("fullName", this.fullName);
if (this.$isApplet) {
info.put ("documentBase", this.appletDocumentBase);
info.put ("codeBase", this.appletCodeBase);
info.put ("registry", this.statusManager.getRegistryInfo ());
}info.put ("version", J.viewer.JC.version);
info.put ("date", J.viewer.JC.date);
info.put ("javaVendor", J.viewer.Viewer.strJavaVendor);
info.put ("javaVersion", J.viewer.Viewer.strJavaVersion + (!this.isJS ? "" : this.isWebGL ? "(WebGL)" : "(HTML5)"));
info.put ("operatingSystem", J.viewer.Viewer.strOSName);
return info;
});
$_M(c$, "initialize", 
function (clearUserVariables) {
this.global = this.stateManager.getGlobalSettings (this.global, clearUserVariables);
this.setStartupBooleans ();
this.global.setI ("_width", this.dimScreen.width);
this.global.setI ("_height", this.dimScreen.height);
if (this.haveDisplay) {
this.global.setB ("_is2D", this.isJS && !this.isWebGL);
this.global.setB ("_multiTouchClient", this.actionManager.isMTClient ());
this.global.setB ("_multiTouchServer", this.actionManager.isMTServer ());
}this.colorManager.resetElementColors ();
this.setObjectColor ("background", "black");
this.setObjectColor ("axis1", "red");
this.setObjectColor ("axis2", "green");
this.setObjectColor ("axis3", "blue");
this.gdata.setAmbientPercent (this.global.ambientPercent);
this.gdata.setDiffusePercent (this.global.diffusePercent);
this.gdata.setSpecular (this.global.specular);
this.gdata.setCel (this.global.celShading);
this.gdata.setSpecularPercent (this.global.specularPercent);
this.gdata.setSpecularPower (-this.global.specularExponent);
this.gdata.setPhongExponent (this.global.phongExponent);
this.gdata.setSpecularPower (this.global.specularPower);
if (this.modelSet != null) this.animationManager.setAnimationOn (false);
this.animationManager.setAnimationFps (this.global.animationFps);
this.statusManager.setAllowStatusReporting (this.global.statusReporting);
this.setBooleanProperty ("antialiasDisplay", this.global.antialiasDisplay);
this.setTransformManagerDefaults ();
}, "~B");
$_M(c$, "listSavedStates", 
function () {
return this.stateManager.listSavedStates ();
});
$_M(c$, "saveOrientation", 
function (saveName, pymolView) {
this.stateManager.saveOrientation (saveName, pymolView);
}, "~S,~A");
$_M(c$, "saveScene", 
function (saveName, scene) {
this.stateManager.saveScene (saveName, scene);
}, "~S,java.util.Map");
$_M(c$, "restoreScene", 
function (saveName, timeSeconds) {
this.stateManager.restoreScene (saveName, timeSeconds);
}, "~S,~N");
$_M(c$, "restoreOrientation", 
function (saveName, timeSeconds) {
return this.stateManager.restoreOrientation (saveName, timeSeconds, true);
}, "~S,~N");
$_M(c$, "restoreRotation", 
function (saveName, timeSeconds) {
this.stateManager.restoreOrientation (saveName, timeSeconds, false);
}, "~S,~N");
$_M(c$, "saveModelOrientation", 
function () {
this.modelSet.saveModelOrientation (this.animationManager.currentModelIndex, this.stateManager.getOrientation ());
});
$_M(c$, "getOrientation", 
function () {
return this.stateManager.getOrientation ();
});
$_M(c$, "restoreModelOrientation", 
function (modelIndex) {
var o = this.modelSet.getModelOrientation (modelIndex);
if (o != null) o.restore (-1, true);
}, "~N");
$_M(c$, "restoreModelRotation", 
function (modelIndex) {
var o = this.modelSet.getModelOrientation (modelIndex);
if (o != null) o.restore (-1, false);
}, "~N");
$_M(c$, "saveBonds", 
function (saveName) {
this.stateManager.saveBonds (saveName);
}, "~S");
$_M(c$, "restoreBonds", 
function (saveName) {
this.clearModelDependentObjects ();
return this.stateManager.restoreBonds (saveName);
}, "~S");
$_M(c$, "saveState", 
function (saveName) {
this.stateManager.saveState (saveName);
}, "~S");
$_M(c$, "deleteSavedState", 
function (saveName) {
this.stateManager.deleteSaved ("State_" + saveName);
}, "~S");
$_M(c$, "getSavedState", 
function (saveName) {
return this.stateManager.getSavedState (saveName);
}, "~S");
$_M(c$, "saveStructure", 
function (saveName) {
this.stateManager.saveStructure (saveName);
}, "~S");
$_M(c$, "getSavedStructure", 
function (saveName) {
return this.stateManager.getSavedStructure (saveName);
}, "~S");
$_M(c$, "saveCoordinates", 
function (saveName, bsSelected) {
this.stateManager.saveCoordinates (saveName, bsSelected);
}, "~S,JU.BS");
$_M(c$, "getSavedCoordinates", 
function (saveName) {
return this.stateManager.getSavedCoordinates (saveName);
}, "~S");
$_M(c$, "saveSelection", 
function (saveName) {
this.stateManager.saveSelection (saveName, this.getSelectionSet (false));
this.stateManager.restoreSelection (saveName);
}, "~S");
$_M(c$, "restoreSelection", 
function (saveName) {
return this.stateManager.restoreSelection (saveName);
}, "~S");
$_M(c$, "getMatrixtransform", 
function () {
return this.transformManager.getMatrixtransform ();
});
$_M(c$, "getRotationQuaternion", 
function () {
return this.transformManager.getRotationQuaternion ();
});
$_M(c$, "setRotationRadius", 
function (angstroms, doAll) {
if (doAll) angstroms = this.transformManager.setRotationRadius (angstroms, false);
if (this.modelSet.setRotationRadius (this.animationManager.currentModelIndex, angstroms)) this.global.setF ("rotationRadius", angstroms);
}, "~N,~B");
$_M(c$, "getRotationCenter", 
function () {
return this.transformManager.getRotationCenter ();
});
$_M(c$, "setCenterAt", 
function (relativeTo, pt) {
if (this.isJmolDataFrame ()) return;
this.transformManager.setCenterAt (relativeTo, pt);
}, "~S,JU.P3");
$_M(c$, "setCenterBitSet", 
function (bsCenter, doScale) {
var center = (J.util.BSUtil.cardinalityOf (bsCenter) > 0 ? this.getAtomSetCenter (bsCenter) : null);
if (this.isJmolDataFrame ()) return;
this.transformManager.setNewRotationCenter (center, doScale);
}, "JU.BS,~B");
$_M(c$, "setNewRotationCenter", 
function (center) {
if (this.isJmolDataFrame ()) return;
this.transformManager.setNewRotationCenter (center, true);
}, "JU.P3");
$_M(c$, "getNavigationCenter", 
function () {
return this.transformManager.getNavigationCenter ();
});
$_M(c$, "getNavigationDepthPercent", 
function () {
return this.transformManager.getNavigationDepthPercent ();
});
$_M(c$, "navigate", 
function (keyWhere, modifiers) {
if (this.isJmolDataFrame ()) return;
this.transformManager.navigateKey (keyWhere, modifiers);
if (!this.transformManager.vibrationOn && keyWhere != 0) this.refresh (1, "Viewer:navigate()");
}, "~N,~N");
$_M(c$, "getNavigationOffset", 
function () {
return this.transformManager.getNavigationOffset ();
});
$_M(c$, "getNavigationOffsetPercent", 
function (XorY) {
return this.transformManager.getNavigationOffsetPercent (XorY);
}, "~S");
$_M(c$, "isNavigating", 
function () {
return this.transformManager.isNavigating ();
});
$_M(c$, "isInPosition", 
function (axis, degrees) {
return this.transformManager.isInPosition (axis, degrees);
}, "JU.V3,~N");
$_M(c$, "move", 
function (eval, dRot, dZoom, dTrans, dSlab, floatSecondsTotal, fps) {
this.transformManager.move (eval, dRot, dZoom, dTrans, dSlab, floatSecondsTotal, fps);
this.moveUpdate (floatSecondsTotal);
}, "J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");
$_M(c$, "stopMotion", 
function () {
this.transformManager.stopMotion ();
});
$_M(c$, "setRotationMatrix", 
function (rotationMatrix) {
this.transformManager.setRotation (rotationMatrix);
}, "JU.M3");
$_M(c$, "moveTo", 
function (eval, floatSecondsTotal, center, rotAxis, degrees, rotationMatrix, zoom, xTrans, yTrans, rotationRadius, navCenter, xNav, yNav, navDepth, cameraDepth, cameraX, cameraY) {
if (!this.haveDisplay) floatSecondsTotal = 0;
this.setTainted (true);
this.transformManager.moveTo (eval, floatSecondsTotal, center, rotAxis, degrees, rotationMatrix, zoom, xTrans, yTrans, rotationRadius, navCenter, xNav, yNav, navDepth, cameraDepth, cameraX, cameraY);
}, "J.api.JmolScriptEvaluator,~N,JU.P3,JU.V3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");
$_M(c$, "moveUpdate", 
function (floatSecondsTotal) {
if (floatSecondsTotal > 0) this.requestRepaintAndWait ("moveUpdate");
 else if (floatSecondsTotal == 0) this.setSync ();
}, "~N");
$_M(c$, "getMoveToText", 
function (timespan) {
return this.transformManager.getMoveToText (timespan, false);
}, "~N");
$_M(c$, "navigateList", 
function (eval, list) {
if (this.isJmolDataFrame ()) return;
this.transformManager.navigateList (eval, list);
}, "J.api.JmolScriptEvaluator,JU.List");
$_M(c$, "navigatePt", 
function (center) {
this.transformManager.setNavigatePt (center);
this.setSync ();
}, "JU.P3");
$_M(c$, "navigateAxis", 
function (rotAxis, degrees) {
this.transformManager.navigateAxis (rotAxis, degrees);
this.setSync ();
}, "JU.V3,~N");
$_M(c$, "navTranslatePercent", 
function (x, y) {
if (this.isJmolDataFrame ()) return;
this.transformManager.navTranslatePercentOrTo (0, x, y);
this.setSync ();
}, "~N,~N");
$_M(c$, "setMouseEnabled", 
function (TF) {
this.mouseEnabled = TF;
}, "~B");
$_V(c$, "processMultitouchEvent", 
function (groupID, eventType, touchID, iData, pt, time) {
this.actionManager.processMultitouchEvent (groupID, eventType, touchID, iData, pt, time);
}, "~N,~N,~N,~N,JU.P3,~N");
$_M(c$, "zoomBy", 
function (pixels) {
if (this.mouseEnabled) this.transformManager.zoomBy (pixels);
this.refresh (2, this.statusManager.syncingMouse ? "Mouse: zoomBy " + pixels : "");
}, "~N");
$_M(c$, "zoomByFactor", 
function (factor, x, y) {
if (this.mouseEnabled) this.transformManager.zoomByFactor (factor, x, y);
this.refresh (2, !this.statusManager.syncingMouse ? "" : "Mouse: zoomByFactor " + factor + (x == 2147483647 ? "" : " " + x + " " + y));
}, "~N,~N,~N");
$_M(c$, "rotateXYBy", 
function (xDelta, yDelta) {
if (this.mouseEnabled) this.transformManager.rotateXYBy (xDelta, yDelta, null);
this.refresh (2, this.statusManager.syncingMouse ? "Mouse: rotateXYBy " + xDelta + " " + yDelta : "");
}, "~N,~N");
$_M(c$, "spinXYBy", 
function (xDelta, yDelta, speed) {
if (this.mouseEnabled) this.transformManager.spinXYBy (xDelta, yDelta, speed);
if (xDelta == 0 && yDelta == 0) return;
this.refresh (2, this.statusManager.syncingMouse ? "Mouse: spinXYBy " + xDelta + " " + yDelta + " " + speed : "");
}, "~N,~N,~N");
$_M(c$, "rotateZBy", 
function (zDelta, x, y) {
if (this.mouseEnabled) this.transformManager.rotateZBy (zDelta, x, y);
this.refresh (2, this.statusManager.syncingMouse ? "Mouse: rotateZBy " + zDelta + (x == 2147483647 ? "" : " " + x + " " + y) : "");
}, "~N,~N,~N");
$_M(c$, "rotateSelected", 
function (deltaX, deltaY, bsSelected) {
if (this.isJmolDataFrame ()) return;
if (this.mouseEnabled) {
this.transformManager.rotateXYBy (deltaX, deltaY, this.setMovableBitSet (bsSelected, false));
this.refreshMeasures (true);
}this.refresh (2, this.statusManager.syncingMouse ? "Mouse: rotateMolecule " + deltaX + " " + deltaY : "");
}, "~N,~N,JU.BS");
$_M(c$, "setMovableBitSet", 
function (bsSelected, checkMolecule) {
if (bsSelected == null) bsSelected = this.getSelectionSet (false);
bsSelected = J.util.BSUtil.copy (bsSelected);
J.util.BSUtil.andNot (bsSelected, this.getMotionFixedAtoms ());
if (checkMolecule && !this.global.allowMoveAtoms) bsSelected = this.modelSet.getMoleculeBitSet (bsSelected);
return bsSelected;
}, "JU.BS,~B");
$_M(c$, "translateXYBy", 
function (xDelta, yDelta) {
if (this.mouseEnabled) this.transformManager.translateXYBy (xDelta, yDelta);
this.refresh (2, this.statusManager.syncingMouse ? "Mouse: translateXYBy " + xDelta + " " + yDelta : "");
}, "~N,~N");
$_V(c$, "rotateFront", 
function () {
this.transformManager.rotateFront ();
this.refresh (1, "Viewer:rotateFront()");
});
$_V(c$, "rotateX", 
function (angleRadians) {
this.transformManager.rotateX (angleRadians);
this.refresh (1, "Viewer:rotateX()");
}, "~N");
$_V(c$, "rotateY", 
function (angleRadians) {
this.transformManager.rotateY (angleRadians);
this.refresh (1, "Viewer:rotateY()");
}, "~N");
$_V(c$, "rotateZ", 
function (angleRadians) {
this.transformManager.rotateZ (angleRadians);
this.refresh (1, "Viewer:rotateZ()");
}, "~N");
$_V(c$, "rotateXDeg", 
function (angleDegrees) {
this.rotateX (angleDegrees * 0.017453292);
}, "~N");
$_V(c$, "rotateYDeg", 
function (angleDegrees) {
this.rotateY (angleDegrees * 0.017453292);
}, "~N");
$_M(c$, "translate", 
function (xyz, x, type, bsAtoms) {
var xy = (type == '\0' ? Clazz_floatToInt (x) : type == '%' ? this.transformManager.percentToPixels (xyz, x) : this.transformManager.angstromsToPixels (x * (type == 'n' ? 10 : 1)));
if (bsAtoms != null) {
if (xy == 0) return;
this.transformManager.setSelectedTranslation (bsAtoms, xyz, xy);
} else {
switch (xyz) {
case 'X':
case 'x':
if (type == '\0') this.transformManager.translateToPercent ('x', x);
 else this.transformManager.translateXYBy (xy, 0);
break;
case 'Y':
case 'y':
if (type == '\0') this.transformManager.translateToPercent ('y', x);
 else this.transformManager.translateXYBy (0, xy);
break;
case 'Z':
case 'z':
if (type == '\0') this.transformManager.translateToPercent ('z', x);
 else this.transformManager.translateZBy (xy);
break;
}
}this.refresh (1, "Viewer:translate()");
}, "~S,~N,~S,JU.BS");
$_M(c$, "getTranslationXPercent", 
function () {
return this.transformManager.getTranslationXPercent ();
});
$_M(c$, "getTranslationYPercent", 
function () {
return this.transformManager.getTranslationYPercent ();
});
$_M(c$, "getTranslationZPercent", 
function () {
return this.transformManager.getTranslationZPercent ();
});
$_M(c$, "getTranslationScript", 
function () {
return this.transformManager.getTranslationScript ();
});
$_M(c$, "getZShadeStart", 
function () {
return this.transformManager.getZShadeStart ();
});
$_M(c$, "isWindowCentered", 
function () {
return this.transformManager.isWindowCentered ();
});
$_V(c$, "getZoomPercent", 
function () {
return Clazz_floatToInt (this.getZoomSetting ());
});
$_M(c$, "getZoomSetting", 
function () {
return this.transformManager.getZoomSetting ();
});
$_V(c$, "getZoomPercentFloat", 
function () {
return this.transformManager.getZoomPercentFloat ();
});
$_M(c$, "getMaxZoomPercent", 
function () {
return 200000;
});
$_M(c$, "slabReset", 
function () {
this.transformManager.slabReset ();
});
$_M(c$, "getZoomEnabled", 
function () {
return this.transformManager.zoomEnabled;
});
$_M(c$, "getSlabEnabled", 
function () {
return this.transformManager.slabEnabled;
});
$_M(c$, "slabByPixels", 
function (pixels) {
this.transformManager.slabByPercentagePoints (pixels);
this.refresh (3, "slabByPixels");
}, "~N");
$_M(c$, "depthByPixels", 
function (pixels) {
this.transformManager.depthByPercentagePoints (pixels);
this.refresh (3, "depthByPixels");
}, "~N");
$_M(c$, "slabDepthByPixels", 
function (pixels) {
this.transformManager.slabDepthByPercentagePoints (pixels);
this.refresh (3, "slabDepthByPixels");
}, "~N");
$_M(c$, "slabInternal", 
function (plane, isDepth) {
this.transformManager.slabInternal (plane, isDepth);
}, "JU.P4,~B");
$_M(c$, "slabToPercent", 
function (percentSlab) {
this.transformManager.slabToPercent (percentSlab);
}, "~N");
$_M(c$, "depthToPercent", 
function (percentDepth) {
this.transformManager.depthToPercent (percentDepth);
}, "~N");
$_M(c$, "setSlabDepthInternal", 
function (isDepth) {
this.transformManager.setSlabDepthInternal (isDepth);
}, "~B");
$_M(c$, "zValueFromPercent", 
function (zPercent) {
return this.transformManager.zValueFromPercent (zPercent);
}, "~N");
$_V(c$, "getUnscaledTransformMatrix", 
function () {
return this.transformManager.getUnscaledTransformMatrix ();
});
$_M(c$, "finalizeTransformParameters", 
function () {
this.transformManager.finalizeTransformParameters ();
this.gdata.setSlab (this.transformManager.slabValue);
this.gdata.setDepth (this.transformManager.depthValue);
this.gdata.setZShade (this.transformManager.zShadeEnabled, this.transformManager.zSlabValue, this.transformManager.zDepthValue, this.global.zShadePower);
});
$_M(c$, "rotatePoint", 
function (pt, ptRot) {
this.transformManager.rotatePoint (pt, ptRot);
}, "JU.P3,JU.P3");
$_M(c$, "transformPt", 
function (pointAngstroms) {
return this.transformManager.transformPoint (pointAngstroms);
}, "JU.P3");
$_M(c$, "transformPtVib", 
function (pointAngstroms, vibrationVector) {
return this.transformManager.transformPointVib (pointAngstroms, vibrationVector);
}, "JU.P3,J.util.Vibration");
$_M(c$, "transformPtScr", 
function (pointAngstroms, pointScreen) {
this.transformManager.transformPointScr (pointAngstroms, pointScreen);
}, "JU.P3,JU.P3i");
$_M(c$, "transformPtNoClip", 
function (pointAngstroms, pt) {
this.transformManager.transformPointNoClip2 (pointAngstroms, pt);
}, "JU.P3,JU.P3");
$_M(c$, "transformPt3f", 
function (pointAngstroms, pointScreen) {
this.transformManager.transformPoint2 (pointAngstroms, pointScreen);
}, "JU.P3,JU.P3");
$_M(c$, "transformPoints", 
function (pointsAngstroms, pointsScreens) {
this.transformManager.transformPoints (pointsAngstroms.length, pointsAngstroms, pointsScreens);
}, "~A,~A");
$_M(c$, "transformVector", 
function (vectorAngstroms, vectorTransformed) {
this.transformManager.transformVector (vectorAngstroms, vectorTransformed);
}, "JU.V3,JU.V3");
$_M(c$, "unTransformPoint", 
function (pointScreen, pointAngstroms) {
this.transformManager.unTransformPoint (pointScreen, pointAngstroms);
}, "JU.P3,JU.P3");
$_M(c$, "getScalePixelsPerAngstrom", 
function (asAntialiased) {
return this.transformManager.scalePixelsPerAngstrom * (asAntialiased || !this.antialiasDisplay ? 1 : 0.5);
}, "~B");
$_M(c$, "scaleToScreen", 
function (z, milliAngstroms) {
return this.transformManager.scaleToScreen (z, milliAngstroms);
}, "~N,~N");
$_M(c$, "unscaleToScreen", 
function (z, screenDistance) {
return this.transformManager.unscaleToScreen (z, screenDistance);
}, "~N,~N");
$_M(c$, "scaleToPerspective", 
function (z, sizeAngstroms) {
return this.transformManager.scaleToPerspective (z, sizeAngstroms);
}, "~N,~N");
$_M(c$, "setSpin", 
function (key, value) {
if (!JU.PT.isOneOf (key, "x;y;z;fps;X;Y;Z;FPS")) return;
var i = "x;y;z;fps;X;Y;Z;FPS".indexOf (key);
switch (i) {
case 0:
this.transformManager.setSpinXYZ (value, NaN, NaN);
break;
case 2:
this.transformManager.setSpinXYZ (NaN, value, NaN);
break;
case 4:
this.transformManager.setSpinXYZ (NaN, NaN, value);
break;
case 6:
default:
this.transformManager.setSpinFps (value);
break;
case 10:
this.transformManager.setNavXYZ (value, NaN, NaN);
break;
case 12:
this.transformManager.setNavXYZ (NaN, value, NaN);
break;
case 14:
this.transformManager.setNavXYZ (NaN, NaN, value);
break;
case 16:
this.transformManager.setNavFps (value);
break;
}
this.global.setI ((i < 10 ? "spin" : "nav") + key, value);
}, "~S,~N");
$_M(c$, "getSpinState", 
function () {
return this.getStateCreator ().getSpinState (false);
});
$_M(c$, "setSpinOn", 
function (spinOn) {
if (spinOn) this.transformManager.setSpinOn ();
 else this.transformManager.setSpinOff ();
}, "~B");
$_M(c$, "getSpinOn", 
function () {
return this.transformManager.getSpinOn ();
});
$_M(c$, "setNavOn", 
function (navOn) {
this.transformManager.setNavOn (navOn);
}, "~B");
$_M(c$, "getNavOn", 
function () {
return this.transformManager.getNavOn ();
});
$_M(c$, "setNavXYZ", 
function (x, y, z) {
this.transformManager.setNavXYZ (Clazz_floatToInt (x), Clazz_floatToInt (y), Clazz_floatToInt (z));
}, "~N,~N,~N");
$_M(c$, "getOrientationText", 
function (type, name) {
switch (type) {
case 1313866247:
case 1073741863:
case 1112541205:
case 1112541206:
case 1112541207:
case 135270417:
return this.modelSet.getBoundBoxOrientation (type, this.getSelectionSet (false));
case 1073742035:
return this.stateManager.getSavedOrientationText (name);
default:
return this.transformManager.getOrientationText (type);
}
}, "~N,~S");
$_M(c$, "getOrientationInfo", 
function () {
return this.transformManager.getOrientationInfo ();
});
$_M(c$, "getMatrixRotate", 
function () {
return this.transformManager.getMatrixRotate ();
});
$_M(c$, "getAxisAngle", 
function (axisAngle) {
this.transformManager.getAxisAngle (axisAngle);
}, "JU.A4");
$_M(c$, "getTransformText", 
function () {
return this.transformManager.getTransformText ();
});
$_M(c$, "getRotation", 
function (matrixRotation) {
this.transformManager.getRotation (matrixRotation);
}, "JU.M3");
$_M(c$, "getCurrentColorRange", 
function () {
return this.colorManager.getPropertyColorRange ();
});
$_M(c$, "setDefaultColors", 
function (isRasmol) {
this.colorManager.setDefaultColors (isRasmol);
this.global.setB ("colorRasmol", isRasmol);
this.global.setS ("defaultColorScheme", (isRasmol ? "rasmol" : "jmol"));
}, "~B");
$_M(c$, "getColorArgbOrGray", 
function (colix) {
return this.gdata.getColorArgbOrGray (colix);
}, "~N");
$_M(c$, "setRubberbandArgb", 
function (argb) {
this.colorManager.setRubberbandArgb (argb);
}, "~N");
$_M(c$, "getColixRubberband", 
function () {
return this.colorManager.colixRubberband;
});
$_M(c$, "setElementArgb", 
function (elementNumber, argb) {
this.global.setS ("=color " + J.util.Elements.elementNameFromNumber (elementNumber), J.util.Escape.escapeColor (argb));
this.colorManager.setElementArgb (elementNumber, argb);
}, "~N,~N");
$_V(c$, "setVectorScale", 
function (scale) {
this.global.setF ("vectorScale", scale);
this.global.vectorScale = scale;
}, "~N");
$_M(c$, "isVibrationOn", 
function () {
return this.transformManager.vibrationOn;
});
$_V(c$, "setVibrationScale", 
function (scale) {
this.transformManager.setVibrationScale (scale);
this.global.vibrationScale = scale;
this.global.setF ("vibrationScale", scale);
}, "~N");
$_M(c$, "setVibrationOff", 
function () {
this.transformManager.setVibrationPeriod (0);
});
$_V(c$, "setVibrationPeriod", 
function (period) {
this.transformManager.setVibrationPeriod (period);
period = Math.abs (period);
this.global.vibrationPeriod = period;
this.global.setF ("vibrationPeriod", period);
}, "~N");
$_M(c$, "setObjectColor", 
function (name, colorName) {
if (colorName == null || colorName.length == 0) return;
this.setObjectArgb (name, JU.CU.getArgbFromString (colorName));
}, "~S,~S");
$_M(c$, "setObjectVisibility", 
function (name, b) {
var objId = J.viewer.StateManager.getObjectIdFromName (name);
if (objId >= 0) {
this.setShapeProperty (objId, "display", b ? Boolean.TRUE : Boolean.FALSE);
}}, "~S,~B");
$_M(c$, "setObjectArgb", 
function (name, argb) {
var objId = J.viewer.StateManager.getObjectIdFromName (name);
if (objId < 0) {
if (name.equalsIgnoreCase ("axes")) {
this.setObjectArgb ("axis1", argb);
this.setObjectArgb ("axis2", argb);
this.setObjectArgb ("axis3", argb);
}return;
}this.global.objColors[objId] = argb;
switch (objId) {
case 0:
this.gdata.setBackgroundArgb (argb);
this.colorManager.setColixBackgroundContrast (argb);
break;
}
this.global.setS (name + "Color", J.util.Escape.escapeColor (argb));
}, "~S,~N");
$_M(c$, "setBackgroundImage", 
function (fileName, image) {
this.global.backgroundImageFileName = fileName;
this.gdata.setBackgroundImage (image);
}, "~S,~O");
$_M(c$, "getObjectArgb", 
function (objId) {
return this.global.objColors[objId];
}, "~N");
$_M(c$, "getObjectColix", 
function (objId) {
var argb = this.getObjectArgb (objId);
if (argb == 0) return this.getColixBackgroundContrast ();
return J.util.C.getColix (argb);
}, "~N");
$_M(c$, "getFontState", 
function (myType, font3d) {
return this.getStateCreator ().getFontState (myType, font3d);
}, "~S,javajs.awt.Font");
$_V(c$, "setColorBackground", 
function (colorName) {
this.setObjectColor ("background", colorName);
}, "~S");
$_V(c$, "getBackgroundArgb", 
function () {
return this.getObjectArgb (0);
});
$_M(c$, "setObjectMad", 
function (iShape, name, mad) {
var objId = J.viewer.StateManager.getObjectIdFromName (name.equalsIgnoreCase ("axes") ? "axis" : name);
if (objId < 0) return;
if (mad == -2 || mad == -4) {
var m = mad + 3;
mad = this.getObjectMad (objId);
if (mad == 0) mad = m;
}this.global.setB ("show" + name, mad != 0);
this.global.objStateOn[objId] = (mad != 0);
if (mad == 0) return;
this.global.objMad[objId] = mad;
this.setShapeSize (iShape, mad, null);
}, "~N,~S,~N");
$_M(c$, "getObjectMad", 
function (objId) {
return (this.global.objStateOn[objId] ? this.global.objMad[objId] : 0);
}, "~N");
$_M(c$, "setPropertyColorScheme", 
function (scheme, isTranslucent, isOverloaded) {
this.global.propertyColorScheme = scheme;
if (scheme.startsWith ("translucent ")) {
isTranslucent = true;
scheme = scheme.substring (12).trim ();
}this.colorManager.setPropertyColorScheme (scheme, isTranslucent, isOverloaded);
}, "~S,~B,~B");
$_M(c$, "getPropertyColorScheme", 
function () {
return this.global.propertyColorScheme;
});
$_M(c$, "getColixBackgroundContrast", 
function () {
return this.colorManager.colixBackgroundContrast;
});
$_M(c$, "getSpecularState", 
function () {
return this.getStateCreator ().getSpecularState ();
});
$_M(c$, "getColixAtomPalette", 
function (atom, pid) {
return this.colorManager.getColixAtomPalette (atom, pid);
}, "J.modelset.Atom,~N");
$_M(c$, "getColixBondPalette", 
function (bond, pid) {
return this.colorManager.getColixBondPalette (bond, pid);
}, "J.modelset.Bond,~N");
$_M(c$, "getColorSchemeList", 
function (colorScheme) {
return this.colorManager.getColorSchemeList (colorScheme);
}, "~S");
$_M(c$, "setUserScale", 
function (scale) {
this.colorManager.setUserScale (scale);
}, "~A");
$_M(c$, "getColixForPropertyValue", 
function (val) {
return this.colorManager.getColixForPropertyValue (val);
}, "~N");
$_M(c$, "getColorPointForPropertyValue", 
function (val) {
return JU.CU.colorPtFromInt2 (this.gdata.getColorArgbOrGray (this.colorManager.getColixForPropertyValue (val)));
}, "~N");
$_M(c$, "select", 
function (bs, isGroup, addRemove, isQuiet) {
if (isGroup) bs = this.getUndeletedGroupAtomBits (bs);
this.selectionManager.select (bs, addRemove, isQuiet);
this.shapeManager.setShapeSizeBs (1, 2147483647, null, null);
}, "JU.BS,~B,~N,~B");
$_V(c$, "setSelectionSet", 
function (set) {
this.select (set, false, 0, true);
}, "JU.BS");
$_M(c$, "selectBonds", 
function (bs) {
this.shapeManager.setShapeSizeBs (1, 2147483647, null, bs);
}, "JU.BS");
$_M(c$, "displayAtoms", 
function (bs, isDisplay, isGroup, addRemove, isQuiet) {
if (isGroup) bs = this.getUndeletedGroupAtomBits (bs);
if (isDisplay) this.selectionManager.display (this.modelSet, bs, addRemove, isQuiet);
 else this.selectionManager.hide (this.modelSet, bs, addRemove, isQuiet);
}, "JU.BS,~B,~B,~N,~B");
$_M(c$, "getUndeletedGroupAtomBits", 
function (bs) {
bs = this.getAtomBits (1087373318, bs);
J.util.BSUtil.andNot (bs, this.selectionManager.getDeletedAtoms ());
return bs;
}, "JU.BS");
$_M(c$, "getHiddenSet", 
function () {
return this.selectionManager.getHiddenSet ();
});
$_M(c$, "isSelected", 
function (atomIndex) {
return this.selectionManager.isSelected (atomIndex);
}, "~N");
$_M(c$, "isInSelectionSubset", 
function (atomIndex) {
return this.selectionManager.isInSelectionSubset (atomIndex);
}, "~N");
$_M(c$, "reportSelection", 
function (msg) {
if (this.modelSet.getSelectionHaloEnabled ()) this.setTainted (true);
if (this.isScriptQueued () || this.global.debugScript) this.scriptStatus (msg);
}, "~S");
$_M(c$, "getAtomSetCenter", 
function (bs) {
return this.modelSet.getAtomSetCenter (bs);
}, "JU.BS");
$_M(c$, "clearAtomSets", 
function () {
this.setSelectionSubset (null);
this.definedAtomSets.clear ();
});
$_M(c$, "getDefinedAtomSet", 
function (name) {
var o = this.definedAtomSets.get (name.toLowerCase ());
return (Clazz_instanceOf (o, JU.BS) ? o :  new JU.BS ());
}, "~S");
$_V(c$, "selectAll", 
function () {
this.selectionManager.selectAll (false);
});
$_M(c$, "setNoneSelected", 
function (noneSelected) {
this.noneSelected = noneSelected;
}, "~B");
$_M(c$, "getNoneSelected", 
function () {
return (this.noneSelected ? Boolean.TRUE : Boolean.FALSE);
});
$_V(c$, "clearSelection", 
function () {
this.selectionManager.clearSelection (true);
this.global.setB ("hideNotSelected", false);
});
$_M(c$, "setSelectionSubset", 
function (subset) {
this.selectionManager.setSelectionSubset (subset);
}, "JU.BS");
$_M(c$, "getSelectionSubset", 
function () {
return this.selectionManager.getSelectionSubset ();
});
$_M(c$, "invertSelection", 
function () {
this.selectionManager.invertSelection ();
});
$_M(c$, "getSelectionSet", 
function (includeDeleted) {
return this.selectionManager.getSelectionSet (includeDeleted);
}, "~B");
$_M(c$, "setSelectedAtom", 
function (atomIndex, TF) {
this.selectionManager.setSelectedAtom (atomIndex, TF);
}, "~N,~B");
$_M(c$, "isAtomSelected", 
function (atomIndex) {
return this.selectionManager.isAtomSelected (atomIndex);
}, "~N");
$_V(c$, "getSelectionCount", 
function () {
return this.selectionManager.getSelectionCount ();
});
$_M(c$, "setFormalCharges", 
function (formalCharge) {
this.modelSet.setFormalCharges (this.getSelectionSet (false), formalCharge);
}, "~N");
$_V(c$, "addSelectionListener", 
function (listener) {
this.selectionManager.addListener (listener);
}, "J.api.JmolSelectionListener");
$_V(c$, "removeSelectionListener", 
function (listener) {
this.selectionManager.addListener (listener);
}, "J.api.JmolSelectionListener");
$_M(c$, "getAtomBitSetEval", 
function (eval, atomExpression) {
if (!this.allowScripting) {
System.out.println ("viewer.getAtomBitSetEval not allowed");
return  new JU.BS ();
}return this.getScriptManager ().getAtomBitSetEval (eval, atomExpression);
}, "J.api.JmolScriptEvaluator,~O");
$_V(c$, "setModeMouse", 
function (modeMouse) {
if (modeMouse == -1) {
if (this.mouse != null) this.disposeMouse ();
this.clearScriptQueue ();
this.clearThreads ();
this.haltScriptExecution ();
if (this.scriptManager != null) this.scriptManager.clear (true);
this.gdata.destroy ();
if (this.jmolpopup != null) this.jmolpopup.jpiDispose ();
if (this.modelkitPopup != null) this.modelkitPopup.jpiDispose ();
try {
if (this.appConsole != null) {
this.appConsole.dispose ();
this.appConsole = null;
}if (this.scriptEditor != null) {
this.scriptEditor.dispose ();
this.scriptEditor = null;
}} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
}}, "~N");
$_M(c$, "getRubberBandSelection", 
function () {
return (this.haveDisplay ? this.actionManager.getRubberBand () : null);
});
$_M(c$, "isBound", 
function (action, gesture) {
return (this.haveDisplay && this.actionManager.isBound (action, gesture));
}, "~N,~N");
$_M(c$, "getCursorX", 
function () {
return (this.haveDisplay ? this.actionManager.getCurrentX () : 0);
});
$_M(c$, "getCursorY", 
function () {
return (this.haveDisplay ? this.actionManager.getCurrentY () : 0);
});
$_M(c$, "getDefaultDirectory", 
function () {
return this.global.defaultDirectory;
});
$_M(c$, "getLocalUrl", 
function (fileName) {
return this.apiPlatform.getLocalUrl (fileName);
}, "~S");
$_V(c$, "getBufferedInputStream", 
function (fullPathName) {
return this.fileManager.getBufferedInputStream (fullPathName);
}, "~S");
$_M(c$, "getBufferedReaderOrErrorMessageFromName", 
function (name, fullPathNameReturn, isBinary) {
return this.fileManager.getBufferedReaderOrErrorMessageFromName (name, fullPathNameReturn, isBinary, true);
}, "~S,~A,~B");
$_M(c$, "setLoadParameters", 
function (htParams, isAppend) {
if (htParams == null) htParams =  new java.util.Hashtable ();
htParams.put ("viewer", this);
if (this.global.atomTypes.length > 0) htParams.put ("atomTypes", this.global.atomTypes);
if (!htParams.containsKey ("lattice")) htParams.put ("lattice", this.global.getDefaultLattice ());
if (this.global.applySymmetryToBonds) htParams.put ("applySymmetryToBonds", Boolean.TRUE);
if (this.global.pdbGetHeader) htParams.put ("getHeader", Boolean.TRUE);
if (this.global.pdbSequential) htParams.put ("isSequential", Boolean.TRUE);
htParams.put ("stateScriptVersionInt", Integer.$valueOf (this.stateScriptVersionInt));
if (!htParams.containsKey ("filter")) {
var filter = this.getDefaultLoadFilter ();
if (filter.length > 0) htParams.put ("filter", filter);
}var merging = (isAppend && !this.global.appendNew && this.getAtomCount () > 0);
htParams.put ("baseAtomIndex", Integer.$valueOf (isAppend ? this.getAtomCount () : 0));
htParams.put ("baseModelIndex", Integer.$valueOf (this.getAtomCount () == 0 ? 0 : this.getModelCount () + (merging ? -1 : 0)));
if (merging) htParams.put ("merging", Boolean.TRUE);
return htParams;
}, "java.util.Map,~B");
$_V(c$, "openFileAsyncSpecial", 
function (fileName, flags) {
this.getScriptManager ().openFileAsync (fileName, flags);
}, "~S,~N");
$_V(c$, "openFile", 
function (fileName) {
this.zap (true, true, false);
return this.loadModelFromFileRepaint (null, fileName, null, null);
}, "~S");
$_V(c$, "openFiles", 
function (fileNames) {
this.zap (true, true, false);
return this.loadModelFromFileRepaint (null, null, fileNames, null);
}, "~A");
$_V(c$, "openReader", 
function (fullPathName, fileName, reader) {
this.zap (true, true, false);
return this.loadModelFromFileRepaint (fullPathName, fileName, null, reader);
}, "~S,~S,java.io.Reader");
$_V(c$, "openDOM", 
function (DOMNode) {
this.zap (true, true, false);
return this.loadModelFromFileRepaint ("?", "?", null, DOMNode);
}, "~O");
$_M(c$, "loadModelFromFileRepaint", 
function (fullPathName, fileName, fileNames, reader) {
var ret = this.loadModelFromFile (fullPathName, fileName, fileNames, reader, false, null, null, 0);
this.refresh (1, "loadModelFromFileRepaint");
return ret;
}, "~S,~S,~A,~O");
$_M(c$, "loadModelFromFile", 
function (fullPathName, fileName, fileNames, reader, isAppend, htParams, loadScript, tokType) {
if (htParams == null) htParams = this.setLoadParameters (null, isAppend);
var atomSetCollection;
var saveInfo = this.fileManager.getFileInfo ();
if (fileNames != null) {
if (loadScript == null) {
loadScript =  new JU.SB ().append ("load files");
for (var i = 0; i < fileNames.length; i++) loadScript.append (" /*file*/$FILENAME" + (i + 1) + "$");

}var timeBegin = System.currentTimeMillis ();
atomSetCollection = this.fileManager.createAtomSetCollectionFromFiles (fileNames, this.setLoadParameters (htParams, isAppend), isAppend);
var ms = System.currentTimeMillis () - timeBegin;
var msg = "";
for (var i = 0; i < fileNames.length; i++) msg += (i == 0 ? "" : ",") + fileNames[i];

J.util.Logger.info ("openFiles(" + fileNames.length + ") " + ms + " ms");
fileNames = htParams.get ("fullPathNames");
var fileTypes = htParams.get ("fileTypes");
var s = loadScript.toString ();
for (var i = 0; i < fileNames.length; i++) {
var fname = fileNames[i];
if (fileTypes != null && fileTypes[i] != null) fname = fileTypes[i] + "::" + fname;
s = JU.PT.simpleReplace (s, "$FILENAME" + (i + 1) + "$", J.util.Escape.eS (fname.$replace ('\\', '/')));
}
loadScript =  new JU.SB ().append (s);
} else if (reader == null) {
if (loadScript == null) loadScript =  new JU.SB ().append ("load /*file*/$FILENAME$");
atomSetCollection = this.openFileFull (fileName, isAppend, htParams, loadScript);
} else if (Clazz_instanceOf (reader, java.io.Reader)) {
atomSetCollection = this.fileManager.createAtomSetCollectionFromReader (fullPathName, fileName, reader, htParams);
} else {
atomSetCollection = this.fileManager.createAtomSetCollectionFromDOM (reader, htParams);
}if (tokType != 0) {
this.fileManager.setFileInfo (saveInfo);
return this.loadAtomDataAndReturnError (atomSetCollection, tokType);
}if (htParams.containsKey ("isData")) return atomSetCollection;
if (loadScript != null) {
var fname = htParams.get ("fullPathName");
if (fname == null) fname = "";
if (htParams.containsKey ("loadScript")) loadScript = htParams.get ("loadScript");
htParams.put ("loadScript", loadScript =  new JU.SB ().append (JU.PT.simpleReplace (loadScript.toString (), "$FILENAME$", J.util.Escape.eS (fname.$replace ('\\', '/')))));
}return this.createModelSetAndReturnError (atomSetCollection, isAppend, loadScript, htParams);
}, "~S,~S,~A,~O,~B,java.util.Map,JU.SB,~N");
$_M(c$, "setLigandModel", 
function (key, data) {
if (this.ligandModels == null) this.ligandModels =  new java.util.Hashtable ();
this.ligandModels.put (key, data);
}, "~S,~S");
$_M(c$, "getLigandModel", 
function (id, prefix, suffix, terminator) {
if (id == null) {
if (this.ligandModelSet != null) {
var e = this.ligandModels.entrySet ().iterator ();
while (e.hasNext ()) {
var entry = e.next ();
if (Clazz_instanceOf (entry.getValue (), Boolean)) e.remove ();
}
}return null;
}var isLigand = prefix.equals ("ligand_");
if (isLigand) id = id.toUpperCase ();
if (this.ligandModelSet == null) this.ligandModelSet =  new java.util.Hashtable ();
this.ligandModelSet.put (id, Boolean.TRUE);
if (this.ligandModels == null) this.ligandModels =  new java.util.Hashtable ();
var model = this.ligandModels.get (id);
var data;
var fname = null;
if (Clazz_instanceOf (model, Boolean)) return null;
if (model == null) model = this.ligandModels.get (id + suffix);
var isError = false;
if (model == null) {
var s;
if (isLigand) {
fname = this.setLoadFormat ("#" + id, '#', false);
if (fname.length == 0) return null;
this.scriptEcho ("fetching " + fname);
s = this.getFileAsString (fname);
} else {
s = this.getFileAsString (prefix);
var pt = (terminator == null ? -1 : s.indexOf (terminator));
if (pt >= 0) s = s.substring (0, pt);
}isError = (s.indexOf ("java.") == 0);
model = s;
if (!isError) this.ligandModels.put (id + suffix, model);
}if (!isLigand) return model;
if (!isError && Clazz_instanceOf (model, String)) {
data = model;
if (data.length != 0) {
var htParams =  new java.util.Hashtable ();
htParams.put ("modelOnly", Boolean.TRUE);
model = this.getModelAdapter ().getAtomSetCollectionReader ("ligand", null, J.io.JmolBinary.getBufferedReaderForString (data), htParams);
isError = (Clazz_instanceOf (model, String));
if (!isError) {
model = this.getModelAdapter ().getAtomSetCollection (model);
isError = (Clazz_instanceOf (model, String));
if (fname != null && !isError) this.scriptEcho (this.getModelAdapter ().getAtomSetCollectionAuxiliaryInfo (model).get ("modelLoadNote"));
}}}if (isError) {
this.scriptEcho (model.toString ());
this.ligandModels.put (id, Boolean.FALSE);
return null;
}return model;
}, "~S,~S,~S,~S");
$_M(c$, "openFileFull", 
function (fileName, isAppend, htParams, loadScript) {
if (fileName == null) return null;
if (fileName.indexOf ("[]") >= 0) {
return null;
}var atomSetCollection;
var msg = "openFile(" + fileName + ")";
J.util.Logger.startTimer (msg);
htParams = this.setLoadParameters (htParams, isAppend);
var isLoadVariable = fileName.startsWith ("@");
var haveFileData = (htParams.containsKey ("fileData"));
if (fileName.indexOf ('$') == 0) htParams.put ("smilesString", fileName.substring (1));
var isString = (fileName.equalsIgnoreCase ("string") || fileName.equals ("Jmol Model Kit"));
var strModel = null;
if (haveFileData) {
strModel = htParams.get ("fileData");
if (htParams.containsKey ("isData")) {
return this.loadInlineScript (strModel, '\0', isAppend, htParams);
}} else if (isString) {
strModel = this.modelSet.getInlineData (-1);
if (strModel == null) if (this.global.modelKitMode) strModel = "5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63";
 else return "cannot find string data";
if (loadScript != null) htParams.put ("loadScript", loadScript =  new JU.SB ().append (JU.PT.simpleReplace (loadScript.toString (), "$FILENAME$", "data \"model inline\"\n" + strModel + "end \"model inline\"")));
}if (strModel != null) {
if (!isAppend) this.zap (true, false, false);
if (!isLoadVariable && (!haveFileData || isString)) this.getStateCreator ().getInlineData (loadScript, strModel, isAppend, this.getDefaultLoadFilter ());
atomSetCollection = this.fileManager.createAtomSetCollectionFromString (strModel, htParams, isAppend);
} else {
atomSetCollection = this.fileManager.createAtomSetCollectionFromFile (fileName, htParams, isAppend);
}J.util.Logger.checkTimer (msg, false);
return atomSetCollection;
}, "~S,~B,java.util.Map,JU.SB");
$_V(c$, "openStringInline", 
function (strModel) {
var ret = this.openStringInlineParamsAppend (strModel, null, false);
this.refresh (1, "openStringInline");
return ret;
}, "~S");
$_M(c$, "loadInline", 
function (strModel) {
return this.loadInlineScriptRepaint (strModel, this.global.inlineNewlineChar, false);
}, "~S");
$_M(c$, "loadInline", 
function (strModel, newLine) {
return this.loadInlineScriptRepaint (strModel, newLine, false);
}, "~S,~S");
$_V(c$, "loadInlineAppend", 
function (strModel, isAppend) {
return this.loadInlineScriptRepaint (strModel, '\0', isAppend);
}, "~S,~B");
$_M(c$, "loadInlineScriptRepaint", 
function (strModel, newLine, isAppend) {
var ret = this.loadInlineScript (strModel, newLine, isAppend, null);
this.refresh (1, "loadInlineScript");
return ret;
}, "~S,~S,~B");
$_M(c$, "loadInline", 
function (arrayModels) {
return this.loadInline (arrayModels, false);
}, "~A");
$_M(c$, "loadInline", 
function (arrayModels, isAppend) {
if (arrayModels == null || arrayModels.length == 0) return null;
var ret = this.openStringsInlineParamsAppend (arrayModels, null, isAppend);
this.refresh (1, "loadInline String[]");
return ret;
}, "~A,~B");
$_M(c$, "loadInline", 
function (arrayData, isAppend) {
if (arrayData == null || arrayData.size () == 0) return null;
if (!isAppend) this.zap (true, false, false);
var list =  new JU.List ();
for (var i = 0; i < arrayData.size (); i++) list.addLast (arrayData.get (i));

var atomSetCollection = this.fileManager.createAtomSeCollectionFromArrayData (list, this.setLoadParameters (null, isAppend), isAppend);
var ret = this.createModelSetAndReturnError (atomSetCollection, isAppend, null, null);
this.refresh (1, "loadInline");
return ret;
}, "java.util.List,~B");
$_M(c$, "loadInlineScript", 
function (strModel, newLine, isAppend, htParams) {
if (strModel == null || strModel.length == 0) return null;
strModel = J.viewer.Viewer.fixInlineString (strModel, newLine);
if (newLine.charCodeAt (0) != 0) J.util.Logger.info ("loading model inline, " + strModel.length + " bytes, with newLine character " + (newLine).charCodeAt (0) + " isAppend=" + isAppend);
if (J.util.Logger.debugging) J.util.Logger.debug (strModel);
var datasep = this.getDataSeparator ();
var i;
if (datasep != null && datasep !== "" && (i = strModel.indexOf (datasep)) >= 0 && strModel.indexOf ("# Jmol state") < 0) {
var n = 2;
while ((i = strModel.indexOf (datasep, i + 1)) >= 0) n++;

var strModels =  new Array (n);
var pt = 0;
var pt0 = 0;
for (i = 0; i < n; i++) {
pt = strModel.indexOf (datasep, pt0);
if (pt < 0) pt = strModel.length;
strModels[i] = strModel.substring (pt0, pt);
pt0 = pt + datasep.length;
}
return this.openStringsInlineParamsAppend (strModels, htParams, isAppend);
}return this.openStringInlineParamsAppend (strModel, htParams, isAppend);
}, "~S,~S,~B,java.util.Map");
c$.fixInlineString = $_M(c$, "fixInlineString", 
function (strModel, newLine) {
var i;
if (strModel.indexOf ("\\/n") >= 0) {
strModel = JU.PT.simpleReplace (strModel, "\n", "");
strModel = JU.PT.simpleReplace (strModel, "\\/n", "\n");
newLine = String.fromCharCode ( 0);
}if (newLine.charCodeAt (0) != 0 && newLine != '\n') {
var repEmpty = (strModel.indexOf ('\n') >= 0);
var len = strModel.length;
for (i = 0; i < len && strModel.charAt (i) == ' '; ++i) {
}
if (i < len && strModel.charAt (i) == newLine) strModel = strModel.substring (i + 1);
if (repEmpty) strModel = JU.PT.simpleReplace (strModel, "" + newLine, "");
 else strModel = strModel.$replace (newLine, '\n');
}return strModel;
}, "~S,~S");
$_M(c$, "openStringInlineParamsAppend", 
function (strModel, htParams, isAppend) {
var br =  new java.io.BufferedReader ( new java.io.StringReader (strModel));
var type = this.getModelAdapter ().getFileTypeName (br);
if (type == null) return "unknown file type";
if (type.equals ("spt")) {
return "cannot open script inline";
}htParams = this.setLoadParameters (htParams, isAppend);
var loadScript = htParams.get ("loadScript");
var isLoadCommand = htParams.containsKey ("isData");
if (loadScript == null) loadScript =  new JU.SB ();
if (!isAppend) this.zap (true, false, false);
if (!isLoadCommand) this.getStateCreator ().getInlineData (loadScript, strModel, isAppend, this.getDefaultLoadFilter ());
var atomSetCollection = this.fileManager.createAtomSetCollectionFromString (strModel, htParams, isAppend);
return this.createModelSetAndReturnError (atomSetCollection, isAppend, loadScript, null);
}, "~S,java.util.Map,~B");
$_M(c$, "openStringsInlineParamsAppend", 
function (arrayModels, htParams, isAppend) {
var loadScript =  new JU.SB ();
if (!isAppend) this.zap (true, false, false);
var atomSetCollection = this.fileManager.createAtomSeCollectionFromStrings (arrayModels, loadScript, this.setLoadParameters (htParams, isAppend), isAppend);
return this.createModelSetAndReturnError (atomSetCollection, isAppend, loadScript, null);
}, "~A,java.util.Map,~B");
$_M(c$, "getInlineChar", 
function () {
return this.global.inlineNewlineChar;
});
$_M(c$, "getDataSeparator", 
function () {
return this.global.getParameter ("dataseparator");
});
$_M(c$, "createModelSetAndReturnError", 
function (atomSetCollection, isAppend, loadScript, htParams) {
var fullPathName = this.fileManager.getFullPathName ();
var fileName = this.fileManager.getFileName ();
var errMsg;
if (loadScript == null) {
this.setBooleanProperty ("preserveState", false);
loadScript =  new JU.SB ().append ("load \"???\"");
}if (Clazz_instanceOf (atomSetCollection, String)) {
errMsg = atomSetCollection;
this.setFileLoadStatus (J.constant.EnumFileStatus.NOT_LOADED, fullPathName, null, null, errMsg, null);
if (this.displayLoadErrors && !isAppend && !errMsg.equals ("#CANCELED#")) this.zapMsg (errMsg);
return errMsg;
}if (isAppend) this.clearAtomSets ();
 else if (this.global.modelKitMode && !fileName.equals ("Jmol Model Kit")) this.setModelKitMode (false);
this.setFileLoadStatus (J.constant.EnumFileStatus.CREATING_MODELSET, fullPathName, fileName, null, null, null);
this.pushHoldRepaint ("createModelSet");
this.setErrorMessage (null, null);
try {
var bsNew =  new JU.BS ();
this.modelManager.createModelSet (fullPathName, fileName, loadScript, atomSetCollection, bsNew, isAppend);
if (bsNew.cardinality () > 0) {
var jmolScript = this.modelSet.getModelSetAuxiliaryInfoValue ("jmolscript");
if (this.modelSet.getModelSetAuxiliaryInfoBoolean ("doMinimize")) this.minimize (2147483647, 0, bsNew, null, 0, true, true, true);
 else this.addHydrogens (bsNew, false, true);
if (jmolScript != null) this.modelSet.getModelSetAuxiliaryInfo ().put ("jmolscript", jmolScript);
}this.initializeModel (isAppend);
} catch (er) {
if (Clazz_exceptionOf (er, Error)) {
this.handleError (er, true);
errMsg = this.getShapeErrorState ();
errMsg = ("ERROR creating model: " + er + (errMsg.length == 0 ? "" : "|" + errMsg));
this.zapMsg (errMsg);
this.setErrorMessage (errMsg, null);
} else {
throw er;
}
}
this.popHoldRepaint ("createModelSet \u0001## REPAINT_IGNORE ##");
errMsg = this.getErrorMessage ();
this.setFileLoadStatus (J.constant.EnumFileStatus.CREATED, fullPathName, fileName, this.getModelSetName (), errMsg, htParams == null ? null : htParams.get ("async"));
if (isAppend) {
this.selectAll ();
this.setTainted (true);
this.axesAreTainted = true;
}atomSetCollection = null;
System.gc ();
return errMsg;
}, "~O,~B,JU.SB,java.util.Map");
$_M(c$, "loadAtomDataAndReturnError", 
function (atomSetCollection, tokType) {
if (Clazz_instanceOf (atomSetCollection, String)) return atomSetCollection;
this.setErrorMessage (null, null);
try {
this.modelManager.createAtomDataSet (atomSetCollection, tokType);
switch (tokType) {
case 4166:
this.setStatusFrameChanged (true);
break;
case 1649412120:
this.shapeManager.deleteVdwDependentShapes (null);
break;
}
} catch (er) {
if (Clazz_exceptionOf (er, Error)) {
this.handleError (er, true);
var errMsg = this.getShapeErrorState ();
errMsg = ("ERROR adding atom data: " + er + (errMsg.length == 0 ? "" : "|" + errMsg));
this.zapMsg (errMsg);
this.setErrorMessage (errMsg, null);
this.setParallel (false);
} else {
throw er;
}
}
return this.getErrorMessage ();
}, "~O,~N");
$_V(c$, "getEmbeddedFileState", 
function (filename) {
return this.fileManager.getEmbeddedFileState (filename);
}, "~S");
$_V(c$, "getFileAsBytes", 
function (pathName, out) {
return this.fileManager.getFileAsBytes (pathName, out, true);
}, "~S,JU.OC");
$_M(c$, "getCurrentFileAsString", 
function () {
var filename = this.getFullPathName ();
if (filename.equals ("string") || filename.equals ("Jmol Model Kit")) return this.modelSet.getInlineData (this.getCurrentModelIndex ());
if (filename.indexOf ("[]") >= 0) return filename;
if (filename === "JSNode") return "<DOM NODE>";
var pathName = this.modelManager.getModelSetPathName ();
if (pathName == null) return null;
return this.getFileAsString4 (pathName, -1, true, false);
});
$_M(c$, "getFullPathName", 
function () {
return this.fileManager.getFullPathName ();
});
$_M(c$, "getFileName", 
function () {
return this.fileManager.getFileName ();
});
$_M(c$, "getFullPathNameOrError", 
function (filename) {
return this.fileManager.getFullPathNameOrError (filename);
}, "~S");
$_V(c$, "getFileAsString", 
function (name) {
return this.getFileAsString4 (name, -1, false, false);
}, "~S");
$_M(c$, "getFileAsString4", 
function (name, nBytesMax, doSpecialLoad, allowBinary) {
if (name == null) return this.getCurrentFileAsString ();
var data =  new Array (2);
data[0] = name;
this.fileManager.getFileDataOrErrorAsString (data, nBytesMax, doSpecialLoad, allowBinary);
return data[1];
}, "~S,~N,~B,~B");
$_M(c$, "getFileAsStringBin", 
function (data) {
return this.fileManager.getFileDataOrErrorAsString (data, -1, false, true);
}, "~A");
$_M(c$, "getFilePath", 
function (name, asShortName) {
return this.fileManager.getFilePath (name, false, asShortName);
}, "~S,~B");
$_M(c$, "getFileInfo", 
function () {
return this.fileManager.getFileInfo ();
});
$_M(c$, "setFileInfo", 
function (fileInfo) {
this.fileManager.setFileInfo (fileInfo);
}, "~A");
$_M(c$, "autoCalculate", 
function (tokProperty) {
switch (tokProperty) {
case 1112539151:
this.modelSet.getSurfaceDistanceMax ();
break;
case 1112539150:
this.modelSet.calculateStraightness ();
break;
}
}, "~N");
$_M(c$, "getSurfaceDistanceMax", 
function () {
return this.modelSet.getSurfaceDistanceMax ();
});
$_M(c$, "calculateStraightness", 
function () {
this.modelSet.setHaveStraightness (false);
this.modelSet.calculateStraightness ();
});
$_M(c$, "calculateSurface", 
function (bsSelected, envelopeRadius) {
if (bsSelected == null) bsSelected = this.getSelectionSet (false);
if (envelopeRadius == 3.4028235E38 || envelopeRadius == -1) this.addStateScriptRet ("calculate surfaceDistance " + (envelopeRadius == 3.4028235E38 ? "FROM" : "WITHIN"), null, bsSelected, null, "", false, true);
return this.modelSet.calculateSurface (bsSelected, envelopeRadius);
}, "JU.BS,~N");
$_M(c$, "getStructureList", 
function () {
return this.global.getStructureList ();
});
$_M(c$, "setStructureList", 
function (list, type) {
this.global.setStructureList (list, type);
this.modelSet.setStructureList (this.getStructureList ());
}, "~A,J.constant.EnumStructure");
$_M(c$, "getDefaultStructure", 
function (bsAtoms, bsAllAtoms) {
if (bsAtoms == null) bsAtoms = this.getSelectionSet (false);
return this.modelSet.getDefaultStructure (bsAtoms, bsAllAtoms);
}, "JU.BS,JU.BS");
$_M(c$, "calculateStructures", 
function (bsAtoms, asDSSP, setStructure) {
if (bsAtoms == null) bsAtoms = this.getSelectionSet (false);
return this.modelSet.calculateStructures (bsAtoms, asDSSP, this.global.dsspCalcHydrogen, setStructure);
}, "JU.BS,~B,~B");
$_V(c$, "getSelectedAtomIterator", 
function (bsSelected, isGreaterOnly, modelZeroBased, isMultiModel) {
return this.modelSet.getSelectedAtomIterator (bsSelected, isGreaterOnly, modelZeroBased, false, isMultiModel);
}, "JU.BS,~B,~B,~B");
$_V(c$, "setIteratorForAtom", 
function (iterator, atomIndex, distance) {
this.modelSet.setIteratorForAtom (iterator, -1, atomIndex, distance, null);
}, "J.api.AtomIndexIterator,~N,~N");
$_V(c$, "setIteratorForPoint", 
function (iterator, modelIndex, pt, distance) {
this.modelSet.setIteratorForPoint (iterator, modelIndex, pt, distance);
}, "J.api.AtomIndexIterator,~N,JU.P3,~N");
$_V(c$, "fillAtomData", 
function (atomData, mode) {
atomData.programInfo = "Jmol Version " + J.viewer.Viewer.getJmolVersion ();
atomData.fileName = this.getFileName ();
this.modelSet.fillAtomData (atomData, mode);
}, "J.atomdata.AtomData,~N");
$_M(c$, "addStateScript", 
function (script, addFrameNumber, postDefinitions) {
return this.addStateScriptRet (script, null, null, null, null, addFrameNumber, postDefinitions);
}, "~S,~B,~B");
$_M(c$, "addStateScriptRet", 
function (script1, bsBonds, bsAtoms1, bsAtoms2, script2, addFrameNumber, postDefinitions) {
return this.modelSet.addStateScript (script1, bsBonds, bsAtoms1, bsAtoms2, script2, addFrameNumber, postDefinitions);
}, "~S,JU.BS,JU.BS,JU.BS,~S,~B,~B");
$_M(c$, "getEchoStateActive", 
function () {
return this.modelSet.getEchoStateActive ();
});
$_M(c$, "setEchoStateActive", 
function (TF) {
this.modelSet.setEchoStateActive (TF);
}, "~B");
$_M(c$, "clearModelDependentObjects", 
function () {
this.setFrameOffsets (null);
this.stopMinimization ();
this.minimizer = null;
if (this.smilesMatcher != null) {
this.smilesMatcher = null;
}if (this.symmetry != null) {
this.symmetry = null;
}});
$_M(c$, "zap", 
function (notify, resetUndo, zapModelKit) {
this.clearThreads ();
if (this.modelSet != null) {
this.ligandModelSet = null;
this.clearModelDependentObjects ();
this.fileManager.clear ();
this.clearRepaintManager (-1);
this.animationManager.clear ();
this.transformManager.clear ();
this.selectionManager.clear ();
this.clearAllMeasurements ();
this.clearMinimization ();
this.gdata.clear ();
this.modelManager.zap ();
if (this.scriptManager != null) this.scriptManager.clear (false);
if (this.nmrCalculation != null) this.getNMRCalculation ().setChemicalShiftReference (null, 0);
if (this.haveDisplay) {
this.mouse.clear ();
this.clearTimeouts ();
this.actionManager.clear ();
}this.stateManager.clear (this.global);
this.tempArray.clear ();
this.chainMap.clear ();
this.chainList.clear ();
this.colorManager.clear ();
this.definedAtomSets.clear ();
if (this.dataManager != null) this.dataManager.clear ();
if (resetUndo) {
if (zapModelKit && this.global.modelKitMode) {
this.openStringInlineParamsAppend ("5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63", null, true);
this.setRotationRadius (5.0, true);
this.setStringProperty ("picking", "assignAtom_C");
this.setStringProperty ("picking", "assignBond_p");
}this.undoClear ();
}System.gc ();
} else {
this.modelManager.zap ();
}this.initializeModel (false);
if (notify) {
this.setFileLoadStatus (J.constant.EnumFileStatus.ZAPPED, null, (resetUndo ? "resetUndo" : this.getZapName ()), null, null, null);
}if (J.util.Logger.debugging) J.util.Logger.checkMemory ();
}, "~B,~B,~B");
$_M(c$, "zapMsg", 
function (msg) {
this.zap (true, true, false);
this.echoMessage (msg);
}, "~S");
$_M(c$, "echoMessage", 
function (msg) {
var iShape = 30;
this.loadShape (iShape);
this.setShapeProperty (iShape, "font", this.getFont3D ("SansSerif", "Plain", 9));
this.setShapeProperty (iShape, "target", "error");
this.setShapeProperty (iShape, "text", msg);
}, "~S");
$_M(c$, "initializeModel", 
function (isAppend) {
this.clearThreads ();
if (isAppend) {
this.animationManager.initializePointers (1);
return;
}this.reset (true);
this.selectAll ();
this.rotatePrev1 = this.rotateBondIndex = -1;
this.movingSelected = false;
this.noneSelected = false;
this.hoverEnabled = true;
this.transformManager.setCenter ();
this.animationManager.initializePointers (1);
if (!this.modelSet.getModelSetAuxiliaryInfoBoolean ("isPyMOL")) {
this.clearAtomSets ();
this.setCurrentModelIndex (0);
}this.setBackgroundModelIndex (-1);
this.setFrankOn (this.getShowFrank ());
this.startHoverWatcher (true);
this.setTainted (true);
this.finalizeTransformParameters ();
}, "~B");
$_V(c$, "startHoverWatcher", 
function (tf) {
if (!this.haveDisplay || tf && (!this.hoverEnabled || this.animationManager.animationOn)) return;
this.actionManager.startHoverWatcher (tf);
}, "~B");
$_V(c$, "getModelSetName", 
function () {
if (this.modelSet == null) return null;
return this.modelSet.modelSetName;
});
$_V(c$, "getModelSetFileName", 
function () {
return this.modelManager.getModelSetFileName ();
});
$_M(c$, "getUnitCellInfoText", 
function () {
return this.modelSet.getUnitCellInfoText ();
});
$_M(c$, "getUnitCellInfo", 
function (infoType) {
var symmetry = this.getCurrentUnitCell ();
if (symmetry == null) return NaN;
return symmetry.getUnitCellInfoType (infoType);
}, "~N");
$_M(c$, "getSpaceGroupInfo", 
function (spaceGroup) {
return this.modelSet.getSymTemp (true).getSpaceGroupInfo (this.modelSet, -1, spaceGroup, 0, null, null, null);
}, "~S");
$_M(c$, "getPolymerPointsAndVectors", 
function (bs, vList) {
this.modelSet.getPolymerPointsAndVectors (bs, vList, this.global.traceAlpha, this.global.sheetSmoothing);
}, "JU.BS,JU.List");
$_M(c$, "getModelSetProperty", 
function (strProp) {
return this.modelSet.getModelSetProperty (strProp);
}, "~S");
$_M(c$, "getModelSetAuxiliaryInfoValue", 
function (strKey) {
return this.modelSet.getModelSetAuxiliaryInfoValue (strKey);
}, "~S");
$_V(c$, "getModelSetPathName", 
function () {
return this.modelManager.getModelSetPathName ();
});
$_M(c$, "getModelSetTypeName", 
function () {
return this.modelSet.getModelSetTypeName ();
});
$_V(c$, "haveFrame", 
function () {
return this.haveModelSet ();
});
$_M(c$, "haveModelSet", 
function () {
return this.modelSet != null;
});
$_M(c$, "clearBfactorRange", 
function () {
this.modelSet.clearBfactorRange ();
});
$_M(c$, "getHybridizationAndAxes", 
function (atomIndex, z, x, lcaoType) {
return this.modelSet.getHybridizationAndAxes (atomIndex, 0, z, x, lcaoType, true, true);
}, "~N,JU.V3,JU.V3,~S");
$_M(c$, "getMoleculeBitSet", 
function (atomIndex) {
return this.modelSet.getMoleculeBitSetForAtom (atomIndex);
}, "~N");
$_M(c$, "getModelUndeletedAtomsBitSet", 
function (modelIndex) {
var bs = this.modelSet.getModelAtomBitSetIncludingDeleted (modelIndex, true);
this.excludeAtoms (bs, false);
return bs;
}, "~N");
$_M(c$, "getModelBitSet", 
function (atomList, allTrajectories) {
return this.modelSet.getModelBitSet (atomList, allTrajectories);
}, "JU.BS,~B");
$_M(c$, "getModelUndeletedAtomsBitSetBs", 
function (bsModels) {
var bs = this.modelSet.getModelAtomBitSetIncludingDeletedBs (bsModels);
this.excludeAtoms (bs, false);
return bs;
}, "JU.BS");
$_M(c$, "excludeAtoms", 
function (bs, ignoreSubset) {
this.selectionManager.excludeAtoms (bs, ignoreSubset);
}, "JU.BS,~B");
$_M(c$, "getModelSet", 
function () {
return this.modelSet;
});
$_M(c$, "getBoundBoxCommand", 
function (withOptions) {
return this.modelSet.getBoundBoxCommand (withOptions);
}, "~B");
$_M(c$, "setBoundBox", 
function (pt1, pt2, byCorner, scale) {
this.modelSet.setBoundBox (pt1, pt2, byCorner, scale);
}, "JU.P3,JU.P3,~B,~N");
$_V(c$, "getBoundBoxCenter", 
function () {
return this.modelSet.getBoundBoxCenter (this.animationManager.currentModelIndex);
});
$_M(c$, "getAverageAtomPoint", 
function () {
return this.modelSet.getAverageAtomPoint ();
});
$_M(c$, "calcBoundBoxDimensions", 
function (bs, scale) {
this.modelSet.calcBoundBoxDimensions (bs, scale);
this.axesAreTainted = true;
}, "JU.BS,~N");
$_M(c$, "getBoxInfo", 
function (bs, scale) {
return this.modelSet.getBoxInfo (bs, scale);
}, "JU.BS,~N");
$_M(c$, "calcRotationRadius", 
function (center) {
return this.modelSet.calcRotationRadius (this.animationManager.currentModelIndex, center);
}, "JU.P3");
$_M(c$, "calcRotationRadiusBs", 
function (bs) {
return this.modelSet.calcRotationRadiusBs (bs);
}, "JU.BS");
$_V(c$, "getBoundBoxCornerVector", 
function () {
return this.modelSet.getBoundBoxCornerVector ();
});
$_M(c$, "getBoundBoxVertices", 
function () {
return this.modelSet.getBboxVertices ();
});
$_M(c$, "getBoundBoxInfo", 
function () {
return this.modelSet.getBoundBoxInfo ();
});
$_M(c$, "getBoundBoxModels", 
function () {
return this.modelSet.getBoundBoxModels ();
});
$_M(c$, "getBoundBoxCenterX", 
function () {
return Clazz_doubleToInt (this.dimScreen.width / 2);
});
$_M(c$, "getBoundBoxCenterY", 
function () {
return Clazz_doubleToInt (this.dimScreen.height / 2);
});
$_V(c$, "getModelCount", 
function () {
return (this.modelSet == null ? 0 : this.modelSet.modelCount);
});
$_M(c$, "getModelInfoAsString", 
function () {
return this.modelSet.getModelInfoAsString ();
});
$_M(c$, "getSymmetryInfoAsString", 
function () {
return this.modelSet.getSymmetryInfoAsString ();
});
$_M(c$, "getSymmetryOperation", 
function (spaceGroup, symop, pt1, pt2, labelOnly) {
return this.modelSet.getSymmetryOperation (this.animationManager.currentModelIndex, spaceGroup, symop, pt1, pt2, null, labelOnly);
}, "~S,~N,JU.P3,JU.P3,~B");
$_V(c$, "getModelSetProperties", 
function () {
return this.modelSet.getModelSetProperties ();
});
$_V(c$, "getModelSetAuxiliaryInfo", 
function () {
return this.modelSet.getModelSetAuxiliaryInfo ();
});
$_V(c$, "getModelNumber", 
function (modelIndex) {
return (modelIndex < 0 ? modelIndex : this.modelSet.getModelNumber (modelIndex));
}, "~N");
$_M(c$, "getModelFileNumber", 
function (modelIndex) {
return (modelIndex < 0 ? 0 : this.modelSet.getModelFileNumber (modelIndex));
}, "~N");
$_V(c$, "getModelNumberDotted", 
function (modelIndex) {
return modelIndex < 0 ? "0" : this.modelSet == null ? null : this.modelSet.getModelNumberDotted (modelIndex);
}, "~N");
$_V(c$, "getModelName", 
function (modelIndex) {
return this.modelSet == null ? null : this.modelSet.getModelName (modelIndex);
}, "~N");
$_V(c$, "getModelProperties", 
function (modelIndex) {
return this.modelSet.getModelProperties (modelIndex);
}, "~N");
$_V(c$, "getModelProperty", 
function (modelIndex, propertyName) {
return this.modelSet.getModelProperty (modelIndex, propertyName);
}, "~N,~S");
$_M(c$, "getModelFileInfo", 
function () {
return this.getPropertyManager ().getModelFileInfo (this.getVisibleFramesBitSet ());
});
$_M(c$, "getModelFileInfoAll", 
function () {
return this.getPropertyManager ().getModelFileInfo (null);
});
$_V(c$, "getModelAuxiliaryInfo", 
function (modelIndex) {
return this.modelSet.getModelAuxiliaryInfo (modelIndex);
}, "~N");
$_V(c$, "getModelAuxiliaryInfoValue", 
function (modelIndex, keyName) {
return this.modelSet.getModelAuxiliaryInfoValue (modelIndex, keyName);
}, "~N,~S");
$_M(c$, "getModelNumberIndex", 
function (modelNumber, useModelNumber, doSetTrajectory) {
return this.modelSet.getModelNumberIndex (modelNumber, useModelNumber, doSetTrajectory);
}, "~N,~B,~B");
$_M(c$, "modelSetHasVibrationVectors", 
function () {
return this.modelSet.modelSetHasVibrationVectors ();
});
$_V(c$, "modelGetLastVibrationIndex", 
function (modelIndex, tok) {
return this.modelSet.getLastVibrationVector (modelIndex, tok);
}, "~N,~N");
$_V(c$, "modelHasVibrationVectors", 
function (modelIndex) {
return (this.modelSet.getLastVibrationVector (modelIndex, 4166) >= 0);
}, "~N");
$_V(c$, "getChainCount", 
function () {
return this.modelSet.getChainCount (true);
});
$_V(c$, "getChainCountInModel", 
function (modelIndex) {
return this.modelSet.getChainCountInModel (modelIndex, false);
}, "~N");
$_M(c$, "getChainCountInModelWater", 
function (modelIndex, countWater) {
return this.modelSet.getChainCountInModel (modelIndex, countWater);
}, "~N,~B");
$_V(c$, "getGroupCount", 
function () {
return this.modelSet.getGroupCount ();
});
$_V(c$, "getGroupCountInModel", 
function (modelIndex) {
return this.modelSet.getGroupCountInModel (modelIndex);
}, "~N");
$_V(c$, "getPolymerCount", 
function () {
return this.modelSet.getBioPolymerCount ();
});
$_V(c$, "getPolymerCountInModel", 
function (modelIndex) {
return this.modelSet.getBioPolymerCountInModel (modelIndex);
}, "~N");
$_V(c$, "getAtomCount", 
function () {
return this.modelSet.getAtomCount ();
});
$_V(c$, "getAtomCountInModel", 
function (modelIndex) {
return this.modelSet.getAtomCountInModel (modelIndex);
}, "~N");
$_V(c$, "getBondCount", 
function () {
return this.modelSet.bondCount;
});
$_V(c$, "getBondCountInModel", 
function (modelIndex) {
return this.modelSet.getBondCountInModel (modelIndex);
}, "~N");
$_M(c$, "getBondsForSelectedAtoms", 
function (bsAtoms) {
return this.modelSet.getBondsForSelectedAtoms (bsAtoms, this.global.bondModeOr || J.util.BSUtil.cardinalityOf (bsAtoms) == 1);
}, "JU.BS");
$_M(c$, "frankClicked", 
function (x, y) {
return !this.global.disablePopupMenu && this.getShowFrank () && this.shapeManager.checkFrankclicked (x, y);
}, "~N,~N");
$_M(c$, "frankClickedModelKit", 
function (x, y) {
return !this.global.disablePopupMenu && this.global.modelKitMode && x >= 0 && y >= 0 && x < 40 && y < 80;
}, "~N,~N");
$_V(c$, "findNearestAtomIndex", 
function (x, y) {
return this.findNearestAtomIndexMovable (x, y, false);
}, "~N,~N");
$_M(c$, "findNearestAtomIndexMovable", 
function (x, y, mustBeMovable) {
return (this.modelSet == null || !this.global.atomPicking ? -1 : this.modelSet.findNearestAtomIndex (x, y, mustBeMovable ? this.selectionManager.getMotionFixedAtoms () : null, this.global.minPixelSelRadius));
}, "~N,~N,~B");
$_M(c$, "findAtomsInRectangle", 
function (rect) {
return this.modelSet.findAtomsInRectangle (rect, this.getVisibleFramesBitSet ());
}, "J.util.Rectangle");
$_M(c$, "toCartesian", 
function (pt, asAbsolute) {
var unitCell = this.getCurrentUnitCell ();
if (unitCell != null) unitCell.toCartesian (pt, asAbsolute);
}, "JU.P3,~B");
$_M(c$, "toFractional", 
function (pt, asAbsolute) {
var unitCell = this.getCurrentUnitCell ();
if (unitCell != null) unitCell.toFractional (pt, asAbsolute);
}, "JU.P3,~B");
$_M(c$, "toUnitCell", 
function (pt, offset) {
var unitCell = this.getCurrentUnitCell ();
if (unitCell != null) unitCell.toUnitCell (pt, offset);
}, "JU.P3,JU.P3");
$_M(c$, "setCurrentCage", 
function (isosurfaceId) {
var data = [isosurfaceId, null];
this.shapeManager.getShapePropertyData (24, "unitCell", data);
this.modelSet.setModelCage (this.getCurrentModelIndex (), data[1]);
}, "~S");
$_M(c$, "setCurrentCagePts", 
function (points) {
this.modelSet.setModelCage (this.getCurrentModelIndex (), this.getSymmetry ().getUnitCell (points));
}, "~A");
$_M(c$, "setCurrentUnitCellOffset", 
function (ijk) {
this.modelSet.setUnitCellOffset (this.animationManager.currentModelIndex, null, ijk);
}, "~N");
$_M(c$, "setCurrentUnitCellOffsetPt", 
function (pt) {
this.modelSet.setUnitCellOffset (this.animationManager.currentModelIndex, pt, 0);
}, "JU.P3");
$_M(c$, "addUnitCellOffset", 
function (pt) {
var unitCell = this.getCurrentUnitCell ();
if (unitCell == null) return;
pt.add (unitCell.getCartesianOffset ());
}, "JU.P3");
$_M(c$, "setAtomData", 
function (type, name, coordinateData, isDefault) {
this.modelSet.setAtomData (type, name, coordinateData, isDefault);
if (type == 2) this.checkCoordinatesChanged ();
this.refreshMeasures (true);
}, "~N,~S,~S,~B");
$_V(c$, "setCenterSelected", 
function () {
this.setCenterBitSet (this.getSelectionSet (false), true);
});
$_M(c$, "setApplySymmetryToBonds", 
function (TF) {
this.global.applySymmetryToBonds = TF;
}, "~B");
$_V(c$, "setBondTolerance", 
function (bondTolerance) {
this.global.setF ("bondTolerance", bondTolerance);
this.global.bondTolerance = bondTolerance;
}, "~N");
$_V(c$, "setMinBondDistance", 
function (minBondDistance) {
this.global.setF ("minBondDistance", minBondDistance);
this.global.minBondDistance = minBondDistance;
}, "~N");
$_M(c$, "getAtomIndices", 
function (bs) {
return this.modelSet.getAtomIndices (bs);
}, "JU.BS");
$_M(c$, "getAtomBits", 
function (tokType, specInfo) {
return this.modelSet.getAtomBits (tokType, specInfo);
}, "~N,~O");
$_M(c$, "getSequenceBits", 
function (specInfo, bs) {
return this.modelSet.getSequenceBits (specInfo, bs);
}, "~S,JU.BS");
$_M(c$, "getAtomsNearPt", 
function (distance, coord) {
var bs =  new JU.BS ();
this.modelSet.getAtomsWithin (distance, coord, bs, -1);
return bs;
}, "~N,JU.P3");
$_M(c$, "getAtomsNearPts", 
function (distance, points, bsInclude) {
return this.modelSet.getAtomsWithinBs (distance, points, bsInclude);
}, "~N,~A,JU.BS");
$_M(c$, "getAtomsNearPlane", 
function (distance, plane) {
return this.modelSet.getAtomsWithin (distance, plane);
}, "~N,JU.P4");
$_M(c$, "getAtomsWithinRadius", 
function (distance, bs, withinAllModels, rd) {
return this.modelSet.getAtomsWithinRD (distance, bs, withinAllModels, rd);
}, "~N,JU.BS,~B,J.atomdata.RadiusData");
$_M(c$, "getAtomsConnected", 
function (min, max, intType, bs) {
return this.modelSet.getAtomsConnected (min, max, intType, bs);
}, "~N,~N,~N,JU.BS");
$_M(c$, "getBranchBitSet", 
function (atomIndex, atomIndexNot, allowCyclic) {
if (atomIndex < 0 || atomIndex >= this.getAtomCount ()) return  new JU.BS ();
return J.util.JmolMolecule.getBranchBitSet (this.modelSet.atoms, atomIndex, this.getModelUndeletedAtomsBitSet (this.modelSet.atoms[atomIndex].modelIndex), null, atomIndexNot, allowCyclic, true);
}, "~N,~N,~B");
$_M(c$, "getAtomIndexFromAtomNumber", 
function (atomNumber) {
return this.modelSet.getAtomIndexFromAtomNumber (atomNumber, this.getVisibleFramesBitSet ());
}, "~N");
$_V(c$, "getElementsPresentBitSet", 
function (modelIndex) {
return this.modelSet.getElementsPresentBitSet (modelIndex);
}, "~N");
$_V(c$, "getHeteroList", 
function (modelIndex) {
return this.modelSet.getHeteroList (modelIndex);
}, "~N");
$_M(c$, "getVisibleSet", 
function () {
return this.modelSet.getVisibleSet ();
});
$_M(c$, "getClickableSet", 
function () {
return this.modelSet.getClickableSet ();
});
$_M(c$, "calcSelectedGroupsCount", 
function () {
this.modelSet.calcSelectedGroupsCount (this.getSelectionSet (false));
});
$_M(c$, "calcSelectedMonomersCount", 
function () {
this.modelSet.calcSelectedMonomersCount (this.getSelectionSet (false));
});
$_M(c$, "calcSelectedMoleculesCount", 
function () {
this.modelSet.calcSelectedMoleculesCount (this.getSelectionSet (false));
});
$_M(c$, "getFileHeader", 
function () {
return this.modelSet.getFileHeader (this.animationManager.currentModelIndex);
});
$_M(c$, "getFileData", 
function () {
return this.modelSet.getFileData (this.animationManager.currentModelIndex);
});
$_M(c$, "getCifData", 
function (modelIndex) {
var name = this.getModelFileName (modelIndex);
var data = this.getFileAsString (name);
if (data == null) return null;
return J.io.CifDataReader.readCifData ( new java.io.BufferedReader ( new java.io.StringReader (data)));
}, "~N");
$_M(c$, "getPDBHeader", 
function () {
return this.modelSet.getPDBHeader (this.animationManager.currentModelIndex);
});
$_M(c$, "getAuxiliaryInfo", 
function (atomExpression) {
return this.modelSet.getAuxiliaryInfo (this.getModelBitSet (this.getAtomBitSet (atomExpression), false));
}, "~O");
$_M(c$, "getChimeInfo", 
function (tok) {
return this.getPropertyManager ().getChimeInfo (tok, this.getSelectionSet (false));
}, "~N");
$_M(c$, "getStateCreator", 
function () {
if (this.sc == null) (this.sc = J.api.Interface.getOptionInterface ("viewer.StateCreator")).setViewer (this);
return this.sc;
});
$_M(c$, "getWrappedStateScript", 
function () {
return this.getOutputManager ().getWrappedState (null, null, null, null);
});
$_V(c$, "getStateInfo", 
function () {
return this.getStateInfo3 (null, 0, 0);
});
$_M(c$, "getStateInfo3", 
function (type, width, height) {
return (this.global.preserveState ? this.getStateCreator ().getStateScript (type, width, height) : "");
}, "~S,~N,~N");
$_M(c$, "getStructureState", 
function () {
return this.getStateCreator ().getModelState (null, false, true);
});
$_M(c$, "getProteinStructureState", 
function () {
return this.modelSet.getProteinStructureState (this.getSelectionSet (false), false, false, 3);
});
$_M(c$, "getCoordinateState", 
function (bsSelected) {
return this.getStateCreator ().getAtomicPropertyState (2, bsSelected);
}, "JU.BS");
$_M(c$, "setCurrentColorRange", 
function (label) {
var data = this.getDataFloat (label);
var bs = (data == null ? null : (this.getDataManager ().getData (label))[2]);
if (bs != null && this.global.rangeSelected) bs.and (this.getSelectionSet (false));
this.setCurrentColorRangeData (data, bs);
}, "~S");
$_M(c$, "setCurrentColorRangeData", 
function (data, bs) {
this.colorManager.setPropertyColorRangeData (data, bs, this.global.propertyColorScheme);
}, "~A,JU.BS");
$_M(c$, "setCurrentColorRange", 
function (min, max) {
this.colorManager.setPropertyColorRange (min, max);
}, "~N,~N");
$_M(c$, "setData", 
function (type, data, arrayCount, matchField, matchFieldColumnCount, field, fieldColumnCount) {
this.getDataManager ().setData (type, data, arrayCount, this.getAtomCount (), matchField, matchFieldColumnCount, field, fieldColumnCount);
}, "~S,~A,~N,~N,~N,~N,~N");
$_M(c$, "getData", 
function (type) {
return this.getDataManager ().getData (type);
}, "~S");
$_M(c$, "getDataFloat", 
function (label) {
return this.getDataManager ().getDataFloatA (label);
}, "~S");
$_M(c$, "getDataFloat2D", 
function (label) {
return this.getDataManager ().getDataFloat2D (label);
}, "~S");
$_M(c$, "getDataFloat3D", 
function (label) {
return this.getDataManager ().getDataFloat3D (label);
}, "~S");
$_M(c$, "getDataFloatAt", 
function (label, atomIndex) {
return this.getDataManager ().getDataFloat (label, atomIndex);
}, "~S,~N");
$_V(c$, "getAltLocListInModel", 
function (modelIndex) {
return this.modelSet.getAltLocListInModel (modelIndex);
}, "~N");
$_M(c$, "setConformation", 
function () {
return this.modelSet.setConformation (this.getSelectionSet (false));
});
$_M(c$, "getConformation", 
function (iModel, conformationIndex, doSet) {
return this.modelSet.getConformation (iModel, conformationIndex, doSet);
}, "~N,~N,~B");
$_M(c$, "autoHbond", 
function (bsFrom, bsTo, onlyIfHaveCalculated) {
if (bsFrom == null) bsFrom = bsTo = this.getSelectionSet (false);
return this.modelSet.autoHbond (bsFrom, bsTo, onlyIfHaveCalculated);
}, "JU.BS,JU.BS,~B");
$_V(c$, "havePartialCharges", 
function () {
return this.modelSet.getPartialCharges () != null;
});
$_M(c$, "getCurrentUnitCell", 
function () {
if (this.animationManager.currentModelIndex >= 0) return this.modelSet.getUnitCell (this.animationManager.currentModelIndex);
var models = this.getVisibleFramesBitSet ();
var ucLast = null;
for (var i = models.nextSetBit (0); i >= 0; i = models.nextSetBit (i + 1)) {
var uc = this.modelSet.getUnitCell (i);
if (uc == null) continue;
if (ucLast == null) {
ucLast = uc;
continue;
}if (!ucLast.unitCellEquals (uc)) return null;
}
return ucLast;
});
$_M(c$, "getModelUnitCell", 
function (modelIndex) {
return this.modelSet.getUnitCell (modelIndex);
}, "~N");
$_M(c$, "getDefaultMeasurementLabel", 
function (nPoints) {
switch (nPoints) {
case 2:
return this.global.defaultDistanceLabel;
case 3:
return this.global.defaultAngleLabel;
default:
return this.global.defaultTorsionLabel;
}
}, "~N");
$_V(c$, "getMeasurementCount", 
function () {
var count = this.getShapePropertyAsInt (6, "count");
return count <= 0 ? 0 : count;
});
$_V(c$, "getMeasurementStringValue", 
function (i) {
var str = "" + this.getShapePropertyIndex (6, "stringValue", i);
return str;
}, "~N");
$_M(c$, "getMeasurementInfo", 
function () {
return this.getShapeProperty (6, "info");
});
$_M(c$, "getMeasurementInfoAsString", 
function () {
return this.getShapeProperty (6, "infostring");
});
$_V(c$, "getMeasurementCountPlusIndices", 
function (i) {
var List = this.getShapePropertyIndex (6, "countPlusIndices", i);
return List;
}, "~N");
$_M(c$, "setPendingMeasurement", 
function (measurementPending) {
this.loadShape (6);
this.setShapeProperty (6, "pending", measurementPending);
}, "J.modelset.MeasurementPending");
$_M(c$, "getPendingMeasurement", 
function () {
return this.getShapeProperty (6, "pending");
});
$_M(c$, "clearAllMeasurements", 
function () {
this.setShapeProperty (6, "clear", null);
});
$_V(c$, "clearMeasurements", 
function () {
this.evalString ("measures delete");
});
$_M(c$, "setAnimation", 
function (tok) {
switch (tok) {
case 1073742098:
this.animationManager.reverseAnimation ();
case 1073742096:
case 266287:
if (!this.animationManager.animationOn) this.animationManager.resumeAnimation ();
return;
case 20487:
if (this.animationManager.animationOn && !this.animationManager.animationPaused) this.animationManager.pauseAnimation ();
return;
case 1073742037:
this.animationManager.setAnimationNext ();
return;
case 1073742108:
this.animationManager.setAnimationPrevious ();
return;
case 1073741942:
case 1073742126:
this.animationManager.rewindAnimation ();
return;
case 1073741993:
this.animationManager.setAnimationLast ();
return;
}
}, "~N");
$_M(c$, "setAnimationDirection", 
function (direction) {
this.animationManager.setAnimationDirection (direction);
}, "~N");
$_M(c$, "getAnimationDirection", 
function () {
return this.animationManager.animationDirection;
});
$_M(c$, "getAnimationInfo", 
function () {
return this.getStateCreator ().getInfo (this.animationManager);
});
$_V(c$, "setAnimationFps", 
function (fps) {
if (fps < 1) fps = 1;
if (fps > 50) fps = 50;
this.animationManager.setAnimationFps (fps);
}, "~N");
$_M(c$, "setAnimationMode", 
function (mode) {
if (mode.equalsIgnoreCase ("once")) {
this.setAnimationReplayMode (J.constant.EnumAnimationMode.ONCE, 0, 0);
} else if (mode.equalsIgnoreCase ("loop")) {
this.setAnimationReplayMode (J.constant.EnumAnimationMode.LOOP, 1, 1);
} else if (mode.startsWith ("pal")) {
this.setAnimationReplayMode (J.constant.EnumAnimationMode.PALINDROME, 1, 1);
}}, "~S");
$_M(c$, "setAnimationReplayMode", 
function (replayMode, firstFrameDelay, lastFrameDelay) {
this.animationManager.setAnimationReplayMode (replayMode, firstFrameDelay, lastFrameDelay);
}, "J.constant.EnumAnimationMode,~N,~N");
$_M(c$, "getAnimationReplayMode", 
function () {
return this.animationManager.animationReplayMode;
});
$_M(c$, "setAnimationOn", 
function (animationOn) {
var wasAnimating = this.animationManager.animationOn;
if (animationOn == wasAnimating) return;
this.animationManager.setAnimationOn (animationOn);
}, "~B");
$_M(c$, "setAnimationRange", 
function (modelIndex1, modelIndex2) {
this.animationManager.setAnimationRange (modelIndex1, modelIndex2);
}, "~N,~N");
$_V(c$, "getVisibleFramesBitSet", 
function () {
return this.modelSet.selectDisplayedTrajectories (J.util.BSUtil.copy (this.animationManager.bsVisibleModels));
});
$_M(c$, "isAnimationOn", 
function () {
return this.animationManager.animationOn;
});
$_M(c$, "setMovie", 
function (info) {
this.animationManager.setMovie (info);
}, "java.util.Map");
$_M(c$, "setAnimMorphCount", 
function (n) {
this.animationManager.setMorphCount (n);
}, "~N");
$_M(c$, "isMovie", 
function () {
return this.animationManager.isMovie;
});
$_M(c$, "getFrameCount", 
function () {
return this.animationManager.getFrameCount ();
});
$_M(c$, "defineAtomSets", 
function (info) {
this.definedAtomSets.putAll (info);
}, "java.util.Map");
$_M(c$, "morph", 
function (frame) {
this.animationManager.morph (frame);
}, "~N");
$_M(c$, "setAnimDisplay", 
function (bs) {
this.animationManager.setDisplay (bs);
if (!this.isAnimationOn ()) this.animationManager.morph (this.animationManager.currentMorphModel + 1);
}, "JU.BS");
$_M(c$, "setCurrentModelIndex", 
function (modelIndex) {
if (modelIndex == -2147483648) {
this.prevFrame = -2147483648;
this.setCurrentModelIndexClear (this.animationManager.currentModelIndex, true);
return;
}this.animationManager.setModel (modelIndex, true);
}, "~N");
$_M(c$, "setTrajectory", 
function (modelIndex) {
this.modelSet.setTrajectory (modelIndex);
}, "~N");
$_M(c$, "setTrajectoryBs", 
function (bsModels) {
this.modelSet.setTrajectoryBs (bsModels);
}, "JU.BS");
$_M(c$, "isTrajectory", 
function (modelIndex) {
return this.modelSet.isTrajectory (modelIndex);
}, "~N");
$_M(c$, "getBitSetTrajectories", 
function () {
return this.modelSet.getBitSetTrajectories ();
});
$_M(c$, "getTrajectoryState", 
function () {
return this.getStateCreator ().getTrajectoryState ();
});
$_M(c$, "setFrameOffset", 
function (modelIndex) {
this.transformManager.setFrameOffset (modelIndex);
}, "~N");
$_M(c$, "setFrameOffsets", 
function (bsAtoms) {
this.bsFrameOffsets = bsAtoms;
this.transformManager.setFrameOffsets (this.frameOffsets = this.modelSet.getFrameOffsets (this.bsFrameOffsets));
}, "JU.BS");
$_M(c$, "getFrameOffsets", 
function () {
return this.bsFrameOffsets;
});
$_M(c$, "setCurrentModelIndexClear", 
function (modelIndex, clearBackground) {
this.animationManager.setModel (modelIndex, clearBackground);
}, "~N,~B");
$_M(c$, "getCurrentModelIndex", 
function () {
return this.animationManager.currentModelIndex;
});
$_V(c$, "getDisplayModelIndex", 
function () {
return this.animationManager.currentModelIndex;
});
$_M(c$, "haveFileSet", 
function () {
return (this.getModelCount () > 1 && this.getModelNumber (2147483647) > 2000000);
});
$_M(c$, "setBackgroundModelIndex", 
function (modelIndex) {
this.animationManager.setBackgroundModelIndex (modelIndex);
this.global.setS ("backgroundModel", this.modelSet.getModelNumberDotted (modelIndex));
}, "~N");
$_M(c$, "setFrameVariables", 
function () {
this.global.setS ("animationMode", this.animationManager.animationReplayMode.name ());
this.global.setI ("animationFps", this.animationManager.animationFps);
this.global.setS ("_firstFrame", this.animationManager.getModelSpecial (-1));
this.global.setS ("_lastFrame", this.animationManager.getModelSpecial (1));
this.global.setF ("_animTimeSec", this.animationManager.getAnimRunTimeSeconds ());
this.global.setB ("_animMovie", this.animationManager.isMovie);
});
$_M(c$, "getInMotion", 
function (includeAnim) {
return (this.inMotion || includeAnim && this.animationManager.animationOn);
}, "~B");
$_V(c$, "getMotionEventNumber", 
function () {
return this.motionEventNumber;
});
$_V(c$, "setInMotion", 
function (inMotion) {
if ( new Boolean (this.inMotion ^ inMotion).valueOf ()) {
this.inMotion = inMotion;
this.resizeImage (0, 0, false, false, true);
if (inMotion) {
this.startHoverWatcher (false);
++this.motionEventNumber;
} else {
this.startHoverWatcher (true);
this.refresh (3, "viewer setInMotion " + inMotion);
}}}, "~B");
$_M(c$, "setRefreshing", 
function (TF) {
this.refreshing = TF;
}, "~B");
$_M(c$, "getRefreshing", 
function () {
return this.refreshing;
});
$_M(c$, "pushHoldRepaint", 
function () {
this.pushHoldRepaint (null);
});
$_M(c$, "pushHoldRepaint", 
function (why) {
if (this.repaintManager != null) this.repaintManager.pushHoldRepaint (why);
}, "~S");
$_V(c$, "popHoldRepaint", 
function (why) {
if (this.repaintManager != null) {
this.repaintManager.popHoldRepaint (why.indexOf ("\u0001## REPAINT_IGNORE ##") < 0, why);
}}, "~S");
$_V(c$, "refresh", 
function (mode, strWhy) {
if (this.repaintManager == null || !this.refreshing) return;
if (mode == 6 && this.getInMotion (true)) return;
{
if (typeof Jmol == "undefined") return; if (!this.isWebGL) {
if (mode == 7)return; if (mode > 0)
this.repaintManager.repaintIfReady(); } else if (mode == 2 ||
mode == 7) {
this.transformManager.finalizeTransformParameters(); if
(Jmol._refresh) Jmol._refresh(this.applet, mode, strWhy,
[this.transformManager.fixedRotationCenter,
this.transformManager.getRotationQuaternion(),
this.transformManager.xTranslationFraction,
this.transformManager.yTranslationFraction,
this.transformManager.modelRadius,
this.transformManager.scalePixelsPerAngstrom,
this.transformManager.zoomPercent ]); if (mode == 7)return; }
}if (mode % 3 != 0 && this.statusManager.doSync ()) this.statusManager.setSync (mode == 2 ? strWhy : null);
}, "~N,~S");
$_M(c$, "requestRepaintAndWait", 
function (why) {
if (!this.haveDisplay || this.repaintManager == null) return;
this.repaintManager.requestRepaintAndWait (why);
this.setSync ();
}, "~S");
$_M(c$, "clearShapeRenderers", 
function () {
this.clearRepaintManager (-1);
});
$_M(c$, "isRepaintPending", 
function () {
return (this.repaintManager == null ? false : this.repaintManager.isRepaintPending ());
});
$_V(c$, "notifyViewerRepaintDone", 
function () {
if (this.repaintManager != null) this.repaintManager.repaintDone ();
this.animationManager.repaintDone ();
});
$_M(c$, "areAxesTainted", 
function () {
var TF = this.axesAreTainted;
this.axesAreTainted = false;
return TF;
});
$_M(c$, "setMaximumSize", 
function (x) {
this.maximumSize = Math.max (x, 100);
}, "~N");
$_V(c$, "setScreenDimension", 
function (width, height) {
height = Math.min (height, this.maximumSize);
width = Math.min (width, this.maximumSize);
if (this.isStereoDouble ()) width = Clazz_doubleToInt ((width + 1) / 2);
if (this.dimScreen.width == width && this.dimScreen.height == height) return;
this.resizeImage (width, height, false, false, true);
}, "~N,~N");
$_M(c$, "getImageFontScaling", 
function () {
return this.imageFontScaling;
});
$_M(c$, "resizeImage", 
function (width, height, isImageWrite, isExport, isReset) {
if (!isImageWrite && this.creatingImage) return;
if (!isExport && !isImageWrite) this.setShapeProperty (5, "clearBoxes", null);
this.antialiasDisplay = (isReset ? this.global.antialiasDisplay && this.checkMotionRendering (603979786) : isImageWrite && !isExport ? this.global.antialiasImages : false);
this.imageFontScaling = (isReset || width <= 0 ? 1 : Clazz_doubleToInt ((this.global.zoomLarge == (height > width) ? height : width) / this.getScreenDim ())) * (this.antialiasDisplay ? 2 : 1);
if (width > 0) {
this.dimScreen.width = width;
this.dimScreen.height = height;
if (!isImageWrite) {
this.global.setI ("_width", width);
this.global.setI ("_height", height);
this.setStatusResized (width, height);
}} else {
width = (this.dimScreen.width == 0 ? this.dimScreen.width = 500 : this.dimScreen.width);
height = (this.dimScreen.height == 0 ? this.dimScreen.height = 500 : this.dimScreen.height);
}this.transformManager.setScreenParameters (width, height, isImageWrite || isReset ? this.global.zoomLarge : false, this.antialiasDisplay, false, false);
this.gdata.setWindowParameters (width, height, this.antialiasDisplay);
}, "~N,~N,~B,~B,~B");
$_V(c$, "getScreenWidth", 
function () {
return this.dimScreen.width;
});
$_V(c$, "getScreenHeight", 
function () {
return this.dimScreen.height;
});
$_M(c$, "getScreenDim", 
function () {
return (this.global.zoomLarge == (this.dimScreen.height > this.dimScreen.width) ? this.dimScreen.height : this.dimScreen.width);
});
$_V(c$, "generateOutputForExport", 
function (params) {
return (this.$noGraphicsAllowed || this.repaintManager == null ? null : this.getOutputManager ().getOutputFromExport (params));
}, "java.util.Map");
$_M(c$, "clearRepaintManager", 
function (iShape) {
if (this.repaintManager != null) this.repaintManager.clear (iShape);
}, "~N");
$_V(c$, "renderScreenImageStereo", 
function (gLeft, gRight, width, height) {
if (this.updateWindow (width, height)) {
if (gRight == null) {
this.getScreenImageBuffer (gLeft, false);
} else {
this.render1 (gRight, this.getImage (true, false), 0, 0);
this.render1 (gLeft, this.getImage (false, false), 0, 0);
}}if (this.captureParams != null && Boolean.FALSE !== this.captureParams.get ("captureEnabled")) {
this.processWriteOrCapture (this.captureParams);
}this.notifyViewerRepaintDone ();
}, "~O,~O,~N,~N");
$_V(c$, "updateJS", 
function (width, height) {
{
if (!this.isWebGL) {
this.renderScreenImageStereo(this.apiPlatform.context, null,
width, height); return; } if (this.updateWindow(width,
height)){ this.render(); } this.notifyViewerRepaintDone();
}}, "~N,~N");
$_M(c$, "updateWindow", 
function (width, height) {
if (!this.refreshing || this.creatingImage) return false;
if (this.isTainted || this.getSlabEnabled ()) this.setModelVisibility ();
this.isTainted = false;
if (this.repaintManager != null) {
if (width != 0) this.setScreenDimension (width, height);
}return true;
}, "~N,~N");
$_M(c$, "renderScreenImage", 
function (g, width, height) {
this.renderScreenImageStereo (g, null, width, height);
}, "~O,~N,~N");
$_M(c$, "getImage", 
function (isDouble, isImageWrite) {
{
if (this.isWebGL)return null;
}var image = null;
try {
this.beginRendering (isDouble, isImageWrite);
this.render ();
this.gdata.endRendering ();
image = this.gdata.getScreenImage (isImageWrite);
} catch (er) {
if (Clazz_exceptionOf (er, Error)) {
this.gdata.getScreenImage (isImageWrite);
this.handleError (er, false);
this.setErrorMessage ("Error during rendering: " + er, null);
} else {
throw er;
}
}
return image;
}, "~B,~B");
$_M(c$, "beginRendering", 
function (isDouble, isImageWrite) {
this.gdata.beginRendering (this.transformManager.getStereoRotationMatrix (isDouble), this.global.translucent, isImageWrite, !this.checkMotionRendering (603979967));
}, "~B,~B");
$_M(c$, "isAntialiased", 
function () {
return this.antialiasDisplay;
});
$_M(c$, "render", 
function () {
if (this.modelSet == null || !this.mustRender || !this.refreshing && !this.creatingImage || this.repaintManager == null) return;
var antialias2 = this.antialiasDisplay && this.global.antialiasTranslucent;
this.finalizeTransformParameters ();
this.shapeManager.finalizeAtoms (this.transformManager.bsSelectedAtoms, this.transformManager.ptOffset);
var minMax = this.shapeManager.transformAtoms ();
this.transformManager.bsSelectedAtoms = null;
{
if (this.isWebGL) { this.repaintManager.renderExport("JS",
this.gdata, this.modelSet, null);
this.notifyViewerRepaintDone(); return; }
}this.repaintManager.render (this.gdata, this.modelSet, true, minMax);
if (this.gdata.setPass2 (antialias2)) {
this.transformManager.setAntialias (antialias2);
this.repaintManager.render (this.gdata, this.modelSet, false, null);
this.transformManager.setAntialias (this.antialiasDisplay);
}});
$_M(c$, "render1", 
function (graphic, img, x, y) {
if (graphic != null && img != null) {
this.apiPlatform.drawImage (graphic, img, x, y, this.dimScreen.width, this.dimScreen.height);
}this.gdata.releaseScreenImage ();
}, "~O,~O,~N,~N");
$_V(c$, "getScreenImageBuffer", 
function (graphic, isImageWrite) {
{
if (this.isWebGL)return null
}{
var mergeImages = (graphic == null && this.isStereoDouble ());
var imageBuffer;
if (this.transformManager.stereoMode.isBiColor ()) {
this.beginRendering (true, isImageWrite);
this.render ();
this.gdata.endRendering ();
this.gdata.snapshotAnaglyphChannelBytes ();
this.beginRendering (false, isImageWrite);
this.render ();
this.gdata.endRendering ();
this.gdata.applyAnaglygh (this.transformManager.stereoMode, this.transformManager.stereoColors);
imageBuffer = this.gdata.getScreenImage (isImageWrite);
} else {
imageBuffer = this.getImage (this.isStereoDouble (), isImageWrite);
}var imageBuffer2 = null;
if (mergeImages) {
imageBuffer2 = this.apiPlatform.newBufferedImage (imageBuffer, this.dimScreen.width << 1, this.dimScreen.height);
graphic = this.apiPlatform.getGraphics (imageBuffer2);
}if (graphic != null) {
if (this.isStereoDouble ()) {
this.render1 (graphic, imageBuffer, this.dimScreen.width, 0);
imageBuffer = this.getImage (false, false);
}this.render1 (graphic, imageBuffer, 0, 0);
}return (mergeImages ? imageBuffer2 : imageBuffer);
}}, "~O,~B");
$_V(c$, "getImageAsBytes", 
function (type, width, height, quality, errMsg) {
{
if (this.isWebGL)return null
}return this.getOutputManager ().getImageAsBytes (type, width, height, quality, errMsg);
}, "~S,~N,~N,~N,~A");
$_V(c$, "releaseScreenImage", 
function () {
this.gdata.releaseScreenImage ();
});
$_V(c$, "evalFile", 
function (strFilename) {
if (!this.allowScripting) return null;
var ptWait = strFilename.indexOf (" -noqueue");
if (ptWait >= 0) {
return this.evalStringWaitStatusQueued ("String", strFilename.substring (0, ptWait), "", true, false, false);
}return this.getScriptManager ().addScript (strFilename, true, false);
}, "~S");
$_M(c$, "getInsertedCommand", 
function () {
var s = this.insertedCommand;
this.insertedCommand = "";
if (J.util.Logger.debugging && s !== "") J.util.Logger.debug ("inserting: " + s);
return s;
});
$_V(c$, "script", 
function (strScript) {
return this.evalStringQuietSync (strScript, false, true);
}, "~S");
$_V(c$, "evalString", 
function (strScript) {
return this.evalStringQuietSync (strScript, false, true);
}, "~S");
$_V(c$, "evalStringQuiet", 
function (strScript) {
return this.evalStringQuietSync (strScript, true, true);
}, "~S");
$_M(c$, "evalStringQuietSync", 
function (strScript, isQuiet, allowSyncScript) {
return (this.getScriptManager () == null ? null : this.scriptManager.evalStringQuietSync (strScript, isQuiet, allowSyncScript));
}, "~S,~B,~B");
$_M(c$, "clearScriptQueue", 
function () {
if (this.scriptManager != null) this.scriptManager.clearQueue ();
});
$_M(c$, "setScriptQueue", 
function (TF) {
this.global.useScriptQueue = TF;
if (!TF) this.clearScriptQueue ();
}, "~B");
$_V(c$, "checkHalt", 
function (str, isInsert) {
return (this.scriptManager != null && this.scriptManager.checkHalt (str, isInsert));
}, "~S,~B");
$_V(c$, "scriptWait", 
function (strScript) {
return this.evalWait ("JSON", strScript, "+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated");
}, "~S");
$_V(c$, "scriptWaitStatus", 
function (strScript, statusList) {
return this.evalWait ("object", strScript, statusList);
}, "~S,~S");
$_M(c$, "evalWait", 
function (returnType, strScript, statusList) {
if (this.getScriptManager () == null) return null;
this.scriptManager.waitForQueue ();
var doTranslateTemp = J.i18n.GT.setDoTranslate (false);
var ret = this.evalStringWaitStatusQueued (returnType, strScript, statusList, false, false, false);
J.i18n.GT.setDoTranslate (doTranslateTemp);
return ret;
}, "~S,~S,~S");
$_M(c$, "evalStringWaitStatusQueued", 
function (returnType, strScript, statusList, isScriptFile, isQuiet, isQueued) {
{
if (strScript.indexOf("JSCONSOLE") == 0) {
this.applet._showInfo(true); return null; }
}if (this.getScriptManager () == null) return null;
return this.scriptManager.evalStringWaitStatusQueued (returnType, strScript, statusList, isScriptFile, isQuiet, isQueued);
}, "~S,~S,~S,~B,~B,~B");
$_M(c$, "exitJmol", 
function () {
if (this.$isApplet) return;
if (this.headlessImageParams != null) {
try {
if (this.isHeadless ()) this.outputToFile (this.headlessImageParams);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
}if (J.util.Logger.debugging) J.util.Logger.debug ("exitJmol -- exiting");
System.out.flush ();
System.exit (0);
});
$_M(c$, "scriptCheckRet", 
function (strScript, returnContext) {
if (this.getScriptManager () == null) return null;
return this.scriptManager.scriptCheckRet (strScript, returnContext);
}, "~S,~B");
$_V(c$, "scriptCheck", 
function (strScript) {
if (this.getScriptManager () == null) return null;
return this.scriptCheckRet (strScript, false);
}, "~S");
$_V(c$, "isScriptExecuting", 
function () {
return (this.eval != null && this.eval.isExecuting ());
});
$_V(c$, "haltScriptExecution", 
function () {
if (this.eval != null) {
this.eval.haltExecution ();
this.eval.stopScriptThreads ();
}this.setStringPropertyTok ("pathForAllFiles", 545259571, "");
this.clearTimeouts ();
});
$_M(c$, "pauseScriptExecution", 
function () {
if (this.eval != null) this.eval.pauseExecution (true);
});
$_M(c$, "getDefaultLoadFilter", 
function () {
return this.global.defaultLoadFilter;
});
$_M(c$, "getDefaultLoadScript", 
function () {
return this.global.defaultLoadScript;
});
$_M(c$, "resolveDatabaseFormat", 
function (fileName) {
if (J.viewer.Viewer.hasDatabasePrefix (fileName)) fileName = this.setLoadFormat (fileName, fileName.charAt (0), false);
return fileName;
}, "~S");
c$.isDatabaseCode = $_M(c$, "isDatabaseCode", 
function (ch) {
return (ch == '$' || ch == '=' || ch == ':');
}, "~S");
c$.hasDatabasePrefix = $_M(c$, "hasDatabasePrefix", 
function (fileName) {
return (fileName.length != 0 && J.viewer.Viewer.isDatabaseCode (fileName.charAt (0)));
}, "~S");
$_M(c$, "setLoadFormat", 
function (name, type, withPrefix) {
var format;
var f = name.substring (1);
switch (type) {
case '=':
if (name.startsWith ("==")) {
f = f.substring (1);
type = '#';
} else if (f.indexOf ("/") > 0) {
try {
var pt = f.indexOf ("/");
var database = f.substring (0, pt);
f = this.global.resolveDataBase (database, f.substring (pt + 1));
return (f == null ? name : f);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return name;
} else {
throw e;
}
}
}case '#':
var s = (type == '=' ? this.global.loadFormat : this.global.loadLigandFormat);
if (f.indexOf (".") > 0 && s.indexOf ("%FILE.") >= 0) s = s.substring (0, s.indexOf ("%FILE") + 5);
return J.util.Txt.formatStringS (s, "FILE", f);
case ':':
format = this.global.pubChemFormat;
var fl = f.toLowerCase ();
var fi = -2147483648;
try {
fi = Integer.parseInt (f);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
if (fi != -2147483648) {
f = "cid/" + fi;
} else {
if (fl.startsWith ("smiles:")) {
format += "?POST?smiles=" + f.substring (7);
f = "smiles";
} else if (fl.startsWith ("cid:")) {
f = "cid/" + f.substring (4);
} else {
if (fl.startsWith ("name:")) f = f.substring (5);
if (fl.startsWith ("cas:")) f = f.substring (4);
f = "name/" + JU.PT.escapeUrl (f);
}}return J.util.Txt.formatStringS (format, "FILE", f);
case '$':
if (name.startsWith ("$$")) {
f = f.substring (1);
format = JU.PT.simpleReplace (this.global.smilesUrlFormat, "&get3d=True", "");
return J.util.Txt.formatStringS (format, "FILE", JU.PT.escapeUrl (f));
}case 'N':
case '2':
case 'I':
case 'K':
case '/':
f = JU.PT.escapeUrl (f);
switch (type) {
case 'N':
format = this.global.nihResolverFormat + "/names";
break;
case '2':
format = this.global.nihResolverFormat + "/image";
break;
case 'I':
format = this.global.nihResolverFormat + "/stdinchi";
break;
case 'K':
format = this.global.nihResolverFormat + "/inchikey";
break;
case '/':
format = this.global.nihResolverFormat + "/";
break;
default:
format = this.global.smilesUrlFormat;
break;
}
return (withPrefix ? "MOL3D::" : "") + J.util.Txt.formatStringS (format, "FILE", f);
case '_':
var server = J.viewer.FileManager.fixFileNameVariables (this.global.edsUrlFormat, f);
var strCutoff = J.viewer.FileManager.fixFileNameVariables (this.global.edsUrlCutoff, f);
return [server, strCutoff];
}
return f;
}, "~S,~S,~B");
$_M(c$, "getElectronDensityLoadInfo", 
function () {
return [this.global.edsUrlFormat, this.global.edsUrlCutoff, this.global.edsUrlOptions];
});
$_M(c$, "getStandardLabelFormat", 
function (type) {
switch (type) {
default:
case 0:
return "%[identify]";
case 1:
return this.global.defaultLabelXYZ;
case 2:
return this.global.defaultLabelPDB;
}
}, "~N");
$_M(c$, "getAdditionalHydrogens", 
function (bsAtoms, doAll, justCarbon, vConnections) {
if (bsAtoms == null) bsAtoms = this.getSelectionSet (false);
var nTotal =  Clazz_newIntArray (1, 0);
var pts = this.modelSet.calculateHydrogens (bsAtoms, nTotal, doAll, justCarbon, vConnections);
var points =  new Array (nTotal[0]);
for (var i = 0, pt = 0; i < pts.length; i++) if (pts[i] != null) for (var j = 0; j < pts[i].length; j++) points[pt++] = pts[i][j];


return points;
}, "JU.BS,~B,~B,JU.List");
$_V(c$, "setMarBond", 
function (marBond) {
this.global.bondRadiusMilliAngstroms = marBond;
this.global.setI ("bondRadiusMilliAngstroms", marBond);
this.setShapeSize (1, marBond * 2, J.util.BSUtil.setAll (this.getAtomCount ()));
}, "~N");
$_M(c$, "setHoverLabel", 
function (strLabel) {
this.loadShape (34);
this.setShapeProperty (34, "label", strLabel);
this.hoverEnabled = (strLabel != null);
if (!this.hoverEnabled) this.startHoverWatcher (false);
}, "~S");
$_M(c$, "hoverOn", 
function (atomIndex, isLabel) {
this.setStatusAtomHovered (atomIndex, this.getAtomInfoXYZ (atomIndex, false));
if (!this.hoverEnabled) return;
if (this.global.modelKitMode) {
if (this.isAtomAssignable (atomIndex)) this.highlight (J.util.BSUtil.newAndSetBit (atomIndex));
this.refresh (3, "hover on atom");
return;
}if (this.eval != null && this.isScriptExecuting () || atomIndex == this.hoverAtomIndex || this.global.hoverDelayMs == 0) return;
if (!this.isInSelectionSubset (atomIndex)) return;
this.loadShape (34);
if (isLabel && this.modelSet.atoms[atomIndex].isShapeVisible (J.viewer.JC.getShapeVisibilityFlag (5))) {
this.setShapeProperty (34, "specialLabel", J.i18n.GT._ ("Drag to move label"));
}this.setShapeProperty (34, "text", null);
this.setShapeProperty (34, "target", Integer.$valueOf (atomIndex));
this.hoverText = null;
this.hoverAtomIndex = atomIndex;
this.refresh (3, "hover on atom");
}, "~N,~B");
$_M(c$, "hoverOnPt", 
function (x, y, text, id, pt) {
if (!this.hoverEnabled) return;
if (this.eval != null && this.isScriptExecuting ()) return;
this.loadShape (34);
this.setShapeProperty (34, "xy", JU.P3i.new3 (x, y, 0));
this.setShapeProperty (34, "target", null);
this.setShapeProperty (34, "specialLabel", null);
this.setShapeProperty (34, "text", text);
this.hoverAtomIndex = -1;
this.hoverText = text;
if (id != null && pt != null) this.setStatusObjectHovered (id, text, pt);
this.refresh (3, "hover on point");
}, "~N,~N,~S,~S,JU.P3");
$_M(c$, "hoverOff", 
function () {
try {
if (this.global.modelKitMode) this.highlight (null);
if (!this.hoverEnabled) return;
var isHover = (this.hoverText != null || this.hoverAtomIndex >= 0);
if (this.hoverAtomIndex >= 0) {
this.setShapeProperty (34, "target", null);
this.hoverAtomIndex = -1;
}if (this.hoverText != null) {
this.setShapeProperty (34, "text", null);
this.hoverText = null;
}this.setShapeProperty (34, "specialLabel", null);
if (isHover) this.refresh (3, "hover off");
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
});
$_M(c$, "getBfactor100Hi", 
function () {
return this.modelSet.getBfactor100Hi ();
});
$_M(c$, "getColix", 
function (object) {
return J.util.C.getColixO (object);
}, "~O");
$_V(c$, "setDebugScript", 
function (debugScript) {
this.global.debugScript = debugScript;
this.global.setB ("debugScript", debugScript);
if (this.eval != null) this.eval.setDebugging ();
}, "~B");
$_M(c$, "clearClickCount", 
function () {
this.setTainted (true);
});
$_M(c$, "getCursor", 
function () {
return this.currentCursor;
});
$_M(c$, "setCursor", 
function (cursor) {
if (this.$isKiosk || this.currentCursor == cursor || this.multiTouch || !this.haveDisplay) return;
this.apiPlatform.setCursor (this.currentCursor = cursor, this.display);
}, "~N");
$_M(c$, "setPickingMode", 
function (strMode, pickingMode) {
if (!this.haveDisplay) return;
this.showSelected = false;
var option = null;
if (strMode != null) {
var pt = strMode.indexOf ("_");
if (pt >= 0) {
option = strMode.substring (pt + 1);
strMode = strMode.substring (0, pt);
}pickingMode = J.viewer.ActionManager.getPickingMode (strMode);
}if (pickingMode < 0) pickingMode = 1;
this.actionManager.setPickingMode (pickingMode);
this.global.setS ("picking", J.viewer.ActionManager.getPickingModeName (this.actionManager.getAtomPickingMode ()));
if (option == null || option.length == 0) return;
option = Character.toUpperCase (option.charAt (0)) + (option.length == 1 ? "" : option.substring (1, 2));
switch (pickingMode) {
case 32:
this.setAtomPickingOption (option);
break;
case 33:
this.setBondPickingOption (option);
break;
default:
J.util.Logger.error ("Bad picking mode: " + strMode + "_" + option);
}
}, "~S,~N");
$_M(c$, "getPickingMode", 
function () {
return (this.haveDisplay ? this.actionManager.getAtomPickingMode () : 0);
});
$_M(c$, "setPickingStyle", 
function (style, pickingStyle) {
if (!this.haveDisplay) return;
if (style != null) pickingStyle = J.viewer.ActionManager.getPickingStyleIndex (style);
if (pickingStyle < 0) pickingStyle = 0;
this.actionManager.setPickingStyle (pickingStyle);
this.global.setS ("pickingStyle", J.viewer.ActionManager.getPickingStyleName (this.actionManager.getPickingStyle ()));
}, "~S,~N");
$_M(c$, "getDrawHover", 
function () {
return this.haveDisplay && this.global.drawHover;
});
$_V(c$, "getAtomInfo", 
function (atomOrPointIndex) {
return (atomOrPointIndex >= 0 ? this.modelSet.getAtomInfo (atomOrPointIndex, null) : this.shapeManager.getShapePropertyIndex (6, "pointInfo", -atomOrPointIndex));
}, "~N");
$_M(c$, "getAtomInfoXYZ", 
function (atomIndex, useChimeFormat) {
return this.modelSet.getAtomInfoXYZ (atomIndex, useChimeFormat);
}, "~N,~B");
$_M(c$, "setSync", 
function () {
if (this.statusManager.doSync ()) this.statusManager.setSync (null);
});
$_V(c$, "setJmolCallbackListener", 
function (jmolCallbackListener) {
this.statusManager.setJmolCallbackListener (jmolCallbackListener);
}, "J.api.JmolCallbackListener");
$_V(c$, "setJmolStatusListener", 
function (jmolStatusListener) {
this.statusManager.setJmolStatusListener (jmolStatusListener, null);
}, "J.api.JmolStatusListener");
$_M(c$, "getMessageQueue", 
function () {
return this.statusManager.getMessageQueue ();
});
$_M(c$, "getStatusChanged", 
function (statusNameList) {
return (statusNameList == null ? null : this.statusManager.getStatusChanged (statusNameList));
}, "~S");
$_M(c$, "menuEnabled", 
function () {
return (!this.global.disablePopupMenu && this.getPopupMenu () != null);
});
$_M(c$, "popupMenu", 
function (x, y, type) {
if (!this.haveDisplay || !this.refreshing || this.$isPreviewOnly || this.global.disablePopupMenu) return;
switch (type) {
case 'j':
try {
this.getPopupMenu ();
this.jmolpopup.jpiShow (x, y);
} catch (e) {
this.global.disablePopupMenu = true;
}
break;
case 'a':
case 'b':
case 'm':
this.modelkitPopup = this.apiPlatform.getMenuPopup (null, type);
if (this.modelkitPopup != null) this.modelkitPopup.jpiShow (x, y);
break;
}
}, "~N,~N,~S");
$_M(c$, "getMenu", 
function (type) {
this.getPopupMenu ();
if (type.equals ("\0")) {
this.popupMenu (this.dimScreen.width - 120, 0, 'j');
return "OK";
}return (this.jmolpopup == null ? "" : this.jmolpopup.jpiGetMenuAsString ("Jmol version " + J.viewer.Viewer.getJmolVersion () + "|_GET_MENU|" + type));
}, "~S");
$_M(c$, "getPopupMenu", 
function () {
if (this.jmolpopup == null) {
this.jmolpopup = (this.allowScripting ? this.apiPlatform.getMenuPopup (this.menuStructure, 'j') : null);
if (this.jmolpopup == null) {
this.global.disablePopupMenu = true;
return null;
}}return this.jmolpopup.jpiGetMenuAsObject ();
});
$_M(c$, "setMenu", 
function (fileOrText, isFile) {
if (isFile) J.util.Logger.info ("Setting menu " + (fileOrText.length == 0 ? "to Jmol defaults" : "from file " + fileOrText));
if (fileOrText.length == 0) fileOrText = null;
 else if (isFile) fileOrText = this.getFileAsString (fileOrText);
this.getProperty ("DATA_API", "setMenu", fileOrText);
this.statusManager.setCallbackFunction ("menu", fileOrText);
}, "~S,~B");
$_M(c$, "setStatusFrameChanged", 
function (isVib) {
if (isVib) {
this.prevFrame = -2147483648;
}var frameNo = this.animationManager.getCurrentModelIndex ();
this.transformManager.setVibrationPeriod (NaN);
var firstIndex = this.animationManager.firstFrameIndex;
var lastIndex = this.animationManager.lastFrameIndex;
var isMovie = this.isMovie ();
var modelIndex = this.animationManager.currentModelIndex;
if (firstIndex == lastIndex && !isMovie) modelIndex = firstIndex;
var frameID = this.getModelFileNumber (modelIndex);
var currentFrame = this.animationManager.getCurrentModelIndex ();
var fileNo = frameID;
var modelNo = frameID % 1000000;
var firstNo = (isMovie ? firstIndex : this.getModelFileNumber (firstIndex));
var lastNo = (isMovie ? lastIndex : this.getModelFileNumber (lastIndex));
var strModelNo;
if (isMovie) {
strModelNo = "" + (frameNo + 1);
} else if (fileNo == 0) {
strModelNo = this.getModelNumberDotted (firstIndex);
if (firstIndex != lastIndex) strModelNo += " - " + this.getModelNumberDotted (lastIndex);
if (Clazz_doubleToInt (firstNo / 1000000) == Clazz_doubleToInt (lastNo / 1000000)) fileNo = firstNo;
} else {
strModelNo = this.getModelNumberDotted (modelIndex);
}if (fileNo != 0) fileNo = (fileNo < 1000000 ? 1 : Clazz_doubleToInt (fileNo / 1000000));
if (!isMovie) {
this.global.setI ("_currentFileNumber", fileNo);
this.global.setI ("_currentModelNumberInFile", modelNo);
}this.global.setI ("_currentFrame", currentFrame);
this.global.setI ("_morphCount", this.animationManager.morphCount);
this.global.setF ("_currentMorphFrame", this.animationManager.currentMorphModel);
this.global.setI ("_frameID", frameID);
this.global.setS ("_modelNumber", strModelNo);
this.global.setS ("_modelName", (modelIndex < 0 ? "" : this.getModelName (modelIndex)));
this.global.setS ("_modelTitle", (modelIndex < 0 ? "" : this.getModelTitle (modelIndex)));
this.global.setS ("_modelFile", (modelIndex < 0 ? "" : this.modelSet.getModelFileName (modelIndex)));
this.global.setS ("_modelType", (modelIndex < 0 ? "" : this.modelSet.getModelFileType (modelIndex)));
if (currentFrame == this.prevFrame) return;
this.prevFrame = currentFrame;
var entryName;
if (isMovie) {
entryName = "" + (this.animationManager.getCurrentModelIndex () + 1);
} else {
entryName = this.getModelName (frameNo);
var script = "" + this.getModelNumberDotted (frameNo);
if (!entryName.equals (script)) entryName = script + ": " + entryName;
if (entryName.length > 50) entryName = entryName.substring (0, 45) + "...";
}this.statusManager.setStatusFrameChanged (frameNo, fileNo, modelNo, (this.animationManager.animationDirection < 0 ? -firstNo : firstNo), (this.animationManager.currentDirection < 0 ? -lastNo : lastNo), currentFrame, entryName);
if (this.doHaveJDX ()) this.getJSV ().setModel (modelIndex);
}, "~B");
$_M(c$, "doHaveJDX", 
function () {
return (this.haveJDX || (this.haveJDX = this.getBooleanProperty ("_JSpecView".toLowerCase ())));
});
$_M(c$, "getJSV", 
function () {
if (this.jsv == null) {
this.jsv = J.api.Interface.getOptionInterface ("viewer.JSpecView");
this.jsv.setViewer (this);
}return this.jsv;
});
$_M(c$, "getJDXBaseModelIndex", 
function (modelIndex) {
if (!this.doHaveJDX ()) return modelIndex;
return this.getJSV ().getBaseModelIndex (modelIndex);
}, "~N");
$_M(c$, "getJspecViewProperties", 
function (myParam) {
var o = this.statusManager.getJspecViewProperties ("" + myParam);
if (o != null) this.haveJDX = true;
return o;
}, "~O");
$_M(c$, "scriptEcho", 
function (strEcho) {
if (!J.util.Logger.isActiveLevel (4)) return;
{
System.out.println(strEcho);
}this.statusManager.setScriptEcho (strEcho, this.isScriptQueued ());
if (this.listCommands && strEcho != null && strEcho.indexOf ("$[") == 0) J.util.Logger.info (strEcho);
}, "~S");
$_M(c$, "isScriptQueued", 
function () {
return this.scriptManager != null && this.scriptManager.isScriptQueued ();
});
$_M(c$, "notifyError", 
function (errType, errMsg, errMsgUntranslated) {
this.global.setS ("_errormessage", errMsgUntranslated);
this.statusManager.notifyError (errType, errMsg, errMsgUntranslated);
}, "~S,~S,~S");
$_M(c$, "jsEval", 
function (strEval) {
return this.statusManager.jsEval (strEval);
}, "~S");
$_M(c$, "setStatusAtomHovered", 
function (atomIndex, info) {
this.global.setI ("_atomhovered", atomIndex);
this.statusManager.setStatusAtomHovered (atomIndex, info);
}, "~N,~S");
$_M(c$, "setStatusObjectHovered", 
function (id, info, pt) {
this.global.setS ("_objecthovered", id);
this.statusManager.setStatusObjectHovered (id, info, pt);
}, "~S,~S,JU.P3");
$_M(c$, "setFileLoadStatus", 
function (ptLoad, fullPathName, fileName, modelName, strError, isAsync) {
this.setErrorMessage (strError, null);
this.global.setI ("_loadPoint", ptLoad.getCode ());
var doCallback = (ptLoad !== J.constant.EnumFileStatus.CREATING_MODELSET);
this.statusManager.setFileLoadStatus (fullPathName, fileName, modelName, strError, ptLoad.getCode (), doCallback, isAsync);
if (doCallback && this.doHaveJDX ()) this.getJSV ().setModel (this.getCurrentModelIndex ());
}, "J.constant.EnumFileStatus,~S,~S,~S,~S,Boolean");
$_M(c$, "getZapName", 
function () {
return (this.global.modelKitMode ? "Jmol Model Kit" : "zapped");
});
$_M(c$, "setStatusMeasuring", 
function (status, intInfo, strMeasure, value) {
this.statusManager.setStatusMeasuring (status, intInfo, strMeasure, value);
}, "~S,~N,~S,~N");
$_M(c$, "notifyMinimizationStatus", 
function () {
var step = this.getParameter ("_minimizationStep");
var ff = this.getParameter ("_minimizationForceField");
this.statusManager.notifyMinimizationStatus (this.getParameter ("_minimizationStatus"), Clazz_instanceOf (step, String) ? Integer.$valueOf (0) : step, this.getParameter ("_minimizationEnergy"), (step.toString ().equals ("0") ? Float.$valueOf (0) : this.getParameter ("_minimizationEnergyDiff")), ff);
});
$_M(c$, "setStatusAtomPicked", 
function (atomIndex, info) {
if (info == null) {
info = this.global.pickLabel;
if (info.length == 0) info = this.getAtomInfoXYZ (atomIndex, this.global.messageStyleChime);
 else info = this.modelSet.getAtomInfo (atomIndex, info);
}this.global.setPicked (atomIndex);
this.global.setS ("_pickinfo", info);
this.statusManager.setStatusAtomPicked (atomIndex, info);
var syncMode = this.statusManager.getSyncMode ();
if (syncMode != 1 || !this.doHaveJDX ()) return;
this.getJSV ().atomPicked (atomIndex);
}, "~N,~S");
$_M(c$, "setStatusResized", 
function (width, height) {
this.statusManager.setStatusResized (width, height);
}, "~N,~N");
$_M(c$, "scriptStatus", 
function (strStatus) {
this.setScriptStatus (strStatus, "", 0, null);
}, "~S");
$_M(c$, "scriptStatusMsg", 
function (strStatus, statusMessage) {
this.setScriptStatus (strStatus, statusMessage, 0, null);
}, "~S,~S");
$_M(c$, "setScriptStatus", 
function (strStatus, statusMessage, msWalltime, strErrorMessageUntranslated) {
this.statusManager.setScriptStatus (strStatus, statusMessage, msWalltime, strErrorMessageUntranslated);
}, "~S,~S,~N,~S");
$_M(c$, "getModelTitle", 
function (modelIndex) {
return this.modelSet == null ? null : this.modelSet.getModelTitle (modelIndex);
}, "~N");
$_V(c$, "getModelFileName", 
function (modelIndex) {
return this.modelSet == null ? null : this.modelSet.getModelFileName (modelIndex);
}, "~N");
$_M(c$, "dialogAsk", 
function (type, fileName) {
{
return prompt(type, fileName);
}}, "~S,~S");
$_V(c$, "showUrl", 
function (urlString) {
if (urlString == null) return;
if (urlString.indexOf (":") < 0) {
var base = this.fileManager.getAppletDocumentBase ();
if (base === "") base = this.fileManager.getFullPathName ();
if (base.indexOf ("/") >= 0) {
base = base.substring (0, base.lastIndexOf ("/") + 1);
} else if (base.indexOf ("\\") >= 0) {
base = base.substring (0, base.lastIndexOf ("\\") + 1);
}urlString = base + urlString;
}J.util.Logger.info ("showUrl:" + urlString);
this.statusManager.showUrl (urlString);
}, "~S");
$_M(c$, "setMeshCreator", 
function (meshCreator) {
this.loadShape (24);
this.setShapeProperty (24, "meshCreator", meshCreator);
}, "~O");
$_M(c$, "showConsole", 
function (showConsole) {
if (!this.haveDisplay) return;
try {
if (this.appConsole == null && showConsole) this.getProperty ("DATA_API", "getAppConsole", Boolean.TRUE);
this.appConsole.setVisible (true);
} catch (e) {
}
}, "~B");
$_M(c$, "clearConsole", 
function () {
this.statusManager.clearConsole ();
});
$_M(c$, "getParameterEscaped", 
function (key) {
return this.global.getParameterEscaped (key, 0);
}, "~S");
$_V(c$, "getParameter", 
function (key) {
return this.global.getParameter (key);
}, "~S");
$_M(c$, "getOrSetNewVariable", 
function (key, doSet) {
return this.global.getOrSetNewVariable (key, doSet);
}, "~S,~B");
$_M(c$, "setUserVariable", 
function (name, value) {
return this.global.setUserVariable (name, value);
}, "~S,J.script.SV");
$_M(c$, "unsetProperty", 
function (key) {
key = key.toLowerCase ();
if (key.equals ("all") || key.equals ("variables")) this.fileManager.setPathForAllFiles ("");
this.global.unsetUserVariable (key);
}, "~S");
$_M(c$, "getVariableList", 
function () {
return this.global.getVariableList ();
});
$_V(c$, "getBooleanProperty", 
function (key) {
key = key.toLowerCase ();
if (this.global.htBooleanParameterFlags.containsKey (key)) return this.global.htBooleanParameterFlags.get (key).booleanValue ();
if (key.endsWith ("p!")) {
if (this.actionManager == null) return false;
var s = this.actionManager.getPickingState ().toLowerCase ();
key = key.substring (0, key.length - 2) + ";";
return (s.indexOf (key) >= 0);
}if (key.equalsIgnoreCase ("__appletReady")) {
this.statusManager.setStatusAppletReady (this.fullName, true);
return true;
}if (key.equalsIgnoreCase ("__appletDestroyed")) {
this.statusManager.setStatusAppletReady (this.htmlName, false);
return true;
}if (key.equalsIgnoreCase ("executionPaused")) return (this.eval != null && this.eval.isPaused ());
if (key.equalsIgnoreCase ("executionStepping")) return (this.eval != null && this.eval.isStepping ());
if (key.equalsIgnoreCase ("haveBFactors")) return (this.modelSet.getBFactors () != null);
if (key.equalsIgnoreCase ("colorRasmol")) return this.colorManager.getDefaultColorRasmol ();
if (key.equalsIgnoreCase ("frank")) return this.getShowFrank ();
if (key.equalsIgnoreCase ("spinOn")) return this.getSpinOn ();
if (key.equalsIgnoreCase ("isNavigating")) return this.isNavigating ();
if (key.equalsIgnoreCase ("showSelections")) return this.modelSet.getSelectionHaloEnabled ();
if (this.global.htUserVariables.containsKey (key)) {
var t = this.global.getUserVariable (key);
if (t.tok == 1048589) return true;
if (t.tok == 1048588) return false;
}J.util.Logger.error ("viewer.getBooleanProperty(" + key + ") - unrecognized");
return false;
}, "~S");
$_V(c$, "getInt", 
function (tok) {
switch (tok) {
case 553648132:
return this.animationManager.animationFps;
case 553648143:
return this.global.dotDensity;
case 553648144:
return this.global.dotScale;
case 553648146:
return this.global.helixStep;
case 553648151:
return this.global.meshScale;
case 553648153:
return this.global.minPixelSelRadius;
case 553648154:
return this.global.percentVdwAtom;
case 553648157:
return this.global.pickingSpinRate;
case 553648158:
return this.global.platformSpeed;
case 553648166:
return this.global.ribbonAspectRatio;
case 536870922:
return this.global.scriptDelay;
case 553648170:
return this.global.smallMoleculeMaxAtoms;
case 553648184:
return this.global.strutSpacing;
}
J.util.Logger.error ("viewer.getInt(" + J.script.T.nameOf (tok) + ") - not listed");
return 0;
}, "~N");
$_M(c$, "getDelayMaximumMs", 
function () {
return (this.haveDisplay ? this.global.delayMaximumMs : 1);
});
$_M(c$, "getHermiteLevel", 
function () {
return (this.getSpinOn () ? 0 : this.global.hermiteLevel);
});
$_M(c$, "getHoverDelay", 
function () {
return (this.global.modelKitMode ? 20 : this.global.hoverDelayMs);
});
$_V(c$, "getBoolean", 
function (tok) {
switch (tok) {
case 1074790662:
return this.modelSet.getModelSetAuxiliaryInfoBoolean ("isPDB");
case 603979780:
return this.global.allowGestures;
case 603979784:
return this.global.allowMultiTouch;
case 603979785:
return this.global.allowRotateSelected;
case 603979792:
return this.global.appendNew;
case 603979794:
return this.global.applySymmetryToBonds;
case 603979796:
return this.global.atomPicking;
case 603979798:
return this.global.autoBond;
case 603979800:
return this.global.autoFps;
case 603979806:
return this.global.axesOrientationRasmol;
case 603979812:
return this.global.bondModeOr;
case 603979817:
return this.global.cartoonBaseEdges;
case 603979819:
return this.global.cartoonFancy;
case 603979820:
return this.global.cartoonLadders;
case 603979818:
return this.global.cartoonRockets;
case 603979822:
return this.global.chainCaseSensitive || this.chainList.size () > 0;
case 603979824:
return this.global.debugScript;
case 603979825:
return this.global.defaultStructureDSSP;
case 603979826:
return this.global.disablePopupMenu;
case 603979828:
return this.global.displayCellParameters;
case 603979830:
return this.global.dotSurface;
case 603979829:
return this.global.dotsSelectedOnly;
case 603979833:
return this.global.drawPicking;
case 603979835:
return this.global.dynamicMeasurements;
case 603979844:
return this.global.fontCaching;
case 603979845:
return this.global.fontScaling;
case 603979846:
return this.global.forceAutoBond;
case 603979848:
return this.global.fractionalRelative;
case 603979850:
return this.global.greyscaleRendering;
case 603979852:
return this.global.hbondsBackbone;
case 603979853:
return this.global.hbondsRasmol;
case 603979854:
return this.global.hbondsSolid;
case 1613758470:
return this.global.rasmolHeteroSetting;
case 603979858:
return this.global.hideNameInPopup;
case 603979864:
return this.global.highResolutionFlag;
case 1613758476:
return this.global.rasmolHydrogenSetting;
case 603979870:
return this.global.isosurfaceKey;
case 603979872:
return this.global.justifyMeasurements;
case 603979874:
return this.global.legacyAutoBonding;
case 603979875:
return this.global.legacyHAddition;
case 603979877:
return this.global.logGestures;
case 603979878:
return this.global.measureAllModels;
case 603979879:
return this.global.measurementLabels;
case 603979880:
return this.global.messageStyleChime;
case 603979883:
return this.global.modelKitMode;
case 603979887:
return this.global.navigationMode;
case 603979888:
return this.global.navigationPeriodic;
case 603979889:
return this.global.partialDots;
case 603979892:
return this.global.pdbSequential;
case 603979894:
return this.global.preserveState;
case 603979898:
return this.global.ribbonBorder;
case 603979900:
return this.global.rocketBarrels;
case 603979906:
return this.global.selectAllModels;
case 603979920:
return this.global.showHiddenSelectionHalos;
case 603979922:
return this.global.showHydrogens;
case 603979926:
return this.global.showMeasurements;
case 603979928:
return this.global.showMultipleBonds;
case 603979934:
return this.global.showTiming;
case 603979938:
return this.global.slabByAtom;
case 603979940:
return this.global.slabByMolecule;
case 603979944:
return this.global.smartAromatic;
case 1613758488:
return this.global.solventOn;
case 603979952:
return this.global.ssbondsBackbone;
case 603979955:
return this.global.strutsMultiple;
case 603979966:
return this.global.traceAlpha;
case 603979967:
return this.global.translucent;
case 603979968:
return this.global.twistedSheets;
case 603979973:
return this.global.vectorSymmetry;
case 603979974:
return this.global.waitForMoveTo;
case 603979978:
return this.global.zeroBasedXyzRasmol;
}
J.util.Logger.error ("viewer.getBoolean(" + J.script.T.nameOf (tok) + ") - not listed");
return false;
}, "~N");
$_M(c$, "allowEmbeddedScripts", 
function () {
return (this.global.allowEmbeddedScripts && !this.$isPreviewOnly);
});
$_M(c$, "getDragSelected", 
function () {
return (this.global.dragSelected && !this.global.modelKitMode);
});
$_M(c$, "getBondPicking", 
function () {
return (this.global.bondPicking || this.global.modelKitMode);
});
$_M(c$, "useMinimizationThread", 
function () {
return (this.global.useMinimizationThread && !this.autoExit);
});
$_V(c$, "getFloat", 
function (tok) {
switch (tok) {
case 570425346:
return this.global.axesScale;
case 570425348:
return this.global.bondTolerance;
case 570425354:
return this.global.defaultTranslucent;
case 570425352:
return this.global.defaultDrawArrowScale;
case 570425355:
return this.global.dipoleScale;
case 570425356:
return this.global.drawFontSize;
case 570425358:
return this.global.exportScale;
case 570425360:
return this.global.hbondsAngleMinimum;
case 570425361:
return this.global.hbondsDistanceMaximum;
case 570425363:
return this.global.loadAtomDataTolerance;
case 570425364:
return this.global.minBondDistance;
case 570425369:
return this.global.multipleBondSpacing;
case 570425368:
return this.global.multipleBondRadiusFactor;
case 570425374:
return this.global.navigationSpeed;
case 570425382:
return this.global.pointGroupDistanceTolerance;
case 570425384:
return this.global.pointGroupLinearTolerance;
case 570425388:
return this.transformManager.getRotationRadius ();
case 570425392:
return this.global.sheetSmoothing;
case 570425394:
return this.global.solventProbeRadius;
case 570425403:
return this.global.starScale;
case 570425406:
return this.global.strutDefaultRadius;
case 570425408:
return this.global.strutLengthMaximum;
case 1649410049:
return this.global.vectorScale;
case 570425412:
return this.global.vibrationPeriod;
}
J.util.Logger.error ("viewer.getFloat(" + J.script.T.nameOf (tok) + ") - not listed");
return 0;
}, "~N");
$_V(c$, "setStringProperty", 
function (key, value) {
if (value == null) return;
if (key.charAt (0) == '_') {
this.global.setS (key, value);
return;
}var tok = J.script.T.getTokFromName (key);
switch (J.script.T.getParamType (tok)) {
case 603979776:
this.setBooleanPropertyTok (key, tok, J.script.SV.newVariable (4, value).asBoolean ());
break;
case 553648128:
this.setIntPropertyTok (key, tok, J.script.SV.newVariable (4, value).asInt ());
break;
case 570425344:
this.setFloatPropertyTok (key, tok, JU.PT.parseFloat (value));
break;
default:
this.setStringPropertyTok (key, tok, value);
}
}, "~S,~S");
$_M(c$, "setStringPropertyTok", 
function (key, tok, value) {
switch (tok) {
case 545259521:
this.setAnimationMode (value);
return;
case 545259569:
this.global.nmrPredictFormat = value;
break;
case 545259548:
this.global.defaultDropScript = value;
break;
case 545259571:
value = this.fileManager.setPathForAllFiles (value);
break;
case 545259558:
this.setUnits (value, false);
return;
case 545259560:
this.global.forceField = value = ("UFF".equalsIgnoreCase (value) ? "UFF" : "MMFF");
this.minimizer = null;
break;
case 545259570:
this.global.nmrUrlFormat = value;
break;
case 545259568:
this.setUnits (value, true);
return;
case 545259566:
this.global.loadLigandFormat = value;
break;
case 545259543:
this.global.defaultLabelPDB = value;
break;
case 545259544:
this.global.defaultLabelXYZ = value;
break;
case 545259549:
this.global.defaultLoadFilter = value;
break;
case 545259567:
value = this.getOutputManager ().setLogFile (value);
if (value == null) return;
break;
case 545259559:
break;
case 545259524:
this.global.atomTypes = value;
break;
case 545259538:
break;
case 545259576:
this.global.pickLabel = value;
break;
case 545259580:
if (value.length == 2 && value.startsWith ("R")) this.global.quaternionFrame = value.substring (0, 2);
 else this.global.quaternionFrame = "" + (value.toLowerCase () + "p").charAt (0);
if (!JU.PT.isOneOf (this.global.quaternionFrame, "RC;RP;a;b;c;n;p;q;x;")) this.global.quaternionFrame = "p";
this.modelSet.setHaveStraightness (false);
break;
case 545259555:
this.setDefaultVdw (value);
return;
case 545259564:
 new J.i18n.GT (value);
this.language = J.i18n.GT.getLanguage ();
this.modelkitPopup = null;
if (this.jmolpopup != null) {
this.jmolpopup.jpiDispose ();
this.jmolpopup = null;
this.getPopupMenu ();
}this.statusManager.setCallbackFunction ("language", this.language);
value = J.i18n.GT.getLanguage ();
break;
case 545259565:
this.global.loadFormat = value;
break;
case 545259534:
this.setObjectColor ("background", value);
return;
case 545259528:
this.setObjectColor ("axis1", value);
return;
case 545259530:
this.setObjectColor ("axis2", value);
return;
case 545259532:
this.setObjectColor ("axis3", value);
return;
case 545259536:
this.setObjectColor ("boundbox", value);
return;
case 545259586:
this.setObjectColor ("unitcell", value);
return;
case 545259578:
this.setPropertyColorScheme (value, false, false);
break;
case 545259562:
this.setShapeProperty (34, "atomLabel", value);
break;
case 545259547:
this.global.defaultDistanceLabel = value;
break;
case 545259542:
this.global.defaultAngleLabel = value;
break;
case 545259554:
this.global.defaultTorsionLabel = value;
break;
case 545259550:
this.global.defaultLoadScript = value;
break;
case 545259522:
this.fileManager.setAppletProxy (value);
break;
case 545259546:
if (value == null) value = "";
value = value.$replace ('\\', '/');
this.global.defaultDirectory = value;
break;
case 545259561:
this.global.helpPath = value;
break;
case 545259552:
if (!value.equalsIgnoreCase ("RasMol") && !value.equalsIgnoreCase ("PyMOL")) value = "Jmol";
this.setDefaultsType (value);
break;
case 545259545:
this.setDefaultColors (value.equalsIgnoreCase ("rasmol"));
return;
case 545259572:
this.setPickingMode (value, 0);
return;
case 545259574:
this.setPickingStyle (value, 0);
return;
case 545259540:
break;
default:
if (key.toLowerCase ().endsWith ("callback")) {
this.statusManager.setCallbackFunction (key, (value.length == 0 || value.equalsIgnoreCase ("none") ? null : value));
break;
}if (!this.global.htNonbooleanParameterValues.containsKey (key.toLowerCase ())) {
this.global.setUserVariable (key, J.script.SV.newVariable (4, value));
return;
}break;
}
this.global.setS (key, value);
}, "~S,~N,~S");
$_V(c$, "setFloatProperty", 
function (key, value) {
if (Float.isNaN (value)) return;
if (key.charAt (0) == '_') {
this.global.setF (key, value);
return;
}var tok = J.script.T.getTokFromName (key);
switch (J.script.T.getParamType (tok)) {
case 545259520:
this.setStringPropertyTok (key, tok, "" + value);
break;
case 603979776:
this.setBooleanPropertyTok (key, tok, value != 0);
break;
case 553648128:
this.setIntPropertyTok (key, tok, Clazz_floatToInt (value));
break;
default:
this.setFloatPropertyTok (key, tok, value);
}
}, "~S,~N");
$_M(c$, "setFloatPropertyTok", 
function (key, tok, value) {
switch (tok) {
case 570425356:
this.global.drawFontSize = value;
break;
case 570425358:
this.global.exportScale = value;
break;
case 570425403:
this.global.starScale = value;
break;
case 570425368:
this.global.multipleBondRadiusFactor = value;
break;
case 570425369:
this.global.multipleBondSpacing = value;
break;
case 570425393:
this.transformManager.setSlabRange (value);
break;
case 570425365:
this.global.minimizationCriterion = value;
break;
case 570425359:
if (this.haveDisplay) this.actionManager.setGestureSwipeFactor (value);
break;
case 570425366:
if (this.haveDisplay) this.actionManager.setMouseDragFactor (value);
break;
case 570425367:
if (this.haveDisplay) this.actionManager.setMouseWheelFactor (value);
break;
case 570425408:
this.global.strutLengthMaximum = value;
break;
case 570425406:
this.global.strutDefaultRadius = value;
break;
case 570425376:
this.setSpin ("X", Clazz_floatToInt (value));
break;
case 570425378:
this.setSpin ("Y", Clazz_floatToInt (value));
break;
case 570425380:
this.setSpin ("Z", Clazz_floatToInt (value));
break;
case 570425370:
if (Float.isNaN (value)) return;
this.setSpin ("FPS", Clazz_floatToInt (value));
break;
case 570425363:
this.global.loadAtomDataTolerance = value;
break;
case 570425360:
this.global.hbondsAngleMinimum = value;
break;
case 570425361:
this.global.hbondsDistanceMaximum = value;
break;
case 570425382:
this.global.pointGroupDistanceTolerance = value;
break;
case 570425384:
this.global.pointGroupLinearTolerance = value;
break;
case 570425357:
this.global.ellipsoidAxisDiameter = value;
break;
case 570425398:
this.setSpin ("x", Clazz_floatToInt (value));
break;
case 570425400:
this.setSpin ("y", Clazz_floatToInt (value));
break;
case 570425402:
this.setSpin ("z", Clazz_floatToInt (value));
break;
case 570425396:
this.setSpin ("fps", Clazz_floatToInt (value));
break;
case 570425352:
this.global.defaultDrawArrowScale = value;
break;
case 570425354:
this.global.defaultTranslucent = value;
break;
case 570425346:
this.setAxesScale (value);
break;
case 570425416:
this.transformManager.setVisualRange (value);
this.refresh (1, "set visualRange");
break;
case 570425371:
this.setNavigationDepthPercent (value);
break;
case 570425374:
this.global.navigationSpeed = value;
break;
case 570425372:
this.transformManager.setNavigationSlabOffsetPercent (value);
break;
case 570425350:
this.transformManager.setCameraDepthPercent (value, false);
this.refresh (1, "set cameraDepth");
return;
case 570425388:
this.setRotationRadius (value, true);
return;
case 570425362:
this.global.hoverDelayMs = Clazz_floatToInt (value * 1000);
break;
case 570425392:
this.global.sheetSmoothing = value;
break;
case 570425355:
value = J.viewer.Viewer.checkFloatRange (value, -10, 10);
this.global.dipoleScale = value;
break;
case 570425404:
this.transformManager.setStereoDegrees (value);
break;
case 1649410049:
this.setVectorScale (value);
return;
case 570425412:
this.setVibrationPeriod (value);
return;
case 570425414:
this.setVibrationScale (value);
return;
case 570425348:
this.setBondTolerance (value);
return;
case 570425364:
this.setMinBondDistance (value);
return;
case 570425390:
this.transformManager.setScaleAngstromsPerInch (value);
break;
case 570425394:
value = J.viewer.Viewer.checkFloatRange (value, 0, 10);
this.global.solventProbeRadius = value;
break;
default:
if (!this.global.htNonbooleanParameterValues.containsKey (key.toLowerCase ())) {
this.global.setUserVariable (key, J.script.SV.newVariable (3, Float.$valueOf (value)));
return;
}}
this.global.setF (key, value);
}, "~S,~N,~N");
$_V(c$, "setIntProperty", 
function (key, value) {
if (value == -2147483648) return;
if (key.charAt (0) == '_') {
this.global.setI (key, value);
return;
}var tok = J.script.T.getTokFromName (key);
switch (J.script.T.getParamType (tok)) {
case 545259520:
this.setStringPropertyTok (key, tok, "" + value);
break;
case 603979776:
this.setBooleanPropertyTok (key, tok, value != 0);
break;
case 570425344:
this.setFloatPropertyTok (key, tok, value);
break;
default:
this.setIntPropertyTok (key, tok, value);
}
}, "~S,~N");
$_M(c$, "setIntPropertyTok", 
function (key, tok, value) {
switch (tok) {
case 553648158:
this.global.platformSpeed = Math.min (Math.max (value, 0), 10);
break;
case 553648151:
this.global.meshScale = value;
break;
case 553648153:
this.global.minPixelSelRadius = value;
break;
case 553648149:
this.global.isosurfacePropertySmoothingPower = value;
break;
case 553648165:
this.global.repaintWaitMs = value;
break;
case 553648170:
this.global.smallMoleculeMaxAtoms = value;
break;
case 553648152:
this.global.minimizationSteps = value;
break;
case 553648184:
this.global.strutSpacing = value;
break;
case 553648156:
value = J.viewer.Viewer.checkIntRange (value, 0, 1000);
this.gdata.setPhongExponent (value);
break;
case 553648146:
this.global.helixStep = value;
this.modelSet.setHaveStraightness (false);
break;
case 553648144:
this.global.dotScale = value;
break;
case 553648143:
this.global.dotDensity = value;
break;
case 553648138:
this.global.delayMaximumMs = value;
break;
case 553648150:
J.util.Logger.setLogLevel (value);
J.util.Logger.info ("logging level set to " + value);
this.global.setI ("logLevel", value);
if (this.eval != null) this.eval.setDebugging ();
return;
case 553648134:
switch (J.constant.EnumAxesMode.getAxesMode (value)) {
case J.constant.EnumAxesMode.MOLECULAR:
this.setAxesModeMolecular (true);
return;
case J.constant.EnumAxesMode.BOUNDBOX:
this.setAxesModeMolecular (false);
return;
case J.constant.EnumAxesMode.UNITCELL:
this.setAxesModeUnitCell (true);
return;
}
return;
case 553648178:
this.setStrandCount (0, value);
return;
case 553648182:
this.setStrandCount (12, value);
return;
case 553648180:
this.setStrandCount (13, value);
return;
case 553648155:
return;
case 536870922:
this.global.scriptDelay = value;
break;
case 553648176:
if (value < 0) value = J.viewer.Viewer.checkIntRange (value, -10, -1);
 else value = J.viewer.Viewer.checkIntRange (value, 0, 100);
this.gdata.setSpecularPower (value);
break;
case 553648172:
value = J.viewer.Viewer.checkIntRange (-value, -10, -1);
this.gdata.setSpecularPower (value);
break;
case 553648136:
this.setMarBond (value);
return;
case 536870924:
this.setBooleanPropertyTok (key, tok, value == 1);
return;
case 553648174:
value = J.viewer.Viewer.checkIntRange (value, 0, 100);
this.gdata.setSpecularPercent (value);
break;
case 553648142:
value = J.viewer.Viewer.checkIntRange (value, 0, 100);
this.gdata.setDiffusePercent (value);
break;
case 553648130:
value = J.viewer.Viewer.checkIntRange (value, 0, 100);
this.gdata.setAmbientPercent (value);
break;
case 553648186:
this.transformManager.zDepthToPercent (value);
break;
case 553648188:
this.transformManager.zSlabToPercent (value);
break;
case 554176526:
this.transformManager.depthToPercent (value);
break;
case 554176565:
this.transformManager.slabToPercent (value);
break;
case 553648190:
this.global.zShadePower = Math.max (value, 1);
break;
case 553648166:
this.global.ribbonAspectRatio = value;
break;
case 553648157:
this.global.pickingSpinRate = (value < 1 ? 1 : value);
break;
case 553648132:
this.setAnimationFps (value);
return;
case 553648154:
this.setPercentVdwAtom (value);
break;
case 553648147:
this.global.hermiteLevel = value;
break;
case 553648145:
case 553648148:
case 553648160:
case 553648159:
case 553648162:
case 553648164:
break;
default:
if (!this.global.htNonbooleanParameterValues.containsKey (key)) {
this.global.setUserVariable (key, J.script.SV.newScriptVariableInt (value));
return;
}}
this.global.setI (key, value);
}, "~S,~N,~N");
c$.checkIntRange = $_M(c$, "checkIntRange", 
function (value, min, max) {
return (value < min ? min : value > max ? max : value);
}, "~N,~N,~N");
c$.checkFloatRange = $_M(c$, "checkFloatRange", 
function (value, min, max) {
return (value < min ? min : value > max ? max : value);
}, "~N,~N,~N");
$_V(c$, "setBooleanProperty", 
function (key, value) {
if (key.charAt (0) == '_') {
this.global.setB (key, value);
return;
}var tok = J.script.T.getTokFromName (key);
switch (J.script.T.getParamType (tok)) {
case 545259520:
this.setStringPropertyTok (key, tok, "");
break;
case 553648128:
this.setIntPropertyTok (key, tok, value ? 1 : 0);
break;
case 570425344:
this.setFloatPropertyTok (key, tok, value ? 1 : 0);
break;
default:
this.setBooleanPropertyTok (key, tok, value);
}
}, "~S,~B");
$_M(c$, "setBooleanPropertyTok", 
function (key, tok, value) {
var doRepaint = true;
switch (tok) {
case 603979837:
this.global.ellipsoidArrows = value;
break;
case 603979967:
this.global.translucent = value;
break;
case 603979820:
this.global.cartoonLadders = value;
break;
case 603979968:
var b = this.global.twistedSheets;
this.global.twistedSheets = value;
if (b != value) this.checkCoordinatesChanged ();
break;
case 603979821:
this.global.celShading = value;
this.gdata.setCel (value);
break;
case 603979819:
this.global.cartoonFancy = value;
break;
case 603979934:
this.global.showTiming = value;
break;
case 603979973:
this.global.vectorSymmetry = value;
break;
case 603979870:
this.global.isosurfaceKey = value;
break;
case 603979889:
this.global.partialDots = value;
break;
case 603979874:
this.global.legacyAutoBonding = value;
break;
case 603979825:
this.global.defaultStructureDSSP = value;
break;
case 603979834:
this.global.dsspCalcHydrogen = value;
break;
case 603979782:
this.global.allowModelkit = value;
if (!value) this.setModelKitMode (false);
break;
case 603979883:
this.setModelKitMode (value);
break;
case 603979885:
this.global.multiProcessor = value && (J.viewer.Viewer.nProcessors > 1);
break;
case 603979884:
this.global.monitorEnergy = value;
break;
case 603979853:
this.global.hbondsRasmol = value;
break;
case 603979881:
this.global.minimizationRefresh = value;
break;
case 603979882:
this.global.minimizationSilent = value;
break;
case 603979969:
this.global.useArcBall = value;
break;
case 603979869:
if (value) {
this.$isKiosk = true;
this.global.disablePopupMenu = true;
if (this.display != null) this.apiPlatform.setTransparentCursor (this.display);
}break;
case 603979974:
this.global.waitForMoveTo = value;
break;
case 603979876:
this.global.logCommands = true;
break;
case 603979877:
this.global.logGestures = true;
break;
case 603979784:
this.global.allowMultiTouch = value;
break;
case 603979894:
this.global.preserveState = value;
this.modelSet.setPreserveState (value);
this.undoClear ();
break;
case 603979955:
this.global.strutsMultiple = value;
break;
case 603979842:
break;
case 603979938:
this.global.slabByAtom = value;
break;
case 603979940:
this.global.slabByMolecule = value;
break;
case 603979902:
this.global.saveProteinStructureState = value;
break;
case 603979780:
this.global.allowGestures = value;
break;
case 603979868:
this.global.imageState = value;
break;
case 603979970:
this.global.useMinimizationThread = value;
break;
case 603979781:
if (this.global.disablePopupMenu) value = false;
this.global.allowKeyStrokes = value;
break;
case 603979831:
this.global.dragSelected = value;
this.showSelected = false;
break;
case 603979924:
this.global.showKeyStrokes = value;
break;
case 603979844:
this.global.fontCaching = value;
break;
case 603979796:
this.global.atomPicking = value;
break;
case 603979814:
this.highlight (null);
this.global.bondPicking = value;
break;
case 603979906:
this.global.selectAllModels = value;
break;
case 603979880:
this.global.messageStyleChime = value;
break;
case 603979892:
this.global.pdbSequential = value;
break;
case 603979890:
this.global.pdbAddHydrogens = value;
break;
case 603979891:
this.global.pdbGetHeader = value;
break;
case 603979838:
this.global.ellipsoidAxes = value;
break;
case 603979836:
this.global.ellipsoidArcs = value;
break;
case 603979839:
this.global.ellipsoidBall = value;
break;
case 603979840:
this.global.ellipsoidDots = value;
break;
case 603979841:
this.global.ellipsoidFill = value;
break;
case 603979845:
this.global.fontScaling = value;
break;
case 603979956:
this.setSyncTarget (0, value);
break;
case 603979958:
this.setSyncTarget (1, value);
break;
case 603979976:
this.global.wireframeRotation = value;
break;
case 603979871:
this.global.isosurfacePropertySmoothing = value;
break;
case 603979833:
this.global.drawPicking = value;
break;
case 603979786:
case 603979790:
case 603979788:
this.setAntialias (tok, value);
break;
case 603979944:
this.global.smartAromatic = value;
break;
case 603979794:
this.setApplySymmetryToBonds (value);
break;
case 603979792:
this.setAppendNew (value);
break;
case 603979800:
this.global.autoFps = value;
break;
case 603979972:
JU.DF.setUseNumberLocalization (this.global.useNumberLocalization = value);
break;
case 1611272202:
key = "showFrank";
this.setFrankOn (value);
break;
case 603979918:
this.setFrankOn (value);
break;
case 1613758488:
key = "solventProbe";
this.global.solventOn = value;
break;
case 603979948:
this.global.solventOn = value;
break;
case 603979835:
this.setDynamicMeasurements (value);
break;
case 603979785:
this.global.allowRotateSelected = value;
break;
case 603979783:
this.global.allowMoveAtoms = value;
this.global.allowRotateSelected = value;
this.global.dragSelected = value;
this.showSelected = false;
break;
case 536870922:
this.setIntPropertyTok ("showScript", tok, value ? 1 : 0);
return;
case 603979778:
this.global.allowEmbeddedScripts = value;
break;
case 603979888:
this.global.navigationPeriodic = value;
break;
case 603979984:
this.transformManager.setZShadeEnabled (value);
return;
case 603979832:
if (this.haveDisplay) this.global.drawHover = value;
break;
case 603979887:
this.setNavigationMode (value);
break;
case 603979886:
return;
case 603979860:
this.global.hideNavigationPoint = value;
break;
case 603979930:
this.global.showNavigationPointAlways = value;
break;
case 603979896:
this.setRefreshing (value);
break;
case 603979872:
this.global.justifyMeasurements = value;
break;
case 603979952:
this.global.ssbondsBackbone = value;
break;
case 603979852:
this.global.hbondsBackbone = value;
break;
case 603979854:
this.global.hbondsSolid = value;
break;
case 536870924:
this.gdata.setSpecular (value);
break;
case 603979942:
this.transformManager.setSlabEnabled (value);
return;
case 603979980:
this.transformManager.setZoomEnabled (value);
return;
case 603979864:
this.global.highResolutionFlag = value;
break;
case 603979966:
this.global.traceAlpha = value;
break;
case 603979983:
this.global.zoomLarge = value;
this.transformManager.setZoomHeight (this.global.zoomHeight, value);
break;
case 603979982:
this.global.zoomHeight = value;
this.transformManager.setZoomHeight (value, this.global.zoomLarge);
break;
case 603979873:
J.i18n.GT.setDoTranslate (value);
break;
case 603979862:
this.selectionManager.setHideNotSelected (value);
break;
case 603979904:
this.setScriptQueue (value);
break;
case 603979830:
this.global.dotSurface = value;
break;
case 603979829:
this.global.dotsSelectedOnly = value;
break;
case 1611141171:
this.setSelectionHalos (value);
break;
case 603979910:
this.global.rasmolHydrogenSetting = value;
break;
case 603979908:
this.global.rasmolHeteroSetting = value;
break;
case 603979928:
this.global.showMultipleBonds = value;
break;
case 603979920:
this.global.showHiddenSelectionHalos = value;
break;
case 603979975:
this.transformManager.setWindowCentered (value);
break;
case 603979828:
this.global.displayCellParameters = value;
break;
case 603979960:
this.global.testFlag1 = value;
break;
case 603979962:
this.global.testFlag2 = value;
break;
case 603979964:
this.global.testFlag3 = value;
break;
case 603979965:
this.jmolTest ();
this.global.testFlag4 = value;
break;
case 603979898:
this.global.ribbonBorder = value;
break;
case 603979817:
this.global.cartoonBaseEdges = value;
break;
case 603979818:
this.global.cartoonRockets = value;
break;
case 603979900:
this.global.rocketBarrels = value;
break;
case 603979850:
this.gdata.setGreyscaleMode (this.global.greyscaleRendering = value);
break;
case 603979879:
this.global.measurementLabels = value;
break;
case 603979810:
this.setAxesModeMolecular (!value);
return;
case 603979804:
this.setAxesModeMolecular (value);
return;
case 603979808:
this.setAxesModeUnitCell (value);
return;
case 603979806:
this.setAxesOrientationRasmol (value);
return;
case 603979823:
this.setStringPropertyTok ("defaultcolorscheme", 545259545, value ? "rasmol" : "jmol");
return;
case 603979824:
this.setDebugScript (value);
return;
case 603979893:
this.setPerspectiveDepth (value);
return;
case 603979798:
this.setAutoBond (value);
return;
case 603979914:
this.setShowAxes (value);
return;
case 603979916:
this.setShowBbcage (value);
return;
case 603979922:
this.setShowHydrogens (value);
return;
case 603979926:
this.setShowMeasurements (value);
return;
case 603979936:
this.setShowUnitCell (value);
return;
case 603979812:
doRepaint = false;
this.global.bondModeOr = value;
break;
case 603979978:
doRepaint = false;
this.global.zeroBasedXyzRasmol = value;
this.reset (true);
break;
case 603979895:
doRepaint = false;
this.global.rangeSelected = value;
break;
case 603979878:
doRepaint = false;
this.global.measureAllModels = value;
break;
case 603979954:
doRepaint = false;
this.statusManager.setAllowStatusReporting (value);
break;
case 603979822:
doRepaint = false;
this.global.chainCaseSensitive = value;
break;
case 603979858:
doRepaint = false;
this.global.hideNameInPopup = value;
break;
case 603979826:
doRepaint = false;
this.global.disablePopupMenu = value;
break;
case 603979846:
doRepaint = false;
this.global.forceAutoBond = value;
break;
case 603979848:
doRepaint = false;
this.global.fractionalRelative = value;
break;
default:
if (!this.global.htBooleanParameterFlags.containsKey (key.toLowerCase ())) {
this.global.setUserVariable (key, J.script.SV.getBoolean (value));
return;
}}
this.global.setB (key, value);
if (doRepaint) this.setTainted (true);
}, "~S,~N,~B");
$_M(c$, "setModelKitMode", 
function (value) {
if (this.actionManager == null || !this.allowScripting) return;
if (value || this.global.modelKitMode) {
this.setPickingMode (null, value ? 33 : 1);
this.setPickingMode (null, value ? 32 : 1);
}var isChange = (this.global.modelKitMode != value);
this.global.modelKitMode = value;
this.highlight (null);
if (value) {
this.setNavigationMode (false);
this.selectAll ();
this.setAtomPickingOption ("C");
this.setBondPickingOption ("p");
if (!this.$isApplet) this.popupMenu (0, 0, 'm');
if (isChange) this.statusManager.setCallbackFunction ("modelkit", "ON");
this.global.modelKitMode = true;
if (this.getAtomCount () == 0) this.zap (false, true, true);
} else {
this.actionManager.setPickingMode (-1);
this.setStringProperty ("pickingStyle", "toggle");
this.setBooleanProperty ("bondPicking", false);
if (isChange) this.statusManager.setCallbackFunction ("modelkit", "OFF");
}}, "~B");
$_M(c$, "getLanguage", 
function () {
return this.language;
});
$_M(c$, "setSmilesString", 
function (s) {
if (s == null) this.global.removeParam ("_smilesString");
 else this.global.setS ("_smilesString", s);
}, "~S");
$_M(c$, "removeUserVariable", 
function (key) {
this.global.removeUserVariable (key);
if (key.endsWith ("callback")) this.statusManager.setCallbackFunction (key, null);
}, "~S");
$_M(c$, "isJmolVariable", 
function (key) {
return this.global.isJmolVariable (key);
}, "~S");
$_M(c$, "jmolTest", 
function () {
});
$_M(c$, "showParameter", 
function (key, ifNotSet, nMax) {
var sv = "" + this.global.getParameterEscaped (key, nMax);
if (ifNotSet || sv.indexOf ("<not defined>") < 0) this.showString (key + " = " + sv, false);
}, "~S,~B,~N");
$_M(c$, "showString", 
function (str, isPrint) {
if (this.isScriptQueued () && (!this.isSilent || isPrint) && !this.isJS) J.util.Logger.warn (str);
this.scriptEcho (str);
}, "~S,~B");
$_M(c$, "getAllSettings", 
function (prefix) {
return this.getStateCreator ().getAllSettings (prefix);
}, "~S");
$_M(c$, "getBindingInfo", 
function (qualifiers) {
return (this.haveDisplay ? this.actionManager.getBindingInfo (qualifiers) : "");
}, "~S");
$_M(c$, "getIsosurfacePropertySmoothing", 
function (asPower) {
return (asPower ? this.global.isosurfacePropertySmoothingPower : this.global.isosurfacePropertySmoothing ? 1 : 0);
}, "~B");
$_M(c$, "setNavigationDepthPercent", 
function (percent) {
this.transformManager.setNavigationDepthPercent (percent);
this.refresh (1, "set navigationDepth");
}, "~N");
$_M(c$, "getShowNavigationPoint", 
function () {
if (!this.global.navigationMode || !this.transformManager.canNavigate ()) return false;
return (this.isNavigating () && !this.global.hideNavigationPoint || this.global.showNavigationPointAlways || this.getInMotion (true));
});
$_M(c$, "getCurrentSolventProbeRadius", 
function () {
return this.global.solventOn ? this.global.solventProbeRadius : 0;
});
$_M(c$, "getTestFlag", 
function (i) {
switch (i) {
case 1:
return this.global.testFlag1;
case 2:
return this.global.testFlag2;
case 3:
return this.global.testFlag3;
case 4:
return this.global.testFlag4;
}
return false;
}, "~N");
$_V(c$, "setPerspectiveDepth", 
function (perspectiveDepth) {
this.transformManager.setPerspectiveDepth (perspectiveDepth);
}, "~B");
$_V(c$, "setAxesOrientationRasmol", 
function (TF) {
this.global.setB ("axesOrientationRasmol", TF);
this.global.axesOrientationRasmol = TF;
this.reset (true);
}, "~B");
$_M(c$, "setAxesScale", 
function (scale) {
scale = J.viewer.Viewer.checkFloatRange (scale, -100, 100);
this.global.axesScale = scale;
this.axesAreTainted = true;
}, "~N");
$_M(c$, "getAxisPoints", 
function () {
return (this.getObjectMad (1) == 0 || this.getAxesMode () !== J.constant.EnumAxesMode.UNITCELL || (this.getShapeProperty (31, "axesTypeXY")).booleanValue () || this.getShapeProperty (31, "origin") != null ? null : this.getShapeProperty (31, "axisPoints"));
});
$_M(c$, "resetError", 
function () {
this.global.removeParam ("_errormessage");
});
$_M(c$, "setAxesModeMolecular", 
function (TF) {
this.global.axesMode = (TF ? J.constant.EnumAxesMode.MOLECULAR : J.constant.EnumAxesMode.BOUNDBOX);
this.axesAreTainted = true;
this.global.removeParam ("axesunitcell");
this.global.removeParam (TF ? "axeswindow" : "axesmolecular");
this.global.setI ("axesMode", this.global.axesMode.getCode ());
this.global.setB (TF ? "axesMolecular" : "axesWindow", true);
}, "~B");
$_M(c$, "setAxesModeUnitCell", 
function (TF) {
this.global.axesMode = (TF ? J.constant.EnumAxesMode.UNITCELL : J.constant.EnumAxesMode.BOUNDBOX);
this.axesAreTainted = true;
this.global.removeParam ("axesmolecular");
this.global.removeParam (TF ? "axeswindow" : "axesunitcell");
this.global.setB (TF ? "axesUnitcell" : "axesWindow", true);
this.global.setI ("axesMode", this.global.axesMode.getCode ());
}, "~B");
$_M(c$, "getAxesMode", 
function () {
return this.global.axesMode;
});
$_V(c$, "getPerspectiveDepth", 
function () {
return this.transformManager.getPerspectiveDepth ();
});
$_V(c$, "setSelectionHalos", 
function (TF) {
if (this.modelSet == null || TF == this.modelSet.getSelectionHaloEnabled ()) return;
this.global.setB ("selectionHalos", TF);
this.loadShape (8);
this.modelSet.setSelectionHaloEnabled (TF);
}, "~B");
$_M(c$, "getSelectionHaloEnabled", 
function (isRenderer) {
var flag = this.modelSet.getSelectionHaloEnabled () || isRenderer && this.showSelected;
if (isRenderer) this.showSelected = false;
return flag;
}, "~B");
$_M(c$, "setStrandCount", 
function (type, value) {
value = J.viewer.Viewer.checkIntRange (value, 0, 20);
switch (type) {
case 12:
this.global.strandCountForStrands = value;
break;
case 13:
this.global.strandCountForMeshRibbon = value;
break;
default:
this.global.strandCountForStrands = value;
this.global.strandCountForMeshRibbon = value;
break;
}
this.global.setI ("strandCount", value);
this.global.setI ("strandCountForStrands", this.global.strandCountForStrands);
this.global.setI ("strandCountForMeshRibbon", this.global.strandCountForMeshRibbon);
}, "~N,~N");
$_M(c$, "getStrandCount", 
function (type) {
return (type == 12 ? this.global.strandCountForStrands : this.global.strandCountForMeshRibbon);
}, "~N");
$_M(c$, "setNavigationMode", 
function (TF) {
this.global.navigationMode = TF;
this.transformManager.setNavigationMode (TF);
}, "~B");
$_M(c$, "setTransformManagerDefaults", 
function () {
this.transformManager.setCameraDepthPercent (this.global.defaultCameraDepth, true);
this.transformManager.setPerspectiveDepth (this.global.defaultPerspectiveDepth);
this.transformManager.setStereoDegrees (-5);
this.transformManager.setVisualRange (this.global.visualRange);
this.transformManager.setSpinOff ();
this.transformManager.setVibrationPeriod (0);
this.transformManager.setFrameOffsets (this.frameOffsets);
});
$_M(c$, "getCameraFactors", 
function () {
return this.transformManager.getCameraFactors ();
});
$_M(c$, "getCameraDepth", 
function () {
return this.transformManager.getCameraDepth ();
});
$_M(c$, "getLoadState", 
function (htParams) {
return this.getStateCreator ().getLoadState (htParams);
}, "java.util.Map");
$_V(c$, "setAutoBond", 
function (TF) {
this.global.setB ("autobond", TF);
this.global.autoBond = TF;
}, "~B");
$_M(c$, "makeConnections", 
function (minDistance, maxDistance, order, connectOperation, bsA, bsB, bsBonds, isBonds, addGroup, energy) {
this.clearModelDependentObjects ();
this.clearMinimization ();
return this.modelSet.makeConnections (minDistance, maxDistance, order, connectOperation, bsA, bsB, bsBonds, isBonds, addGroup, energy);
}, "~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");
$_V(c$, "rebond", 
function () {
this.rebondState (false);
});
$_M(c$, "rebondState", 
function (isStateScript) {
this.clearModelDependentObjects ();
this.modelSet.deleteAllBonds ();
var isLegacy = isStateScript && this.global.legacyAutoBonding;
this.modelSet.autoBondBs4 (null, null, null, null, this.getMadBond (), isLegacy);
this.addStateScript ((isLegacy ? "set legacyAutoBonding TRUE;connect;set legacyAutoBonding FALSE;" : "connect;"), false, true);
}, "~B");
$_M(c$, "setPdbConectBonding", 
function (isAuto, isStateScript) {
this.clearModelDependentObjects ();
this.modelSet.deleteAllBonds ();
var bsExclude =  new JU.BS ();
this.modelSet.setPdbConectBonding (0, 0, bsExclude);
if (isAuto) {
var isLegacy = isStateScript && this.global.legacyAutoBonding;
this.modelSet.autoBondBs4 (null, null, bsExclude, null, this.getMadBond (), isLegacy);
this.addStateScript ((isLegacy ? "set legacyAutoBonding TRUE;connect PDB AUTO;set legacyAutoBonding FALSE;" : "connect PDB auto;"), false, true);
return;
}this.addStateScript ("connect PDB;", false, true);
}, "~B,~B");
$_V(c$, "setPercentVdwAtom", 
function (value) {
this.global.setI ("percentVdwAtom", value);
this.global.percentVdwAtom = value;
this.rd.value = value / 100;
this.rd.factorType = J.atomdata.RadiusData.EnumType.FACTOR;
this.rd.vdwType = J.constant.EnumVdw.AUTO;
this.setShapeSizeRD (0, this.rd, null);
}, "~N");
$_M(c$, "getDefaultRadiusData", 
function () {
return this.rd;
});
$_V(c$, "getMadBond", 
function () {
return (this.global.bondRadiusMilliAngstroms * 2);
});
$_M(c$, "getMarBond", 
function () {
return this.global.bondRadiusMilliAngstroms;
});
$_M(c$, "getModeMultipleBond", 
function () {
return this.global.modeMultipleBond;
});
$_V(c$, "setShowHydrogens", 
function (TF) {
this.global.setB ("showHydrogens", TF);
this.global.showHydrogens = TF;
}, "~B");
$_V(c$, "setShowBbcage", 
function (value) {
this.setObjectMad (32, "boundbox", (value ? -4 : 0));
this.global.setB ("showBoundBox", value);
}, "~B");
$_V(c$, "getShowBbcage", 
function () {
return this.getObjectMad (4) != 0;
});
$_M(c$, "setShowUnitCell", 
function (value) {
this.setObjectMad (33, "unitcell", (value ? -2 : 0));
this.global.setB ("showUnitCell", value);
}, "~B");
$_M(c$, "getShowUnitCell", 
function () {
return this.getObjectMad (5) != 0;
});
$_V(c$, "setShowAxes", 
function (value) {
this.setObjectMad (31, "axes", (value ? -2 : 0));
this.global.setB ("showAxes", value);
}, "~B");
$_V(c$, "getShowAxes", 
function () {
return this.getObjectMad (1) != 0;
});
$_V(c$, "setFrankOn", 
function (TF) {
if (this.$isPreviewOnly) TF = false;
this.frankOn = TF;
this.setObjectMad (35, "frank", (TF ? 1 : 0));
}, "~B");
$_M(c$, "getShowFrank", 
function () {
if (this.$isPreviewOnly || this.$isApplet && this.creatingImage) return false;
return (!this.isJS && this.$isSignedApplet && !this.isSignedAppletLocal || this.frankOn);
});
$_V(c$, "setShowMeasurements", 
function (TF) {
this.global.setB ("showMeasurements", TF);
this.global.showMeasurements = TF;
}, "~B");
$_M(c$, "setUnits", 
function (units, isDistance) {
this.global.setUnits (units);
if (isDistance) {
this.global.setUnits (units);
this.setShapeProperty (6, "reformatDistances", null);
} else {
}}, "~S,~B");
$_M(c$, "getMeasureDistanceUnits", 
function () {
return this.global.measureDistanceUnits;
});
$_M(c$, "getEnergyUnits", 
function () {
return this.global.energyUnits;
});
$_M(c$, "setAppendNew", 
function (value) {
this.global.appendNew = value;
}, "~B");
$_V(c$, "setRasmolDefaults", 
function () {
this.setDefaultsType ("RasMol");
});
$_V(c$, "setJmolDefaults", 
function () {
this.setDefaults ();
});
$_M(c$, "setDefaultsType", 
function (type) {
if (type.equalsIgnoreCase ("RasMol")) {
this.stateManager.setRasMolDefaults ();
return;
}if (type.equalsIgnoreCase ("PyMOL")) {
this.stateManager.setPyMOLDefaults ();
return;
}this.setDefaults ();
}, "~S");
$_M(c$, "setDefaults", 
function () {
this.setShapeSizeRD (0, this.rd, this.getModelUndeletedAtomsBitSet (-1));
});
$_M(c$, "setAntialias", 
function (tok, TF) {
switch (tok) {
case 603979786:
this.global.antialiasDisplay = TF;
break;
case 603979790:
this.global.antialiasTranslucent = TF;
break;
case 603979788:
this.global.antialiasImages = TF;
return;
}
this.resizeImage (0, 0, false, false, true);
}, "~N,~B");
$_M(c$, "allocTempPoints", 
function (size) {
return this.tempArray.allocTempPoints (size);
}, "~N");
$_M(c$, "freeTempPoints", 
function (tempPoints) {
this.tempArray.freeTempPoints (tempPoints);
}, "~A");
$_M(c$, "allocTempScreens", 
function (size) {
return this.tempArray.allocTempScreens (size);
}, "~N");
$_M(c$, "freeTempScreens", 
function (tempScreens) {
this.tempArray.freeTempScreens (tempScreens);
}, "~A");
$_M(c$, "allocTempEnum", 
function (size) {
return this.tempArray.allocTempEnum (size);
}, "~N");
$_M(c$, "freeTempEnum", 
function (temp) {
this.tempArray.freeTempEnum (temp);
}, "~A");
$_M(c$, "getFont3D", 
function (fontFace, fontStyle, fontSize) {
return this.gdata.getFont3DFSS (fontFace, fontStyle, fontSize);
}, "~S,~S,~N");
$_M(c$, "formatText", 
function (text0) {
var i;
if ((i = text0.indexOf ("@{")) < 0 && (i = text0.indexOf ("%{")) < 0) return text0;
var text = text0;
var isEscaped = (text.indexOf ("\\") >= 0);
if (isEscaped) {
text = JU.PT.simpleReplace (text, "\\%", "\1");
text = JU.PT.simpleReplace (text, "\\@", "\2");
isEscaped = !text.equals (text0);
}text = JU.PT.simpleReplace (text, "%{", "@{");
var name;
while ((i = text.indexOf ("@{")) >= 0) {
i++;
var i0 = i + 1;
var len = text.length;
i = J.util.Txt.ichMathTerminator (text, i, len);
if (i >= len) return text;
name = text.substring (i0, i);
if (name.length == 0) return text;
var v = this.evaluateExpression (name);
if (Clazz_instanceOf (v, JU.P3)) v = J.util.Escape.eP (v);
text = text.substring (0, i0 - 2) + v.toString () + text.substring (i + 1);
}
if (isEscaped) {
text = JU.PT.simpleReplace (text, "\2", "@");
text = JU.PT.simpleReplace (text, "\1", "%");
}return text;
}, "~S");
$_M(c$, "getElementSymbol", 
function (i) {
return this.modelSet.getElementSymbol (i);
}, "~N");
$_M(c$, "getElementNumber", 
function (i) {
return this.modelSet.getElementNumber (i);
}, "~N");
$_V(c$, "getAtomName", 
function (i) {
return this.modelSet.getAtomName (i);
}, "~N");
$_V(c$, "getAtomNumber", 
function (i) {
return this.modelSet.getAtomNumber (i);
}, "~N");
$_M(c$, "getAtomGroupQuaternions", 
function (bsAtoms, nMax) {
return this.modelSet.getAtomGroupQuaternions (bsAtoms, nMax, this.getQuaternionFrame ());
}, "JU.BS,~N");
$_M(c$, "getAtomQuaternion", 
function (i) {
return this.modelSet.getQuaternion (i, this.getQuaternionFrame ());
}, "~N");
$_V(c$, "getAtomPoint3f", 
function (i) {
return this.modelSet.atoms[i];
}, "~N");
$_M(c$, "getAtomPointVector", 
function (bs) {
return this.modelSet.getAtomPointVector (bs);
}, "JU.BS");
$_V(c$, "getAtomRadius", 
function (i) {
return this.modelSet.getAtomRadius (i);
}, "~N");
$_V(c$, "getAtomArgb", 
function (i) {
return this.gdata.getColorArgbOrGray (this.modelSet.getAtomColix (i));
}, "~N");
$_V(c$, "getAtomModelIndex", 
function (i) {
return this.modelSet.atoms[i].modelIndex;
}, "~N");
$_V(c$, "getBondRadius", 
function (i) {
return this.modelSet.getBondRadius (i);
}, "~N");
$_V(c$, "getBondOrder", 
function (i) {
return this.modelSet.getBondOrder (i);
}, "~N");
$_M(c$, "assignAromaticBonds", 
function () {
this.modelSet.assignAromaticBonds ();
});
$_M(c$, "resetAromatic", 
function () {
this.modelSet.resetAromatic ();
});
$_V(c$, "getBondArgb1", 
function (i) {
return this.gdata.getColorArgbOrGray (this.modelSet.getBondColix1 (i));
}, "~N");
$_V(c$, "getBondModelIndex", 
function (i) {
return this.modelSet.getBondModelIndex (i);
}, "~N");
$_V(c$, "getBondArgb2", 
function (i) {
return this.gdata.getColorArgbOrGray (this.modelSet.getBondColix2 (i));
}, "~N");
$_V(c$, "getPolymerLeadMidPoints", 
function (modelIndex, polymerIndex) {
return this.modelSet.getPolymerLeadMidPoints (modelIndex, polymerIndex);
}, "~N,~N");
$_M(c$, "setStereoMode", 
function (twoColors, stereoMode, degrees) {
this.setFloatProperty ("stereoDegrees", degrees);
this.setBooleanProperty ("greyscaleRendering", stereoMode.isBiColor ());
if (twoColors != null) this.transformManager.setStereoMode2 (twoColors);
 else this.transformManager.setStereoMode (stereoMode);
}, "~A,J.constant.EnumStereoMode,~N");
$_M(c$, "isStereoDouble", 
function () {
return this.transformManager.stereoMode === J.constant.EnumStereoMode.DOUBLE;
});
$_V(c$, "getOperatingSystemName", 
function () {
return J.viewer.Viewer.strOSName + (!this.isJS ? "" : this.isWebGL ? "(WebGL)" : "(HTML5)");
});
$_V(c$, "getJavaVendor", 
function () {
return J.viewer.Viewer.strJavaVendor;
});
$_V(c$, "getJavaVersion", 
function () {
return J.viewer.Viewer.strJavaVersion;
});
$_M(c$, "getGraphicsData", 
function () {
return this.gdata;
});
$_V(c$, "getProperty", 
function (returnType, infoType, paramInfo) {
if (!"DATA_API".equals (returnType)) return this.getPropertyManager ().getProperty (returnType, infoType, paramInfo);
switch (("scriptCheck.........consoleText.........scriptEditor........scriptEditorState...getAppConsole.......getScriptEditor.....setMenu.............spaceGroupInfo......disablePopupMenu....defaultDirectory....getPopupMenu........shapeManager........").indexOf (infoType)) {
case 0:
return this.scriptCheckRet (paramInfo, true);
case 20:
return (this.appConsole == null ? "" : this.appConsole.getText ());
case 40:
this.showEditor (paramInfo);
return null;
case 60:
this.scriptEditorVisible = (paramInfo).booleanValue ();
return null;
case 80:
if (this.$isKiosk) {
this.appConsole = null;
} else if (Clazz_instanceOf (paramInfo, J.api.JmolAppConsoleInterface)) {
this.appConsole = paramInfo;
} else if (paramInfo != null && !(paramInfo).booleanValue ()) {
this.appConsole = null;
} else if (this.appConsole == null && paramInfo != null && (paramInfo).booleanValue ()) {
{
this.appConsole = J.api.Interface
.getOptionInterface("consolejs.AppletConsole"); if
(this.appConsole != null) { this.appConsole.start(this);
return this.appConsole; }
}if (this.appConsole != null) this.appConsole.start (this);
}this.scriptEditor = (this.appConsole == null ? null : this.appConsole.getScriptEditor ());
return this.appConsole;
case 100:
if (this.appConsole == null && paramInfo != null && (paramInfo).booleanValue ()) {
this.getProperty ("DATA_API", "getAppConsole", Boolean.TRUE);
this.scriptEditor = (this.appConsole == null ? null : this.appConsole.getScriptEditor ());
}return this.scriptEditor;
case 120:
if (this.jmolpopup != null) this.jmolpopup.jpiDispose ();
this.jmolpopup = null;
return this.menuStructure = paramInfo;
case 140:
return this.getSpaceGroupInfo (null);
case 160:
this.global.disablePopupMenu = true;
return null;
case 180:
return this.global.defaultDirectory;
case 200:
if (Clazz_instanceOf (paramInfo, String)) return this.getMenu (paramInfo);
return this.getPopupMenu ();
case 220:
return this.shapeManager.getProperty (paramInfo);
}
J.util.Logger.error ("ERROR in getProperty DATA_API: " + infoType);
return null;
}, "~S,~S,~O");
$_M(c$, "showEditor", 
function (file_text) {
var scriptEditor = this.getProperty ("DATA_API", "getScriptEditor", Boolean.TRUE);
if (scriptEditor == null) return;
scriptEditor.show (file_text);
}, "~A");
$_M(c$, "getPropertyManager", 
function () {
if (this.pm == null) (this.pm = J.api.Interface.getOptionInterface ("viewer.PropertyManager")).setViewer (this);
return this.pm;
});
$_M(c$, "getModelExtract", 
function (atomExpression, doTransform, isModelKit, type) {
return this.getPropertyManager ().getModelExtract (this.getAtomBitSet (atomExpression), doTransform, isModelKit, type);
}, "~O,~B,~B,~S");
$_M(c$, "setTainted", 
function (TF) {
this.isTainted = this.axesAreTainted = (TF && (this.refreshing || this.creatingImage));
}, "~B");
$_M(c$, "notifyMouseClicked", 
function (x, y, action, mode) {
var modifiers = J.viewer.binding.Binding.getButtonMods (action);
var clickCount = J.viewer.binding.Binding.getClickCount (action);
this.global.setI ("_mouseX", x);
this.global.setI ("_mouseY", this.dimScreen.height - y);
this.global.setI ("_mouseAction", action);
this.global.setI ("_mouseModifiers", modifiers);
this.global.setI ("_clickCount", clickCount);
return this.statusManager.setStatusClicked (x, this.dimScreen.height - y, action, clickCount, mode);
}, "~N,~N,~N,~N");
$_M(c$, "checkObjectClicked", 
function (x, y, modifiers) {
return this.shapeManager.checkObjectClicked (x, y, modifiers, this.getVisibleFramesBitSet (), this.global.drawPicking);
}, "~N,~N,~N");
$_M(c$, "checkObjectHovered", 
function (x, y) {
return (x >= 0 && this.shapeManager != null && this.shapeManager.checkObjectHovered (x, y, this.getVisibleFramesBitSet (), this.getBondPicking ()));
}, "~N,~N");
$_M(c$, "checkObjectDragged", 
function (prevX, prevY, x, y, action) {
var iShape = 0;
switch (this.getPickingMode ()) {
case 2:
iShape = 5;
break;
case 4:
iShape = 22;
break;
}
if (this.shapeManager.checkObjectDragged (prevX, prevY, x, y, action, this.getVisibleFramesBitSet (), iShape)) {
this.refresh (1, "checkObjectDragged");
if (iShape == 22) this.scriptEcho (this.getShapeProperty (22, "command"));
}}, "~N,~N,~N,~N,~N");
$_M(c$, "rotateAxisAngleAtCenter", 
function (eval, rotCenter, rotAxis, degreesPerSecond, endDegrees, isSpin, bsSelected) {
var isOK = this.transformManager.rotateAxisAngleAtCenter (eval, rotCenter, rotAxis, degreesPerSecond, endDegrees, isSpin, bsSelected);
if (isOK) this.refresh (-1, "rotateAxisAngleAtCenter");
return isOK;
}, "J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");
$_M(c$, "rotateAboutPointsInternal", 
function (eval, point1, point2, degreesPerSecond, endDegrees, isSpin, bsSelected, translation, finalPoints, dihedralList) {
var isOK = this.transformManager.rotateAboutPointsInternal (eval, point1, point2, degreesPerSecond, endDegrees, false, isSpin, bsSelected, false, translation, finalPoints, dihedralList);
if (isOK) this.refresh (-1, "rotateAxisAboutPointsInternal");
return isOK;
}, "J.api.JmolScriptEvaluator,JU.P3,JU.P3,~N,~N,~B,JU.BS,JU.V3,JU.List,~A");
$_M(c$, "startSpinningAxis", 
function (pt1, pt2, isClockwise) {
if (this.getSpinOn () || this.getNavOn ()) {
this.setSpinOn (false);
this.setNavOn (false);
return;
}this.transformManager.rotateAboutPointsInternal (null, pt1, pt2, this.global.pickingSpinRate, 3.4028235E38, isClockwise, true, null, false, null, null, null);
}, "JU.P3,JU.P3,~B");
$_M(c$, "getModelDipole", 
function () {
return this.modelSet.getModelDipole (this.animationManager.currentModelIndex);
});
$_M(c$, "calculateMolecularDipole", 
function () {
return this.modelSet.calculateMolecularDipole (this.animationManager.currentModelIndex);
});
$_M(c$, "getAtomIdentityInfo", 
function (atomIndex, info) {
this.modelSet.getAtomIdentityInfo (atomIndex, info);
}, "~N,java.util.Map");
$_M(c$, "setDefaultLattice", 
function (ptLattice) {
this.global.setDefaultLattice (ptLattice);
this.global.setS ("defaultLattice", J.util.Escape.eP (ptLattice));
}, "JU.P3");
$_M(c$, "getDefaultLattice", 
function () {
return this.global.getDefaultLattice ();
});
$_M(c$, "getTaintedAtoms", 
function (type) {
return this.modelSet.getTaintedAtoms (type);
}, "~N");
$_M(c$, "setTaintedAtoms", 
function (bs, type) {
this.modelSet.setTaintedAtoms (bs, type);
}, "JU.BS,~N");
$_M(c$, "getData", 
function (atomExpression, type) {
var exp = "";
if (type.equalsIgnoreCase ("MOL") || type.equalsIgnoreCase ("SDF") || type.equalsIgnoreCase ("V2000") || type.equalsIgnoreCase ("V3000") || type.equalsIgnoreCase ("XYZVIB") || type.equalsIgnoreCase ("CD")) return this.getModelExtract (atomExpression, false, false, type);
if (type.toLowerCase ().indexOf ("property_") == 0) exp = "{selected}.label(\"%{" + type + "}\")";
 else if (type.equalsIgnoreCase ("CML")) return this.getModelCml (this.getAtomBitSet (atomExpression), 2147483647, true);
 else if (type.equalsIgnoreCase ("PDB")) exp = "{selected and not hetero}.label(\"ATOM  %5i %-4a%1A%3.3n %1c%4R%1E   %8.3x%8.3y%8.3z%6.2Q%6.2b          %2e  \").lines+{selected and hetero}.label(\"HETATM%5i %-4a%1A%3.3n %1c%4R%1E   %8.3x%8.3y%8.3z%6.2Q%6.2b          %2e  \").lines";
 else if (type.equalsIgnoreCase ("XYZRN")) exp = "\"\" + {selected}.size + \"\n\n\"+{selected}.label(\"%-2e %8.3x %8.3y %8.3z %4.2[vdw] 1 [%n]%r.%a#%i\").lines";
 else if (type.startsWith ("USER:")) exp = "{selected}.label(\"" + type.substring (5) + "\").lines";
 else exp = "\"\" + {selected}.size + \"\n\n\"+{selected}.label(\"%-2e %10.5x %10.5y %10.5z\").lines";
if (!atomExpression.equals ("selected")) exp = JU.PT.simpleReplace (exp, "selected", atomExpression);
return this.evaluateExpression (exp);
}, "~S,~S");
$_M(c$, "getModelCml", 
function (bs, nAtomsMax, addBonds) {
return this.modelSet.getModelCml (bs, nAtomsMax, addBonds);
}, "JU.BS,~N,~B");
$_M(c$, "getHelixData", 
function (bs, tokType) {
return this.modelSet.getHelixData (bs, tokType);
}, "JU.BS,~N");
$_M(c$, "getPdbAtomData", 
function (bs, sb) {
return this.modelSet.getPdbAtomData (bs == null ? this.getSelectionSet (true) : bs, sb);
}, "JU.BS,JU.OC");
$_M(c$, "isJmolDataFrameForModel", 
function (modelIndex) {
return this.modelSet.isJmolDataFrameForModel (modelIndex);
}, "~N");
$_M(c$, "isJmolDataFrame", 
function () {
return this.modelSet.isJmolDataFrameForModel (this.animationManager.currentModelIndex);
});
$_M(c$, "getJmolDataFrameIndex", 
function (modelIndex, type) {
return this.modelSet.getJmolDataFrameIndex (modelIndex, type);
}, "~N,~S");
$_M(c$, "setJmolDataFrame", 
function (type, modelIndex, dataIndex) {
this.modelSet.setJmolDataFrame (type, modelIndex, dataIndex);
}, "~S,~N,~N");
$_M(c$, "setFrameTitle", 
function (modelIndex, title) {
this.modelSet.setFrameTitle (J.util.BSUtil.newAndSetBit (modelIndex), title);
}, "~N,~S");
$_M(c$, "setFrameTitleObj", 
function (title) {
this.loadShape (30);
this.modelSet.setFrameTitle (this.getVisibleFramesBitSet (), title);
}, "~O");
$_M(c$, "getFrameTitle", 
function () {
return this.modelSet.getFrameTitle (this.animationManager.currentModelIndex);
});
$_M(c$, "getJmolFrameType", 
function (modelIndex) {
return this.modelSet.getJmolFrameType (modelIndex);
}, "~N");
$_M(c$, "getJmolDataSourceFrame", 
function (modelIndex) {
return this.modelSet.getJmolDataSourceFrame (modelIndex);
}, "~N");
$_M(c$, "setAtomProperty", 
function (bs, tok, iValue, fValue, sValue, values, list) {
if (tok == 1649412120) this.shapeManager.deleteVdwDependentShapes (bs);
this.clearMinimization ();
this.modelSet.setAtomProperty (bs, tok, iValue, fValue, sValue, values, list);
switch (tok) {
case 1112541185:
case 1112541186:
case 1112541187:
case 1112541188:
case 1112541189:
case 1112541190:
case 1112539153:
case 1112539154:
case 1112539155:
case 1087375365:
this.refreshMeasures (true);
}
}, "JU.BS,~N,~N,~N,~S,~A,~A");
$_M(c$, "checkCoordinatesChanged", 
function () {
this.modelSet.recalculatePositionDependentQuantities (null, null);
this.refreshMeasures (true);
});
$_M(c$, "setAtomCoord", 
function (atomIndex, x, y, z) {
this.modelSet.setAtomCoord (atomIndex, x, y, z);
}, "~N,~N,~N,~N");
$_M(c$, "setAtomCoordRelative", 
function (atomIndex, x, y, z) {
this.modelSet.setAtomCoordRelative (atomIndex, x, y, z);
}, "~N,~N,~N,~N");
$_M(c$, "setAtomCoords", 
function (bs, tokType, xyzValues) {
if (bs.cardinality () == 0) return;
this.modelSet.setAtomCoords (bs, tokType, xyzValues);
this.checkMinimization ();
this.statusManager.setStatusAtomMoved (bs);
}, "JU.BS,~N,~O");
$_M(c$, "setAtomCoordsRelative", 
function (offset, bs) {
if (bs == null) bs = this.getSelectionSet (false);
if (bs.cardinality () == 0) return;
this.modelSet.setAtomCoordsRelative (offset, bs);
this.checkMinimization ();
this.statusManager.setStatusAtomMoved (bs);
}, "JU.T3,JU.BS");
$_M(c$, "invertAtomCoordPt", 
function (pt, bs) {
this.modelSet.invertSelected (pt, null, -1, null, bs);
this.checkMinimization ();
this.statusManager.setStatusAtomMoved (bs);
}, "JU.P3,JU.BS");
$_M(c$, "invertAtomCoordPlane", 
function (plane, bs) {
this.modelSet.invertSelected (null, plane, -1, null, bs);
this.checkMinimization ();
this.statusManager.setStatusAtomMoved (bs);
}, "JU.P4,JU.BS");
$_M(c$, "invertSelected", 
function (pt, plane, iAtom, invAtoms) {
var bs = this.getSelectionSet (false);
if (bs.cardinality () == 0) return;
this.modelSet.invertSelected (pt, plane, iAtom, invAtoms, bs);
this.checkMinimization ();
this.statusManager.setStatusAtomMoved (bs);
}, "JU.P3,JU.P4,~N,JU.BS");
$_M(c$, "moveAtoms", 
function (mNew, matrixRotate, translation, center, isInternal, bsAtoms) {
if (bsAtoms.cardinality () == 0) return;
this.modelSet.moveAtoms (mNew, matrixRotate, translation, bsAtoms, center, isInternal);
this.checkMinimization ();
this.statusManager.setStatusAtomMoved (bsAtoms);
}, "JU.M3,JU.M3,JU.V3,JU.P3,~B,JU.BS");
$_M(c$, "moveSelected", 
function (deltaX, deltaY, deltaZ, x, y, bsSelected, isTranslation, asAtoms) {
if (deltaZ == 0) return;
if (x == -2147483648) this.rotateBondIndex = -1;
if (this.isJmolDataFrame ()) return;
if (deltaX == -2147483648) {
this.showSelected = true;
this.loadShape (8);
this.refresh (6, "moveSelected");
return;
}if (deltaX == 2147483647) {
if (!this.showSelected) return;
this.showSelected = false;
this.refresh (6, "moveSelected");
return;
}if (this.movingSelected) return;
this.movingSelected = true;
this.stopMinimization ();
if (this.rotateBondIndex >= 0 && x != -2147483648) {
this.actionRotateBond (deltaX, deltaY, x, y);
} else {
bsSelected = this.setMovableBitSet (bsSelected, !asAtoms);
if (bsSelected.cardinality () != 0) {
if (isTranslation) {
var ptCenter = this.getAtomSetCenter (bsSelected);
this.transformManager.finalizeTransformParameters ();
var f = (this.global.antialiasDisplay ? 2 : 1);
var ptScreen = this.transformPt (ptCenter);
var ptScreenNew;
if (deltaZ != -2147483648) ptScreenNew = JU.P3.new3 (ptScreen.x, ptScreen.y, ptScreen.z + deltaZ + 0.5);
 else ptScreenNew = JU.P3.new3 (ptScreen.x + deltaX * f + 0.5, ptScreen.y + deltaY * f + 0.5, ptScreen.z);
var ptNew =  new JU.P3 ();
this.unTransformPoint (ptScreenNew, ptNew);
ptNew.sub (ptCenter);
this.setAtomCoordsRelative (ptNew, bsSelected);
} else {
this.transformManager.rotateXYBy (deltaX, deltaY, bsSelected);
}}}this.refresh (2, "");
this.movingSelected = false;
}, "~N,~N,~N,~N,~N,JU.BS,~B,~B");
$_M(c$, "highlightBond", 
function (index, isHover) {
if (isHover && !this.hoverEnabled) return;
var bs = null;
if (index >= 0) {
var b = this.modelSet.bonds[index];
var i = b.getAtomIndex2 ();
if (!this.isAtomAssignable (i)) return;
bs = J.util.BSUtil.newAndSetBit (i);
bs.set (b.getAtomIndex1 ());
}this.highlight (bs);
this.refresh (3, "highlightBond");
}, "~N,~B");
$_M(c$, "highlight", 
function (bs) {
if (bs != null) this.loadShape (8);
this.setShapeProperty (8, "highlight", bs);
}, "JU.BS");
$_M(c$, "setRotateBondIndex", 
function (index) {
var haveBond = (this.rotateBondIndex >= 0);
if (!haveBond && index < 0) return;
this.rotatePrev1 = -1;
this.bsRotateBranch = null;
if (index == -2147483648) return;
this.rotateBondIndex = index;
this.highlightBond (index, false);
}, "~N");
$_M(c$, "getRotateBondIndex", 
function () {
return this.rotateBondIndex;
});
$_M(c$, "actionRotateBond", 
function (deltaX, deltaY, x, y) {
if (this.rotateBondIndex < 0) return;
var bsBranch = this.bsRotateBranch;
var atom1;
var atom2;
if (bsBranch == null) {
var b = this.modelSet.bonds[this.rotateBondIndex];
atom1 = b.getAtom1 ();
atom2 = b.getAtom2 ();
this.undoMoveActionClear (atom1.index, 2, true);
var pt = JU.P3.new3 (x, y, Clazz_doubleToInt ((atom1.screenZ + atom2.screenZ) / 2));
this.transformManager.unTransformPoint (pt, pt);
if (atom2.getCovalentBondCount () == 1 || pt.distance (atom1) < pt.distance (atom2) && atom1.getCovalentBondCount () != 1) {
var a = atom1;
atom1 = atom2;
atom2 = a;
}if (J.util.Measure.computeAngleABC (pt, atom1, atom2, true) > 90 || J.util.Measure.computeAngleABC (pt, atom2, atom1, true) > 90) {
bsBranch = this.getBranchBitSet (atom2.index, atom1.index, true);
}if (bsBranch != null) for (var n = 0, i = atom1.getBonds ().length; --i >= 0; ) {
if (bsBranch.get (atom1.getBondedAtomIndex (i)) && ++n == 2) {
bsBranch = null;
break;
}}
if (bsBranch == null) {
bsBranch = this.getMoleculeBitSet (atom1.index);
}this.bsRotateBranch = bsBranch;
this.rotatePrev1 = atom1.index;
this.rotatePrev2 = atom2.index;
} else {
atom1 = this.modelSet.atoms[this.rotatePrev1];
atom2 = this.modelSet.atoms[this.rotatePrev2];
}var v1 = JU.V3.new3 (atom2.screenX - atom1.screenX, atom2.screenY - atom1.screenY, 0);
var v2 = JU.V3.new3 (deltaX, deltaY, 0);
v1.cross (v1, v2);
var degrees = (v1.z > 0 ? 1 : -1) * v2.length ();
var bs = J.util.BSUtil.copy (bsBranch);
bs.andNot (this.selectionManager.getMotionFixedAtoms ());
this.rotateAboutPointsInternal (this.eval, atom1, atom2, 0, degrees, false, bs, null, null, null);
}, "~N,~N,~N,~N");
$_M(c$, "refreshMeasures", 
function (andStopMinimization) {
this.setShapeProperty (6, "refresh", null);
if (andStopMinimization) this.stopMinimization ();
}, "~B");
$_M(c$, "setDynamicMeasurements", 
function (TF) {
this.global.dynamicMeasurements = TF;
}, "~B");
$_M(c$, "functionXY", 
function (functionName, nX, nY) {
var data = null;
if (functionName.indexOf ("file:") == 0) data = this.getFileAsString (functionName.substring (5));
 else if (functionName.indexOf ("data2d_") != 0) return this.statusManager.functionXY (functionName, nX, nY);
nX = Math.abs (nX);
nY = Math.abs (nY);
var fdata;
if (data == null) {
fdata = this.getDataFloat2D (functionName);
if (fdata != null) return fdata;
data = "";
}fdata =  Clazz_newFloatArray (nX, nY, 0);
var f =  Clazz_newFloatArray (nX * nY, 0);
J.util.Parser.parseStringInfestedFloatArray (data, null, f);
for (var i = 0, n = 0; i < nX; i++) for (var j = 0; j < nY; j++) fdata[i][j] = f[n++];


return fdata;
}, "~S,~N,~N");
$_M(c$, "functionXYZ", 
function (functionName, nX, nY, nZ) {
var data = null;
if (functionName.indexOf ("file:") == 0) data = this.getFileAsString (functionName.substring (5));
 else if (functionName.indexOf ("data3d_") != 0) return this.statusManager.functionXYZ (functionName, nX, nY, nZ);
nX = Math.abs (nX);
nY = Math.abs (nY);
nZ = Math.abs (nZ);
var xyzdata;
if (data == null) {
xyzdata = this.getDataFloat3D (functionName);
if (xyzdata != null) return xyzdata;
data = "";
}xyzdata =  Clazz_newFloatArray (nX, nY, nZ, 0);
var f =  Clazz_newFloatArray (nX * nY * nZ, 0);
J.util.Parser.parseStringInfestedFloatArray (data, null, f);
for (var i = 0, n = 0; i < nX; i++) for (var j = 0; j < nY; j++) for (var k = 0; k < nZ; k++) xyzdata[i][j][k] = f[n++];



return xyzdata;
}, "~S,~N,~N,~N");
$_V(c$, "extractMolData", 
function (what) {
if (what == null) {
var i = this.getCurrentModelIndex ();
if (i < 0) return null;
what = this.getModelNumberDotted (i);
}return this.getModelExtract (what, true, false, "V2000");
}, "~S");
$_M(c$, "getNMRPredict", 
function (openURL) {
var molFile = this.getModelExtract ("selected", true, false, "V2000");
var pt = molFile.indexOf ("\n");
molFile = "Jmol " + J.viewer.Viewer.version_date + molFile.substring (pt);
if (openURL) {
if (this.$isApplet) {
this.showUrl (this.global.nmrUrlFormat + molFile);
} else {
this.syncScript ("true", "*", 0);
this.syncScript ("JSpecView:", ".", 0);
}return null;
}var url = this.global.nmrPredictFormat + molFile;
return this.getFileAsString (url);
}, "~B");
$_M(c$, "getHelp", 
function (what) {
if (this.global.helpPath.indexOf ("?") < 0) {
if (what.length > 0 && what.indexOf ("?") != 0) what = "?search=" + JU.PT.simpleReplace (what, " ", "%20");
what += (what.length == 0 ? "?ver=" : "&ver=") + J.viewer.JC.version;
} else {
what = "&" + what;
}this.showUrl (this.global.helpPath + what);
}, "~S");
$_M(c$, "show2D", 
function (smiles) {
this.showUrl (this.setLoadFormat ("_" + smiles, '2', false));
}, "~S");
$_M(c$, "getChemicalInfo", 
function (smiles, type, info) {
var s = this.setLoadFormat ("_" + smiles, type, false);
if (type == '/') s += JU.PT.simpleReplace (info, " ", "%20");
return this.getFileAsString4 (s, -1, false, false);
}, "~S,~S,~S");
$_M(c$, "addCommand", 
function (command) {
if (this.autoExit || !this.haveDisplay || !this.getPreserveState ()) return;
this.commandHistory.addCommand (JU.PT.replaceAllCharacters (command, "\r\n\t", " "));
}, "~S");
$_M(c$, "removeCommand", 
function () {
return this.commandHistory.removeCommand ();
});
$_V(c$, "getSetHistory", 
function (howFarBack) {
return this.commandHistory.getSetHistory (howFarBack);
}, "~N");
$_M(c$, "getOutputChannel", 
function (localName, fullPath) {
return this.getOutputManager ().getOutputChannel (localName, fullPath);
}, "~S,~A");
$_V(c$, "writeTextFile", 
function (fileName, data) {
var params =  new java.util.Hashtable ();
params.put ("fileName", fileName);
params.put ("type", "txt");
params.put ("text", data);
this.outputToFile (params);
}, "~S,~S");
$_V(c$, "clipImageOrPasteText", 
function (text) {
if (!this.haveAccess (J.viewer.Viewer.ACCESS.ALL)) return "no";
return this.getOutputManager ().clipImageOrPasteText (text);
}, "~S");
$_V(c$, "getClipboardText", 
function () {
if (!this.haveAccess (J.viewer.Viewer.ACCESS.ALL)) return "no";
try {
return this.getOutputManager ().getClipboardText ();
} catch (er) {
if (Clazz_exceptionOf (er, Error)) {
return J.i18n.GT._ ("clipboard is not accessible -- use signed applet");
} else {
throw er;
}
}
});
$_M(c$, "processWriteOrCapture", 
function (params) {
return this.getOutputManager ().processWriteOrCapture (params);
}, "java.util.Map");
$_M(c$, "createZip", 
function (fileName, type, scripts) {
var params =  new java.util.Hashtable ();
params.put ("fileName", fileName);
params.put ("type", type);
params.put ("text", this.getStateInfo ());
if (scripts != null) params.put ("scripts", scripts);
return this.getOutputManager ().outputToFile (params);
}, "~S,~S,~A");
$_V(c$, "outputToFile", 
function (params) {
return this.getOutputManager ().outputToFile (params);
}, "java.util.Map");
$_M(c$, "getOutputManager", 
function () {
if (this.outputManager != null) return this.outputManager;
return (this.outputManager = J.api.Interface.getOptionInterface (this.isJS && !this.isWebGL ? "viewer.OutputManagerJS" : "viewer.OutputManagerAwt")).setViewer (this, this.privateKey);
});
$_M(c$, "setSyncTarget", 
function (mode, TF) {
switch (mode) {
case 0:
this.statusManager.syncingMouse = TF;
break;
case 1:
this.statusManager.syncingScripts = TF;
break;
case 2:
this.statusManager.syncSend (TF ? "GET_GRAPHICS" : "SET_GRAPHICS_OFF", "*", 0);
if (Float.isNaN (this.transformManager.stereoDegrees)) this.setFloatProperty ("stereoDegrees", -5);
if (TF) {
this.setBooleanProperty ("_syncMouse", false);
this.setBooleanProperty ("_syncScript", false);
}return;
}
if (!this.statusManager.syncingScripts && !this.statusManager.syncingMouse) this.refresh (-1, "set sync");
}, "~N,~B");
$_V(c$, "syncScript", 
function (script, applet, port) {
this.getStateCreator ().syncScript (script, applet, port);
}, "~S,~S,~N");
$_M(c$, "getModelIndexFromId", 
function (id) {
return this.modelSet.getModelIndexFromId (id);
}, "~S");
$_M(c$, "setSyncDriver", 
function (mode) {
this.statusManager.setSyncDriver (mode);
}, "~N");
$_M(c$, "getPartialCharges", 
function () {
return this.modelSet.getPartialCharges ();
});
$_M(c$, "getAtomicPotentials", 
function (isMep, bsSelected, bsIgnore, fileName) {
var potentials =  Clazz_newFloatArray (this.getAtomCount (), 0);
var m = J.api.Interface.getOptionInterface ("quantum.MlpCalculation");
m.set (this);
var data = (fileName == null ? null : this.getFileAsString (fileName));
m.assignPotentials (this.modelSet.atoms, potentials, this.getSmartsMatch ("a", bsSelected), this.getSmartsMatch ("/noAromatic/[$(C=O),$(O=C),$(NC=O)]", bsSelected), bsIgnore, data);
return potentials;
}, "~B,JU.BS,JU.BS,~S");
$_M(c$, "setProteinType", 
function (type, bs) {
this.modelSet.setProteinType (bs == null ? this.getSelectionSet (false) : bs, type);
}, "J.constant.EnumStructure,JU.BS");
$_V(c$, "getBondPoint3f1", 
function (i) {
return this.modelSet.getBondAtom1 (i);
}, "~N");
$_V(c$, "getBondPoint3f2", 
function (i) {
return this.modelSet.getBondAtom2 (i);
}, "~N");
$_M(c$, "getVibration", 
function (atomIndex) {
return this.modelSet.getVibration (atomIndex, false);
}, "~N");
$_M(c$, "getVanderwaalsMar", 
function (i) {
return (this.defaultVdw === J.constant.EnumVdw.USER ? this.userVdwMars[i] : J.util.Elements.getVanderwaalsMar (i, this.defaultVdw));
}, "~N");
$_M(c$, "getVanderwaalsMarType", 
function (atomicAndIsotopeNumber, type) {
if (type == null) type = this.defaultVdw;
 else switch (type) {
case J.constant.EnumVdw.USER:
if (this.bsUserVdws == null) type = this.defaultVdw;
 else return this.userVdwMars[atomicAndIsotopeNumber & 127];
break;
case J.constant.EnumVdw.AUTO:
case J.constant.EnumVdw.JMOL:
case J.constant.EnumVdw.BABEL:
case J.constant.EnumVdw.RASMOL:
if (this.defaultVdw !== J.constant.EnumVdw.AUTO) type = this.defaultVdw;
break;
}
return (J.util.Elements.getVanderwaalsMar (atomicAndIsotopeNumber, type));
}, "~N,J.constant.EnumVdw");
$_M(c$, "setDefaultVdw", 
function (type) {
var vType = J.constant.EnumVdw.getVdwType (type);
if (vType == null) vType = J.constant.EnumVdw.AUTO;
this.setDefaultVdw (vType);
this.global.setS ("defaultVDW", this.getDefaultVdwNameOrData (-2147483648, null, null));
}, "~S");
$_M(c$, "setDefaultVdw", 
function (type) {
switch (type) {
case J.constant.EnumVdw.JMOL:
case J.constant.EnumVdw.BABEL:
case J.constant.EnumVdw.RASMOL:
case J.constant.EnumVdw.AUTO:
case J.constant.EnumVdw.USER:
break;
default:
type = J.constant.EnumVdw.JMOL;
}
if (type !== this.defaultVdw && type === J.constant.EnumVdw.USER && this.bsUserVdws == null) this.setUserVdw (this.defaultVdw);
this.defaultVdw = type;
}, "J.constant.EnumVdw");
$_M(c$, "setUserVdw", 
function (mode) {
this.userVdwMars =  Clazz_newIntArray (J.util.Elements.elementNumberMax, 0);
this.userVdws =  Clazz_newFloatArray (J.util.Elements.elementNumberMax, 0);
this.bsUserVdws =  new JU.BS ();
if (mode === J.constant.EnumVdw.USER) mode = J.constant.EnumVdw.JMOL;
for (var i = 1; i < J.util.Elements.elementNumberMax; i++) {
this.userVdwMars[i] = J.util.Elements.getVanderwaalsMar (i, mode);
this.userVdws[i] = this.userVdwMars[i] / 1000;
}
}, "J.constant.EnumVdw");
$_M(c$, "getDefaultVdwNameOrData", 
function (mode, type, bs) {
switch (mode) {
case -2147483648:
return this.defaultVdw.getVdwLabel ();
case 2147483647:
if ((bs = this.bsUserVdws) == null) return "";
type = J.constant.EnumVdw.USER;
break;
}
if (type == null || type === J.constant.EnumVdw.AUTO) type = this.defaultVdw;
if (type === J.constant.EnumVdw.USER && this.bsUserVdws == null) this.setUserVdw (this.defaultVdw);
return this.getDataManager ().getDefaultVdwNameOrData (type, bs);
}, "~N,J.constant.EnumVdw,JU.BS");
$_M(c$, "deleteAtoms", 
function (bs, fullModels) {
var atomIndex = (bs == null ? -1 : bs.nextSetBit (0));
if (atomIndex < 0) return 0;
this.clearModelDependentObjects ();
if (!fullModels) {
this.statusManager.modifySend (atomIndex, this.modelSet.atoms[atomIndex].modelIndex, 4);
this.modelSet.deleteAtoms (bs);
var n = this.selectionManager.deleteAtoms (bs);
this.setTainted (true);
this.statusManager.modifySend (atomIndex, this.modelSet.atoms[atomIndex].modelIndex, -4);
return n;
}var modelIndex = this.modelSet.atoms[atomIndex].modelIndex;
this.statusManager.modifySend (-1, modelIndex, 5);
this.setCurrentModelIndexClear (0, false);
this.animationManager.setAnimationOn (false);
var bsD0 = J.util.BSUtil.copy (this.getDeletedAtoms ());
var bsDeleted = this.modelSet.deleteModels (bs);
this.selectionManager.processDeletedModelAtoms (bsDeleted);
this.setAnimationRange (0, 0);
if (this.eval != null) this.eval.deleteAtomsInVariables (bsDeleted);
this.clearRepaintManager (-1);
this.animationManager.clear ();
this.animationManager.initializePointers (1);
this.setCurrentModelIndexClear (this.getModelCount () > 1 ? -1 : 0, this.getModelCount () > 1);
this.hoverAtomIndex = -1;
this.setFileLoadStatus (J.constant.EnumFileStatus.DELETED, null, null, null, null, null);
this.refreshMeasures (true);
if (bsD0 != null) bsDeleted.andNot (bsD0);
this.statusManager.modifySend (-1, modelIndex, -5);
return J.util.BSUtil.cardinalityOf (bsDeleted);
}, "JU.BS,~B");
$_M(c$, "deleteBonds", 
function (bsDeleted) {
this.modelSet.deleteBonds (bsDeleted, false);
}, "JU.BS");
$_M(c$, "deleteModelAtoms", 
function (firstAtomIndex, nAtoms, bsDeleted) {
this.selectionManager.deleteModelAtoms (bsDeleted);
J.util.BSUtil.deleteBits (this.getFrameOffsets (), bsDeleted);
this.setFrameOffsets (this.getFrameOffsets ());
this.getDataManager ().deleteModelAtoms (firstAtomIndex, nAtoms, bsDeleted);
}, "~N,~N,JU.BS");
$_M(c$, "getDeletedAtoms", 
function () {
return this.selectionManager.getDeletedAtoms ();
});
$_M(c$, "getQuaternionFrame", 
function () {
return this.global.quaternionFrame.charAt (this.global.quaternionFrame.length == 2 ? 1 : 0);
});
$_M(c$, "calculatePointGroup", 
function () {
return this.modelSet.calculatePointGroup (this.getSelectionSet (false));
});
$_M(c$, "getPointGroupInfo", 
function (atomExpression) {
return this.modelSet.getPointGroupInfo (this.getAtomBitSet (atomExpression));
}, "~O");
$_M(c$, "getPointGroupAsString", 
function (asDraw, type, index, scale) {
return this.modelSet.getPointGroupAsString (this.getSelectionSet (false), asDraw, type, index, scale);
}, "~B,~S,~N,~N");
$_M(c$, "loadImage", 
function (pathName, echoName) {
this.fileManager.loadImage (pathName, echoName);
}, "~S,~S");
$_M(c$, "loadImageData", 
function (image, nameOrError, echoName, sc) {
if (image == null) J.util.Logger.info (nameOrError);
if (echoName == null) {
this.setBackgroundImage ((image == null ? null : nameOrError), image);
} else {
this.loadShape (30);
this.setShapeProperty (30, "text", nameOrError);
if (image != null) this.setShapeProperty (30, "image", image);
}if (sc != null) {
sc.mustResumeEval = true;
this.eval.resumeEval (sc);
}}, "~O,~S,~S,J.script.ScriptContext");
$_M(c$, "cd", 
function (dir) {
if (dir == null) {
dir = ".";
} else if (dir.length == 0) {
this.setStringProperty ("defaultDirectory", "");
dir = ".";
}dir = this.fileManager.getDefaultDirectory (dir + (dir.equals ("=") ? "" : dir.endsWith ("/") ? "X.spt" : "/X.spt"));
if (dir.length > 0) this.setStringProperty ("defaultDirectory", dir);
var path = this.fileManager.getFilePath (dir + "/", true, false);
if (path.startsWith ("file:/")) J.viewer.FileManager.setLocalPath (this, dir, false);
return dir;
}, "~S");
$_M(c$, "setErrorMessage", 
function (errMsg, errMsgUntranslated) {
this.errorMessageUntranslated = errMsgUntranslated;
if (errMsg != null) this.eval.stopScriptThreads ();
return (this.errorMessage = errMsg);
}, "~S,~S");
$_V(c$, "getErrorMessage", 
function () {
return this.errorMessage;
});
$_V(c$, "getErrorMessageUn", 
function () {
return this.errorMessageUntranslated == null ? this.errorMessage : this.errorMessageUntranslated;
});
$_M(c$, "setShapeErrorState", 
function (shapeID, state) {
this.currentShapeID = shapeID;
this.currentShapeState = state;
}, "~N,~S");
$_M(c$, "getShapeErrorState", 
function () {
if (this.currentShapeID < 0) return "";
if (this.modelSet != null) this.shapeManager.releaseShape (this.currentShapeID);
this.clearRepaintManager (this.currentShapeID);
return J.viewer.JC.getShapeClassName (this.currentShapeID, false) + " " + this.currentShapeState;
});
$_M(c$, "handleError", 
function (er, doClear) {
try {
if (doClear) this.zapMsg ("" + er);
this.undoClear ();
if (J.util.Logger.getLogLevel () == 0) J.util.Logger.setLogLevel (4);
this.setCursor (0);
this.setBooleanProperty ("refreshing", true);
this.fileManager.setPathForAllFiles ("");
J.util.Logger.error ("viewer handling error condition: " + er + "  ");
if (!this.isJS) er.printStackTrace ();
this.notifyError ("Error", "doClear=" + doClear + "; " + er, "" + er);
} catch (e1) {
try {
J.util.Logger.error ("Could not notify error " + er + ": due to " + e1);
} catch (er2) {
}
}
}, "Error,~B");
$_M(c$, "getAtomicCharges", 
function () {
return this.modelSet.getAtomicCharges ();
});
$_M(c$, "getFunctions", 
function (isStatic) {
return (isStatic ? J.viewer.Viewer.staticFunctions : this.localFunctions);
}, "~B");
$_M(c$, "removeFunction", 
function (name) {
var $function = this.getFunction (name);
if ($function == null) return;
J.viewer.Viewer.staticFunctions.remove (name);
this.localFunctions.remove (name);
}, "~S");
$_M(c$, "getFunction", 
function (name) {
if (name == null) return null;
var $function = (J.viewer.Viewer.isStaticFunction (name) ? J.viewer.Viewer.staticFunctions : this.localFunctions).get (name);
return ($function == null || $function.geTokens () == null ? null : $function);
}, "~S");
c$.isStaticFunction = $_M(c$, "isStaticFunction", 
function (name) {
return name.startsWith ("static_");
}, "~S");
$_M(c$, "isFunction", 
function (name) {
return (J.viewer.Viewer.isStaticFunction (name) ? J.viewer.Viewer.staticFunctions : this.localFunctions).containsKey (name);
}, "~S");
$_M(c$, "clearFunctions", 
function () {
J.viewer.Viewer.staticFunctions.clear ();
this.localFunctions.clear ();
});
$_M(c$, "addFunction", 
function ($function) {
var name = $function.getName ();
(J.viewer.Viewer.isStaticFunction (name) ? J.viewer.Viewer.staticFunctions : this.localFunctions).put (name, $function);
}, "J.api.JmolScriptFunction");
$_M(c$, "getFunctionCalls", 
function (selectedFunction) {
return this.getStateCreator ().getFunctionCalls (selectedFunction);
}, "~S");
$_M(c$, "showMessage", 
function (s) {
if (!this.isPrintOnly) J.util.Logger.warn (s);
}, "~S");
$_M(c$, "getMoInfo", 
function (modelIndex) {
return this.modelSet.getMoInfo (modelIndex);
}, "~N");
$_M(c$, "checkPrivateKey", 
function (privateKey) {
return privateKey == this.privateKey;
}, "~N");
$_M(c$, "bindAction", 
function (desc, name) {
if (this.haveDisplay) this.actionManager.bindAction (desc, name);
}, "~S,~S");
$_M(c$, "unBindAction", 
function (desc, name) {
if (this.haveDisplay) this.actionManager.unbindAction (desc, name);
}, "~S,~S");
$_M(c$, "getMouseInfo", 
function () {
return (this.haveDisplay ? this.actionManager.getMouseInfo () : null);
});
$_M(c$, "getFrontPlane", 
function () {
return this.transformManager.getFrontPlane ();
});
$_M(c$, "getPlaneIntersection", 
function (type, plane, scale, flags) {
return this.modelSet.getPlaneIntersection (type, plane, scale, flags, this.animationManager.currentModelIndex);
}, "~N,JU.P4,~N,~N");
$_M(c$, "calculateStruts", 
function (bs1, bs2) {
return this.modelSet.calculateStruts (bs1 == null ? this.getSelectionSet (false) : bs1, bs2 == null ? this.getSelectionSet (false) : bs2);
}, "JU.BS,JU.BS");
$_M(c$, "getPreserveState", 
function () {
return (this.global.preserveState && this.scriptManager != null);
});
$_M(c$, "isKiosk", 
function () {
return this.$isKiosk;
});
$_M(c$, "hasFocus", 
function () {
return (this.haveDisplay && (this.$isKiosk || this.apiPlatform.hasFocus (this.display)));
});
$_M(c$, "setFocus", 
function () {
if (this.haveDisplay && !this.apiPlatform.hasFocus (this.display)) this.apiPlatform.requestFocusInWindow (this.display);
});
$_M(c$, "getMinimizer", 
function (createNew) {
if (this.minimizer == null && createNew) {
this.minimizer = J.api.Interface.getOptionInterface ("minimize.Minimizer");
this.minimizer.setProperty ("viewer", this);
}return this.minimizer;
}, "~B");
$_M(c$, "stopMinimization", 
function () {
if (this.minimizer != null) {
this.minimizer.setProperty ("stop", null);
}});
$_M(c$, "clearMinimization", 
function () {
if (this.minimizer != null) this.minimizer.setProperty ("clear", null);
});
$_M(c$, "getMinimizationInfo", 
function () {
return (this.minimizer == null ? "" : this.minimizer.getProperty ("log", 0));
});
$_M(c$, "checkMinimization", 
function () {
this.refreshMeasures (true);
if (!this.global.monitorEnergy) return;
this.minimize (0, 0, this.getModelUndeletedAtomsBitSet (-1), null, 0, false, true, false);
this.echoMessage (this.getParameter ("_minimizationForceField") + " Energy = " + this.getParameter ("_minimizationEnergy"));
});
$_M(c$, "minimize", 
function (steps, crit, bsSelected, bsFixed, rangeFixed, addHydrogen, isSilent, isLoad2D) {
var ff = this.global.forceField;
var bsInFrame = this.getModelUndeletedAtomsBitSetBs (this.getVisibleFramesBitSet ());
if (bsSelected == null) bsSelected = this.getModelUndeletedAtomsBitSet (this.getVisibleFramesBitSet ().length () - 1);
 else bsSelected.and (bsInFrame);
if (rangeFixed <= 0) rangeFixed = 5.0;
var bsMotionFixed = J.util.BSUtil.copy (bsFixed == null ? this.selectionManager.getMotionFixedAtoms () : bsFixed);
var haveFixed = (bsMotionFixed.cardinality () > 0);
if (haveFixed) bsSelected.andNot (bsMotionFixed);
var bsNearby = this.getAtomsWithinRadius (rangeFixed, bsSelected, true, null);
bsNearby.andNot (bsSelected);
if (haveFixed) {
bsMotionFixed.and (bsNearby);
} else {
bsMotionFixed = bsNearby;
}bsMotionFixed.and (bsInFrame);
if (addHydrogen) bsSelected.or (this.addHydrogens (bsSelected, isLoad2D, isSilent));
if (bsSelected.cardinality () > 200) {
J.util.Logger.error ("Too many atoms for minimization (>200)");
return;
}try {
if (!isSilent) J.util.Logger.info ("Minimizing " + bsSelected.cardinality () + " atoms");
this.getMinimizer (true).minimize (steps, crit, bsSelected, bsMotionFixed, haveFixed, isSilent, ff);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
J.util.Logger.error ("Minimization error: " + e.toString ());
if (!this.isJS) e.printStackTrace ();
} else {
throw e;
}
}
}, "~N,~N,JU.BS,JU.BS,~N,~B,~B,~B");
$_M(c$, "setMotionFixedAtoms", 
function (bs) {
this.selectionManager.setMotionFixedAtoms (bs);
}, "JU.BS");
$_M(c$, "getMotionFixedAtoms", 
function () {
return this.selectionManager.getMotionFixedAtoms ();
});
$_M(c$, "rotateArcBall", 
function (x, y, factor) {
this.transformManager.rotateArcBall (x, y, factor);
this.refresh (2, this.statusManager.syncingMouse ? "Mouse: rotateArcBall " + x + " " + y + " " + factor : "");
}, "~N,~N,~N");
$_M(c$, "getAtomicPropertyState", 
function (commands, type, bs, name, data) {
this.getStateCreator ().getAtomicPropertyStateBuffer (commands, type, bs, name, data);
}, "JU.SB,~N,JU.BS,~S,~A");
$_M(c$, "getCenterAndPoints", 
function (atomSets, addCenter) {
return this.modelSet.getCenterAndPoints (atomSets, addCenter);
}, "JU.List,~B");
$_M(c$, "writeFileData", 
function (fileName, type, modelIndex, parameters) {
return this.getOutputManager ().writeFileData (fileName, type, modelIndex, parameters);
}, "~S,~S,~N,~A");
$_M(c$, "getPdbData", 
function (modelIndex, type, parameters) {
return this.modelSet.getPdbData (modelIndex, type, this.getSelectionSet (false), parameters, null);
}, "~N,~S,~A");
$_M(c$, "getGroupsWithin", 
function (nResidues, bs) {
return this.modelSet.getGroupsWithin (nResidues, bs);
}, "~N,JU.BS");
$_M(c$, "getExecutor", 
function () {
if (this.executor != null || J.viewer.Viewer.nProcessors < 2) return this.executor;
try {
this.executor = (J.api.Interface.getOptionInterface ("parallel.ScriptParallelProcessor")).getExecutor ();
} catch (e$$) {
if (Clazz_exceptionOf (e$$, Exception)) {
var e = e$$;
{
this.executor = null;
}
} else if (Clazz_exceptionOf (e$$, Error)) {
var er = e$$;
{
this.executor = null;
}
} else {
throw e$$;
}
}
if (this.executor == null) J.util.Logger.error ("parallel processing is not available");
return this.executor;
});
$_M(c$, "getShapeInfo", 
function () {
return this.shapeManager.getShapeInfo ();
});
$_M(c$, "togglePickingLabel", 
function (bs) {
if (bs == null) bs = this.getSelectionSet (false);
this.loadShape (5);
this.shapeManager.setShapePropertyBs (5, "toggleLabel", null, bs);
}, "JU.BS");
$_M(c$, "loadShape", 
function (shapeID) {
this.shapeManager.loadShape (shapeID);
}, "~N");
$_M(c$, "setShapeSize", 
function (shapeID, mad, bsSelected) {
if (bsSelected == null) bsSelected = this.getSelectionSet (false);
this.shapeManager.setShapeSizeBs (shapeID, mad, null, bsSelected);
}, "~N,~N,JU.BS");
$_M(c$, "setShapeSizeRD", 
function (shapeID, rd, bsAtoms) {
this.shapeManager.setShapeSizeBs (shapeID, 0, rd, bsAtoms);
}, "~N,J.atomdata.RadiusData,JU.BS");
$_M(c$, "setShapeProperty", 
function (shapeID, propertyName, value) {
if (shapeID < 0) return;
this.shapeManager.setShapePropertyBs (shapeID, propertyName, value, null);
}, "~N,~S,~O");
$_M(c$, "getShapeProperty", 
function (shapeType, propertyName) {
return this.shapeManager.getShapePropertyIndex (shapeType, propertyName, -2147483648);
}, "~N,~S");
$_M(c$, "getShapePropertyData", 
function (shapeType, propertyName, data) {
return this.shapeManager.getShapePropertyData (shapeType, propertyName, data);
}, "~N,~S,~A");
$_M(c$, "getShapePropertyIndex", 
function (shapeType, propertyName, index) {
return this.shapeManager.getShapePropertyIndex (shapeType, propertyName, index);
}, "~N,~S,~N");
$_M(c$, "getShapePropertyAsInt", 
function (shapeID, propertyName) {
var value = this.getShapeProperty (shapeID, propertyName);
return value == null || !(Clazz_instanceOf (value, Integer)) ? -2147483648 : (value).intValue ();
}, "~N,~S");
$_M(c$, "setModelVisibility", 
function () {
if (this.shapeManager == null) return;
this.shapeManager.setModelVisibility ();
});
$_M(c$, "resetShapes", 
function (andCreateNew) {
this.shapeManager.resetShapes ();
if (andCreateNew) {
this.shapeManager.loadDefaultShapes (this.modelSet);
this.clearRepaintManager (-1);
}}, "~B");
$_M(c$, "setAtomLabel", 
function (value, i) {
this.shapeManager.setAtomLabel (value, i);
}, "~S,~N");
$_M(c$, "deleteShapeAtoms", 
function (value, bs) {
this.shapeManager.deleteShapeAtoms (value, bs);
}, "~A,JU.BS");
$_M(c$, "resetBioshapes", 
function (bsAllAtoms) {
this.shapeManager.resetBioshapes (bsAllAtoms);
}, "JU.BS");
$_M(c$, "getAtomShapeValue", 
function (tok, group, atomIndex) {
return this.shapeManager.getAtomShapeValue (tok, group, atomIndex);
}, "~N,J.modelset.Group,~N");
$_M(c$, "mergeShapes", 
function (newShapes) {
this.shapeManager.mergeShapes (newShapes);
}, "~A");
$_M(c$, "getShapeManager", 
function () {
return this.shapeManager;
});
$_M(c$, "setParallel", 
function (TF) {
return (this.$isParallel = this.global.multiProcessor && TF);
}, "~B");
$_M(c$, "isParallel", 
function () {
return this.global.multiProcessor && this.$isParallel;
});
$_M(c$, "getRenderableBitSet", 
function () {
return this.shapeManager.getRenderableBitSet ();
});
$_M(c$, "setAtomPickingOption", 
function (option) {
if (this.haveDisplay) this.actionManager.setAtomPickingOption (option);
}, "~S");
$_M(c$, "setBondPickingOption", 
function (option) {
if (this.haveDisplay) this.actionManager.setBondPickingOption (option);
}, "~S");
$_M(c$, "undoClear", 
function () {
this.actionStates.clear ();
this.actionStatesRedo.clear ();
});
$_M(c$, "undoMoveAction", 
function (action, n) {
this.getStateCreator ().undoMoveAction (action, n);
}, "~N,~N");
$_M(c$, "undoMoveActionClear", 
function (taintedAtom, type, clearRedo) {
if (!this.global.preserveState) return;
this.getStateCreator ().undoMoveActionClear (taintedAtom, type, clearRedo);
}, "~N,~N,~B");
$_M(c$, "assignBond", 
function (bondIndex, type) {
try {
var bsAtoms = this.modelSet.setBondOrder (bondIndex, type);
if (bsAtoms == null || type == '0') this.refresh (3, "setBondOrder");
 else this.addHydrogens (bsAtoms, false, true);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
J.util.Logger.error ("assignBond failed");
} else {
throw e;
}
}
}, "~N,~S");
$_M(c$, "assignAtom", 
function (atomIndex, pt, type) {
if (type.equals ("X")) this.setRotateBondIndex (-1);
if (this.modelSet.atoms[atomIndex].modelIndex != this.modelSet.modelCount - 1) return;
this.clearModelDependentObjects ();
if (pt == null) {
this.statusManager.modifySend (atomIndex, this.modelSet.atoms[atomIndex].modelIndex, 1);
var atomCount = this.modelSet.getAtomCount ();
this.modelSet.assignAtom (atomIndex, type, true);
if (!JU.PT.isOneOf (type, ";Mi;Pl;X;")) this.modelSet.setAtomNamesAndNumbers (atomIndex, -atomCount, null);
this.statusManager.modifySend (atomIndex, this.modelSet.atoms[atomIndex].modelIndex, -1);
this.refresh (3, "assignAtom");
return;
}var atom = this.modelSet.atoms[atomIndex];
var bs = J.util.BSUtil.newAndSetBit (atomIndex);
var pts = [pt];
var vConnections =  new JU.List ();
vConnections.addLast (atom);
var modelIndex = atom.modelIndex;
this.statusManager.modifySend (atomIndex, modelIndex, 3);
try {
bs = this.addHydrogensInline (bs, vConnections, pts);
atomIndex = bs.nextSetBit (0);
this.modelSet.assignAtom (atomIndex, type, false);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
this.modelSet.setAtomNamesAndNumbers (atomIndex, -1, null);
this.statusManager.modifySend (atomIndex, modelIndex, -3);
}, "~N,JU.P3,~S");
$_M(c$, "assignConnect", 
function (index, index2) {
this.clearModelDependentObjects ();
var connections = JU.AU.newFloat2 (1);
connections[0] = [index, index2];
var modelIndex = this.modelSet.atoms[index].modelIndex;
this.statusManager.modifySend (index, modelIndex, 2);
this.modelSet.connect (connections);
this.modelSet.assignAtom (index, ".", true);
this.modelSet.assignAtom (index2, ".", true);
this.statusManager.modifySend (index, modelIndex, -2);
this.refresh (3, "assignConnect");
}, "~N,~N");
$_M(c$, "moveAtomWithHydrogens", 
function (atomIndex, deltaX, deltaY, deltaZ, bsAtoms) {
this.stopMinimization ();
if (bsAtoms == null) {
var atom = this.modelSet.atoms[atomIndex];
bsAtoms = J.util.BSUtil.newAndSetBit (atomIndex);
var bonds = atom.getBonds ();
if (bonds != null) for (var i = 0; i < bonds.length; i++) {
var atom2 = bonds[i].getOtherAtom (atom);
if (atom2.getElementNumber () == 1) bsAtoms.set (atom2.index);
}
}this.moveSelected (deltaX, deltaY, deltaZ, -2147483648, -2147483648, bsAtoms, true, true);
}, "~N,~N,~N,~N,JU.BS");
$_M(c$, "isAtomPDB", 
function (i) {
return this.modelSet.isAtomPDB (i);
}, "~N");
$_M(c$, "isModelPDB", 
function (i) {
return this.modelSet.models[i].isBioModel;
}, "~N");
$_M(c$, "isAtomAssignable", 
function (i) {
return this.modelSet.isAtomAssignable (i);
}, "~N");
$_V(c$, "deleteMeasurement", 
function (i) {
this.setShapeProperty (6, "delete", Integer.$valueOf (i));
}, "~N");
$_M(c$, "haveModelKit", 
function () {
return this.modelSet.haveModelKit ();
});
$_M(c$, "getModelKitStateBitSet", 
function (bs, bsDeleted) {
return this.modelSet.getModelKitStateBitset (bs, bsDeleted);
}, "JU.BS,JU.BS");
$_M(c$, "getSmiles", 
function (index1, index2, bsSelected, isBioSmiles, allowUnmatchedRings, addCrossLinks, addComment) {
var atoms = this.modelSet.atoms;
if (bsSelected == null) {
if (index1 < 0 || index2 < 0) {
bsSelected = this.getSelectionSet (true);
} else {
if (isBioSmiles) {
if (index1 > index2) {
var i = index1;
index1 = index2;
index2 = i;
}index1 = atoms[index1].getGroup ().firstAtomIndex;
index2 = atoms[index2].getGroup ().lastAtomIndex;
}bsSelected =  new JU.BS ();
bsSelected.setBits (index1, index2 + 1);
}}var comment = (addComment ? J.viewer.Viewer.getJmolVersion () + " " + this.getModelName (this.getCurrentModelIndex ()) : null);
return this.getSmilesMatcher ().getSmiles (atoms, this.getAtomCount (), bsSelected, isBioSmiles, allowUnmatchedRings, addCrossLinks, comment);
}, "~N,~N,JU.BS,~B,~B,~B,~B");
$_M(c$, "connect", 
function (connections) {
this.modelSet.connect (connections);
}, "~A");
$_M(c$, "prompt", 
function (label, data, list, asButtons) {
return (this.$isKiosk ? "null" : this.apiPlatform.prompt (label, data, list, asButtons));
}, "~S,~S,~A,~B");
$_M(c$, "getColorEncoder", 
function (colorScheme) {
return this.colorManager.getColorEncoder (colorScheme);
}, "~S");
$_M(c$, "displayBonds", 
function (bs, isDisplay) {
this.modelSet.displayBonds (bs, isDisplay);
}, "J.modelset.Bond.BondSet,~B");
$_M(c$, "getModelAtomProperty", 
function (atom, text) {
return this.modelSet.getModelAtomProperty (atom, text);
}, "J.modelset.Atom,~S");
$_M(c$, "setStateScriptVersion", 
function (version) {
if (version != null) {
var tokens = JU.PT.getTokens (version.$replace ('.', ' ').$replace ('_', ' '));
try {
var main = JU.PT.parseInt (tokens[0]);
var sub = JU.PT.parseInt (tokens[1]);
var minor = JU.PT.parseInt (tokens[2]);
if (minor == -2147483648) minor = 0;
if (main != -2147483648 && sub != -2147483648) {
this.stateScriptVersionInt = main * 10000 + sub * 100 + minor;
this.global.legacyAutoBonding = (this.stateScriptVersionInt < 110924);
this.global.legacyHAddition = (this.stateScriptVersionInt < 130117);
return;
}} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
}this.setBooleanProperty ("legacyautobonding", false);
this.stateScriptVersionInt = 2147483647;
}, "~S");
$_M(c$, "initializeExporter", 
function (params) {
var isJS = params.get ("type").equals ("JS");
var cname;
if (isJS) {
if (this.jsExporter3D != null) {
this.jsExporter3D.initializeOutput (this, this.privateKey, this.gdata, params);
return this.jsExporter3D;
}cname = "J.exportjs.Export3D";
} else {
var fileName = params.get ("fileName");
var fullPath = params.get ("fullPath");
var out = this.getOutputChannel (fileName, fullPath);
if (out == null) return null;
params.put ("outputChannel", out);
cname = "J.export.Export3D";
}var export3D = null;
try {
var export3Dclass = Class.forName (cname);
export3D = export3Dclass.newInstance ();
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return null;
} else {
throw e;
}
}
var exporter = export3D.initializeExporter (this, this.privateKey, this.gdata, params);
if (isJS && exporter != null) this.jsExporter3D = export3D;
return (exporter == null ? null : export3D);
}, "java.util.Map");
$_M(c$, "getMouseEnabled", 
function () {
return this.refreshing && !this.creatingImage;
});
$_M(c$, "setZslabPoint", 
function (pt) {
this.transformManager.setZslabPoint (pt);
}, "JU.P3");
$_V(c$, "calcAtomsMinMax", 
function (bs, boxInfo) {
this.modelSet.calcAtomsMinMax (bs, boxInfo);
}, "JU.BS,J.util.BoxInfo");
$_M(c$, "getObjectMap", 
function (map, c) {
switch (c) {
case '{':
if (this.getScriptManager () != null) {
var m = map;
var sets = this.eval.getDefinedAtomSets ();
if (sets != null) m.putAll (sets);
J.script.T.getTokensType (m, 3145728);
}return;
case '$':
case '0':
this.shapeManager.getObjectMap (map, c == '$');
return;
}
}, "java.util.Map,~S");
$_M(c$, "getPdbBondInfo", 
function (group3) {
if (this.htPdbBondInfo == null) this.htPdbBondInfo =  new java.util.Hashtable ();
var info = this.htPdbBondInfo.get (group3);
if (info != null) return info;
info = J.viewer.JC.getPdbBondInfo (J.modelset.Group.lookupGroupID (group3), this.global.legacyHAddition);
this.htPdbBondInfo.put (group3, info);
return info;
}, "~S");
$_M(c$, "setPicked", 
function (iAtom) {
this.global.setPicked (iAtom);
}, "~N");
$_V(c$, "runScript", 
function (script) {
var outputBuffer =  new JU.SB ();
try {
if (this.getScriptManager () == null) return null;
this.eval.runScriptBuffer (script, outputBuffer);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return this.eval.getErrorMessage ();
} else {
throw e;
}
}
return outputBuffer.toString ();
}, "~S");
$_M(c$, "allowSpecAtom", 
function () {
return this.modelSet.allowSpecAtom ();
});
$_M(c$, "setFrameDelayMs", 
function (millis) {
this.modelSet.setFrameDelayMs (millis, this.getVisibleFramesBitSet ());
}, "~N");
$_M(c$, "getFrameDelayMs", 
function (i) {
return this.modelSet.getFrameDelayMs (i);
}, "~N");
$_M(c$, "getBaseModelBitSet", 
function () {
return this.modelSet.getModelAtomBitSetIncludingDeleted (this.getJDXBaseModelIndex (this.getCurrentModelIndex ()), true);
});
$_M(c$, "getTimeouts", 
function () {
return this.timeouts;
});
$_M(c$, "clearTimeouts", 
function () {
if (this.timeouts != null) J.thread.TimeoutThread.clear (this.timeouts);
});
$_M(c$, "setTimeout", 
function (name, mSec, script) {
if (!this.haveDisplay || this.isHeadless () || this.autoExit) return;
if (name == null) {
this.clearTimeouts ();
return;
}if (this.timeouts == null) {
this.timeouts =  new java.util.Hashtable ();
}J.thread.TimeoutThread.setTimeout (this, this.timeouts, name, mSec, script);
}, "~S,~N,~S");
$_M(c$, "triggerTimeout", 
function (name) {
if (!this.haveDisplay || this.timeouts == null) return;
J.thread.TimeoutThread.trigger (this.timeouts, name);
}, "~S");
$_M(c$, "clearTimeout", 
function (name) {
this.setTimeout (name, 0, null);
}, "~S");
$_M(c$, "showTimeout", 
function (name) {
return (this.haveDisplay ? J.thread.TimeoutThread.showTimeout (this.timeouts, name) : "");
}, "~S");
$_M(c$, "calculatePartialCharges", 
function (bsSelected) {
if (bsSelected == null || bsSelected.cardinality () == 0) bsSelected = this.getModelUndeletedAtomsBitSetBs (this.getVisibleFramesBitSet ());
this.getMinimizer (true).calculatePartialCharges (this.modelSet.bonds, this.modelSet.bondCount, this.modelSet.atoms, bsSelected);
}, "JU.BS");
$_M(c$, "setCurrentModelID", 
function (id) {
var modelIndex = this.getCurrentModelIndex ();
if (modelIndex >= 0) this.modelSet.setModelAuxiliaryInfo (modelIndex, "modelID", id);
}, "~S");
$_M(c$, "setCentroid", 
function (bs, minmax) {
this.modelSet.setCentroid (bs, minmax);
}, "JU.BS,~A");
$_M(c$, "getPathForAllFiles", 
function () {
return this.fileManager.getPathForAllFiles ();
});
$_M(c$, "cacheGet", 
function (key) {
return this.fileManager.cacheGet (key, false);
}, "~S");
$_M(c$, "cacheClear", 
function () {
this.fileManager.cacheClear ();
});
$_V(c$, "cachePut", 
function (key, data) {
J.util.Logger.info ("Viewer cachePut " + key);
this.fileManager.cachePut (key, data);
}, "~S,~O");
$_V(c$, "cacheFileByName", 
function (fileName, isAdd) {
return this.fileManager.cacheFileByNameAdd (fileName, isAdd);
}, "~S,~B");
$_M(c$, "cacheList", 
function () {
return this.fileManager.cacheList ();
});
$_M(c$, "clearThreads", 
function () {
if (this.eval != null) this.eval.stopScriptThreads ();
this.stopMinimization ();
this.setVibrationOff ();
this.setSpinOn (false);
this.setNavOn (false);
this.setAnimationOn (false);
});
$_M(c$, "getEvalContextAndHoldQueue", 
function (jse) {
if (jse == null || !this.isJS) return null;
jse.pushContextDown ("getEvalContextAndHoldQueue");
var sc = jse.getThisContext ();
var sc0 = sc;
while (sc0 != null) {
sc0.mustResumeEval = true;
sc0 = sc0.parentContext;
}
sc.isJSThread = true;
this.queueOnHold = true;
return sc;
}, "J.api.JmolScriptEvaluator");
$_M(c$, "checkInheritedShapes", 
function () {
this.shapeManager.checkInheritedShapes ();
});
$_V(c$, "resizeInnerPanel", 
function (width, height) {
if (this.autoExit || !this.haveDisplay) {
this.setScreenDimension (width, height);
return this.dimScreen;
}return this.statusManager.resizeInnerPanel (width, height);
}, "~N,~N");
$_M(c$, "getFontLineShapeState", 
function (s, myType, tickInfos) {
return this.getStateCreator ().getFontLineShapeState (s, myType, tickInfos);
}, "~S,~S,~A");
$_M(c$, "getShapeSetState", 
function (atomShape, shape, monomerCount, monomers, bsSizeDefault, temp, temp2) {
this.getStateCreator ().getShapeSetState (atomShape, shape, monomerCount, monomers, bsSizeDefault, temp, temp2);
}, "J.shape.AtomShape,J.shape.Shape,~N,~A,JU.BS,java.util.Map,java.util.Map");
$_M(c$, "getMeasurementState", 
function (measures, mList, measurementCount, font3d, ti) {
return this.getStateCreator ().getMeasurementState (measures, mList, measurementCount, font3d, ti);
}, "J.shape.Measures,JU.List,~N,javajs.awt.Font,J.modelset.TickInfo");
$_M(c$, "getBondState", 
function (shape, bsOrderSet, reportAll) {
return this.getStateCreator ().getBondState (shape, bsOrderSet, reportAll);
}, "J.shape.Shape,JU.BS,~B");
$_M(c$, "getAtomShapeSetState", 
function (shape, shapes) {
return this.getStateCreator ().getAtomShapeSetState (shape, shapes);
}, "J.shape.Shape,~A");
$_M(c$, "getShapeState", 
function (shape) {
return this.getStateCreator ().getShapeState (shape);
}, "J.shape.Shape");
$_M(c$, "getAtomShapeState", 
function (shape) {
return this.getStateCreator ().getAtomShapeState (shape);
}, "J.shape.AtomShape");
$_M(c$, "getDefaultPropertyParam", 
function (propertyID) {
return this.getPropertyManager ().getDefaultPropertyParam (propertyID);
}, "~N");
$_M(c$, "getPropertyNumber", 
function (name) {
return this.getPropertyManager ().getPropertyNumber (name);
}, "~S");
$_M(c$, "checkPropertyParameter", 
function (name) {
return this.getPropertyManager ().checkPropertyParameter (name);
}, "~S");
$_M(c$, "extractProperty", 
function (property, args, pt) {
return this.getPropertyManager ().extractProperty (property, args, pt);
}, "~O,~A,~N");
$_M(c$, "addHydrogens", 
function (bsAtoms, is2DLoad, isSilent) {
var doAll = (bsAtoms == null);
if (bsAtoms == null) bsAtoms = this.getModelUndeletedAtomsBitSet (this.getVisibleFramesBitSet ().length () - 1);
var bsB =  new JU.BS ();
if (bsAtoms.cardinality () == 0) return bsB;
var modelIndex = this.modelSet.atoms[bsAtoms.nextSetBit (0)].modelIndex;
if (modelIndex != this.modelSet.modelCount - 1) return bsB;
var vConnections =  new JU.List ();
var pts = this.getAdditionalHydrogens (bsAtoms, doAll, false, vConnections);
var wasAppendNew = false;
wasAppendNew = this.global.appendNew;
if (pts.length > 0) {
this.clearModelDependentObjects ();
try {
bsB = (is2DLoad ? this.modelSet.addHydrogens (vConnections, pts) : this.addHydrogensInline (bsAtoms, vConnections, pts));
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
System.out.println (e.toString ());
} else {
throw e;
}
}
if (wasAppendNew) this.setAppendNew (true);
}if (!isSilent) this.scriptStatus (J.i18n.GT._ ("{0} hydrogens added", pts.length));
return bsB;
}, "JU.BS,~B,~B");
$_M(c$, "addHydrogensInline", 
function (bsAtoms, vConnections, pts) {
if (this.getScriptManager () == null) return null;
return this.eval.addHydrogensInline (bsAtoms, vConnections, pts);
}, "JU.BS,JU.List,~A");
$_V(c$, "evalFunctionFloat", 
function (func, params, values) {
return (this.getScriptManager () == null ? 0 : this.eval.evalFunctionFloat (func, params, values));
}, "~O,~O,~A");
$_M(c$, "evalParallel", 
function (context, shapeManager) {
this.displayLoadErrors = false;
var isOK = this.getScriptManager () != null && this.eval.evaluateParallel (context, (shapeManager == null ? this.shapeManager : shapeManager));
this.displayLoadErrors = true;
return isOK;
}, "J.script.ScriptContext,J.viewer.ShapeManager");
$_V(c$, "evaluateExpression", 
function (stringOrTokens) {
if (this.getScriptManager () == null) return null;
return this.eval.evaluateExpression (stringOrTokens, false);
}, "~O");
$_M(c$, "evaluateExpressionAsVariable", 
function (stringOrTokens) {
if (this.getScriptManager () == null) return null;
return this.eval.evaluateExpression (stringOrTokens, true);
}, "~O");
$_M(c$, "getAtomBitSet", 
function (atomExpression) {
if (Clazz_instanceOf (atomExpression, JU.BS)) return atomExpression;
this.getScriptManager ();
return this.getAtomBitSetEval (this.eval, atomExpression);
}, "~O");
$_M(c$, "getAtomBitSetVector", 
function (atomExpression) {
if (this.getScriptManager () == null) return null;
return this.eval.getAtomBitSetVector (this.getAtomCount (), atomExpression);
}, "~O");
$_M(c$, "getContextVariables", 
function () {
if (this.getScriptManager () == null) return null;
return this.eval.getContextVariables ();
});
$_M(c$, "getScriptContext", 
function (why) {
return (this.getScriptManager () == null ? null : this.eval.getScriptContext (why));
}, "~S");
$_V(c$, "getAtomDefs", 
function (names) {
return this.getStateCreator ().getAtomDefs (names);
}, "java.util.Map");
$_M(c$, "createModels", 
function (n) {
this.modelSet.createModels (n);
}, "~N");
$_M(c$, "setCGO", 
function (info) {
this.shapeManager.loadShape (23);
this.shapeManager.setShapePropertyBs (23, "setCGO", info, null);
}, "JU.List");
$_M(c$, "setFrame", 
function (i) {
this.animationManager.setFrame (i - 1);
}, "~N");
$_M(c$, "movePyMOL", 
function (eval, floatSecondsTotal, pymolView) {
this.transformManager.moveToPyMOL (eval, floatSecondsTotal, pymolView);
return true;
}, "J.api.JmolScriptEvaluator,~N,~A");
$_M(c$, "getCamera", 
function () {
return this.transformManager.camera;
});
$_M(c$, "setModelSet", 
function (modelSet) {
this.modelSet = this.modelManager.modelSet = modelSet;
}, "J.modelset.ModelSet");
$_M(c$, "setObjectProp", 
function (id, tokCommand) {
this.getScriptManager ();
if (id == null) id = "*";
return (this.eval == null ? null : this.eval.setObjectPropSafe (id, tokCommand, -1));
}, "~S,~N");
$_M(c$, "getSceneList", 
function () {
try {
return this.getModelSetAuxiliaryInfoValue ("scenes");
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return null;
} else {
throw e;
}
}
});
$_M(c$, "setBondParameters", 
function (modelIndex, i, bsBonds, rad, pymolValence, argb, trans) {
this.modelSet.setBondParametersBS (modelIndex, i, bsBonds, rad, pymolValence, argb, trans);
}, "~N,~N,JU.BS,~N,~N,~N,~N");
$_M(c$, "getDihedralMap", 
function (atoms) {
return this.modelSet.getDihedralMap (atoms);
}, "~A");
$_M(c$, "setDihedrals", 
function (dihedralList, bsBranches, rate) {
if (bsBranches == null) bsBranches = this.getBsBranches (dihedralList);
this.modelSet.setDihedrals (dihedralList, bsBranches, rate);
}, "~A,~A,~N");
$_M(c$, "getBsBranches", 
function (dihedralList) {
return this.modelSet.getBsBranches (dihedralList);
}, "~A");
$_M(c$, "getChainID", 
function (id) {
var iboxed = this.chainMap.get (id);
if (iboxed != null) return iboxed.intValue ();
var i = id.charCodeAt (0);
if (id.length > 1) {
i = 256 + this.chainList.size ();
this.chainList.addLast (id);
}iboxed = Integer.$valueOf (i);
this.chainMap.put (iboxed, id);
this.chainMap.put (id, iboxed);
return i;
}, "~S");
$_M(c$, "getChainIDStr", 
function (id) {
return this.chainMap.get (Integer.$valueOf (id));
}, "~N");
$_M(c$, "getScriptQueueInfo", 
function () {
return (this.scriptManager != null && this.scriptManager.isQueueProcessing () ? Boolean.TRUE : Boolean.FALSE);
});
$_M(c$, "getNMRCalculation", 
function () {
return (this.nmrCalculation == null ? (this.nmrCalculation = J.api.Interface.getOptionInterface ("quantum.NMRCalculation")).setViewer (this) : this.nmrCalculation);
});
$_M(c$, "getDistanceUnits", 
function (s) {
if (s == null) s = this.getDefaultMeasurementLabel (2);
var pt = s.indexOf ("//");
return (pt < 0 ? this.getMeasureDistanceUnits () : s.substring (pt + 2));
}, "~S");
$_M(c$, "calculateFormalCharges", 
function (bs) {
if (bs == null) bs = this.getSelectionSet (false);
return this.modelSet.fixFormalCharges (bs);
}, "JU.BS");
$_M(c$, "cachePngFiles", 
function () {
return (!this.getTestFlag (1));
});
$_M(c$, "setModulation", 
function (isOn, t1, t2, isThread) {
var t = (t1 == null ? 2147483647 : t1[0]);
if (t2 == 2147483647) {
if (!isThread) this.animationManager.setModulationPlay (2147483647, 0);
if (t1 != null) this.global.setI ("_modt", t1[0]);
this.modelSet.setModulation (this.getSelectionSet (false), isOn, t);
} else {
this.animationManager.setModulationPlay (t, t2);
}this.refreshMeasures (true);
}, "~B,~A,~N,~B");
$_M(c$, "setModulationFps", 
function (fps) {
this.animationManager.setModulationFps (fps);
}, "~N");
$_M(c$, "checkInMotion", 
function (state) {
switch (state) {
case 0:
this.setTimeout ("_SET_IN_MOTION_", 0, null);
break;
case 1:
if (!this.inMotion) this.setTimeout ("_SET_IN_MOTION_", this.global.hoverDelayMs * 2, "!setInMotion");
break;
case 2:
this.setInMotion (true);
this.refresh (3, "timeoutThread set in motion");
break;
}
}, "~N");
$_M(c$, "checkMotionRendering", 
function (tok) {
if (!this.getInMotion (true) && !this.transformManager.spinOn && !this.transformManager.vibrationOn && !this.animationManager.animationOn) return true;
if (this.global.wireframeRotation) return false;
var n = 0;
switch (tok) {
case 1678770178:
case 1141899265:
n = 2;
break;
case 1113198596:
n = 3;
break;
case 1113198597:
n = 4;
break;
case 1113200642:
n = 5;
break;
case 1073742018:
n = 6;
break;
case 603979967:
n = 7;
break;
case 603979786:
n = 8;
break;
}
return this.global.platformSpeed >= n;
}, "~N");
$_M(c$, "openExportChannel", 
function (privateKey, fileName, asWriter) {
return this.getOutputManager ().openOutputChannel (privateKey, fileName, asWriter, false);
}, "~N,~S,~B");
$_V(c$, "log", 
function (data) {
if (data != null) this.getOutputManager ().logToFile (data);
}, "~S");
$_M(c$, "getLogFileName", 
function () {
return (this.logFileName == null ? "" : this.logFileName);
});
$_M(c$, "getCommands", 
function (htDefine, htMore, select) {
return this.getStateCreator ().getCommands (htDefine, htMore, select);
}, "java.util.Map,java.util.Map,~S");
$_M(c$, "allowCapture", 
function () {
return !this.$isApplet || this.$isSignedApplet;
});
$_M(c$, "getMP", 
function () {
return (J.api.Interface.getOptionInterface ("modelset.MeasurementPending")).set (this.modelSet);
});
$_V(c$, "getApplet", 
function () {
return this.applet;
});
Clazz_pu$h ();
c$ = Clazz_declareType (J.viewer.Viewer, "ACCESS", Enum);
Clazz_defineEnumConstant (c$, "NONE", 0, []);
Clazz_defineEnumConstant (c$, "READSPT", 1, []);
Clazz_defineEnumConstant (c$, "ALL", 2, []);
c$ = Clazz_p0p ();
Clazz_defineStatics (c$,
"jsDocumentBase", "");
c$.strJavaVendor = c$.prototype.strJavaVendor = System.getProperty ("java.vendor", "j2s");
c$.strOSName = c$.prototype.strOSName = System.getProperty ("os.name", "j2s");
c$.strJavaVersion = c$.prototype.strJavaVersion = System.getProperty ("java.version", "0.0");
Clazz_defineStatics (c$,
"version_date", null,
"SYNC_GRAPHICS_MESSAGE", "GET_GRAPHICS",
"SYNC_NO_GRAPHICS_MESSAGE", "SET_GRAPHICS_OFF");
c$.staticFunctions = c$.prototype.staticFunctions =  new java.util.Hashtable ();
Clazz_defineStatics (c$,
"nProcessors", 1);
{
{
}}});
$_L(null,"java.lang.Thread",["java.lang.IllegalArgumentException","$.ThreadGroup","java.util.Date"],function(){
c$=$_C(function(){
this.target=null;
this.group=null;
this.name=null;
this.priority=0;
$_Z(this,arguments);
},java.lang,"Thread",null,Runnable);
c$.currentThread=$_M(c$,"currentThread",
function(){
if(Thread.J2S_THREAD==null){
($t$=Thread.J2S_THREAD=new Thread(),Thread.prototype.J2S_THREAD=Thread.J2S_THREAD,$t$);
}return Thread.J2S_THREAD;
});
c$.sleep=$_M(c$,"sleep",
function(millis){
Clazz_alert("Thread.sleep is not implemented in Java2Script!");
},"~N");
$_K(c$,
function(){
});
$_K(c$,
function(target){
this.init(null,target,"Thread-"+new java.util.Date().getTime()+Math.random(),0);
},"Runnable");
$_K(c$,
function(group,target){
this.init(group,target,"Thread-"+new java.util.Date().getTime()+Math.random(),0);
},"ThreadGroup,Runnable");
$_K(c$,
function(name){
this.init(null,null,name,0);
},"~S");
$_K(c$,
function(group,name){
this.init(group,null,name,0);
},"ThreadGroup,~S");
$_K(c$,
function(target,name){
this.init(null,target,name,0);
},"Runnable,~S");
$_K(c$,
function(group,target,name){
this.init(group,target,name,0);
},"ThreadGroup,Runnable,~S");
$_K(c$,
function(group,target,name,stackSize){
this.init(group,target,name,stackSize);
},"ThreadGroup,Runnable,~S,~N");
$_M(c$,"init",
($fz=function(g,target,name,stackSize){
if(g==null){
g=new ThreadGroup();
}this.group=g;
this.target=target;
this.name=name;
this.priority=5;
},$fz.isPrivate=true,$fz),"ThreadGroup,Runnable,~S,~N");
$_M(c$,"start",
function(){
window.setTimeout((function(runnable){
return function(){
runnable.run();
};
})(this),0);
});
$_M(c$,"run",
function(){
if(this.target!=null){
this.target.run();
}});
$_M(c$,"setPriority",
function(newPriority){
if(newPriority>10||newPriority<1){
throw new IllegalArgumentException();
}this.priority=newPriority;
},"~N");
$_M(c$,"getPriority",
function(){
return this.priority;
});


$_M(c$,"interrupt",
function(){
 //not implemented
});

$_M(c$,"setName",
function(name){
this.name=name;
},"~S");
$_M(c$,"getName",
function(){
return String.valueOf(this.name);
});
$_M(c$,"getThreadGroup",
function(){
return this.group;
});
$_V(c$,"toString",
function(){
var group=this.getThreadGroup();
if(group!=null){
return"Thread["+this.getName()+","+this.getPriority()+","+group.getName()+"]";
}else{
return"Thread["+this.getName()+","+this.getPriority()+","+""+"]";
}});
$_S(c$,
"MIN_PRIORITY",1,
"NORM_PRIORITY",5,
"MAX_PRIORITY",10,
"J2S_THREAD",null);
});
Clazz_declarePackage ("J.constant");
Clazz_load (["java.lang.Enum"], "J.constant.EnumQuantumShell", ["JU.SB"], function () {
c$ = Clazz_decorateAsClass (function () {
this.tag = null;
this.tag2 = null;
this.id = 0;
this.idSpherical = 0;
Clazz_instantialize (this, arguments);
}, J.constant, "EnumQuantumShell", Enum);
Clazz_makeConstructor (c$, 
function (tag, tag2, id, idSpherical) {
this.tag = tag;
this.tag2 = tag2;
this.id = id;
this.idSpherical = idSpherical;
}, "~S,~S,~N,~N");
c$.getNewDfCoefMap = $_M(c$, "getNewDfCoefMap", 
function () {
return [ Clazz_newIntArray (1, 0),  Clazz_newIntArray (3, 0),  Clazz_newIntArray (4, 0),  Clazz_newIntArray (5, 0),  Clazz_newIntArray (6, 0),  Clazz_newIntArray (7, 0),  Clazz_newIntArray (10, 0),  Clazz_newIntArray (9, 0),  Clazz_newIntArray (15, 0),  Clazz_newIntArray (11, 0),  Clazz_newIntArray (21, 0),  Clazz_newIntArray (13, 0),  Clazz_newIntArray (28, 0)];
});
c$.getQuantumShellTagID = $_M(c$, "getQuantumShellTagID", 
function (tag) {
if (tag.equals ("L")) return J.constant.EnumQuantumShell.SP.id;
var item = J.constant.EnumQuantumShell.getQuantumShell (tag);
return (item == null ? -1 : item.id);
}, "~S");
c$.getQuantumShell = $_M(c$, "getQuantumShell", 
function (tag) {
for (var item, $item = 0, $$item = J.constant.EnumQuantumShell.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (item.tag.equals (tag) || item.tag2.equals (tag)) return item;

return null;
}, "~S");
c$.getQuantumShellTagIDSpherical = $_M(c$, "getQuantumShellTagIDSpherical", 
function (tag) {
if (tag.equals ("L")) return J.constant.EnumQuantumShell.SP.idSpherical;
var item = J.constant.EnumQuantumShell.getQuantumShell (tag);
return (item == null ? -1 : item.idSpherical);
}, "~S");
c$.getItem = $_M(c$, "getItem", 
function (id) {
switch (id) {
case 0:
return J.constant.EnumQuantumShell.S;
case 1:
return J.constant.EnumQuantumShell.P;
case 2:
return J.constant.EnumQuantumShell.SP;
case 3:
return J.constant.EnumQuantumShell.D_SPHERICAL;
case 4:
return J.constant.EnumQuantumShell.D_CARTESIAN;
case 5:
return J.constant.EnumQuantumShell.F_SPHERICAL;
case 6:
return J.constant.EnumQuantumShell.F_CARTESIAN;
case 7:
return J.constant.EnumQuantumShell.G_SPHERICAL;
case 8:
return J.constant.EnumQuantumShell.G_CARTESIAN;
case 9:
return J.constant.EnumQuantumShell.H_SPHERICAL;
case 10:
return J.constant.EnumQuantumShell.H_CARTESIAN;
case 11:
return J.constant.EnumQuantumShell.I_SPHERICAL;
case 12:
return J.constant.EnumQuantumShell.I_CARTESIAN;
}
return null;
}, "~N");
c$.getQuantumShellTag = $_M(c$, "getQuantumShellTag", 
function (id) {
for (var item, $item = 0, $$item = J.constant.EnumQuantumShell.values (); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (item.id == id) return item.tag;

return "" + id;
}, "~N");
c$.getMOString = $_M(c$, "getMOString", 
function (lc) {
var sb =  new JU.SB ();
if (lc.length == 2) return "" + Clazz_floatToInt (lc[0] < 0 ? -lc[1] : lc[1]);
sb.appendC ('[');
for (var i = 0; i < lc.length; i += 2) {
if (i > 0) sb.append (", ");
sb.appendF (lc[i]).append (" ").appendI (Clazz_floatToInt (lc[i + 1]));
}
sb.appendC (']');
return sb.toString ();
}, "~A");
c$.SUPPORTED_BASIS_FUNCTIONS = "SPLDF";
Clazz_defineEnumConstant (c$, "S", 0, ["S", "S", 0, 0]);
Clazz_defineEnumConstant (c$, "P", 1, ["P", "X", 1, 1]);
Clazz_defineEnumConstant (c$, "SP", 2, ["SP", "SP", 2, 2]);
Clazz_defineEnumConstant (c$, "D_SPHERICAL", 3, ["5D", "5D", 3, 3]);
Clazz_defineEnumConstant (c$, "D_CARTESIAN", 4, ["D", "XX", 4, 3]);
Clazz_defineEnumConstant (c$, "F_SPHERICAL", 5, ["7F", "7F", 5, 5]);
Clazz_defineEnumConstant (c$, "F_CARTESIAN", 6, ["F", "XXX", 6, 5]);
Clazz_defineEnumConstant (c$, "G_SPHERICAL", 7, ["9G", "9G", 7, 7]);
Clazz_defineEnumConstant (c$, "G_CARTESIAN", 8, ["G", "XXXX", 8, 7]);
Clazz_defineEnumConstant (c$, "H_SPHERICAL", 9, ["11H", "11H", 9, 9]);
Clazz_defineEnumConstant (c$, "H_CARTESIAN", 10, ["H", "XXXXX", 10, 9]);
Clazz_defineEnumConstant (c$, "I_SPHERICAL", 11, ["13I", "13I", 11, 11]);
Clazz_defineEnumConstant (c$, "I_CARTESIAN", 12, ["I", "XXXXXX", 12, 11]);
});
Clazz_declarePackage ("J.api");
Clazz_load (["J.constant.EnumQuantumShell"], "J.api.JmolAdapter", ["java.util.Hashtable", "J.api.JmolViewer", "J.modelset.Group", "J.util.Elements", "J.viewer.JC"], function () {
c$ = Clazz_decorateAsClass (function () {
this.adapterName = null;
Clazz_instantialize (this, arguments);
}, J.api, "JmolAdapter");
c$.getShellEnumeration = $_M(c$, "getShellEnumeration", 
function (i) {
return J.constant.EnumQuantumShell.getItem (i);
}, "~N");
c$.getNewDfCoefMap = $_M(c$, "getNewDfCoefMap", 
function () {
return J.constant.EnumQuantumShell.getNewDfCoefMap ();
});
c$.getElementSymbol = $_M(c$, "getElementSymbol", 
function (elementNumber) {
return J.util.Elements.elementSymbolFromNumber (elementNumber);
}, "~N");
c$.getElementNumber = $_M(c$, "getElementNumber", 
function (elementSymbol) {
return J.util.Elements.elementNumberFromSymbol (elementSymbol, false);
}, "~S");
c$.getNaturalIsotope = $_M(c$, "getNaturalIsotope", 
function (elementNumber) {
return J.util.Elements.getNaturalIsotope (elementNumber);
}, "~N");
c$.isHetero = $_M(c$, "isHetero", 
function (group3) {
return J.viewer.JC.isHetero (group3);
}, "~S");
c$.getQuantumShellTag = $_M(c$, "getQuantumShellTag", 
function (id) {
return J.constant.EnumQuantumShell.getQuantumShellTag (id);
}, "~N");
c$.getQuantumShellTagID = $_M(c$, "getQuantumShellTagID", 
function (tag) {
return J.constant.EnumQuantumShell.getQuantumShellTagID (tag);
}, "~S");
c$.getQuantumShellTagIDSpherical = $_M(c$, "getQuantumShellTagIDSpherical", 
function (tag) {
return J.constant.EnumQuantumShell.getQuantumShellTagIDSpherical (tag);
}, "~S");
c$.lookupGroupID = $_M(c$, "lookupGroupID", 
function (group3) {
return J.modelset.Group.lookupGroupID (group3);
}, "~S");
c$.getBondingRadiusFloat = $_M(c$, "getBondingRadiusFloat", 
function (atomicNumberWithIsotope, charge) {
return J.util.Elements.getBondingRadiusFloat (atomicNumberWithIsotope, charge);
}, "~N,~N");
Clazz_makeConstructor (c$, 
function (adapterName) {
this.adapterName = adapterName;
}, "~S");
$_M(c$, "getAdapterName", 
function () {
return this.adapterName;
});
$_M(c$, "getAtomSetCollectionFromReader", 
function (name, type, bufferedReader, htParams) {
if (htParams == null) htParams =  new java.util.Hashtable ();
if (!htParams.containsKey ("viewer")) htParams.put ("viewer", J.api.JmolViewer.allocateViewer (null, this));
var a = this.getAtomSetCollectionReader (name, type, bufferedReader, htParams);
if (Clazz_instanceOf (a, String)) return a;
return this.getAtomSetCollection (a);
}, "~S,~S,~O,java.util.Map");
$_M(c$, "openBufferedReader", 
function (name, bufferedReader) {
return this.getAtomSetCollectionFromReader (name, null, bufferedReader, null);
}, "~S,java.io.BufferedReader");
$_M(c$, "openBufferedReader", 
function (name, bufferedReader, htParams) {
return this.getAtomSetCollectionFromReader (name, null, bufferedReader, htParams);
}, "~S,java.io.BufferedReader,java.util.Map");
$_M(c$, "openBufferedReader", 
function (name, type, bufferedReader) {
return this.getAtomSetCollectionFromReader (name, type, bufferedReader, null);
}, "~S,~S,java.io.BufferedReader");
c$.canonizeAlphaDigit = $_M(c$, "canonizeAlphaDigit", 
function (ch) {
return ((ch >= 'A' && ch <= 'Z') || (ch >= 'a' && ch <= 'z') || (ch >= '0' && ch <= '9') ? ch : '\0');
}, "~S");
c$.canonizeInsertionCode = $_M(c$, "canonizeInsertionCode", 
function (insertionCode) {
return J.api.JmolAdapter.canonizeAlphaDigit (insertionCode);
}, "~S");
c$.canonizeAlternateLocationID = $_M(c$, "canonizeAlternateLocationID", 
function (altLoc) {
return J.api.JmolAdapter.canonizeAlphaDigit (altLoc);
}, "~S");
Clazz_defineStatics (c$,
"ORDER_COVALENT_SINGLE", 1,
"ORDER_COVALENT_DOUBLE", 2,
"ORDER_COVALENT_TRIPLE", 3,
"ORDER_AROMATIC", 515,
"ORDER_AROMATIC_SINGLE", 513,
"ORDER_AROMATIC_DOUBLE", 514,
"ORDER_HBOND", 2048,
"ORDER_STEREO_NEAR", 1025,
"ORDER_STEREO_FAR", 1041,
"ORDER_PARTIAL01", 33,
"ORDER_PARTIAL12", 66,
"ORDER_PARTIAL23", 97,
"ORDER_PARTIAL32", 100,
"ORDER_UNSPECIFIED", 17,
"ORDER_AS_SINGLE", 65536);
c$.SHELL_S = c$.prototype.SHELL_S = J.constant.EnumQuantumShell.S.id;
c$.SHELL_P = c$.prototype.SHELL_P = J.constant.EnumQuantumShell.P.id;
c$.SHELL_SP = c$.prototype.SHELL_SP = J.constant.EnumQuantumShell.SP.id;
c$.SHELL_L = c$.prototype.SHELL_L = J.constant.EnumQuantumShell.SP.id;
c$.SHELL_D_SPHERICAL = c$.prototype.SHELL_D_SPHERICAL = J.constant.EnumQuantumShell.D_SPHERICAL.id;
c$.SHELL_D_CARTESIAN = c$.prototype.SHELL_D_CARTESIAN = J.constant.EnumQuantumShell.D_CARTESIAN.id;
c$.SHELL_F_SPHERICAL = c$.prototype.SHELL_F_SPHERICAL = J.constant.EnumQuantumShell.F_SPHERICAL.id;
c$.SHELL_F_CARTESIAN = c$.prototype.SHELL_F_CARTESIAN = J.constant.EnumQuantumShell.F_CARTESIAN.id;
c$.SHELL_G_SPHERICAL = c$.prototype.SHELL_G_SPHERICAL = J.constant.EnumQuantumShell.G_SPHERICAL.id;
c$.SHELL_G_CARTESIAN = c$.prototype.SHELL_G_CARTESIAN = J.constant.EnumQuantumShell.G_CARTESIAN.id;
c$.SHELL_H_SPHERICAL = c$.prototype.SHELL_H_SPHERICAL = J.constant.EnumQuantumShell.H_SPHERICAL.id;
c$.SHELL_H_CARTESIAN = c$.prototype.SHELL_H_CARTESIAN = J.constant.EnumQuantumShell.H_CARTESIAN.id;
c$.SUPPORTED_BASIS_FUNCTIONS = c$.prototype.SUPPORTED_BASIS_FUNCTIONS = "SPLDF";
c$.NOTE_SCRIPT_FILE = c$.prototype.NOTE_SCRIPT_FILE = "NOTE: file recognized as a script file: ";
Clazz_defineStatics (c$,
"cellParamNames", ["_cell_length_a", "_cell_length_b", "_cell_length_c", "_cell_angle_alpha", "_cell_angle_beta", "_cell_angle_gamma"]);
});
Clazz_declarePackage ("J.adapter.smarter");
Clazz_load (["J.api.JmolAdapter"], "J.adapter.smarter.SmarterJmolAdapter", ["J.adapter.smarter.AtomIterator", "$.AtomSetCollection", "$.BondIterator", "$.Resolver", "$.StructureIterator", "J.util.Logger"], function () {
c$ = Clazz_declareType (J.adapter.smarter, "SmarterJmolAdapter", J.api.JmolAdapter);
Clazz_makeConstructor (c$, 
function () {
Clazz_superConstructor (this, J.adapter.smarter.SmarterJmolAdapter, ["SmarterJmolAdapter"]);
});
$_V(c$, "getFileTypeName", 
function (atomSetCollectionOrReader) {
if (Clazz_instanceOf (atomSetCollectionOrReader, J.adapter.smarter.AtomSetCollection)) return (atomSetCollectionOrReader).getFileTypeName ();
if (Clazz_instanceOf (atomSetCollectionOrReader, java.io.BufferedReader)) return J.adapter.smarter.Resolver.getFileType (atomSetCollectionOrReader);
return null;
}, "~O");
$_V(c$, "getAtomSetCollectionReader", 
function (name, type, bufferedReader, htParams) {
return J.adapter.smarter.SmarterJmolAdapter.staticGetAtomSetCollectionReader (name, type, bufferedReader, htParams);
}, "~S,~S,~O,java.util.Map");
c$.staticGetAtomSetCollectionReader = $_M(c$, "staticGetAtomSetCollectionReader", 
function (name, type, bufferedReader, htParams) {
try {
var ret = J.adapter.smarter.Resolver.getAtomCollectionReader (name, type, bufferedReader, htParams, -1);
if (Clazz_instanceOf (ret, String)) {
try {
J.adapter.smarter.SmarterJmolAdapter.close (bufferedReader);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
} else {
(ret).setup (name, htParams, bufferedReader);
}return ret;
} catch (e) {
try {
J.adapter.smarter.SmarterJmolAdapter.close (bufferedReader);
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
} else {
throw ex;
}
}
bufferedReader = null;
J.util.Logger.error ("" + e);
return "" + e;
}
}, "~S,~S,~O,java.util.Map");
$_M(c$, "getAtomSetCollectionFromReader", 
function (fname, reader, htParams) {
var ret = J.adapter.smarter.Resolver.getAtomCollectionReader (fname, null, reader, htParams, -1);
if (Clazz_instanceOf (ret, J.adapter.smarter.AtomSetCollectionReader)) {
(ret).setup (fname, htParams, reader);
return (ret).readData ();
}return "" + ret;
}, "~S,~O,java.util.Map");
$_V(c$, "getAtomSetCollection", 
function (atomSetCollectionReader) {
return J.adapter.smarter.SmarterJmolAdapter.staticGetAtomSetCollection (atomSetCollectionReader);
}, "~O");
c$.staticGetAtomSetCollection = $_M(c$, "staticGetAtomSetCollection", 
function (a) {
var br = null;
try {
br = a.reader;
var ret = a.readData ();
if (!(Clazz_instanceOf (ret, J.adapter.smarter.AtomSetCollection))) return ret;
var atomSetCollection = ret;
if (atomSetCollection.errorMessage != null) return atomSetCollection.errorMessage;
return atomSetCollection;
} catch (e) {
try {
System.out.println (e.toString ());
} catch (ee) {
if (Clazz_exceptionOf (ee, Exception)) {
J.util.Logger.error (e.toString ());
} else {
throw ee;
}
}
try {
br.close ();
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
} else {
throw ex;
}
}
br = null;
J.util.Logger.error ("" + e);
return "" + e;
}
}, "J.adapter.smarter.AtomSetCollectionReader");
$_V(c$, "getAtomSetCollectionReaders", 
function (filesReader, names, types, htParams, getReadersOnly) {
var size = names.length;
var readers = (getReadersOnly ?  new Array (size) : null);
var atomsets = (getReadersOnly ? null :  new Array (size));
var r = null;
var viewer = htParams.get ("viewer");
for (var i = 0; i < size; i++) {
try {
if (r != null) htParams.put ("viewer", viewer);
var reader = filesReader.getBufferedReaderOrBinaryDocument (i, false);
if (!(Clazz_instanceOf (reader, java.io.BufferedReader) || Clazz_instanceOf (reader, J.api.JmolDocument))) return reader;
var ret = J.adapter.smarter.Resolver.getAtomCollectionReader (names[i], (types == null ? null : types[i]), reader, htParams, i);
if (!(Clazz_instanceOf (ret, J.adapter.smarter.AtomSetCollectionReader))) return ret;
r = ret;
r.setup (null, null, null);
if (r.isBinary) {
r.setup (names[i], htParams, filesReader.getBufferedReaderOrBinaryDocument (i, true));
} else {
r.setup (names[i], htParams, reader);
}if (getReadersOnly) {
readers[i] = r;
} else {
ret = r.readData ();
if (!(Clazz_instanceOf (ret, J.adapter.smarter.AtomSetCollection))) return ret;
atomsets[i] = ret;
if (atomsets[i].errorMessage != null) return atomsets[i].errorMessage;
}} catch (e) {
J.util.Logger.error ("" + e);
if (!viewer.isJS) e.printStackTrace ();
return "" + e;
}
}
if (getReadersOnly) return readers;
return this.getAtomSetCollectionFromSet (readers, atomsets, htParams);
}, "J.api.JmolFilesReaderInterface,~A,~A,java.util.Map,~B");
$_V(c$, "getAtomSetCollectionFromSet", 
function (readerSet, atomsets, htParams) {
var readers = readerSet;
var asc = (atomsets == null ?  new Array (readers.length) : atomsets);
if (atomsets == null) {
for (var i = 0; i < readers.length; i++) {
try {
var ret = readers[i].readData ();
if (!(Clazz_instanceOf (ret, J.adapter.smarter.AtomSetCollection))) return ret;
asc[i] = ret;
if (asc[i].errorMessage != null) return asc[i].errorMessage;
} catch (e) {
J.util.Logger.error ("" + e);
return "" + e;
}
}
}var result;
if (htParams.containsKey ("trajectorySteps")) {
result = asc[0];
try {
result.finalizeTrajectoryAs (htParams.get ("trajectorySteps"), htParams.get ("vibrationSteps"));
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
if (result.errorMessage == null) result.errorMessage = "" + e;
} else {
throw e;
}
}
} else if (asc[0].isTrajectory) {
result = asc[0];
for (var i = 1; i < asc.length; i++) asc[0].mergeTrajectories (asc[i]);

} else {
result =  new J.adapter.smarter.AtomSetCollection ("Array", null, asc, null);
}return (result.errorMessage == null ? result : result.errorMessage);
}, "~O,~O,java.util.Map");
$_V(c$, "getAtomSetCollectionFromDOM", 
function (DOMNode, htParams) {
try {
var ret = J.adapter.smarter.Resolver.DOMResolve (DOMNode, htParams);
if (!(Clazz_instanceOf (ret, J.adapter.smarter.AtomSetCollectionReader))) return ret;
var a = ret;
a.setup ("DOM node", htParams, null);
ret = a.readDataObject (DOMNode);
if (!(Clazz_instanceOf (ret, J.adapter.smarter.AtomSetCollection))) return ret;
var asc = ret;
if (asc.errorMessage != null) return asc.errorMessage;
return asc;
} catch (e) {
J.util.Logger.error ("" + e);
return "" + e;
}
}, "~O,java.util.Map");
$_V(c$, "finish", 
function (atomSetCollection) {
(atomSetCollection).finish ();
}, "~O");
$_V(c$, "getAtomSetCollectionName", 
function (atomSetCollection) {
return (atomSetCollection).getCollectionName ();
}, "~O");
$_V(c$, "getAtomSetCollectionAuxiliaryInfo", 
function (atomSetCollection) {
return (atomSetCollection).getAtomSetCollectionAuxiliaryInfoMap ();
}, "~O");
$_V(c$, "getAtomSetCount", 
function (atomSetCollection) {
return (atomSetCollection).getAtomSetCount ();
}, "~O");
$_V(c$, "getAtomSetNumber", 
function (atomSetCollection, atomSetIndex) {
return (atomSetCollection).getAtomSetNumber (atomSetIndex);
}, "~O,~N");
$_V(c$, "getAtomSetName", 
function (atomSetCollection, atomSetIndex) {
return (atomSetCollection).getAtomSetName (atomSetIndex);
}, "~O,~N");
$_V(c$, "getAtomSetAuxiliaryInfo", 
function (atomSetCollection, atomSetIndex) {
return (atomSetCollection).getAtomSetAuxiliaryInfo (atomSetIndex);
}, "~O,~N");
$_V(c$, "getHydrogenAtomCount", 
function (atomSetCollection) {
return (atomSetCollection).getHydrogenAtomCount ();
}, "~O");
$_V(c$, "getBondList", 
function (atomSetCollection) {
return (atomSetCollection).getBondList ();
}, "~O");
$_V(c$, "getAtomCount", 
function (atomSetCollection) {
var a = atomSetCollection;
return (a.bsAtoms == null ? a.getAtomCount () : a.bsAtoms.cardinality ());
}, "~O");
$_V(c$, "coordinatesAreFractional", 
function (atomSetCollection) {
return (atomSetCollection).coordinatesAreFractional;
}, "~O");
$_V(c$, "getNotionalUnitcell", 
function (atomSetCollection) {
return (atomSetCollection).notionalUnitCell;
}, "~O");
$_V(c$, "getPdbScaleMatrix", 
function (atomSetCollection) {
var a = (atomSetCollection).notionalUnitCell;
if (a.length < 22) return null;
var b =  Clazz_newFloatArray (16, 0);
for (var i = 0; i < 16; i++) b[i] = a[6 + i];

return b;
}, "~O");
$_V(c$, "getPdbScaleTranslate", 
function (atomSetCollection) {
var a = (atomSetCollection).notionalUnitCell;
if (a.length < 22) return null;
var b =  Clazz_newFloatArray (3, 0);
b[0] = a[9];
b[1] = a[13];
b[2] = a[17];
return b;
}, "~O");
$_V(c$, "getAtomIterator", 
function (atomSetCollection) {
return  new J.adapter.smarter.AtomIterator (atomSetCollection);
}, "~O");
$_V(c$, "getBondIterator", 
function (atomSetCollection) {
return  new J.adapter.smarter.BondIterator (atomSetCollection);
}, "~O");
$_V(c$, "getStructureIterator", 
function (atomSetCollection) {
return (atomSetCollection).getStructureCount () == 0 ? null :  new J.adapter.smarter.StructureIterator (atomSetCollection);
}, "~O");
c$.close = $_M(c$, "close", 
function (bufferedReader) {
if (Clazz_instanceOf (bufferedReader, java.io.BufferedReader)) (bufferedReader).close ();
 else (bufferedReader).close ();
}, "~O");
Clazz_defineStatics (c$,
"PATH_KEY", ".PATH");
c$.PATH_SEPARATOR = c$.prototype.PATH_SEPARATOR = System.getProperty ("path.separator", "/");
});
Clazz_declarePackage ("J.api");
Clazz_load (null, "J.api.Interface", ["J.util.Logger"], function () {
c$ = Clazz_declareType (J.api, "Interface");
c$.getOptionInterface = $_M(c$, "getOptionInterface", 
function (name) {
return J.api.Interface.getInterface ("J." + name);
}, "~S");
c$.getApplicationInterface = $_M(c$, "getApplicationInterface", 
function (name) {
return J.api.Interface.getInterface ("org.openscience.jmol.app." + name);
}, "~S");
c$.getInterface = $_M(c$, "getInterface", 
function (name) {
try {
var x = Class.forName (name);
return (x == null ? null : x.newInstance ());
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
J.util.Logger.error ("Interface.java Error creating instance for " + name + ": \n" + e);
return null;
} else {
throw e;
}
}
}, "~S");
});
$_L(null,"java.lang.ThreadGroup",["java.lang.NullPointerException","$.Thread"],function(){
c$=$_C(function(){
this.parent=null;
this.name=null;
this.maxPriority=0;
$_Z(this,arguments);
},java.lang,"ThreadGroup");
$_K(c$,
function(){
this.name="system";
this.maxPriority=10;
});
$_K(c$,
function(name){
this.construct(Thread.currentThread().getThreadGroup(),name);
},"~S");
$_K(c$,
function(parent,name){
if(parent==null){
throw new NullPointerException();
}this.name=name;
this.parent=parent;
this.maxPriority=10;
},"ThreadGroup,~S");
$_M(c$,"getName",
function(){
return this.name;
});
$_M(c$,"getParent",
function(){
return this.parent;
});
$_M(c$,"getMaxPriority",
function(){
return this.maxPriority;
});
});
Clazz_declarePackage ("J.constant");
Clazz_load (["java.lang.Enum"], "J.constant.EnumAxesMode", null, function () {
c$ = Clazz_decorateAsClass (function () {
this.code = 0;
Clazz_instantialize (this, arguments);
}, J.constant, "EnumAxesMode", Enum);
Clazz_makeConstructor (c$, 
function (code) {
this.code = code;
}, "~N");
$_M(c$, "getCode", 
function () {
return this.code;
});
c$.getAxesMode = $_M(c$, "getAxesMode", 
function (code) {
for (var mode, $mode = 0, $$mode = J.constant.EnumAxesMode.values (); $mode < $$mode.length && ((mode = $$mode[$mode]) || true); $mode++) {
if (mode.getCode () == code) {
return mode;
}}
return null;
}, "~N");
Clazz_defineEnumConstant (c$, "BOUNDBOX", 0, [0]);
Clazz_defineEnumConstant (c$, "MOLECULAR", 1, [1]);
Clazz_defineEnumConstant (c$, "UNITCELL", 2, [2]);
});
Clazz_declarePackage ("J.constant");
Clazz_load (["java.lang.Enum"], "J.constant.EnumFileStatus", null, function () {
c$ = Clazz_decorateAsClass (function () {
this.code = 0;
Clazz_instantialize (this, arguments);
}, J.constant, "EnumFileStatus", Enum);
$_M(c$, "getCode", 
function () {
return this.code;
});
Clazz_makeConstructor (c$, 
function (code) {
this.code = code;
}, "~N");
Clazz_defineEnumConstant (c$, "DELETED", 0, [5]);
Clazz_defineEnumConstant (c$, "CREATED", 1, [3]);
Clazz_defineEnumConstant (c$, "CREATING_MODELSET", 2, [2]);
Clazz_defineEnumConstant (c$, "ZAPPED", 3, [0]);
Clazz_defineEnumConstant (c$, "NOT_LOADED", 4, [-1]);
});
Clazz_declarePackage ("J.api");
Clazz_declareInterface (J.api, "JmolAdapterAtomIterator");
Clazz_declarePackage ("J.adapter.smarter");
Clazz_load (["J.api.JmolAdapterAtomIterator"], "J.adapter.smarter.AtomIterator", ["java.lang.Float", "J.api.JmolAdapter"], function () {
c$ = Clazz_decorateAsClass (function () {
this.iatom = 0;
this.atom = null;
this.atomCount = 0;
this.atoms = null;
this.bsAtoms = null;
Clazz_instantialize (this, arguments);
}, J.adapter.smarter, "AtomIterator", null, J.api.JmolAdapterAtomIterator);
Clazz_makeConstructor (c$, 
function (atomSetCollection) {
this.atomCount = atomSetCollection.getAtomCount ();
this.atoms = atomSetCollection.getAtoms ();
this.bsAtoms = atomSetCollection.bsAtoms;
this.iatom = 0;
}, "J.adapter.smarter.AtomSetCollection");
$_V(c$, "hasNext", 
function () {
if (this.iatom == this.atomCount) return false;
while ((this.atom = this.atoms[this.iatom++]) == null || (this.bsAtoms != null && !this.bsAtoms.get (this.atom.index))) if (this.iatom == this.atomCount) return false;

this.atoms[this.iatom - 1] = null;
return true;
});
$_V(c$, "getAtomSetIndex", 
function () {
return this.atom.atomSetIndex;
});
$_V(c$, "getAtomSymmetry", 
function () {
return this.atom.bsSymmetry;
});
$_V(c$, "getAtomSite", 
function () {
return this.atom.atomSite + 1;
});
$_V(c$, "getUniqueID", 
function () {
return Integer.$valueOf (this.atom.index);
});
$_V(c$, "getElementNumber", 
function () {
return (this.atom.elementNumber > 0 ? this.atom.elementNumber : J.api.JmolAdapter.getElementNumber (this.atom.getElementSymbol ()));
});
$_V(c$, "getAtomName", 
function () {
return this.atom.atomName;
});
$_V(c$, "getFormalCharge", 
function () {
return this.atom.formalCharge;
});
$_V(c$, "getPartialCharge", 
function () {
return this.atom.partialCharge;
});
$_V(c$, "getTensors", 
function () {
return this.atom.tensors;
});
$_V(c$, "getRadius", 
function () {
return this.atom.radius;
});
$_V(c$, "getVib", 
function () {
return (this.atom.vib == null || Float.isNaN (this.atom.vib.z) ? null : this.atom.vib);
});
$_V(c$, "getBfactor", 
function () {
return Float.isNaN (this.atom.bfactor) && this.atom.anisoBorU != null ? this.atom.anisoBorU[7] * 100 : this.atom.bfactor;
});
$_V(c$, "getOccupancy", 
function () {
return Clazz_floatToInt (this.atom.foccupancy * 100);
});
$_V(c$, "getIsHetero", 
function () {
return this.atom.isHetero;
});
$_V(c$, "getAtomSerial", 
function () {
return this.atom.atomSerial;
});
$_V(c$, "getChainID", 
function () {
return this.atom.chainID;
});
$_V(c$, "getAlternateLocationID", 
function () {
return J.api.JmolAdapter.canonizeAlternateLocationID (this.atom.alternateLocationID);
});
$_V(c$, "getGroup3", 
function () {
return this.atom.group3;
});
$_V(c$, "getSequenceNumber", 
function () {
return this.atom.sequenceNumber;
});
$_V(c$, "getInsertionCode", 
function () {
return J.api.JmolAdapter.canonizeInsertionCode (this.atom.insertionCode);
});
$_V(c$, "getXYZ", 
function () {
return this.atom;
});
});
Clazz_declarePackage ("J.adapter.smarter");
Clazz_load (["java.util.Hashtable", "JU.P3"], "J.adapter.smarter.AtomSetCollection", ["java.lang.Boolean", "$.Float", "java.util.Collections", "$.Properties", "JU.AU", "$.BS", "$.List", "$.M3", "$.M4", "$.P3i", "$.PT", "$.SB", "$.V3", "J.adapter.smarter.Atom", "$.Bond", "$.SmarterJmolAdapter", "J.api.Interface", "J.util.BSUtil", "$.Escape", "$.Logger"], function () {
c$ = Clazz_decorateAsClass (function () {
this.bsAtoms = null;
this.fileTypeName = null;
this.collectionName = null;
this.atomSetCollectionAuxiliaryInfo = null;
this.atomCount = 0;
this.atoms = null;
this.bondCount = 0;
this.bonds = null;
this.structureCount = 0;
this.structures = null;
this.atomSetCount = 0;
this.currentAtomSetIndex = -1;
this.atomSetNumbers = null;
this.atomSetAtomIndexes = null;
this.atomSetAtomCounts = null;
this.atomSetBondCounts = null;
this.atomSetAuxiliaryInfo = null;
this.latticeCells = null;
this.errorMessage = null;
this.coordinatesAreFractional = false;
this.isTrajectory = false;
this.trajectoryStepCount = 0;
this.trajectorySteps = null;
this.vibrationSteps = null;
this.trajectoryNames = null;
this.doFixPeriodic = false;
this.notionalUnitCell = null;
this.allowMultiple = false;
this.reader = null;
this.readerList = null;
this.vConnect = null;
this.connectNextAtomIndex = 0;
this.connectNextAtomSet = 0;
this.connectLast = null;
this.bsStructuredModels = null;
this.symmetryRange = 0;
this.doCentroidUnitCell = false;
this.centroidPacked = false;
this.ptSupercell = null;
this.fmatSupercell = null;
this.symmetry = null;
this.haveUnitCell = false;
this.doNormalize = true;
this.doPackUnitCell = false;
this.rminx = 0;
this.rminy = 0;
this.rminz = 0;
this.rmaxx = 0;
this.rmaxy = 0;
this.rmaxz = 0;
this.ptOffset = null;
this.unitCellOffset = null;
this.minXYZ = null;
this.maxXYZ = null;
this.minXYZ0 = null;
this.maxXYZ0 = null;
this.haveAnisou = false;
this.dtype = 3;
this.unitCellTranslations = null;
this.baseSymmetryAtomCount = 0;
this.checkLatticeOnly = false;
this.latticeOp = 0;
this.latticeOnly = false;
this.bondCount0 = 0;
this.bondIndex0 = 0;
this.applySymmetryToBonds = false;
this.checkSpecial = true;
this.checkAll = false;
this.ptTemp = null;
this.mTemp = null;
this.atomSymbolicMap = null;
this.haveMappedSerials = false;
Clazz_instantialize (this, arguments);
}, J.adapter.smarter, "AtomSetCollection");
Clazz_prepareFields (c$, function () {
this.atomSetCollectionAuxiliaryInfo =  new java.util.Hashtable ();
this.atoms =  new Array (256);
this.bonds =  new Array (256);
this.structures =  new Array (16);
this.atomSetNumbers =  Clazz_newIntArray (16, 0);
this.atomSetAtomIndexes =  Clazz_newIntArray (16, 0);
this.atomSetAtomCounts =  Clazz_newIntArray (16, 0);
this.atomSetBondCounts =  Clazz_newIntArray (16, 0);
this.atomSetAuxiliaryInfo =  new Array (16);
this.notionalUnitCell =  Clazz_newFloatArray (6, 0);
this.ptOffset =  new JU.P3 ();
this.atomSymbolicMap =  new java.util.Hashtable ();
});
$_M(c$, "getFileTypeName", 
function () {
return this.fileTypeName;
});
$_M(c$, "getCollectionName", 
function () {
return this.collectionName;
});
$_M(c$, "setCollectionName", 
function (collectionName) {
if (collectionName != null) {
collectionName = collectionName.trim ();
if (collectionName.length == 0) return;
this.collectionName = collectionName;
}}, "~S");
$_M(c$, "getAtomSetCollectionAuxiliaryInfoMap", 
function () {
return this.atomSetCollectionAuxiliaryInfo;
});
$_M(c$, "clearGlobalBoolean", 
function (globalIndex) {
this.atomSetCollectionAuxiliaryInfo.remove (J.adapter.smarter.AtomSetCollection.globalBooleans[globalIndex]);
}, "~N");
$_M(c$, "setGlobalBoolean", 
function (globalIndex) {
this.setAtomSetCollectionAuxiliaryInfo (J.adapter.smarter.AtomSetCollection.globalBooleans[globalIndex], Boolean.TRUE);
}, "~N");
$_M(c$, "getGlobalBoolean", 
function (globalIndex) {
return (this.getAtomSetCollectionAuxiliaryInfo (J.adapter.smarter.AtomSetCollection.globalBooleans[globalIndex]) === Boolean.TRUE);
}, "~N");
$_M(c$, "getAtomCount", 
function () {
return this.atomCount;
});
$_M(c$, "getHydrogenAtomCount", 
function () {
var n = 0;
for (var i = 0; i < this.atomCount; i++) if (this.atoms[i].elementNumber == 1 || this.atoms[i].elementSymbol.equals ("H")) n++;

return n;
});
$_M(c$, "getAtoms", 
function () {
return this.atoms;
});
$_M(c$, "getAtom", 
function (i) {
return this.atoms[i];
}, "~N");
$_M(c$, "getBondCount", 
function () {
return this.bondCount;
});
$_M(c$, "getBonds", 
function () {
return this.bonds;
});
$_M(c$, "getBond", 
function (i) {
return this.bonds[i];
}, "~N");
$_M(c$, "getStructureCount", 
function () {
return this.structureCount;
});
$_M(c$, "getStructures", 
function () {
return this.structures;
});
$_M(c$, "getAtomSetCount", 
function () {
return this.atomSetCount;
});
$_M(c$, "getCurrentAtomSetIndex", 
function () {
return this.currentAtomSetIndex;
});
$_M(c$, "setCurrentAtomSetIndex", 
function (i) {
this.currentAtomSetIndex = i;
}, "~N");
$_M(c$, "setDoFixPeriodic", 
function () {
this.doFixPeriodic = true;
});
Clazz_makeConstructor (c$, 
function (fileTypeName, reader, array, list) {
this.fileTypeName = fileTypeName;
this.reader = reader;
this.allowMultiple = (reader == null || reader.desiredVibrationNumber < 0);
var p =  new java.util.Properties ();
p.put ("PATH_KEY", ".PATH");
p.put ("PATH_SEPARATOR", J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR);
this.setAtomSetCollectionAuxiliaryInfo ("properties", p);
if (array != null) {
var n = 0;
this.readerList =  new JU.List ();
for (var i = 0; i < array.length; i++) if (array[i].atomCount > 0 || array[i].reader != null && array[i].reader.mustFinalizeModelSet) this.appendAtomSetCollection (n++, array[i]);

if (n > 1) this.setAtomSetCollectionAuxiliaryInfo ("isMultiFile", Boolean.TRUE);
} else if (list != null) {
this.setAtomSetCollectionAuxiliaryInfo ("isMultiFile", Boolean.TRUE);
this.appendAtomSetCollectionList (list);
}}, "~S,J.adapter.smarter.AtomSetCollectionReader,~A,JU.List");
$_M(c$, "appendAtomSetCollectionList", 
function (list) {
var n = list.size ();
if (n == 0) {
this.errorMessage = "No file found!";
return;
}for (var i = 0; i < n; i++) {
var o = list.get (i);
if (Clazz_instanceOf (o, JU.List)) this.appendAtomSetCollectionList (o);
 else this.appendAtomSetCollection (i, o);
}
}, "JU.List");
$_M(c$, "setTrajectory", 
function () {
if (!this.isTrajectory) {
this.trajectorySteps =  new JU.List ();
}this.isTrajectory = true;
this.addTrajectoryStep ();
});
$_M(c$, "appendAtomSetCollection", 
function (collectionIndex, collection) {
if (collection.reader != null && collection.reader.mustFinalizeModelSet) this.readerList.addLast (collection.reader);
var existingAtomsCount = this.atomCount;
this.setAtomSetCollectionAuxiliaryInfo ("loadState", collection.getAtomSetCollectionAuxiliaryInfo ("loadState"));
if (collection.bsAtoms != null) {
if (this.bsAtoms == null) this.bsAtoms =  new JU.BS ();
for (var i = collection.bsAtoms.nextSetBit (0); i >= 0; i = collection.bsAtoms.nextSetBit (i + 1)) this.bsAtoms.set (existingAtomsCount + i);

}var clonedAtoms = 0;
var atomSetCount0 = this.atomSetCount;
for (var atomSetNum = 0; atomSetNum < collection.atomSetCount; atomSetNum++) {
this.newAtomSet ();
var info = this.atomSetAuxiliaryInfo[this.currentAtomSetIndex] = collection.atomSetAuxiliaryInfo[atomSetNum];
var atomInfo = info.get ("PDB_CONECT_firstAtom_count_max");
if (atomInfo != null) atomInfo[0] += existingAtomsCount;
this.setAtomSetAuxiliaryInfo ("title", collection.collectionName);
this.setAtomSetName (collection.getAtomSetName (atomSetNum));
for (var atomNum = 0; atomNum < collection.atomSetAtomCounts[atomSetNum]; atomNum++) {
try {
if (this.bsAtoms != null) this.bsAtoms.set (this.atomCount);
this.newCloneAtom (collection.atoms[clonedAtoms]);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
this.errorMessage = "appendAtomCollection error: " + e;
} else {
throw e;
}
}
clonedAtoms++;
}
this.atomSetNumbers[this.currentAtomSetIndex] = (collectionIndex < 0 ? this.currentAtomSetIndex + 1 : ((collectionIndex + 1) * 1000000) + collection.atomSetNumbers[atomSetNum]);
}
for (var bondNum = 0; bondNum < collection.bondCount; bondNum++) {
var bond = collection.bonds[bondNum];
this.addNewBondWithOrder (bond.atomIndex1 + existingAtomsCount, bond.atomIndex2 + existingAtomsCount, bond.order);
}
for (var i = J.adapter.smarter.AtomSetCollection.globalBooleans.length; --i >= 0; ) if (collection.getGlobalBoolean (i)) this.setGlobalBoolean (i);

for (var i = 0; i < collection.structureCount; i++) {
var s = collection.structures[i];
this.addStructure (s);
s.modelStartEnd[0] += atomSetCount0;
s.modelStartEnd[1] += atomSetCount0;
}
}, "~N,J.adapter.smarter.AtomSetCollection");
$_M(c$, "setNoAutoBond", 
function () {
this.setAtomSetCollectionAuxiliaryInfo ("noAutoBond", Boolean.TRUE);
});
$_M(c$, "freeze", 
function (reverseModels) {
if (this.atomSetCount == 1 && this.collectionName == null) this.collectionName = this.getAtomSetAuxiliaryInfoValue (0, "name");
if (reverseModels) this.reverseAtomSets ();
if (this.trajectoryStepCount > 1) this.finalizeTrajectory ();
this.getList (true);
this.getList (false);
for (var i = 0; i < this.atomSetCount; i++) {
this.setAtomSetAuxiliaryInfoForSet ("initialAtomCount", Integer.$valueOf (this.atomSetAtomCounts[i]), i);
this.setAtomSetAuxiliaryInfoForSet ("initialBondCount", Integer.$valueOf (this.atomSetBondCounts[i]), i);
}
}, "~B");
$_M(c$, "reverseAtomSets", 
function () {
this.reverseArray (this.atomSetAtomIndexes);
this.reverseArray (this.atomSetNumbers);
this.reverseArray (this.atomSetAtomCounts);
this.reverseArray (this.atomSetBondCounts);
J.adapter.smarter.AtomSetCollection.reverseList (this.trajectorySteps);
J.adapter.smarter.AtomSetCollection.reverseList (this.trajectoryNames);
J.adapter.smarter.AtomSetCollection.reverseList (this.vibrationSteps);
this.reverseObject (this.atomSetAuxiliaryInfo);
for (var i = 0; i < this.atomCount; i++) this.atoms[i].atomSetIndex = this.atomSetCount - 1 - this.atoms[i].atomSetIndex;

for (var i = 0; i < this.structureCount; i++) {
var m = this.structures[i].modelStartEnd[0];
if (m >= 0) {
this.structures[i].modelStartEnd[0] = this.atomSetCount - 1 - this.structures[i].modelStartEnd[1];
this.structures[i].modelStartEnd[1] = this.atomSetCount - 1 - m;
}}
for (var i = 0; i < this.bondCount; i++) this.bonds[i].atomSetIndex = this.atomSetCount - 1 - this.atoms[this.bonds[i].atomIndex1].atomSetIndex;

this.reverseSets (this.bonds, this.bondCount);
var lists = JU.AU.createArrayOfArrayList (this.atomSetCount);
for (var i = 0; i < this.atomSetCount; i++) lists[i] =  new JU.List ();

for (var i = 0; i < this.atomCount; i++) lists[this.atoms[i].atomSetIndex].addLast (this.atoms[i]);

var newIndex =  Clazz_newIntArray (this.atomCount, 0);
var n = this.atomCount;
for (var i = this.atomSetCount; --i >= 0; ) for (var j = lists[i].size (); --j >= 0; ) {
var a = this.atoms[--n] = lists[i].get (j);
newIndex[a.index] = n;
a.index = n;
}

for (var i = 0; i < this.bondCount; i++) {
this.bonds[i].atomIndex1 = newIndex[this.bonds[i].atomIndex1];
this.bonds[i].atomIndex2 = newIndex[this.bonds[i].atomIndex2];
}
for (var i = 0; i < this.atomSetCount; i++) {
var conect = this.getAtomSetAuxiliaryInfoValue (i, "PDB_CONECT_firstAtom_count_max");
if (conect == null) continue;
conect[0] = newIndex[conect[0]];
conect[1] = this.atomSetAtomCounts[i];
}
});
$_M(c$, "reverseSets", 
function (o, n) {
var lists = JU.AU.createArrayOfArrayList (this.atomSetCount);
for (var i = 0; i < this.atomSetCount; i++) lists[i] =  new JU.List ();

for (var i = 0; i < n; i++) {
var index = o[i].atomSetIndex;
if (index < 0) return;
lists[o[i].atomSetIndex].addLast (o[i]);
}
for (var i = this.atomSetCount; --i >= 0; ) for (var j = lists[i].size (); --j >= 0; ) o[--n] = lists[i].get (j);


}, "~A,~N");
$_M(c$, "reverseObject", 
function (o) {
var n = this.atomSetCount;
for (var i = Clazz_doubleToInt (n / 2); --i >= 0; ) JU.AU.swap (o, i, n - 1 - i);

}, "~A");
c$.reverseList = $_M(c$, "reverseList", 
function (list) {
if (list == null) return;
java.util.Collections.reverse (list);
}, "JU.List");
$_M(c$, "reverseArray", 
function (a) {
var n = this.atomSetCount;
for (var i = Clazz_doubleToInt (n / 2); --i >= 0; ) JU.AU.swapInt (a, i, n - 1 - i);

}, "~A");
$_M(c$, "getList", 
function (isAltLoc) {
var i;
for (i = this.atomCount; --i >= 0; ) if (this.atoms[i] != null && (isAltLoc ? this.atoms[i].alternateLocationID : this.atoms[i].insertionCode) != '\0') break;

if (i < 0) return;
var lists =  new Array (this.atomSetCount);
for (i = 0; i < this.atomSetCount; i++) lists[i] = "";

var pt;
for (i = 0; i < this.atomCount; i++) {
if (this.atoms[i] == null) continue;
var id = (isAltLoc ? this.atoms[i].alternateLocationID : this.atoms[i].insertionCode);
if (id != '\0' && lists[pt = this.atoms[i].atomSetIndex].indexOf (id) < 0) lists[pt] += id;
}
var type = (isAltLoc ? "altLocs" : "insertionCodes");
for (i = 0; i < this.atomSetCount; i++) if (lists[i].length > 0) this.setAtomSetAuxiliaryInfoForSet (type, lists[i], i);

}, "~B");
$_M(c$, "finish", 
function () {
if (this.reader != null) this.reader.finalizeModelSet ();
 else if (this.readerList != null) for (var i = 0; i < this.readerList.size (); i++) this.readerList.get (i).finalizeModelSet ();

this.atoms = null;
this.atomSetAtomCounts =  Clazz_newIntArray (16, 0);
this.atomSetAuxiliaryInfo =  new Array (16);
this.atomSetCollectionAuxiliaryInfo =  new java.util.Hashtable ();
this.atomSetCount = 0;
this.atomSetNumbers =  Clazz_newIntArray (16, 0);
this.atomSymbolicMap =  new java.util.Hashtable ();
this.bonds = null;
this.connectLast = null;
this.currentAtomSetIndex = -1;
this.latticeCells = null;
this.notionalUnitCell = null;
this.readerList = null;
this.symmetry = null;
this.structures =  new Array (16);
this.structureCount = 0;
this.trajectorySteps = null;
this.vibrationSteps = null;
this.vConnect = null;
});
$_M(c$, "discardPreviousAtoms", 
function () {
for (var i = this.atomCount; --i >= 0; ) this.atoms[i] = null;

this.atomCount = 0;
this.clearSymbolicMap ();
this.atomSetCount = 0;
this.currentAtomSetIndex = -1;
for (var i = this.atomSetAuxiliaryInfo.length; --i >= 0; ) {
this.atomSetAtomCounts[i] = 0;
this.atomSetBondCounts[i] = 0;
this.atomSetAuxiliaryInfo[i] = null;
}
});
$_M(c$, "removeAtomSet", 
function (imodel) {
if (this.bsAtoms == null) {
this.bsAtoms =  new JU.BS ();
this.bsAtoms.setBits (0, this.atomCount);
}var i0 = this.atomSetAtomIndexes[imodel];
var nAtoms = this.atomSetAtomCounts[imodel];
var i1 = i0 + nAtoms;
this.bsAtoms.clearBits (i0, i1);
for (var i = i1; i < this.atomCount; i++) this.atoms[i].atomSetIndex--;

for (var i = imodel + 1; i < this.atomSetCount; i++) {
this.atomSetAuxiliaryInfo[i - 1] = this.atomSetAuxiliaryInfo[i];
this.atomSetAtomIndexes[i - 1] = this.atomSetAtomIndexes[i];
this.atomSetBondCounts[i - 1] = this.atomSetBondCounts[i];
this.atomSetAtomCounts[i - 1] = this.atomSetAtomCounts[i];
this.atomSetNumbers[i - 1] = this.atomSetNumbers[i];
}
var n = 0;
for (var i = 0; i < this.structureCount; i++) {
var s = this.structures[i];
if (s.modelStartEnd[0] == imodel && s.modelStartEnd[1] == imodel) {
this.structures[i] = null;
n++;
}}
if (n > 0) {
var ss =  new Array (this.structureCount - n);
for (var i = 0, pt = 0; i < this.structureCount; i++) if (this.structures[i] != null) ss[pt++] = this.structures[i];

this.structures = ss;
}for (var i = 0; i < this.bondCount; i++) this.bonds[i].atomSetIndex = this.atoms[this.bonds[i].atomIndex1].atomSetIndex;

this.atomSetAuxiliaryInfo[--this.atomSetCount] = null;
}, "~N");
$_M(c$, "removeCurrentAtomSet", 
function () {
if (this.currentAtomSetIndex < 0) return;
this.currentAtomSetIndex--;
this.atomSetCount--;
});
$_M(c$, "newCloneAtom", 
function (atom) {
var clone = atom.getClone ();
this.addAtom (clone);
return clone;
}, "J.adapter.smarter.Atom");
$_M(c$, "cloneFirstAtomSet", 
function (atomCount) {
if (!this.allowMultiple) return;
this.newAtomSet ();
if (atomCount == 0) atomCount = this.atomSetAtomCounts[0];
for (var i = 0; i < atomCount; ++i) this.newCloneAtom (this.atoms[i]);

}, "~N");
$_M(c$, "cloneFirstAtomSetWithBonds", 
function (nBonds) {
if (!this.allowMultiple) return;
this.cloneFirstAtomSet (0);
var firstCount = this.atomSetAtomCounts[0];
for (var bondNum = 0; bondNum < nBonds; bondNum++) {
var bond = this.bonds[this.bondCount - nBonds];
this.addNewBondWithOrder (bond.atomIndex1 + firstCount, bond.atomIndex2 + firstCount, bond.order);
}
}, "~N");
$_M(c$, "cloneLastAtomSet", 
function () {
this.cloneLastAtomSetFromPoints (0, null);
});
$_M(c$, "cloneLastAtomSetFromPoints", 
function (atomCount, pts) {
if (!this.allowMultiple) return;
var count = (atomCount > 0 ? atomCount : this.getLastAtomSetAtomCount ());
var atomIndex = this.getLastAtomSetAtomIndex ();
this.newAtomSet ();
for (var i = 0; i < count; ++i) {
var atom = this.newCloneAtom (this.atoms[atomIndex++]);
if (pts != null) atom.setT (pts[i]);
}
}, "~N,~A");
$_M(c$, "getFirstAtomSetAtomCount", 
function () {
return this.atomSetAtomCounts[0];
});
$_M(c$, "getLastAtomSetAtomCount", 
function () {
return this.atomSetAtomCounts[this.currentAtomSetIndex];
});
$_M(c$, "getLastAtomSetAtomIndex", 
function () {
return this.atomCount - this.atomSetAtomCounts[this.currentAtomSetIndex];
});
$_M(c$, "addNewAtom", 
function () {
var atom =  new J.adapter.smarter.Atom ();
this.addAtom (atom);
return atom;
});
$_M(c$, "addAtom", 
function (atom) {
if (this.atomCount == this.atoms.length) {
if (this.atomCount > 200000) this.atoms = JU.AU.ensureLength (this.atoms, this.atomCount + 50000);
 else this.atoms = JU.AU.doubleLength (this.atoms);
}if (this.atomSetCount == 0) this.newAtomSet ();
atom.index = this.atomCount;
this.atoms[this.atomCount++] = atom;
atom.atomSetIndex = this.currentAtomSetIndex;
atom.atomSite = this.atomSetAtomCounts[this.currentAtomSetIndex]++;
}, "J.adapter.smarter.Atom");
$_M(c$, "addAtomWithMappedName", 
function (atom) {
this.addAtom (atom);
this.mapMostRecentAtomName ();
}, "J.adapter.smarter.Atom");
$_M(c$, "addAtomWithMappedSerialNumber", 
function (atom) {
this.addAtom (atom);
this.mapMostRecentAtomSerialNumber ();
}, "J.adapter.smarter.Atom");
$_M(c$, "addNewBondWithOrder", 
function (atomIndex1, atomIndex2, order) {
if (atomIndex1 < 0 || atomIndex1 >= this.atomCount || atomIndex2 < 0 || atomIndex2 >= this.atomCount) return null;
var bond =  new J.adapter.smarter.Bond (atomIndex1, atomIndex2, order);
this.addBond (bond);
return bond;
}, "~N,~N,~N");
$_M(c$, "addNewBondFromNames", 
function (atomName1, atomName2, order) {
return this.addNewBondWithOrder (this.getAtomIndexFromName (atomName1), this.getAtomIndexFromName (atomName2), order);
}, "~S,~S,~N");
$_M(c$, "addNewBondWithMappedSerialNumbers", 
function (atomSerial1, atomSerial2, order) {
return this.addNewBondWithOrder (this.getAtomIndexFromSerial (atomSerial1), this.getAtomIndexFromSerial (atomSerial2), order);
}, "~N,~N,~N");
$_M(c$, "addConnection", 
function (is) {
if (this.vConnect == null) {
this.connectLast = null;
this.vConnect =  new JU.List ();
}if (this.connectLast != null) {
if (is[0] == this.connectLast[0] && is[1] == this.connectLast[1] && is[2] != 2048) {
this.connectLast[2]++;
return;
}}this.vConnect.addLast (this.connectLast = is);
}, "~A");
$_M(c$, "connectAllBad", 
function (maxSerial) {
var firstAtom = this.connectNextAtomIndex;
for (var i = this.connectNextAtomSet; i < this.atomSetCount; i++) {
this.setAtomSetAuxiliaryInfoForSet ("PDB_CONECT_firstAtom_count_max", [firstAtom, this.atomSetAtomCounts[i], maxSerial], i);
if (this.vConnect != null) {
this.setAtomSetAuxiliaryInfoForSet ("PDB_CONECT_bonds", this.vConnect, i);
this.setGlobalBoolean (3);
}firstAtom += this.atomSetAtomCounts[i];
}
this.vConnect = null;
this.connectNextAtomSet = this.currentAtomSetIndex + 1;
this.connectNextAtomIndex = firstAtom;
}, "~N");
$_M(c$, "connectAll", 
function (maxSerial, isConnectStateBug) {
if (this.currentAtomSetIndex < 0) return;
if (isConnectStateBug) {
this.connectAllBad (maxSerial);
return;
}this.setAtomSetAuxiliaryInfo ("PDB_CONECT_firstAtom_count_max", [this.atomSetAtomIndexes[this.currentAtomSetIndex], this.atomSetAtomCounts[this.currentAtomSetIndex], maxSerial]);
if (this.vConnect == null) return;
var firstAtom = this.connectNextAtomIndex;
for (var i = this.connectNextAtomSet; i < this.atomSetCount; i++) {
this.setAtomSetAuxiliaryInfoForSet ("PDB_CONECT_bonds", this.vConnect, i);
this.setGlobalBoolean (3);
firstAtom += this.atomSetAtomCounts[i];
}
this.vConnect = null;
this.connectNextAtomSet = this.currentAtomSetIndex + 1;
this.connectNextAtomIndex = firstAtom;
}, "~N,~B");
$_M(c$, "addBond", 
function (bond) {
if (this.trajectoryStepCount > 0) return;
if (bond.atomIndex1 < 0 || bond.atomIndex2 < 0 || bond.order < 0 || this.atoms[bond.atomIndex1].atomSetIndex != this.atoms[bond.atomIndex2].atomSetIndex) {
if (J.util.Logger.debugging) {
J.util.Logger.debug (">>>>>>BAD BOND:" + bond.atomIndex1 + "-" + bond.atomIndex2 + " order=" + bond.order);
}return;
}if (this.bondCount == this.bonds.length) this.bonds = JU.AU.arrayCopyObject (this.bonds, this.bondCount + 1024);
this.bonds[this.bondCount++] = bond;
this.atomSetBondCounts[this.currentAtomSetIndex]++;
}, "J.adapter.smarter.Bond");
$_M(c$, "finalizeStructures", 
function () {
if (this.structureCount == 0) return;
this.bsStructuredModels =  new JU.BS ();
var map =  new java.util.Hashtable ();
for (var i = 0; i < this.structureCount; i++) {
var s = this.structures[i];
if (s.modelStartEnd[0] == -1) {
s.modelStartEnd[0] = 0;
s.modelStartEnd[1] = this.atomSetCount - 1;
}this.bsStructuredModels.setBits (s.modelStartEnd[0], s.modelStartEnd[1] + 1);
if (s.strandCount == 0) continue;
var key = s.structureID + " " + s.modelStartEnd[0];
var v = map.get (key);
var count = (v == null ? 0 : v.intValue ()) + 1;
map.put (key, Integer.$valueOf (count));
}
for (var i = 0; i < this.structureCount; i++) {
var s = this.structures[i];
if (s.strandCount == 1) s.strandCount = map.get (s.structureID + " " + s.modelStartEnd[0]).intValue ();
}
});
$_M(c$, "addStructure", 
function (structure) {
if (this.structureCount == this.structures.length) this.structures = JU.AU.arrayCopyObject (this.structures, this.structureCount + 32);
this.structures[this.structureCount++] = structure;
}, "J.adapter.smarter.Structure");
$_M(c$, "addVibrationVectorWithSymmetry", 
function (iatom, vx, vy, vz, withSymmetry) {
if (!withSymmetry) {
this.addVibrationVector (iatom, vx, vy, vz);
return;
}var atomSite = this.atoms[iatom].atomSite;
var atomSetIndex = this.atoms[iatom].atomSetIndex;
for (var i = iatom; i < this.atomCount && this.atoms[i].atomSetIndex == atomSetIndex; i++) {
if (this.atoms[i].atomSite == atomSite) this.addVibrationVector (i, vx, vy, vz);
}
}, "~N,~N,~N,~N,~B");
$_M(c$, "addVibrationVector", 
function (iatom, x, y, z) {
if (!this.allowMultiple) iatom = iatom % this.atomCount;
this.atoms[iatom].vib = JU.V3.new3 (x, y, z);
}, "~N,~N,~N,~N");
$_M(c$, "setAtomSetSpaceGroupName", 
function (spaceGroupName) {
this.setAtomSetAuxiliaryInfo ("spaceGroup", spaceGroupName + "");
}, "~S");
$_M(c$, "setCoordinatesAreFractional", 
function (tf) {
this.coordinatesAreFractional = tf;
this.setAtomSetAuxiliaryInfo ("coordinatesAreFractional", Boolean.$valueOf (tf));
if (tf) this.setGlobalBoolean (0);
}, "~B");
$_M(c$, "setSymmetryRange", 
function (factor) {
this.symmetryRange = factor;
this.setAtomSetCollectionAuxiliaryInfo ("symmetryRange", Float.$valueOf (factor));
}, "~N");
$_M(c$, "setLatticeCells", 
function (latticeCells, applySymmetryToBonds, doPackUnitCell, doCentroidUnitCell, centroidPacked, strSupercell, ptSupercell) {
this.latticeCells = latticeCells;
var isLatticeRange = (latticeCells[0] <= 555 && latticeCells[1] >= 555 && (latticeCells[2] == 0 || latticeCells[2] == 1 || latticeCells[2] == -1));
this.doNormalize = latticeCells[0] != 0 && (!isLatticeRange || latticeCells[2] == 1);
this.applySymmetryToBonds = applySymmetryToBonds;
this.doPackUnitCell = doPackUnitCell;
this.doCentroidUnitCell = doCentroidUnitCell;
this.centroidPacked = centroidPacked;
if (strSupercell != null) this.setSuperCell (strSupercell);
 else this.ptSupercell = ptSupercell;
}, "~A,~B,~B,~B,~B,~S,JU.P3");
$_M(c$, "setSupercellFromPoint", 
function (pt) {
this.ptSupercell = pt;
J.util.Logger.info ("Using supercell " + J.util.Escape.eP (pt));
}, "JU.P3");
$_M(c$, "setSuperCell", 
function (supercell) {
if (this.fmatSupercell != null) return;
this.fmatSupercell =  Clazz_newFloatArray (16, 0);
if (this.getSymmetry ().getMatrixFromString (supercell, this.fmatSupercell, true) == null) {
this.fmatSupercell = null;
return;
}J.util.Logger.info ("Using supercell \n" + JU.M4.newA (this.fmatSupercell));
}, "~S");
$_M(c$, "getSymmetry", 
function () {
if (this.symmetry == null) this.symmetry = J.api.Interface.getOptionInterface ("symmetry.Symmetry");
return this.symmetry;
});
$_M(c$, "setNotionalUnitCell", 
function (info, matUnitCellOrientation, unitCellOffset) {
this.notionalUnitCell =  Clazz_newFloatArray (info.length, 0);
this.unitCellOffset = unitCellOffset;
for (var i = 0; i < info.length; i++) this.notionalUnitCell[i] = info[i];

this.haveUnitCell = true;
this.setAtomSetAuxiliaryInfo ("notionalUnitcell", this.notionalUnitCell);
this.setGlobalBoolean (2);
this.getSymmetry ().setUnitCell (this.notionalUnitCell);
if (unitCellOffset != null) {
this.symmetry.setOffsetPt (unitCellOffset);
this.setAtomSetAuxiliaryInfo ("unitCellOffset", unitCellOffset);
}if (matUnitCellOrientation != null) {
this.symmetry.setUnitCellOrientation (matUnitCellOrientation);
this.setAtomSetAuxiliaryInfo ("matUnitCellOrientation", matUnitCellOrientation);
}}, "~A,JU.M3,JU.P3");
$_M(c$, "addSpaceGroupOperation", 
function (xyz) {
this.getSymmetry ().setSpaceGroup (this.doNormalize);
return this.symmetry.addSpaceGroupOperation (xyz, 0);
}, "~S");
$_M(c$, "setLatticeParameter", 
function (latt) {
this.getSymmetry ().setSpaceGroup (this.doNormalize);
this.symmetry.setLattice (latt);
}, "~N");
$_M(c$, "applySymmetry", 
function (symmetry) {
if (symmetry != null) this.getSymmetry ().setSpaceGroupS (symmetry);
this.applySymmetryLattice (this.latticeCells[0], this.latticeCells[1], Math.abs (this.latticeCells[2]));
}, "J.api.SymmetryInterface");
$_M(c$, "applySymmetryLattice", 
function (maxX, maxY, maxZ) {
if (!this.coordinatesAreFractional || !this.getSymmetry ().haveSpaceGroup ()) return;
if (this.fmatSupercell != null) {
this.rminx = 3.4028235E38;
this.rminy = 3.4028235E38;
this.rminz = 3.4028235E38;
this.rmaxx = -3.4028235E38;
this.rmaxy = -3.4028235E38;
this.rmaxz = -3.4028235E38;
var ptx = this.setSym (0, 1, 2);
var pty = this.setSym (4, 5, 6);
var ptz = this.setSym (8, 9, 10);
this.minXYZ = JU.P3i.new3 (Clazz_floatToInt (this.rminx), Clazz_floatToInt (this.rminy), Clazz_floatToInt (this.rminz));
this.maxXYZ = JU.P3i.new3 (Clazz_floatToInt (this.rmaxx), Clazz_floatToInt (this.rmaxy), Clazz_floatToInt (this.rmaxz));
this.applyAllSymmetry ();
var iAtomFirst = this.getLastAtomSetAtomIndex ();
for (var i = iAtomFirst; i < this.atomCount; i++) this.symmetry.toCartesian (this.atoms[i], true);

this.symmetry = null;
this.setNotionalUnitCell ([0, 0, 0, 0, 0, 0, ptx.x, ptx.y, ptx.z, pty.x, pty.y, pty.z, ptz.x, ptz.y, ptz.z], null, this.getAtomSetAuxiliaryInfoValue (-1, "unitCellOffset"));
this.setAtomSetSpaceGroupName ("P1");
this.getSymmetry ().setSpaceGroup (this.doNormalize);
this.symmetry.addSpaceGroupOperation ("x,y,z", 0);
for (var i = iAtomFirst; i < this.atomCount; i++) this.symmetry.toFractional (this.atoms[i], true);

this.haveAnisou = false;
this.atomSetAuxiliaryInfo[this.currentAtomSetIndex].remove ("matUnitCellOrientation");
this.doPackUnitCell = false;
}this.minXYZ =  new JU.P3i ();
this.maxXYZ = JU.P3i.new3 (maxX, maxY, maxZ);
this.applyAllSymmetry ();
this.fmatSupercell = null;
}, "~N,~N,~N");
$_M(c$, "setSym", 
function (i, j, k) {
var pt =  new JU.P3 ();
pt.set (this.fmatSupercell[i], this.fmatSupercell[j], this.fmatSupercell[k]);
this.setSymmetryMinMax (pt);
this.symmetry.toCartesian (pt, false);
return pt;
}, "~N,~N,~N");
$_M(c$, "setSymmetryMinMax", 
function (c) {
if (this.rminx > c.x) this.rminx = c.x;
if (this.rminy > c.y) this.rminy = c.y;
if (this.rminz > c.z) this.rminz = c.z;
if (this.rmaxx < c.x) this.rmaxx = c.x;
if (this.rmaxy < c.y) this.rmaxy = c.y;
if (this.rmaxz < c.z) this.rmaxz = c.z;
}, "JU.P3");
$_M(c$, "isInSymmetryRange", 
function (c) {
return (c.x >= this.rminx && c.y >= this.rminy && c.z >= this.rminz && c.x <= this.rmaxx && c.y <= this.rmaxy && c.z <= this.rmaxz);
}, "JU.P3");
c$.isWithinCell = $_M(c$, "isWithinCell", 
function (dtype, pt, minX, maxX, minY, maxY, minZ, maxZ) {
var slop = 0.02;
return (pt.x > minX - slop && pt.x < maxX + slop && (dtype < 2 || pt.y > minY - slop && pt.y < maxY + slop) && (dtype < 3 || pt.z > minZ - slop && pt.z < maxZ + slop));
}, "~N,JU.P3,~N,~N,~N,~N,~N,~N");
$_M(c$, "setAnisoBorU", 
function (atom, data, type) {
this.haveAnisou = true;
atom.anisoBorU = data;
data[6] = type;
}, "J.adapter.smarter.Atom,~A,~N");
$_M(c$, "getAnisoBorU", 
function (atom) {
return atom.anisoBorU;
}, "J.adapter.smarter.Atom");
$_M(c$, "setTensors", 
function () {
if (!this.haveAnisou) return;
this.getSymmetry ();
for (var i = this.getLastAtomSetAtomIndex (); i < this.atomCount; i++) this.atoms[i].addTensor (this.symmetry.getTensor (this.atoms[i].anisoBorU), null, false);

});
$_M(c$, "setLatticeOnly", 
function (b) {
this.checkLatticeOnly = b;
}, "~B");
$_M(c$, "setBaseSymmetryAtomCount", 
function (n) {
this.baseSymmetryAtomCount = n;
}, "~N");
$_M(c$, "applyAllSymmetry", 
function () {
var noSymmetryCount = (this.baseSymmetryAtomCount == 0 ? this.getLastAtomSetAtomCount () : this.baseSymmetryAtomCount);
var iAtomFirst = this.getLastAtomSetAtomIndex ();
this.setTensors ();
this.bondCount0 = this.bondCount;
this.finalizeSymmetry (iAtomFirst, noSymmetryCount);
var operationCount = this.symmetry.getSpaceGroupOperationCount ();
this.getSymmetry ().setMinMaxLatticeParameters (this.minXYZ, this.maxXYZ);
this.dtype = Clazz_floatToInt (this.getSymmetry ().getUnitCellInfoType (6));
if (this.doCentroidUnitCell) this.setAtomSetCollectionAuxiliaryInfo ("centroidMinMax", [this.minXYZ.x, this.minXYZ.y, this.minXYZ.z, this.maxXYZ.x, this.maxXYZ.y, this.maxXYZ.z, (this.centroidPacked ? 1 : 0)]);
if (this.ptSupercell != null) {
this.setAtomSetAuxiliaryInfo ("supercell", this.ptSupercell);
switch (this.dtype) {
case 3:
this.minXYZ.z *= Clazz_floatToInt (Math.abs (this.ptSupercell.z));
this.maxXYZ.z *= Clazz_floatToInt (Math.abs (this.ptSupercell.z));
case 2:
this.minXYZ.y *= Clazz_floatToInt (Math.abs (this.ptSupercell.y));
this.maxXYZ.y *= Clazz_floatToInt (Math.abs (this.ptSupercell.y));
case 1:
this.minXYZ.x *= Clazz_floatToInt (Math.abs (this.ptSupercell.x));
this.maxXYZ.x *= Clazz_floatToInt (Math.abs (this.ptSupercell.x));
}
}if (this.doCentroidUnitCell || this.doPackUnitCell || this.symmetryRange != 0 && this.maxXYZ.x - this.minXYZ.x == 1 && this.maxXYZ.y - this.minXYZ.y == 1 && this.maxXYZ.z - this.minXYZ.z == 1) {
this.minXYZ0 = JU.P3i.new3 (this.minXYZ.x, this.minXYZ.y, this.minXYZ.z);
this.maxXYZ0 = JU.P3i.new3 (this.maxXYZ.x, this.maxXYZ.y, this.maxXYZ.z);
switch (this.dtype) {
case 3:
this.minXYZ.z--;
this.maxXYZ.z++;
case 2:
this.minXYZ.y--;
this.maxXYZ.y++;
case 1:
this.minXYZ.x--;
this.maxXYZ.x++;
}
}var nCells = (this.maxXYZ.x - this.minXYZ.x) * (this.maxXYZ.y - this.minXYZ.y) * (this.maxXYZ.z - this.minXYZ.z);
var cartesianCount = (this.checkSpecial ? noSymmetryCount * operationCount * nCells : this.symmetryRange > 0 ? noSymmetryCount * operationCount : this.symmetryRange < 0 ? 1 : 1);
var cartesians =  new Array (cartesianCount);
for (var i = 0; i < noSymmetryCount; i++) this.atoms[i + iAtomFirst].bsSymmetry = J.util.BSUtil.newBitSet (operationCount * (nCells + 1));

var pt = 0;
var unitCells =  Clazz_newIntArray (nCells, 0);
this.unitCellTranslations =  new Array (nCells);
var iCell = 0;
var cell555Count = 0;
var absRange = Math.abs (this.symmetryRange);
var checkSymmetryRange = (this.symmetryRange != 0);
var checkRangeNoSymmetry = (this.symmetryRange < 0);
var checkRange111 = (this.symmetryRange > 0);
if (checkSymmetryRange) {
this.rminx = 3.4028235E38;
this.rminy = 3.4028235E38;
this.rminz = 3.4028235E38;
this.rmaxx = -3.4028235E38;
this.rmaxy = -3.4028235E38;
this.rmaxz = -3.4028235E38;
}this.latticeOp = this.symmetry.getLatticeOp ();
this.checkAll = (this.atomSetCount == 1 && this.checkSpecial && this.latticeOp >= 0);
this.latticeOnly = (this.checkLatticeOnly && this.latticeOp >= 0);
var op = this.symmetry.getSpaceGroupOperation (0);
if (this.doPackUnitCell) this.ptOffset.set (0, 0, 0);
for (var tx = this.minXYZ.x; tx < this.maxXYZ.x; tx++) for (var ty = this.minXYZ.y; ty < this.maxXYZ.y; ty++) for (var tz = this.minXYZ.z; tz < this.maxXYZ.z; tz++) {
this.unitCellTranslations[iCell] = JU.V3.new3 (tx, ty, tz);
unitCells[iCell++] = 555 + tx * 100 + ty * 10 + tz;
if (tx != 0 || ty != 0 || tz != 0 || cartesians.length == 0) continue;
for (pt = 0; pt < noSymmetryCount; pt++) {
var atom = this.atoms[iAtomFirst + pt];
var c = JU.P3.newP (atom);
op.transform (c);
this.symmetry.toCartesian (c, false);
if (this.doPackUnitCell) {
this.symmetry.toUnitCell (c, this.ptOffset);
atom.setT (c);
this.symmetry.toFractional (atom, false);
}atom.bsSymmetry.set (iCell * operationCount);
atom.bsSymmetry.set (0);
if (checkSymmetryRange) this.setSymmetryMinMax (c);
if (pt < cartesianCount) cartesians[pt] = c;
}
if (checkRangeNoSymmetry) {
this.rminx -= absRange;
this.rminy -= absRange;
this.rminz -= absRange;
this.rmaxx += absRange;
this.rmaxy += absRange;
this.rmaxz += absRange;
}cell555Count = pt = this.symmetryAddAtoms (iAtomFirst, noSymmetryCount, 0, 0, 0, 0, pt, iCell * operationCount, cartesians);
}


if (checkRange111) {
this.rminx -= absRange;
this.rminy -= absRange;
this.rminz -= absRange;
this.rmaxx += absRange;
this.rmaxy += absRange;
this.rmaxz += absRange;
}iCell = 0;
for (var tx = this.minXYZ.x; tx < this.maxXYZ.x; tx++) for (var ty = this.minXYZ.y; ty < this.maxXYZ.y; ty++) for (var tz = this.minXYZ.z; tz < this.maxXYZ.z; tz++) {
iCell++;
if (tx != 0 || ty != 0 || tz != 0) pt = this.symmetryAddAtoms (iAtomFirst, noSymmetryCount, tx, ty, tz, cell555Count, pt, iCell * operationCount, cartesians);
}


if (iCell * noSymmetryCount == this.atomCount - iAtomFirst) this.appendAtomProperties (iCell);
this.setSymmetryOps ();
this.setAtomSetAuxiliaryInfo ("presymmetryAtomIndex", Integer.$valueOf (iAtomFirst));
this.setAtomSetAuxiliaryInfo ("presymmetryAtomCount", Integer.$valueOf (noSymmetryCount));
this.setAtomSetAuxiliaryInfo ("latticeDesignation", this.symmetry.getLatticeDesignation ());
this.setAtomSetAuxiliaryInfo ("unitCellRange", unitCells);
this.setAtomSetAuxiliaryInfo ("unitCellTranslations", this.unitCellTranslations);
this.notionalUnitCell =  Clazz_newFloatArray (6, 0);
this.coordinatesAreFractional = false;
this.setAtomSetAuxiliaryInfo ("hasSymmetry", Boolean.TRUE);
this.setGlobalBoolean (1);
});
$_M(c$, "finalizeSymmetry", 
function (iAtomFirst, noSymmetryCount) {
var name = this.getAtomSetAuxiliaryInfoValue (-1, "spaceGroup");
this.symmetry.setFinalOperations (name, this.atoms, iAtomFirst, noSymmetryCount, this.doNormalize);
if (name == null || name.equals ("unspecified!")) this.setAtomSetSpaceGroupName (this.symmetry.getSpaceGroupName ());
}, "~N,~N");
$_M(c$, "setSymmetryOps", 
function () {
var operationCount = this.symmetry.getSpaceGroupOperationCount ();
if (operationCount > 0) {
var symmetryList =  new Array (operationCount);
for (var i = 0; i < operationCount; i++) symmetryList[i] = "" + this.symmetry.getSpaceGroupXyz (i, this.doNormalize);

this.setAtomSetAuxiliaryInfo ("symmetryOperations", symmetryList);
}this.setAtomSetAuxiliaryInfo ("symmetryCount", Integer.$valueOf (operationCount));
});
$_M(c$, "setCheckSpecial", 
function (TF) {
this.checkSpecial = TF;
}, "~B");
$_M(c$, "symmetryAddAtoms", 
function (iAtomFirst, noSymmetryCount, transX, transY, transZ, baseCount, pt, iCellOpPt, cartesians) {
var isBaseCell = (baseCount == 0);
var addBonds = (this.bondCount0 > this.bondIndex0 && this.applySymmetryToBonds);
var atomMap = (addBonds ?  Clazz_newIntArray (noSymmetryCount, 0) : null);
if (this.doPackUnitCell) this.ptOffset.set (transX, transY, transZ);
var range2 = this.symmetryRange * this.symmetryRange;
var checkRangeNoSymmetry = (this.symmetryRange < 0);
var checkRange111 = (this.symmetryRange > 0);
var checkSymmetryMinMax = (isBaseCell && checkRange111);
checkRange111 = new Boolean (checkRange111 & !isBaseCell).valueOf ();
var nOperations = this.symmetry.getSpaceGroupOperationCount ();
if (nOperations == 1) this.checkSpecial = false;
var checkSymmetryRange = (checkRangeNoSymmetry || checkRange111);
var checkDistances = (this.checkSpecial || checkSymmetryRange);
var addCartesian = (this.checkSpecial || checkSymmetryMinMax);
if (checkRangeNoSymmetry) baseCount = noSymmetryCount;
var atomMax = iAtomFirst + noSymmetryCount;
var ptAtom =  new JU.P3 ();
for (var iSym = 0; iSym < nOperations; iSym++) {
if (isBaseCell && iSym == 0 || this.latticeOnly && iSym > 0 && iSym != this.latticeOp) continue;
var pt0 = (this.checkSpecial ? pt : checkRange111 ? baseCount : 0);
for (var i = iAtomFirst; i < atomMax; i++) {
if (this.atoms[i].ignoreSymmetry) continue;
if (this.bsAtoms != null && !this.bsAtoms.get (i)) continue;
this.symmetry.newSpaceGroupPoint (iSym, this.atoms[i], ptAtom, transX, transY, transZ);
var special = null;
var cartesian = JU.P3.newP (ptAtom);
this.symmetry.toCartesian (cartesian, false);
if (this.doPackUnitCell) {
this.symmetry.toUnitCell (cartesian, this.ptOffset);
ptAtom.setT (cartesian);
this.symmetry.toFractional (ptAtom, false);
if (!J.adapter.smarter.AtomSetCollection.isWithinCell (this.dtype, ptAtom, this.minXYZ0.x, this.maxXYZ0.x, this.minXYZ0.y, this.maxXYZ0.y, this.minXYZ0.z, this.maxXYZ0.z)) continue;
}if (checkSymmetryMinMax) this.setSymmetryMinMax (cartesian);
if (checkDistances) {
var minDist2 = 3.4028235E38;
if (checkSymmetryRange && !this.isInSymmetryRange (cartesian)) continue;
var j0 = (this.checkAll ? this.atomCount : pt0);
for (var j = j0; --j >= 0; ) {
var d2 = cartesian.distanceSquared (cartesians[j]);
if (this.checkSpecial && d2 < 0.0001) {
special = this.atoms[iAtomFirst + j];
if (special.atomName == null || special.atomName.equals (this.atoms[i].atomName)) break;
special = null;
}if (checkRange111 && j < baseCount && d2 < minDist2) minDist2 = d2;
}
if (checkRange111 && minDist2 > range2) continue;
}var atomSite = this.atoms[i].atomSite;
if (special != null) {
if (addBonds) atomMap[atomSite] = special.index;
special.bsSymmetry.set (iCellOpPt + iSym);
special.bsSymmetry.set (iSym);
} else {
if (addBonds) atomMap[atomSite] = this.atomCount;
var atom1 = this.newCloneAtom (this.atoms[i]);
atom1.setT (ptAtom);
atom1.atomSite = atomSite;
atom1.bsSymmetry = J.util.BSUtil.newAndSetBit (iCellOpPt + iSym);
atom1.bsSymmetry.set (iSym);
if (addCartesian) cartesians[pt++] = cartesian;
if (this.atoms[i].tensors != null) {
atom1.tensors = null;
for (var j = this.atoms[i].tensors.size (); --j >= 0; ) {
var t = this.atoms[i].tensors.get (j);
if (t == null) continue;
if (nOperations == 1) atom1.addTensor (t.copyTensor (), null, false);
 else this.addRotatedTensor (atom1, t, iSym, false);
}
}}}
if (addBonds) {
for (var bondNum = this.bondIndex0; bondNum < this.bondCount0; bondNum++) {
var bond = this.bonds[bondNum];
var atom1 = this.atoms[bond.atomIndex1];
var atom2 = this.atoms[bond.atomIndex2];
if (atom1 == null || atom2 == null) continue;
var iAtom1 = atomMap[atom1.atomSite];
var iAtom2 = atomMap[atom2.atomSite];
if (iAtom1 >= atomMax || iAtom2 >= atomMax) this.addNewBondWithOrder (iAtom1, iAtom2, bond.order);
}
}}
return pt;
}, "~N,~N,~N,~N,~N,~N,~N,~N,~A");
$_M(c$, "addRotatedTensor", 
function (a, t, iSym, reset) {
if (this.ptTemp == null) {
this.ptTemp =  new JU.P3 ();
this.mTemp =  new JU.M3 ();
}return a.addTensor ((J.api.Interface.getOptionInterface ("util.Tensor")).setFromEigenVectors (this.symmetry.rotateAxes (iSym, t.eigenVectors, this.ptTemp, this.mTemp), t.eigenValues, t.isIsotropic ? "iso" : t.type, t.id), null, reset);
}, "J.adapter.smarter.Atom,J.util.Tensor,~N,~B");
$_M(c$, "applySymmetryBio", 
function (thisBiomolecule, notionalUnitCell, applySymmetryToBonds, filter) {
if (this.latticeCells != null && this.latticeCells[0] != 0) {
J.util.Logger.error ("Cannot apply biomolecule when lattice cells are indicated");
return;
}var particleMode = (filter.indexOf ("BYCHAIN") >= 0 ? 1 : filter.indexOf ("BYSYMOP") >= 0 ? 2 : 0);
this.doNormalize = false;
this.symmetry = null;
var biomts = thisBiomolecule.get ("biomts");
if (biomts.size () < 2) return;
if (!Float.isNaN (notionalUnitCell[0])) this.setNotionalUnitCell (notionalUnitCell, null, this.unitCellOffset);
this.getSymmetry ().setSpaceGroup (this.doNormalize);
this.symmetry.setUnitCell (null);
this.addSpaceGroupOperation ("x,y,z");
var name = thisBiomolecule.get ("name");
this.setAtomSetSpaceGroupName (name);
var len = biomts.size ();
this.applySymmetryToBonds = applySymmetryToBonds;
this.bondCount0 = this.bondCount;
var addBonds = (this.bondCount0 > this.bondIndex0 && applySymmetryToBonds);
var atomMap = (addBonds ?  Clazz_newIntArray (this.atomCount, 0) : null);
var iAtomFirst = this.getLastAtomSetAtomIndex ();
var atomMax = this.atomCount;
var ht =  new java.util.Hashtable ();
var nChain = 0;
switch (particleMode) {
case 1:
for (var i = atomMax; --i >= iAtomFirst; ) {
var id = Integer.$valueOf (this.atoms[i].chainID);
var bs = ht.get (id);
if (bs == null) {
nChain++;
ht.put (id, bs =  new JU.BS ());
}bs.set (i);
}
this.bsAtoms =  new JU.BS ();
for (var i = 0; i < nChain; i++) {
this.bsAtoms.set (atomMax + i);
var a =  new J.adapter.smarter.Atom ();
a.set (0, 0, 0);
this.addAtom (a);
}
var ichain = 0;
for (var e, $e = ht.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var a = this.atoms[atomMax + ichain++];
var bs = e.getValue ();
for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) a.add (this.atoms[i]);

a.scale (1 / bs.cardinality ());
a.atomName = "Pt" + ichain;
}
iAtomFirst = atomMax;
atomMax += nChain;
break;
case 2:
this.bsAtoms =  new JU.BS ();
this.bsAtoms.set (atomMax);
var a = this.atoms[atomMax] =  new J.adapter.smarter.Atom ();
a.set (0, 0, 0);
for (var i = atomMax; --i >= iAtomFirst; ) a.add (this.atoms[i]);

a.scale (1 / (atomMax - iAtomFirst));
a.atomName = "Pt";
iAtomFirst = atomMax++;
break;
}
if (filter.indexOf ("#<") >= 0) {
len = Math.min (len, JU.PT.parseInt (filter.substring (filter.indexOf ("#<") + 2)) - 1);
filter = JU.PT.simpleReplace (filter, "#<", "_<");
}for (var iAtom = iAtomFirst; iAtom < atomMax; iAtom++) this.atoms[iAtom].bsSymmetry = J.util.BSUtil.newAndSetBit (0);

for (var i = 1; i < len; i++) {
if (filter.indexOf ("!#") >= 0) {
if (filter.indexOf ("!#" + (i + 1) + ";") >= 0) continue;
} else if (filter.indexOf ("#") >= 0 && filter.indexOf ("#" + (i + 1) + ";") < 0) {
continue;
}var mat = biomts.get (i);
for (var iAtom = iAtomFirst; iAtom < atomMax; iAtom++) {
if (this.bsAtoms != null && !this.bsAtoms.get (iAtom)) continue;
try {
var atomSite = this.atoms[iAtom].atomSite;
var atom1;
if (addBonds) atomMap[atomSite] = this.atomCount;
atom1 = this.newCloneAtom (this.atoms[iAtom]);
if (this.bsAtoms != null) this.bsAtoms.set (atom1.index);
atom1.atomSite = atomSite;
mat.transform (atom1);
atom1.bsSymmetry = J.util.BSUtil.newAndSetBit (i);
if (addBonds) {
for (var bondNum = this.bondIndex0; bondNum < this.bondCount0; bondNum++) {
var bond = this.bonds[bondNum];
var iAtom1 = atomMap[this.atoms[bond.atomIndex1].atomSite];
var iAtom2 = atomMap[this.atoms[bond.atomIndex2].atomSite];
if (iAtom1 >= atomMax || iAtom2 >= atomMax) this.addNewBondWithOrder (iAtom1, iAtom2, bond.order);
}
}} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
this.errorMessage = "appendAtomCollection error: " + e;
} else {
throw e;
}
}
}
mat.m03 /= notionalUnitCell[0];
if (Float.isNaN (mat.m03)) mat.m03 = 1;
mat.m13 /= notionalUnitCell[1];
mat.m23 /= notionalUnitCell[2];
if (i > 0) this.symmetry.addBioMoleculeOperation (mat, false);
}
var noSymmetryCount = atomMax - iAtomFirst;
this.setAtomSetAuxiliaryInfo ("presymmetryAtomIndex", Integer.$valueOf (iAtomFirst));
this.setAtomSetAuxiliaryInfo ("presymmetryAtomCount", Integer.$valueOf (noSymmetryCount));
this.setAtomSetAuxiliaryInfo ("biosymmetryCount", Integer.$valueOf (len));
this.setAtomSetAuxiliaryInfo ("biosymmetry", this.symmetry);
this.finalizeSymmetry (iAtomFirst, noSymmetryCount);
this.setSymmetryOps ();
this.symmetry = null;
this.coordinatesAreFractional = false;
this.setAtomSetAuxiliaryInfo ("hasSymmetry", Boolean.TRUE);
this.setGlobalBoolean (1);
}, "java.util.Map,~A,~B,~S");
$_M(c$, "mapMostRecentAtomName", 
function () {
if (this.atomCount > 0) {
var index = this.atomCount - 1;
var atomName = this.atoms[index].atomName;
if (atomName != null) this.atomSymbolicMap.put (atomName, Integer.$valueOf (index));
}});
$_M(c$, "clearSymbolicMap", 
function () {
this.atomSymbolicMap.clear ();
this.haveMappedSerials = false;
});
$_M(c$, "mapMostRecentAtomSerialNumber", 
function () {
if (this.atomCount == 0) return;
var index = this.atomCount - 1;
var atomSerial = this.atoms[index].atomSerial;
if (atomSerial != -2147483648) this.atomSymbolicMap.put (Integer.$valueOf (atomSerial), Integer.$valueOf (index));
this.haveMappedSerials = true;
});
$_M(c$, "createAtomSerialMap", 
function () {
if (this.haveMappedSerials || this.currentAtomSetIndex < 0) return;
for (var i = this.getLastAtomSetAtomCount (); i < this.atomCount; i++) {
var atomSerial = this.atoms[i].atomSerial;
if (atomSerial != -2147483648) this.atomSymbolicMap.put (Integer.$valueOf (atomSerial), Integer.$valueOf (i));
}
this.haveMappedSerials = true;
});
$_M(c$, "getAtomIndexFromName", 
function (atomName) {
return this.getMapIndex (atomName);
}, "~S");
$_M(c$, "getAtomIndexFromSerial", 
function (serialNumber) {
return this.getMapIndex (Integer.$valueOf (serialNumber));
}, "~N");
$_M(c$, "getMapIndex", 
function (nameOrNum) {
var value = this.atomSymbolicMap.get (nameOrNum);
return (value == null ? -1 : value.intValue ());
}, "~O");
$_M(c$, "setAtomSetCollectionAuxiliaryInfo", 
function (key, value) {
if (value == null) this.atomSetCollectionAuxiliaryInfo.remove (key);
 else this.atomSetCollectionAuxiliaryInfo.put (key, value);
}, "~S,~O");
$_M(c$, "setAtomSetCollectionPartialCharges", 
function (auxKey) {
if (!this.atomSetCollectionAuxiliaryInfo.containsKey (auxKey)) {
return false;
}var atomData = this.atomSetCollectionAuxiliaryInfo.get (auxKey);
for (var i = atomData.size (); --i >= 0; ) this.atoms[i].partialCharge = atomData.get (i).floatValue ();

J.util.Logger.info ("Setting partial charges type " + auxKey);
return true;
}, "~S");
$_M(c$, "mapPartialCharge", 
function (atomName, charge) {
this.atoms[this.getAtomIndexFromName (atomName)].partialCharge = charge;
}, "~S,~N");
$_M(c$, "getAtomSetCollectionAuxiliaryInfo", 
function (key) {
return this.atomSetCollectionAuxiliaryInfo.get (key);
}, "~S");
$_M(c$, "addTrajectoryStep", 
function () {
var trajectoryStep =  new Array (this.atomCount);
var haveVibrations = (this.atomCount > 0 && this.atoms[0].vib != null && !Float.isNaN (this.atoms[0].vib.z));
var vibrationStep = (haveVibrations ?  new Array (this.atomCount) : null);
var prevSteps = (this.trajectoryStepCount == 0 ? null : this.trajectorySteps.get (this.trajectoryStepCount - 1));
for (var i = 0; i < this.atomCount; i++) {
var pt = JU.P3.newP (this.atoms[i]);
if (this.doFixPeriodic && prevSteps != null) pt = J.adapter.smarter.AtomSetCollection.fixPeriodic (pt, prevSteps[i]);
trajectoryStep[i] = pt;
if (haveVibrations) vibrationStep[i] = this.atoms[i].vib;
}
if (haveVibrations) {
if (this.vibrationSteps == null) {
this.vibrationSteps =  new JU.List ();
for (var i = 0; i < this.trajectoryStepCount; i++) this.vibrationSteps.addLast (null);

}this.vibrationSteps.addLast (vibrationStep);
}this.trajectorySteps.addLast (trajectoryStep);
this.trajectoryStepCount++;
});
c$.fixPeriodic = $_M(c$, "fixPeriodic", 
function (pt, pt0) {
pt.x = J.adapter.smarter.AtomSetCollection.fixPoint (pt.x, pt0.x);
pt.y = J.adapter.smarter.AtomSetCollection.fixPoint (pt.y, pt0.y);
pt.z = J.adapter.smarter.AtomSetCollection.fixPoint (pt.z, pt0.z);
return pt;
}, "JU.P3,JU.P3");
c$.fixPoint = $_M(c$, "fixPoint", 
function (x, x0) {
while (x - x0 > 0.9) {
x -= 1;
}
while (x - x0 < -0.9) {
x += 1;
}
return x;
}, "~N,~N");
$_M(c$, "finalizeTrajectoryAs", 
function (trajectorySteps, vibrationSteps) {
this.trajectorySteps = trajectorySteps;
this.vibrationSteps = vibrationSteps;
this.trajectoryStepCount = trajectorySteps.size ();
this.finalizeTrajectory ();
}, "JU.List,JU.List");
$_M(c$, "finalizeTrajectory", 
function () {
if (this.trajectoryStepCount == 0) return;
var trajectory = this.trajectorySteps.get (0);
var vibrations = (this.vibrationSteps == null ? null : this.vibrationSteps.get (0));
var v =  new JU.V3 ();
if (this.vibrationSteps != null && vibrations != null && vibrations.length < this.atomCount || trajectory.length < this.atomCount) {
this.errorMessage = "File cannot be loaded as a trajectory";
return;
}for (var i = 0; i < this.atomCount; i++) {
if (this.vibrationSteps != null) this.atoms[i].vib = (vibrations == null ? v : vibrations[i]);
if (trajectory[i] != null) this.atoms[i].setT (trajectory[i]);
}
this.setAtomSetCollectionAuxiliaryInfo ("trajectorySteps", this.trajectorySteps);
if (this.vibrationSteps != null) this.setAtomSetCollectionAuxiliaryInfo ("vibrationSteps", this.vibrationSteps);
});
$_M(c$, "newAtomSet", 
function () {
this.newAtomSetClear (true);
});
$_M(c$, "newAtomSetClear", 
function (doClearMap) {
if (!this.allowMultiple && this.currentAtomSetIndex >= 0) this.discardPreviousAtoms ();
this.bondIndex0 = this.bondCount;
if (this.isTrajectory) {
this.discardPreviousAtoms ();
}this.currentAtomSetIndex = this.atomSetCount++;
if (this.atomSetCount > this.atomSetNumbers.length) {
this.atomSetAtomIndexes = JU.AU.doubleLengthI (this.atomSetAtomIndexes);
this.atomSetAtomCounts = JU.AU.doubleLengthI (this.atomSetAtomCounts);
this.atomSetBondCounts = JU.AU.doubleLengthI (this.atomSetBondCounts);
this.atomSetAuxiliaryInfo = JU.AU.doubleLength (this.atomSetAuxiliaryInfo);
}this.atomSetAtomIndexes[this.currentAtomSetIndex] = this.atomCount;
if (this.atomSetCount + this.trajectoryStepCount > this.atomSetNumbers.length) {
this.atomSetNumbers = JU.AU.doubleLengthI (this.atomSetNumbers);
}if (this.isTrajectory) {
this.atomSetNumbers[this.currentAtomSetIndex + this.trajectoryStepCount] = this.atomSetCount + this.trajectoryStepCount;
} else {
this.atomSetNumbers[this.currentAtomSetIndex] = this.atomSetCount;
}if (doClearMap) this.atomSymbolicMap.clear ();
this.setAtomSetAuxiliaryInfo ("title", this.collectionName);
}, "~B");
$_M(c$, "getAtomSetAtomIndex", 
function (i) {
return this.atomSetAtomIndexes[i];
}, "~N");
$_M(c$, "getAtomSetAtomCount", 
function (i) {
return this.atomSetAtomCounts[i];
}, "~N");
$_M(c$, "getAtomSetBondCount", 
function (i) {
return this.atomSetBondCounts[i];
}, "~N");
$_M(c$, "setAtomSetName", 
function (atomSetName) {
if (this.isTrajectory) {
this.setTrajectoryName (atomSetName);
return;
}this.setAtomSetAuxiliaryInfoForSet ("name", atomSetName, this.currentAtomSetIndex);
if (!this.allowMultiple) this.setCollectionName (atomSetName);
}, "~S");
$_M(c$, "setTrajectoryName", 
function (name) {
if (this.trajectoryStepCount == 0) return;
if (this.trajectoryNames == null) {
this.trajectoryNames =  new JU.List ();
}for (var i = this.trajectoryNames.size (); i < this.trajectoryStepCount; i++) this.trajectoryNames.addLast (null);

this.trajectoryNames.set (this.trajectoryStepCount - 1, name);
}, "~S");
$_M(c$, "setAtomSetNames", 
function (atomSetName, n, namedSets) {
for (var i = this.currentAtomSetIndex; --n >= 0 && i >= 0; --i) if (namedSets == null || !namedSets.get (i)) this.setAtomSetAuxiliaryInfoForSet ("name", atomSetName, i);

}, "~S,~N,JU.BS");
$_M(c$, "setCurrentAtomSetNumber", 
function (atomSetNumber) {
this.setAtomSetNumber (this.currentAtomSetIndex + (this.isTrajectory ? this.trajectoryStepCount : 0), atomSetNumber);
}, "~N");
$_M(c$, "setAtomSetNumber", 
function (index, atomSetNumber) {
this.atomSetNumbers[index] = atomSetNumber;
}, "~N,~N");
$_M(c$, "setAtomSetModelProperty", 
function (key, value) {
this.setAtomSetModelPropertyForSet (key, value, this.currentAtomSetIndex);
}, "~S,~S");
$_M(c$, "setAtomSetModelPropertyForSet", 
function (key, value, atomSetIndex) {
var p = this.getAtomSetAuxiliaryInfoValue (atomSetIndex, "modelProperties");
if (p == null) this.setAtomSetAuxiliaryInfoForSet ("modelProperties", p =  new java.util.Properties (), atomSetIndex);
p.put (key, value);
}, "~S,~S,~N");
$_M(c$, "setAtomSetAtomProperty", 
function (key, data, atomSetIndex) {
if (!data.endsWith ("\n")) data += "\n";
if (atomSetIndex < 0) atomSetIndex = this.currentAtomSetIndex;
var p = this.getAtomSetAuxiliaryInfoValue (atomSetIndex, "atomProperties");
if (p == null) this.setAtomSetAuxiliaryInfoForSet ("atomProperties", p =  new java.util.Hashtable (), atomSetIndex);
p.put (key, data);
}, "~S,~S,~N");
$_M(c$, "appendAtomProperties", 
function (nTimes) {
var p = this.getAtomSetAuxiliaryInfoValue (-1, "atomProperties");
if (p == null) {
return;
}for (var entry, $entry = p.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) {
var key = entry.getKey ();
var data = entry.getValue ();
var s =  new JU.SB ();
for (var i = nTimes; --i >= 0; ) s.append (data);

p.put (key, s.toString ());
}
}, "~N");
$_M(c$, "setAtomSetPartialCharges", 
function (auxKey) {
if (!this.atomSetAuxiliaryInfo[this.currentAtomSetIndex].containsKey (auxKey)) {
return false;
}var atomData = this.getAtomSetAuxiliaryInfoValue (this.currentAtomSetIndex, auxKey);
for (var i = atomData.size (); --i >= 0; ) {
this.atoms[i].partialCharge = atomData.get (i).floatValue ();
}
return true;
}, "~S");
$_M(c$, "getAtomSetAuxiliaryInfoValue", 
function (index, key) {
return this.atomSetAuxiliaryInfo[index >= 0 ? index : this.currentAtomSetIndex].get (key);
}, "~N,~S");
$_M(c$, "setAtomSetAuxiliaryInfo", 
function (key, value) {
this.setAtomSetAuxiliaryInfoForSet (key, value, this.currentAtomSetIndex);
}, "~S,~O");
$_M(c$, "setAtomSetAuxiliaryInfoForSet", 
function (key, value, atomSetIndex) {
if (atomSetIndex < 0) return;
if (this.atomSetAuxiliaryInfo[atomSetIndex] == null) this.atomSetAuxiliaryInfo[atomSetIndex] =  new java.util.Hashtable ();
if (value == null) this.atomSetAuxiliaryInfo[atomSetIndex].remove (key);
 else this.atomSetAuxiliaryInfo[atomSetIndex].put (key, value);
}, "~S,~O,~N");
$_M(c$, "setAtomSetPropertyForSets", 
function (key, value, n) {
for (var idx = this.currentAtomSetIndex; --n >= 0 && idx >= 0; --idx) this.setAtomSetModelPropertyForSet (key, value, idx);

}, "~S,~S,~N");
$_M(c$, "cloneLastAtomSetProperties", 
function () {
this.cloneAtomSetProperties (this.currentAtomSetIndex - 1);
});
$_M(c$, "cloneAtomSetProperties", 
function (index) {
var p = this.getAtomSetAuxiliaryInfoValue (index, "modelProperties");
if (p != null) this.setAtomSetAuxiliaryInfoForSet ("modelProperties", p.clone (), this.currentAtomSetIndex);
}, "~N");
$_M(c$, "getAtomSetNumber", 
function (atomSetIndex) {
return this.atomSetNumbers[atomSetIndex >= this.atomSetCount ? 0 : atomSetIndex];
}, "~N");
$_M(c$, "getAtomSetName", 
function (atomSetIndex) {
if (this.trajectoryNames != null && atomSetIndex < this.trajectoryNames.size ()) return this.trajectoryNames.get (atomSetIndex);
if (atomSetIndex >= this.atomSetCount) atomSetIndex = this.atomSetCount - 1;
return this.getAtomSetAuxiliaryInfoValue (atomSetIndex, "name");
}, "~N");
$_M(c$, "getAtomSetAuxiliaryInfo", 
function (atomSetIndex) {
return this.atomSetAuxiliaryInfo[atomSetIndex >= this.atomSetCount ? this.atomSetCount - 1 : atomSetIndex];
}, "~N");
$_M(c$, "setAtomNames", 
function (atomIdNames) {
if (atomIdNames == null) return null;
var s;
for (var i = 0; i < this.atomCount; i++) if ((s = atomIdNames.getProperty (this.atoms[i].atomName)) != null) this.atoms[i].atomName = s;

return null;
}, "java.util.Properties");
$_M(c$, "setAtomSetEnergy", 
function (energyString, value) {
if (this.currentAtomSetIndex < 0) return;
J.util.Logger.info ("Energy for model " + (this.currentAtomSetIndex + 1) + " = " + energyString);
this.setAtomSetAuxiliaryInfo ("EnergyString", energyString);
this.setAtomSetAuxiliaryInfo ("Energy", Float.$valueOf (value));
this.setAtomSetModelProperty ("Energy", "" + value);
}, "~S,~N");
$_M(c$, "setAtomSetFrequency", 
function (pathKey, label, freq, units) {
freq += " " + (units == null ? "cm^-1" : units);
var name = (label == null ? "" : label + " ") + freq;
this.setAtomSetName (name);
this.setAtomSetModelProperty ("Frequency", freq);
if (label != null) this.setAtomSetModelProperty ("FrequencyLabel", label);
this.setAtomSetModelProperty (".PATH", (pathKey == null ? "" : pathKey + J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR + "Frequencies") + "Frequencies");
return name;
}, "~S,~S,~S,~S");
$_M(c$, "toCartesian", 
function (symmetry) {
for (var i = this.getLastAtomSetAtomIndex (); i < this.atomCount; i++) symmetry.toCartesian (this.atoms[i], true);

}, "J.api.SymmetryInterface");
$_M(c$, "getBondList", 
function () {
var info =  new Array (this.bondCount);
for (var i = 0; i < this.bondCount; i++) {
info[i] = [this.atoms[this.bonds[i].atomIndex1].atomName, this.atoms[this.bonds[i].atomIndex2].atomName, "" + this.bonds[i].order];
}
return info;
});
$_M(c$, "centralize", 
function () {
var pt =  new JU.P3 ();
for (var i = 0; i < this.atomSetCount; i++) {
var n = this.atomSetAtomCounts[i];
var atom0 = this.atomSetAtomIndexes[i];
pt.set (0, 0, 0);
for (var j = atom0 + n; --j >= atom0; ) pt.add (this.atoms[j]);

pt.scale (1 / n);
for (var j = atom0 + n; --j >= atom0; ) this.atoms[j].sub (pt);

}
});
$_M(c$, "mergeTrajectories", 
function (a) {
if (!this.isTrajectory || !a.isTrajectory || this.vibrationSteps != null) return;
for (var i = 0; i < a.trajectoryStepCount; i++) this.trajectorySteps.add (this.trajectoryStepCount++, a.trajectorySteps.get (i));

this.setAtomSetCollectionAuxiliaryInfo ("trajectorySteps", this.trajectorySteps);
}, "J.adapter.smarter.AtomSetCollection");
Clazz_defineStatics (c$,
"globalBooleans", ["someModelsHaveFractionalCoordinates", "someModelsHaveSymmetry", "someModelsHaveUnitcells", "someModelsHaveCONECT", "isPDB"],
"GLOBAL_FRACTCOORD", 0,
"GLOBAL_SYMMETRY", 1,
"GLOBAL_UNITCELLS", 2,
"GLOBAL_CONECT", 3,
"GLOBAL_ISPDB", 4,
"notionalUnitcellTags", ["a", "b", "c", "alpha", "beta", "gamma"],
"PARTICLE_NONE", 0,
"PARTICLE_CHAIN", 1,
"PARTICLE_SYMOP", 2);
});
Clazz_declarePackage ("J.api");
c$ = Clazz_declareType (J.api, "JmolAdapterBondIterator");
Clazz_declarePackage ("J.adapter.smarter");
Clazz_load (["J.api.JmolAdapterBondIterator"], "J.adapter.smarter.BondIterator", null, function () {
c$ = Clazz_decorateAsClass (function () {
this.bsAtoms = null;
this.bonds = null;
this.ibond = 0;
this.bond = null;
this.bondCount = 0;
Clazz_instantialize (this, arguments);
}, J.adapter.smarter, "BondIterator", J.api.JmolAdapterBondIterator);
Clazz_makeConstructor (c$, 
function (atomSetCollection) {
Clazz_superConstructor (this, J.adapter.smarter.BondIterator, []);
this.bsAtoms = atomSetCollection.bsAtoms;
this.bonds = atomSetCollection.getBonds ();
this.bondCount = atomSetCollection.getBondCount ();
this.ibond = 0;
}, "J.adapter.smarter.AtomSetCollection");
$_V(c$, "hasNext", 
function () {
if (this.ibond == this.bondCount) return false;
while ((this.bond = this.bonds[this.ibond++]) == null || (this.bsAtoms != null && (!this.bsAtoms.get (this.bond.atomIndex1) || !this.bsAtoms.get (this.bond.atomIndex2)))) if (this.ibond == this.bondCount) return false;

return true;
});
$_V(c$, "getAtomUniqueID1", 
function () {
return Integer.$valueOf (this.bond.atomIndex1);
});
$_V(c$, "getAtomUniqueID2", 
function () {
return Integer.$valueOf (this.bond.atomIndex2);
});
$_V(c$, "getEncodedOrder", 
function () {
return this.bond.order;
});
$_V(c$, "getRadius", 
function () {
return this.bond.radius;
});
$_V(c$, "getColix", 
function () {
return this.bond.colix;
});
});
Clazz_declarePackage ("J.adapter.smarter");
Clazz_load (null, "J.adapter.smarter.Resolver", ["java.lang.Character", "$.Float", "java.util.StringTokenizer", "JU.PT", "J.adapter.smarter.AtomSetCollectionReader", "$.SmarterJmolAdapter", "J.io.LimitedLineReader", "J.util.Logger"], function () {
c$ = Clazz_declareType (J.adapter.smarter, "Resolver");
c$.getReaderClassBase = $_M(c$, "getReaderClassBase", 
function (type) {
var name = type + "Reader";
if (type.startsWith ("Xml")) return "J.adapter.readers." + "xml." + name;
var key = ";" + type + ";";
for (var i = 1; i < J.adapter.smarter.Resolver.readerSets.length; i += 2) if (J.adapter.smarter.Resolver.readerSets[i].indexOf (key) >= 0) return "J.adapter.readers." + J.adapter.smarter.Resolver.readerSets[i - 1] + name;

return "J.adapter.readers." + "???." + name;
}, "~S");
c$.getFileType = $_M(c$, "getFileType", 
function (br) {
try {
return J.adapter.smarter.Resolver.determineAtomSetCollectionReader (br, false);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return null;
} else {
throw e;
}
}
}, "java.io.BufferedReader");
c$.getAtomCollectionReader = $_M(c$, "getAtomCollectionReader", 
function (fullName, type, bufferedReader, htParams, ptFile) {
var atomSetCollectionReader = null;
var readerName;
fullName = fullName.$replace ('\\', '/');
var errMsg = null;
if (type != null) {
readerName = J.adapter.smarter.Resolver.getReaderFromType (type);
if (readerName == null) errMsg = "unrecognized file format type " + type;
 else J.util.Logger.info ("The Resolver assumes " + readerName);
} else {
readerName = J.adapter.smarter.Resolver.determineAtomSetCollectionReader (bufferedReader, true);
if (readerName.charAt (0) == '\n') {
type = htParams.get ("defaultType");
if (type != null) {
type = J.adapter.smarter.Resolver.getReaderFromType (type);
if (type != null) readerName = type;
}}if (readerName.charAt (0) == '\n') errMsg = "unrecognized file format for file " + fullName + "\n" + readerName;
 else if (readerName.equals ("spt")) errMsg = "NOTE: file recognized as a script file: " + fullName + "\n";
 else if (!fullName.equals ("ligand")) J.util.Logger.info ("The Resolver thinks " + readerName);
}if (errMsg != null) {
J.adapter.smarter.SmarterJmolAdapter.close (bufferedReader);
return errMsg;
}htParams.put ("ptFile", Integer.$valueOf (ptFile));
if (ptFile <= 0) htParams.put ("readerName", readerName);
if (readerName.indexOf ("Xml") == 0) readerName = "Xml";
var className = null;
var atomSetCollectionReaderClass;
var err = null;
try {
try {
className = J.adapter.smarter.Resolver.getReaderClassBase (readerName);
atomSetCollectionReaderClass = Class.forName (className);
atomSetCollectionReader = atomSetCollectionReaderClass.newInstance ();
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
err = "File reader was not found:" + className;
J.util.Logger.error (err);
return err;
} else {
throw e;
}
}
return atomSetCollectionReader;
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
err = "uncaught error in file loading for " + className;
J.util.Logger.error (err);
System.out.println (e.getMessage ());
return err;
} else {
throw e;
}
}
}, "~S,~S,~O,java.util.Map,~N");
c$.DOMResolve = $_M(c$, "DOMResolve", 
function (DOMNode, htParams) {
var className = null;
var atomSetCollectionReaderClass;
var atomSetCollectionReader;
var atomSetCollectionReaderName = J.adapter.smarter.Resolver.getXmlType (htParams.get ("nameSpaceInfo"));
if (J.util.Logger.debugging) {
J.util.Logger.debug ("The Resolver thinks " + atomSetCollectionReaderName);
}htParams.put ("readerName", atomSetCollectionReaderName);
try {
className = "J.adapter.readers.xml.XmlReader";
atomSetCollectionReaderClass = Class.forName (className);
atomSetCollectionReader = atomSetCollectionReaderClass.newInstance ();
return atomSetCollectionReader;
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
var err = "File reader was not found:" + className;
J.util.Logger.errorEx (err, e);
return err;
} else {
throw e;
}
}
}, "~O,java.util.Map");
c$.determineAtomSetCollectionReader = $_M(c$, "determineAtomSetCollectionReader", 
function (readerOrDocument, returnLines) {
if (Clazz_instanceOf (readerOrDocument, J.api.JmolDocument)) {
return "PyMOL";
}var llr =  new J.io.LimitedLineReader (readerOrDocument, 16384);
var leader = llr.getHeader (64).trim ();
for (var i = 0; i < J.adapter.smarter.Resolver.fileStartsWithRecords.length; ++i) {
var recordTags = J.adapter.smarter.Resolver.fileStartsWithRecords[i];
for (var j = 1; j < recordTags.length; ++j) {
var recordTag = recordTags[j];
if (leader.startsWith (recordTag)) return recordTags[0];
}
}
if (leader.indexOf ("PNG") == 1 && leader.indexOf ("PNGJ") >= 0) return "pngj";
if (leader.indexOf ("PNG") == 1 || leader.indexOf ("JPG") == 1 || leader.indexOf ("JFIF") == 6) return "spt";
if (leader.startsWith ("##TITLE")) return "Jcampdx";
var lines =  new Array (16);
var nLines = 0;
for (var i = 0; i < lines.length; ++i) {
lines[i] = llr.readLineWithNewline ();
if (lines[i].length > 0) nLines++;
}
var readerName;
if ((readerName = J.adapter.smarter.Resolver.checkSpecial (nLines, lines, false)) != null) return readerName;
if ((readerName = J.adapter.smarter.Resolver.checkLineStarts (lines)) != null) {
if (readerName.equals ("Cif") && llr.getHeader (0).contains ("mmcif_pdbx.dic")) readerName = "MMCIF_PDBX";
return readerName;
}if ((readerName = J.adapter.smarter.Resolver.checkHeaderContains (llr.getHeader (0))) != null) return readerName;
if ((readerName = J.adapter.smarter.Resolver.checkSpecial (nLines, lines, true)) != null) return readerName;
return (returnLines ? "\n" + lines[0] + "\n" + lines[1] + "\n" + lines[2] + "\n" : null);
}, "~O,~B");
c$.checkHeaderContains = $_M(c$, "checkHeaderContains", 
function (header) {
for (var i = 0; i < J.adapter.smarter.Resolver.headerContainsRecords.length; ++i) {
var recordTags = J.adapter.smarter.Resolver.headerContainsRecords[i];
for (var j = 1; j < recordTags.length; ++j) {
var recordTag = recordTags[j];
if (header.indexOf (recordTag) < 0) continue;
var type = recordTags[0];
return (!type.equals ("Xml") ? type : header.indexOf ("<!DOCTYPE HTML PUBLIC") < 0 && header.indexOf ("XHTML") < 0 && (header.indexOf ("xhtml") < 0 || header.indexOf ("<cml") >= 0) ? J.adapter.smarter.Resolver.getXmlType (header) : null);
}
}
return null;
}, "~S");
c$.checkLineStarts = $_M(c$, "checkLineStarts", 
function (lines) {
for (var i = 0; i < J.adapter.smarter.Resolver.lineStartsWithRecords.length; ++i) {
var recordTags = J.adapter.smarter.Resolver.lineStartsWithRecords[i];
for (var j = 1; j < recordTags.length; ++j) {
var recordTag = recordTags[j];
for (var k = 0; k < lines.length; ++k) {
if (lines[k].startsWith (recordTag)) return recordTags[0];
}
}
}
return null;
}, "~A");
c$.getXmlType = $_M(c$, "getXmlType", 
function (header) {
if (header.indexOf ("http://www.molpro.net/") >= 0) {
return J.adapter.smarter.Resolver.specialTags[19][0];
}if (header.indexOf ("odyssey") >= 0) {
return J.adapter.smarter.Resolver.specialTags[20][0];
}if (header.indexOf ("C3XML") >= 0) {
return J.adapter.smarter.Resolver.specialTags[18][0];
}if (header.indexOf ("arguslab") >= 0) {
return J.adapter.smarter.Resolver.specialTags[16][0];
}if (header.indexOf ("jvxl") >= 0) {
return J.adapter.smarter.Resolver.specialTags[17][0];
}if (header.indexOf ("http://www.xml-cml.org/schema") >= 0 || header.indexOf ("cml:") >= 0) {
return J.adapter.smarter.Resolver.specialTags[17][0];
}if (header.indexOf ("XSD") >= 0) {
return J.adapter.smarter.Resolver.specialTags[21][0];
}if (header.indexOf (">vasp") >= 0) {
return J.adapter.smarter.Resolver.specialTags[22][0];
}if (header.indexOf ("<GEOMETRY_INFO>") >= 0) {
return J.adapter.smarter.Resolver.specialTags[23][0];
}return J.adapter.smarter.Resolver.specialTags[17][0] + "(unidentified)";
}, "~S");
c$.getReaderFromType = $_M(c$, "getReaderFromType", 
function (type) {
type = type.toLowerCase ();
var base = null;
if ((base = J.adapter.smarter.Resolver.checkType (J.adapter.smarter.Resolver.specialTags, type)) != null) return base;
if ((base = J.adapter.smarter.Resolver.checkType (J.adapter.smarter.Resolver.fileStartsWithRecords, type)) != null) return base;
if ((base = J.adapter.smarter.Resolver.checkType (J.adapter.smarter.Resolver.lineStartsWithRecords, type)) != null) return base;
return J.adapter.smarter.Resolver.checkType (J.adapter.smarter.Resolver.headerContainsRecords, type);
}, "~S");
c$.checkType = $_M(c$, "checkType", 
function (typeTags, type) {
for (var i = 0; i < typeTags.length; ++i) if (typeTags[i][0].toLowerCase ().equals (type)) return typeTags[i][0];

return null;
}, "~A,~S");
c$.checkSpecial = $_M(c$, "checkSpecial", 
function (nLines, lines, isEnd) {
if (isEnd) {
if (J.adapter.smarter.Resolver.checkGromacs (lines)) return J.adapter.smarter.Resolver.specialTags[14][0];
if (J.adapter.smarter.Resolver.checkCrystal (lines)) return J.adapter.smarter.Resolver.specialTags[12][0];
if (J.adapter.smarter.Resolver.checkCastep (lines)) return J.adapter.smarter.Resolver.specialTags[10][0];
if (J.adapter.smarter.Resolver.checkVaspposcar (lines)) return J.adapter.smarter.Resolver.specialTags[13][0];
} else {
if (nLines == 1 && lines[0].length > 0 && Character.isDigit (lines[0].charAt (0))) return J.adapter.smarter.Resolver.specialTags[0][0];
if (J.adapter.smarter.Resolver.checkMopacGraphf (lines)) return J.adapter.smarter.Resolver.specialTags[1][0];
if (J.adapter.smarter.Resolver.checkOdyssey (lines)) return J.adapter.smarter.Resolver.specialTags[3][0];
if (J.adapter.smarter.Resolver.checkMol (lines)) return J.adapter.smarter.Resolver.specialTags[4][0];
if (J.adapter.smarter.Resolver.checkXyz (lines)) return J.adapter.smarter.Resolver.specialTags[5][0];
if (J.adapter.smarter.Resolver.checkAlchemy (lines[0])) return J.adapter.smarter.Resolver.specialTags[8][0];
if (J.adapter.smarter.Resolver.checkFoldingXyz (lines)) return J.adapter.smarter.Resolver.specialTags[6][0];
if (J.adapter.smarter.Resolver.checkCube (lines)) return J.adapter.smarter.Resolver.specialTags[7][0];
if (J.adapter.smarter.Resolver.checkWien2k (lines)) return J.adapter.smarter.Resolver.specialTags[9][0];
if (J.adapter.smarter.Resolver.checkAims (lines)) return J.adapter.smarter.Resolver.specialTags[11][0];
if (J.adapter.smarter.Resolver.checkGenNBO (lines)) return J.adapter.smarter.Resolver.specialTags[15][0];
}return null;
}, "~N,~A,~B");
c$.checkAims = $_M(c$, "checkAims", 
function (lines) {
for (var i = 0; i < lines.length; i++) {
if (lines[i].startsWith ("mol 1")) return false;
var tokens = JU.PT.getTokens (lines[i]);
if (tokens.length == 0) continue;
if (tokens[0].startsWith ("atom") && tokens.length >= 5 || tokens[0].startsWith ("multipole") && tokens.length >= 6 || tokens[0].startsWith ("lattice_vector") && tokens.length >= 4) return true;
}
return false;
}, "~A");
c$.checkAlchemy = $_M(c$, "checkAlchemy", 
function (line) {
var pt;
if ((pt = line.indexOf ("ATOMS")) >= 0 && line.indexOf ("BONDS") > pt) try {
var n = Integer.parseInt (line.substring (0, pt).trim ());
return (n > 0);
} catch (nfe) {
if (Clazz_exceptionOf (nfe, NumberFormatException)) {
} else {
throw nfe;
}
}
return false;
}, "~S");
c$.checkCastep = $_M(c$, "checkCastep", 
function (lines) {
for (var i = 0; i < lines.length; i++) {
if (lines[i].indexOf ("Frequencies in         cm-1") == 1 || lines[i].contains ("CASTEP") || lines[i].toUpperCase ().startsWith ("%BLOCK LATTICE_ABC") || lines[i].toUpperCase ().startsWith ("%BLOCK LATTICE_CART") || lines[i].toUpperCase ().startsWith ("%BLOCK POSITIONS_FRAC") || lines[i].toUpperCase ().startsWith ("%BLOCK POSITIONS_ABS") || lines[i].contains ("<-- E")) return true;
}
return false;
}, "~A");
c$.checkVaspposcar = $_M(c$, "checkVaspposcar", 
function (lines) {
var select = lines[8].trim ().toLowerCase ();
if (select.contains ("direct") || select.contains ("cartesian") || select.contains ("selective")) return true;
var normal = lines[7].trim ().toLowerCase ();
if (normal.contains ("direct") || normal.contains ("cartesian")) return true;
return false;
}, "~A");
c$.checkCrystal = $_M(c$, "checkCrystal", 
function (lines) {
var s = lines[1].trim ();
if (s.equals ("SLAB") || s.equals ("MOLECULE") || s.equals ("CRYSTAL") || s.equals ("POLYMER") || (s = lines[3]).equals ("SLAB") || s.equals ("MOLECULE") || s.equals ("POLYMER")) return true;
for (var i = 0; i < lines.length; i++) {
if (lines[i].trim ().equals ("OPTGEOM")) return true;
}
return false;
}, "~A");
c$.checkCube = $_M(c$, "checkCube", 
function (lines) {
try {
for (var j = 2; j <= 5; j++) {
var tokens2 =  new java.util.StringTokenizer (lines[j]);
var n = tokens2.countTokens ();
if (!(n == 4 || j == 2 && n == 5)) return false;
Integer.parseInt (tokens2.nextToken ());
for (var i = 3; --i >= 0; ) JU.PT.fVal (tokens2.nextToken ());

if (n == 5) Integer.parseInt (tokens2.nextToken ());
}
return true;
} catch (nfe) {
if (Clazz_exceptionOf (nfe, NumberFormatException)) {
} else {
throw nfe;
}
}
return false;
}, "~A");
c$.checkFoldingXyz = $_M(c$, "checkFoldingXyz", 
function (lines) {
var tokens =  new java.util.StringTokenizer (lines[0].trim (), " \t");
if (tokens.countTokens () < 2) return false;
try {
Integer.parseInt (tokens.nextToken ().trim ());
} catch (nfe) {
if (Clazz_exceptionOf (nfe, NumberFormatException)) {
return false;
} else {
throw nfe;
}
}
var secondLine = lines[1].trim ();
if (secondLine.length == 0) secondLine = lines[2].trim ();
tokens =  new java.util.StringTokenizer (secondLine, " \t");
if (tokens.countTokens () == 0) return false;
try {
Integer.parseInt (tokens.nextToken ().trim ());
} catch (nfe) {
if (Clazz_exceptionOf (nfe, NumberFormatException)) {
return false;
} else {
throw nfe;
}
}
return true;
}, "~A");
c$.checkGenNBO = $_M(c$, "checkGenNBO", 
function (lines) {
return (lines[1].startsWith (" Basis set information needed for plotting orbitals") || lines[1].indexOf ("s in the AO basis:") >= 0 || lines[2].indexOf (" N A T U R A L   A T O M I C   O R B I T A L") >= 0);
}, "~A");
c$.checkGromacs = $_M(c$, "checkGromacs", 
function (lines) {
if (JU.PT.parseInt (lines[1]) == -2147483648) return false;
var len = -1;
for (var i = 2; i < 16 && len != 0; i++) if ((len = lines[i].length) != 69 && len != 45 && len != 0) return false;

return true;
}, "~A");
c$.checkMol = $_M(c$, "checkMol", 
function (lines) {
var line4trimmed = ("X" + lines[3]).trim ().toUpperCase ();
if (line4trimmed.length < 7 || line4trimmed.indexOf (".") >= 0) return false;
if (line4trimmed.endsWith ("V2000") || line4trimmed.endsWith ("V3000")) return true;
try {
var n1 = Integer.parseInt (lines[3].substring (0, 3).trim ());
var n2 = Integer.parseInt (lines[3].substring (3, 6).trim ());
return (n1 > 0 && n2 >= 0 && lines[0].indexOf ("@<TRIPOS>") != 0 && lines[1].indexOf ("@<TRIPOS>") != 0 && lines[2].indexOf ("@<TRIPOS>") != 0);
} catch (nfe) {
if (Clazz_exceptionOf (nfe, NumberFormatException)) {
} else {
throw nfe;
}
}
return false;
}, "~A");
c$.checkMopacGraphf = $_M(c$, "checkMopacGraphf", 
function (lines) {
return (lines[0].indexOf ("MOPAC-Graphical data") > 2);
}, "~A");
c$.checkOdyssey = $_M(c$, "checkOdyssey", 
function (lines) {
var i;
for (i = 0; i < lines.length; i++) if (!lines[i].startsWith ("C ") && lines[i].length != 0) break;

if (i >= lines.length || lines[i].charAt (0) != ' ' || (i = i + 2) + 1 >= lines.length) return false;
try {
var spin = Integer.parseInt (lines[i].substring (2).trim ());
var charge = Integer.parseInt (lines[i].substring (0, 2).trim ());
var atom1 = Integer.parseInt (lines[++i].substring (0, 2).trim ());
if (spin < 0 || spin > 5 || atom1 <= 0 || charge > 5) return false;
var atomline = J.adapter.smarter.AtomSetCollectionReader.getTokensFloat (lines[i], null, 5);
return !Float.isNaN (atomline[1]) && !Float.isNaN (atomline[2]) && !Float.isNaN (atomline[3]) && Float.isNaN (atomline[4]);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
return false;
}, "~A");
c$.checkWien2k = $_M(c$, "checkWien2k", 
function (lines) {
return (lines[2].startsWith ("MODE OF CALC=") || lines[2].startsWith ("             RELA") || lines[2].startsWith ("             NREL"));
}, "~A");
c$.checkXyz = $_M(c$, "checkXyz", 
function (lines) {
try {
Integer.parseInt (lines[0].trim ());
return true;
} catch (nfe) {
if (Clazz_exceptionOf (nfe, NumberFormatException)) {
} else {
throw nfe;
}
}
return false;
}, "~A");
Clazz_defineStatics (c$,
"classBase", "J.adapter.readers.");
c$.readerSets = c$.prototype.readerSets = ["cif.", ";Cif;MMCIF_PDBX;", "molxyz.", ";Mol3D;Mol;Xyz;", "more.", ";BinaryDcd;Gromacs;Jcampdx;MdCrd;MdTop;Mol2;Pqr;P2n;TlsDataOnly;", "quantum.", ";Adf;Csf;Dgrid;GamessUK;GamessUS;Gaussian;GausianWfn;Jaguar;Molden;MopacGraphf;GenNBO;NWChem;Odyssey;Psi;Qchem;Spartan;SpartanSmol;WebMO;", "pdb.", ";Pdb;", "pymol.", ";PyMOL;", "simple.", ";Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;Mopac;MopacArchive;ZMatrix;", "xtal.", ";Abinit;Aims;Castep;Crystal;Dmol;Espresso;Gulp;Jana;Magres;Shelx;Siesta;VaspOutcar;VaspPoscar;Wien2k;Xcrysden;"];
Clazz_defineStatics (c$,
"CML_NAMESPACE_URI", "http://www.xml-cml.org/schema",
"SPECIAL_JME", 0,
"SPECIAL_MOPACGRAPHF", 1,
"SPECIAL_ODYSSEY", 3,
"SPECIAL_MOL", 4,
"SPECIAL_XYZ", 5,
"SPECIAL_FOLDINGXYZ", 6,
"SPECIAL_CUBE", 7,
"SPECIAL_ALCHEMY", 8,
"SPECIAL_WIEN", 9,
"SPECIAL_CASTEP", 10,
"SPECIAL_AIMS", 11,
"SPECIAL_CRYSTAL", 12,
"SPECIAL_VASPPOSCAR", 13,
"SPECIAL_GROMACS", 14,
"SPECIAL_GENNBO", 15,
"SPECIAL_ARGUS_XML", 16,
"SPECIAL_CML_XML", 17,
"SPECIAL_CHEM3D_XML", 18,
"SPECIAL_MOLPRO_XML", 19,
"SPECIAL_ODYSSEY_XML", 20,
"SPECIAL_XSD_XML", 21,
"SPECIAL_VASP_XML", 22,
"SPECIAL_QE_XML", 23,
"SPECIAL_ARGUS_DOM", 24,
"SPECIAL_CML_DOM", 25,
"SPECIAL_CHEM3D_DOM", 26,
"SPECIAL_MOLPRO_DOM", 27,
"SPECIAL_ODYSSEY_DOM", 28,
"SPECIAL_XSD_DOM", 29,
"SPECIAL_VASP_DOM", 30,
"specialTags", [["Jme"], ["MopacGraphf"], ["Mol3D"], ["Odyssey"], ["Mol"], ["Xyz"], ["FoldingXyz"], ["Cube"], ["Alchemy"], ["Wien2k"], ["Castep"], ["Aims"], ["Crystal"], ["VaspPoscar"], ["Gromacs"], ["GenNBO"], ["XmlArgus"], ["XmlCml"], ["XmlChem3d"], ["XmlMolpro"], ["XmlOdyssey"], ["XmlXsd"], ["XmlVasp"], ["XmlQE"], ["XmlArgus(DOM)"], ["XmlCml(DOM)"], ["XmlChem3d(DOM)"], ["XmlMolpro(DOM)"], ["XmlOdyssey(DOM)"], ["XmlXsd(DOM)"], ["XmlVasp(DOM)"], ["MdCrd"]],
"LEADER_CHAR_MAX", 64,
"sptContainsRecords", ["spt", "# Jmol state", "# Jmol script", "JmolManifest"],
"cubeFileStartRecords", ["Cube", "JVXL", "#JVXL"],
"mol2Records", ["Mol2", "mol2", "@<TRIPOS>"],
"webmoFileStartRecords", ["WebMO", "[HEADER]"],
"moldenFileStartRecords", ["Molden", "[Molden"],
"dcdFileStartRecords", ["BinaryDcd", "T\0\0\0CORD", "\0\0\0TCORD"],
"tlsDataOnlyFileStartRecords", ["TlsDataOnly", "REFMAC\n\nTL", "REFMAC\r\n\r\n", "REFMAC\r\rTL"],
"zMatrixFileStartRecords", ["ZMatrix", "#ZMATRIX"],
"magresFileStartRecords", ["Magres", "#$magres", "# magres"],
"pymolStartRecords", ["PyMOL", "}q"],
"janaStartRecords", ["Jana", "Version Jana"]);
c$.fileStartsWithRecords = c$.prototype.fileStartsWithRecords = [J.adapter.smarter.Resolver.sptContainsRecords, J.adapter.smarter.Resolver.cubeFileStartRecords, J.adapter.smarter.Resolver.mol2Records, J.adapter.smarter.Resolver.webmoFileStartRecords, J.adapter.smarter.Resolver.moldenFileStartRecords, J.adapter.smarter.Resolver.dcdFileStartRecords, J.adapter.smarter.Resolver.tlsDataOnlyFileStartRecords, J.adapter.smarter.Resolver.zMatrixFileStartRecords, J.adapter.smarter.Resolver.magresFileStartRecords, J.adapter.smarter.Resolver.pymolStartRecords, J.adapter.smarter.Resolver.janaStartRecords];
Clazz_defineStatics (c$,
"pqrLineStartRecords", ["Pqr", "REMARK   1 PQR"],
"p2nLineStartRecords", ["P2n", "REMARK   1 P2N"],
"pdbLineStartRecords", ["Pdb", "HEADER", "OBSLTE", "TITLE ", "CAVEAT", "COMPND", "SOURCE", "KEYWDS", "EXPDTA", "AUTHOR", "REVDAT", "SPRSDE", "JRNL  ", "REMARK ", "DBREF ", "SEQADV", "SEQRES", "MODRES", "HELIX ", "SHEET ", "TURN  ", "CRYST1", "ORIGX1", "ORIGX2", "ORIGX3", "SCALE1", "SCALE2", "SCALE3", "ATOM  ", "HETATM", "MODEL ", "LINK  "],
"shelxLineStartRecords", ["Shelx", "TITL ", "ZERR ", "LATT ", "SYMM ", "CELL "],
"cifLineStartRecords", ["Cif", "data_", "_publ"],
"ghemicalMMLineStartRecords", ["GhemicalMM", "!Header mm1gp", "!Header gpr"],
"jaguarLineStartRecords", ["Jaguar", "  |  Jaguar version"],
"mdlLineStartRecords", ["Mol", "$MDL "],
"spartanSmolLineStartRecords", ["SpartanSmol", "INPUT="],
"csfLineStartRecords", ["Csf", "local_transform"],
"mdTopLineStartRecords", ["MdTop", "%FLAG TITLE"],
"hyperChemLineStartRecords", ["HyperChem", "mol 1"],
"vaspOutcarLineStartRecords", ["VaspOutcar", " vasp.", " INCAR:"]);
c$.lineStartsWithRecords = c$.prototype.lineStartsWithRecords = [J.adapter.smarter.Resolver.cifLineStartRecords, J.adapter.smarter.Resolver.pqrLineStartRecords, J.adapter.smarter.Resolver.p2nLineStartRecords, J.adapter.smarter.Resolver.pdbLineStartRecords, J.adapter.smarter.Resolver.shelxLineStartRecords, J.adapter.smarter.Resolver.ghemicalMMLineStartRecords, J.adapter.smarter.Resolver.jaguarLineStartRecords, J.adapter.smarter.Resolver.mdlLineStartRecords, J.adapter.smarter.Resolver.spartanSmolLineStartRecords, J.adapter.smarter.Resolver.csfLineStartRecords, J.adapter.smarter.Resolver.mol2Records, J.adapter.smarter.Resolver.mdTopLineStartRecords, J.adapter.smarter.Resolver.hyperChemLineStartRecords, J.adapter.smarter.Resolver.vaspOutcarLineStartRecords];
Clazz_defineStatics (c$,
"xmlContainsRecords", ["Xml", "<?xml", "<atom", "<molecule", "<reaction", "<cml", "<bond", ".dtd\"", "<list>", "<entry", "<identifier", "http://www.xml-cml.org/schema/cml2/core"],
"gaussianContainsRecords", ["Gaussian", "Entering Gaussian System", "Entering Link 1", "1998 Gaussian, Inc."],
"ampacContainsRecords", ["Ampac", "AMPAC Version"],
"mopacContainsRecords", ["Mopac", "MOPAC 93 (c) Fujitsu", "MOPAC FOR LINUX (PUBLIC DOMAIN VERSION)", "MOPAC:  VERSION  6", "MOPAC   7", "MOPAC2", "MOPAC (PUBLIC"],
"qchemContainsRecords", ["Qchem", "Welcome to Q-Chem", "A Quantum Leap Into The Future Of Chemistry"],
"gamessUKContainsRecords", ["GamessUK", "GAMESS-UK", "G A M E S S - U K"],
"gamessUSContainsRecords", ["GamessUS", "GAMESS"],
"spartanBinaryContainsRecords", ["SpartanSmol", "|PropertyArchive", "_spartan", "spardir", "BEGIN Directory Entry Molecule"],
"spartanContainsRecords", ["Spartan", "Spartan"],
"adfContainsRecords", ["Adf", "Amsterdam Density Functional"],
"dgridContainsRecords", ["Dgrid", "BASISFILE   created by DGrid"],
"dmolContainsRecords", ["Dmol", "DMol^3"],
"gulpContainsRecords", ["Gulp", "GENERAL UTILITY LATTICE PROGRAM"],
"psiContainsRecords", ["Psi", "    PSI  3", "PSI3:"],
"nwchemContainsRecords", ["NWChem", " argument  1 = "],
"uicrcifContainsRecords", ["Cif", "Crystallographic Information File"],
"crystalContainsRecords", ["Crystal", "*                                CRYSTAL"],
"espressoContainsRecords", ["Espresso", "Program PWSCF", "Program PHONON"],
"siestaContainsRecords", ["Siesta", "MD.TypeOfRun", "SolutionMethod", "MeshCutoff", "WELCOME TO SIESTA"],
"xcrysDenContainsRecords", ["Xcrysden", "PRIMVEC", "CONVVEC", "PRIMCOORD"],
"mopacArchiveContainsRecords", ["MopacArchive", "SUMMARY OF PM"],
"abinitContainsRecords", ["Abinit", "http://www.abinit.org", "Catholique", "Louvain"]);
c$.headerContainsRecords = c$.prototype.headerContainsRecords = [J.adapter.smarter.Resolver.sptContainsRecords, J.adapter.smarter.Resolver.xmlContainsRecords, J.adapter.smarter.Resolver.gaussianContainsRecords, J.adapter.smarter.Resolver.ampacContainsRecords, J.adapter.smarter.Resolver.mopacContainsRecords, J.adapter.smarter.Resolver.qchemContainsRecords, J.adapter.smarter.Resolver.gamessUKContainsRecords, J.adapter.smarter.Resolver.gamessUSContainsRecords, J.adapter.smarter.Resolver.spartanBinaryContainsRecords, J.adapter.smarter.Resolver.spartanContainsRecords, J.adapter.smarter.Resolver.mol2Records, J.adapter.smarter.Resolver.adfContainsRecords, J.adapter.smarter.Resolver.psiContainsRecords, J.adapter.smarter.Resolver.nwchemContainsRecords, J.adapter.smarter.Resolver.uicrcifContainsRecords, J.adapter.smarter.Resolver.dgridContainsRecords, J.adapter.smarter.Resolver.crystalContainsRecords, J.adapter.smarter.Resolver.dmolContainsRecords, J.adapter.smarter.Resolver.gulpContainsRecords, J.adapter.smarter.Resolver.espressoContainsRecords, J.adapter.smarter.Resolver.siestaContainsRecords, J.adapter.smarter.Resolver.xcrysDenContainsRecords, J.adapter.smarter.Resolver.mopacArchiveContainsRecords, J.adapter.smarter.Resolver.abinitContainsRecords];
});
Clazz_declarePackage ("J.api");
c$ = Clazz_declareType (J.api, "JmolAdapterStructureIterator");
Clazz_declarePackage ("J.adapter.smarter");
Clazz_load (["J.api.JmolAdapterStructureIterator"], "J.adapter.smarter.StructureIterator", ["J.api.JmolAdapter"], function () {
c$ = Clazz_decorateAsClass (function () {
this.structureCount = 0;
this.structures = null;
this.structure = null;
this.istructure = 0;
this.bsModelsDefined = null;
Clazz_instantialize (this, arguments);
}, J.adapter.smarter, "StructureIterator", J.api.JmolAdapterStructureIterator);
Clazz_makeConstructor (c$, 
function (atomSetCollection) {
Clazz_superConstructor (this, J.adapter.smarter.StructureIterator, []);
this.structureCount = atomSetCollection.getStructureCount ();
this.structures = atomSetCollection.getStructures ();
this.istructure = 0;
this.bsModelsDefined = atomSetCollection.bsStructuredModels;
}, "J.adapter.smarter.AtomSetCollection");
$_V(c$, "hasNext", 
function () {
if (this.istructure == this.structureCount) return false;
this.structure = this.structures[this.istructure++];
return true;
});
$_V(c$, "getStructureType", 
function () {
return this.structure.structureType;
});
$_V(c$, "getSubstructureType", 
function () {
return this.structure.substructureType;
});
$_V(c$, "getStructureID", 
function () {
return this.structure.structureID;
});
$_V(c$, "getSerialID", 
function () {
return this.structure.serialID;
});
$_V(c$, "getStartChainID", 
function () {
return this.structure.startChainID;
});
$_V(c$, "getStartSequenceNumber", 
function () {
return this.structure.startSequenceNumber;
});
$_V(c$, "getStartInsertionCode", 
function () {
return J.api.JmolAdapter.canonizeInsertionCode (this.structure.startInsertionCode);
});
$_V(c$, "getEndChainID", 
function () {
return this.structure.endChainID;
});
$_V(c$, "getEndSequenceNumber", 
function () {
return this.structure.endSequenceNumber;
});
$_V(c$, "getEndInsertionCode", 
function () {
return this.structure.endInsertionCode;
});
$_V(c$, "getStrandCount", 
function () {
return this.structure.strandCount;
});
$_V(c$, "getStructuredModels", 
function () {
return this.bsModelsDefined;
});
$_V(c$, "getAtomIndices", 
function () {
return this.structure.atomStartEnd;
});
$_V(c$, "getModelIndices", 
function () {
return this.structure.modelStartEnd;
});
});
Clazz_declarePackage ("J.modelset");
Clazz_load (["java.lang.Short", "java.util.Hashtable", "J.viewer.JC"], "J.modelset.Group", ["java.lang.Float", "JU.AU", "$.BS", "$.P3", "$.V3", "J.constant.EnumStructure", "J.util.BSUtil", "$.Logger", "$.Quaternion"], function () {
c$ = Clazz_decorateAsClass (function () {
this.groupIndex = 0;
this.chain = null;
this.firstAtomIndex = -1;
this.leadAtomIndex = -1;
this.lastAtomIndex = 0;
this.seqcode = 0;
this.groupID = 0;
this.$isProtein = false;
this.selectedIndex = 0;
this.shapeVisibilityFlags = 0;
this.phi = NaN;
this.psi = NaN;
this.omega = NaN;
this.straightness = NaN;
this.mu = NaN;
this.theta = NaN;
this.bsAdded = null;
Clazz_instantialize (this, arguments);
}, J.modelset, "Group");
$_M(c$, "getGroupIndex", 
function () {
return this.groupIndex;
});
$_M(c$, "setGroupIndex", 
function (groupIndex) {
this.groupIndex = groupIndex;
}, "~N");
Clazz_makeConstructor (c$, 
function () {
});
$_M(c$, "setGroup", 
function (chain, group3, seqcode, firstAtomIndex, lastAtomIndex) {
this.chain = chain;
this.seqcode = seqcode;
if (group3 == null) group3 = "";
this.groupID = J.modelset.Group.getGroupIdFor (group3);
this.$isProtein = (this.groupID >= 1 && this.groupID < 24);
this.firstAtomIndex = firstAtomIndex;
this.lastAtomIndex = lastAtomIndex;
return this;
}, "J.modelset.Chain,~S,~N,~N,~N");
$_M(c$, "calcBioParameters", 
function () {
return false;
});
$_M(c$, "haveParameters", 
function () {
return true;
});
$_M(c$, "setGroupParameter", 
function (tok, f) {
switch (tok) {
case 1112539145:
this.phi = f;
break;
case 1112539146:
this.psi = f;
break;
case 1112539144:
this.omega = f;
break;
case 1112539141:
this.mu = f;
break;
case 1112539152:
this.theta = f;
break;
case 1112539150:
this.straightness = f;
break;
}
}, "~N,~N");
$_M(c$, "getGroupParameter", 
function (tok) {
if (!this.haveParameters ()) this.calcBioParameters ();
switch (tok) {
case 1112539144:
return this.omega;
case 1112539145:
return this.phi;
case 1112539146:
return this.psi;
case 1112539141:
return this.mu;
case 1112539152:
return this.theta;
case 1112539150:
return this.straightness;
}
return NaN;
}, "~N");
$_M(c$, "setModelSet", 
function (modelSet) {
this.chain.model.modelSet = modelSet;
}, "J.modelset.ModelSet");
$_M(c$, "setShapeVisibility", 
function (visFlag, isVisible) {
if (isVisible) {
this.shapeVisibilityFlags |= visFlag;
} else {
this.shapeVisibilityFlags &= ~visFlag;
}}, "~N,~B");
$_M(c$, "getGroup3", 
function () {
return J.modelset.Group.group3Names[this.groupID];
});
c$.getGroup3For = $_M(c$, "getGroup3For", 
function (groupID) {
return J.modelset.Group.group3Names[groupID];
}, "~N");
$_M(c$, "getGroup1", 
function () {
if (this.groupID >= J.viewer.JC.predefinedGroup1Names.length) return '?';
return J.viewer.JC.predefinedGroup1Names[this.groupID];
});
$_M(c$, "getGroupID", 
function () {
return this.groupID;
});
$_M(c$, "getChainID", 
function () {
return this.chain.chainID;
});
$_M(c$, "getBioPolymerLength", 
function () {
return 0;
});
$_M(c$, "getMonomerIndex", 
function () {
return -1;
});
$_M(c$, "getGroups", 
function () {
return null;
});
$_M(c$, "getStructure", 
function () {
return null;
});
$_M(c$, "getStrucNo", 
function () {
return 0;
});
$_M(c$, "getProteinStructureType", 
function () {
return J.constant.EnumStructure.NOT;
});
$_M(c$, "getProteinStructureSubType", 
function () {
return this.getProteinStructureType ();
});
$_M(c$, "setProteinStructureType", 
function (type, monomerIndexCurrent) {
return -1;
}, "J.constant.EnumStructure,~N");
$_M(c$, "isProtein", 
function () {
return this.$isProtein;
});
$_M(c$, "isNucleic", 
function () {
return (this.groupID >= 24 && this.groupID < 42);
});
$_M(c$, "isDna", 
function () {
return false;
});
$_M(c$, "isRna", 
function () {
return false;
});
$_M(c$, "isPurine", 
function () {
return false;
});
$_M(c$, "isPyrimidine", 
function () {
return false;
});
$_M(c$, "isCarbohydrate", 
function () {
return false;
});
c$.addGroup3Name = $_M(c$, "addGroup3Name", 
function (group3) {
if (J.modelset.Group.group3NameCount == J.modelset.Group.group3Names.length) ($t$ = J.modelset.Group.group3Names = JU.AU.doubleLengthS (J.modelset.Group.group3Names), J.modelset.Group.prototype.group3Names = J.modelset.Group.group3Names, $t$);
var groupID = ($t$ = J.modelset.Group.group3NameCount ++, J.modelset.Group.prototype.group3NameCount = J.modelset.Group.group3NameCount, $t$);
J.modelset.Group.group3Names[groupID] = group3;
J.modelset.Group.htGroup.put (group3, Short.$valueOf (groupID));
return groupID;
}, "~S");
c$.getGroupIdFor = $_M(c$, "getGroupIdFor", 
function (group3) {
if (group3 == null) return -1;
var groupID = J.modelset.Group.lookupGroupID (group3);
return (groupID != -1) ? groupID : J.modelset.Group.addGroup3Name (group3);
}, "~S");
c$.lookupGroupID = $_M(c$, "lookupGroupID", 
function (group3) {
if (group3 != null) {
var boxedGroupID = J.modelset.Group.htGroup.get (group3);
if (boxedGroupID != null) return boxedGroupID.shortValue ();
}return -1;
}, "~S");
$_M(c$, "getResno", 
function () {
return (this.seqcode == -2147483648 ? 0 : this.seqcode >> 8);
});
c$.getSeqNumberFor = $_M(c$, "getSeqNumberFor", 
function (seqcode) {
return (J.modelset.Group.haveSequenceNumber (seqcode) ? seqcode >> 8 : 2147483647);
}, "~N");
c$.haveSequenceNumber = $_M(c$, "haveSequenceNumber", 
function (seqcode) {
return ((seqcode & 128) != 0);
}, "~N");
$_M(c$, "getSeqcodeString", 
function () {
return J.modelset.Group.getSeqcodeStringFor (this.seqcode);
});
c$.getSeqcodeFor = $_M(c$, "getSeqcodeFor", 
function (seqNo, insCode) {
if (seqNo == -2147483648) return seqNo;
if (!((insCode >= 'A' && insCode <= 'Z') || (insCode >= 'a' && insCode <= 'z') || (insCode >= '0' && insCode <= '9') || insCode == '?' || insCode == '*')) {
if (insCode != ' ' && insCode != '\0') J.util.Logger.warn ("unrecognized insertionCode:" + insCode);
insCode = '\0';
}return ((seqNo == 2147483647 ? 0 : (seqNo << 8) | 128)) + insCode.charCodeAt (0);
}, "~N,~S");
c$.getSeqcodeStringFor = $_M(c$, "getSeqcodeStringFor", 
function (seqcode) {
if (seqcode == -2147483648) return null;
return (seqcode & 127) == 0 ? "" + (seqcode >> 8) : "" + (seqcode >> 8) + '^' + String.fromCharCode (seqcode & 127);
}, "~N");
$_M(c$, "getInsertionCode", 
function () {
if (this.seqcode == -2147483648) return '\0';
return String.fromCharCode (this.seqcode & 127);
});
c$.getInsertionCodeFor = $_M(c$, "getInsertionCodeFor", 
function (seqcode) {