// JmolApplet.js -- Jmol._Applet and Jmol._Image // BH 11/24/2013 11:41:31 AM streamlined createApplet, with added JNLP for local reading // BH 10/11/2013 7:17:10 AM streamlined and made consistent with JSV and JSME // BH 7/16/2012 1:50:03 PM adds server-side scripting for image // BH 8/11/2012 11:00:01 AM adds Jmol._readyCallback for MSIE not in Quirks mode // BH 8/12/2012 3:56:40 AM allows .min.png to be replaced by .all.png in Image file name // BH 8/13/2012 6:16:55 PM fix for no-java message not displaying // BH 11/18/2012 1:06:39 PM adds option ">" in database query box for quick command execution // BH 12/17/2012 6:25:00 AM change ">" option to "!" ;(function (Jmol, document) { // _Applet -- the main, full-featured, Jmol object Jmol._Applet = function(id, Info, checkOnly){ window[id] = this; this._jmolType = "Jmol._Applet" + (Info.isSigned ? " (signed)" : ""); this._isJava = true; this._syncKeyword = "Select:"; if (checkOnly) return this; this._isSigned = Info.isSigned; this._readyFunction = Info.readyFunction; this._ready = false; this._isJava = true; this._isInfoVisible = false; this._applet = null; this._memoryLimit = Info.memoryLimit || 512; this._canScript = function(script) {return true;}; this._savedOrientations = []; this._initialize = function(jarPath, jarFile) { var doReport = false; Jmol._jarFile && (jarFile = Jmol._jarFile); if(this._jarFile) { var f = this._jarFile; if(f.indexOf("/") >= 0) { alert("This web page URL is requesting that the applet used be " + f + ". This is a possible security risk, particularly if the applet is signed, because signed applets can read and write files on your local machine or network."); var ok = prompt("Do you want to use applet " + f + "? ", "yes or no") if(ok == "yes") { jarPath = f.substring(0, f.lastIndexOf("/")); jarFile = f.substring(f.lastIndexOf("/") + 1); } else { doReport = true; } } else { jarFile = f; } this_isSigned = Info.isSigned = (jarFile.indexOf("Signed") >= 0); } this._jarPath = Info.jarPath = jarPath || "."; this._jarFile = Info.jarFile = (typeof(jarFile) == "string" ? jarFile : (jarFile ? "JmolAppletSigned" : "JmolApplet") + "0.jar"); if (doReport) alert("The web page URL was ignored. Continuing using " + this._jarFile + ' in directory "' + this._jarPath + '"'); Jmol.controls == undefined || Jmol.controls._onloadResetForms(); } this._create(id, Info); return this; } Jmol._Applet._get = function(id, Info, checkOnly) { // note that the variable name the return is assigned to MUST match the first parameter in quotes // applet = Jmol.getApplet("applet", Info) checkOnly || (checkOnly = false); Info || (Info = {}); var DefaultInfo = { color: "#FFFFFF", // applet object background color, as for older jmolSetBackgroundColor(s) width: 300, height: 300, addSelectionOptions: false, serverURL: "http://your.server.here/jsmol.php", defaultModel: "", script: null, src: null, readyFunction: null, use: "HTML5",//other options include JAVA, WEBGL, and IMAGE jarPath: "java", jarFile: "JmolApplet0.jar", isSigned: false, j2sPath: "j2s", coverImage: null, // URL for image to display coverTitle: "", // tip that is displayed before model starts to load coverCommand: "", // Jmol command executed upon clicking image deferApplet: false, // true == the model should not be loaded until the image is clicked deferUncover: false, // true == the image should remain until command execution is complete disableJ2SLoadMonitor: false, disableInitialConsole: false, debug: false }; Jmol._addDefaultInfo(Info, DefaultInfo); Jmol._debugAlert = Info.debug; if (!Jmol.featureDetection.allowHTML5)Info.use = "JAVA"; //alert(Info.use) Info.serverURL && (Jmol._serverUrl = Info.serverURL); var javaAllowed = false; var applet = null; var List = Info.use.toUpperCase().split("#")[0].split(" "); for (var i = 0; i < List.length; i++) { switch (List[i]) { case "JAVA": javaAllowed = true; if (Jmol.featureDetection.supportsJava()) applet = new Jmol._Applet(id, Info, checkOnly); break; case "WEBGL": applet = Jmol._Applet._getCanvas(id, Info, checkOnly, true); break; case "HTML5": applet = Jmol._Applet._getCanvas(id, Info, checkOnly, false); break; case "IMAGE": applet = new Jmol._Image(id, Info, checkOnly); break; } if (applet != null) break; } if (applet == null) { if (checkOnly || !javaAllowed) applet = {_jmolType : "none" }; else if (javaAllowed) applet = new Jmol._Applet(id, Info); } // keyed to both its string id and itself return (checkOnly ? applet : Jmol._registerApplet(id, applet)); } Jmol._Applet._getCanvas = function(id, Info, checkOnly, webGL) { if (webGL && Jmol.featureDetection.supportsWebGL()) { Jmol._Canvas3D.prototype = Jmol._jsSetPrototype(new Jmol._Applet(id, Info, true)); GLmol.setRefresh(Jmol._Canvas3D.prototype); return new Jmol._Canvas3D(id, Info, "Jmol", checkOnly); } if (!webGL) { Jmol._Canvas2D.prototype = Jmol._jsSetPrototype(new Jmol._Applet(id, Info, true)); return new Jmol._Canvas2D(id, Info, "Jmol", checkOnly); } return null; }; /* AngelH, mar2007: By (re)setting these variables in the webpage before calling Jmol.getApplet(), a custom message can be provided (e.g. localized for user's language) when no Java is installed. */ Jmol._Applet._noJavaMsg = "Either you do not have Java applets enabled in your webbrowser or your browser is blocking this applet.\ Check the warning message from your browser and/or enable Java applets in\ your web browser preferences, or install the Java Runtime Environment from www.java.com"; Jmol._Applet._setCommonMethods = function(proto) { proto._showInfo = Jmol._Applet.prototype._showInfo; proto._search = Jmol._Applet.prototype._search; proto._readyCallback = Jmol._Applet.prototype._readyCallback; } Jmol._Applet._createApplet = function(applet, Info, params) { applet._initialize(Info.jarPath, Info.jarFile); var jarFile = applet._jarFile; var jnlp = "" if (Jmol._isLocal && Info.jarPath.indexOf("http") != 0) { // local installations need jnlp here and should reference JmolApplet(Signed).jar, not JmolApplet(Signed)0.jar jarFile = jarFile.replace(/0\.jar/,".jar"); jnlp = " jnlp_href=\"" + jarFile.replace(/\.jar/,".jnlp") + "\""; } // size is set to 100% of containers' size, but only if resizable. // Note that resizability in MSIE requires: // var w = (applet._containerWidth.indexOf("px") >= 0 ? applet._containerWidth : "100%"); var h = (applet._containerHeight.indexOf("px") >= 0 ? applet._containerHeight : "100%"); var widthAndHeight = " style=\"width:" + w + ";height:" + h + "\" "; var attributes = "name='" + applet._id + "_object' id='" + applet._id + "_object' " + "\n" + widthAndHeight + jnlp + "\n" params.codebase = applet._jarPath; params.codePath = params.codebase + "/"; if (params.codePath.indexOf("://") < 0) { var base = document.location.href.split("#")[0].split("?")[0].split("/"); base[base.length - 1] = params.codePath; params.codePath = base.join("/"); } params.archive = jarFile; params.mayscript = 'true'; params.java_arguments = "-Xmx" + Math.round(Info.memoryLimit || applet._memoryLimit) + "m"; params.permissions = (applet._isSigned ? "all-permissions" : "sandbox"); params.documentLocation = document.location.href; params.documentBase = document.location.href.split("#")[0].split("?")[0]; params.jarPath = Info.jarPath; Jmol._syncedApplets.length && (params.synccallback = "Jmol._mySyncCallback"); applet._startupScript && (params.script = applet._startupScript); var t = "\n"; for (var i in params) if(params[i]) t += " \n"; if (Jmol.featureDetection.useIEObject || Jmol.featureDetection.useHtml4Object) { t = "" : " type='application/x-java-applet'>") + t + "\n" + Jmol._Applet._noJavaMsg + "\n"; } else { // use applet tag t = "\n" + t + "\n" + Jmol._Applet._noJavaMsg + "\n"; } t = Jmol._getWrapper(applet, true) + t + Jmol._getWrapper(applet, false) + (Info.addSelectionOptions ? Jmol._getGrabberOptions(applet) : ""); if (Jmol._debugAlert) alert(t); applet._code = Jmol._documentWrite(t); } var japroto = Jmol._Applet.prototype; japroto._create = function(id, Info){ Jmol._setObject(this, id, Info); var params = { syncId: ("" + Math.random()).substring(3), progressbar: "true", progresscolor: "blue", boxbgcolor: this._color || "black", boxfgcolor: "white", boxmessage: "Downloading JmolApplet ...", script: (this._color ? "background " + this._color : ""), code: "JmolApplet.class" }; Jmol._setJmolParams(params, Info); function sterilizeInline(model) { model = model.replace(/\r|\n|\r\n/g, (model.indexOf("|") >= 0 ? "\\/n" : "|")).replace(/'/g, "'"); if(Jmol._debugAlert) alert("inline model:\n" + model); return model; } params.loadInline = (Info.inlineModel ? sterilizeInline(Info.inlineModel) : ""); params.appletReadyCallback = "Jmol._readyCallback"; if (Jmol._syncedApplets.length) params.synccallback = "Jmol._mySyncCallback"; params.java_arguments = "-Xmx" + Math.round(Info.memoryLimit || this._memoryLimit) + "m"; this._initialize(Info.jarPath, Info.jarFile); Jmol._Applet._createApplet(this, Info, params); } japroto._readyCallback = function(id, fullid, isReady, applet) { if (!isReady) return; // ignore -- page is closing Jmol._setDestroy(this); this._ready = true; var script = this._readyScript; this._applet = applet; if (this._defaultModel) Jmol._search(this, this._defaultModel, (script ? ";" + script : "")); else if (script) this._script(script); else if (this._src) this._script('load "' + this._src + '"'); this._showInfo(true); this._showInfo(false); this._setDragDrop(); var me = this; this._readyFunction && this._readyFunction(me); Jmol._setReady(this); var app = this._2dapplet; if (app && app._isEmbedded && app._ready && app.__Info.visible) { this._show2d(true); } } japroto._setDragDrop = function() { var me = this; Jmol.$appEvent(me, "appletdiv", "dragover", function(e) { e = e.originalEvent; e.stopPropagation(); e.preventDefault(); e.dataTransfer.dropEffect = 'copy'; }); Jmol.$appEvent(me, "appletdiv", "drop", function(e) { var e = e.originalEvent; e.stopPropagation(); e.preventDefault(); var file = e.dataTransfer.files[0]; var reader = new FileReader(); reader.onloadend = function(evt) { if (evt.target.readyState == FileReader.DONE) { var cacheName = "cache://DROP_" + file.name; var bytes = Jmol._toBytes(evt.target.result); me._applet.viewer.cacheFileByName("cache://DROP_*",false); me._applet.viewer.cachePut(cacheName, bytes); me._applet.viewer.openFileAsyncSpecial(cacheName, 1); //Jmol.script(me, "load '" + cacheName + "'"); } }; reader.readAsArrayBuffer(file); }); } japroto._showInfo = function(tf) { if(tf && this._2dapplet) this._2dapplet._show(false); Jmol.$html(Jmol.$(this, "infoheaderspan"), this._infoHeader); if (this._info) Jmol.$html(Jmol.$(this, "infodiv"), this._info); if ((!this._isInfoVisible) == (!tf)) return; this._isInfoVisible = tf; // 1px does not work for MSIE if (this._isJava) { var x = (tf ? 2 : "100%"); Jmol.$setSize(Jmol.$(this, "appletdiv"), x, x); } Jmol.$setVisible(Jmol.$(this, "infotablediv"), tf); Jmol.$setVisible(Jmol.$(this, "infoheaderdiv"), tf); this._show(!tf); } japroto._show2d = function(tf) { this._2dapplet._show2d(tf); if (this._2dapplet._isEmbedded) { this._showInfo(false); this._show(!tf); } } japroto._show = function(tf) { var x = (!tf ? 2 : "100%"); Jmol.$setSize(Jmol.$(this, "object"), x, x); if (!this._isJava) Jmol.$setVisible(Jmol.$(this, "appletdiv"), tf); } japroto._search = function(query, script){ Jmol._search(this, query, script); } japroto._loadModel = function(mol, params) { if (!params && this._noscript) { this._applet.viewer.loadInline(mol, '\0'); return; } var script = 'load DATA "model"\n' + mol + '\nEND "model" ' + params; this._applet.script(script); } japroto._clearConsole = function () { if (this._console == this._id + "_infodiv") this.info = ""; if (!self.Clazz)return; Jmol._setConsoleDiv(this._console); Clazz.Console.clear(); } japroto._addScript = function(script) { this._readyScript || (this. Script = ";"); this._readyScript += ";" + script; return true; } japroto._script = function(script) { if (!this._ready) return this._addScript(script); Jmol._setConsoleDiv(this._console); this._applet.script(script); } japroto._syncScript = function(script) { this._applet.syncScript(script); } japroto._scriptWait = function(script) { var Ret = this._scriptWaitAsArray(script); var s = ""; for(var i = Ret.length; --i >= 0; ) for(var j = 0, jj = Ret[i].length; j < jj; j++) s += Ret[i][j] + "\n"; return s; } japroto._scriptEcho = function(script) { // returns a newline-separated list of all echos from a script var Ret = this._scriptWaitAsArray(script); var s = ""; for(var i = Ret.length; --i >= 0; ) for(var j = Ret[i].length; --j >= 0; ) if(Ret[i][j][1] == "scriptEcho") s += Ret[i][j][3] + "\n"; return s.replace(/ \| /g, "\n"); } japroto._scriptMessage = function(script) { // returns a newline-separated list of all messages from a script, ending with "script completed\n" var Ret = this._scriptWaitAsArray(script); var s = ""; for(var i = Ret.length; --i >= 0; ) for(var j = Ret[i].length; --j >= 0; ) if(Ret[i][j][1] == "scriptStatus") s += Ret[i][j][3] + "\n"; return s.replace(/ \| /g, "\n"); } japroto._scriptWaitOutput = function(script) { var ret = ""; try { if(script) { ret += this._applet.scriptWaitOutput(script); } } catch(e) { } return ret; } japroto._scriptWaitAsArray = function(script) { var ret = ""; try { this._getStatus("scriptEcho,scriptMessage,scriptStatus,scriptError"); if(script) { ret += this._applet.scriptWait(script); ret = Jmol._evalJSON(ret, "jmolStatus"); if( typeof ret == "object") return ret; } } catch(e) { } return [[ret]]; } japroto._getStatus = function(strStatus) { return Jmol._sortMessages(this._getPropertyAsArray("jmolStatus",strStatus)); } japroto._getPropertyAsArray = function(sKey,sValue) { return Jmol._evalJSON(this._getPropertyAsJSON(sKey,sValue),sKey); } japroto._getPropertyAsString = function(sKey,sValue) { sValue == undefined && ( sValue = ""); return this._applet.getPropertyAsString(sKey, sValue) + ""; } japroto._getPropertyAsJSON = function(sKey,sValue) { sValue == undefined && ( sValue = ""); try { return (this._applet.getPropertyAsJSON(sKey, sValue) + ""); } catch(e) { return ""; } } japroto._getPropertyAsJavaObject = function(sKey,sValue) { sValue == undefined && ( sValue = ""); return this._applet.getProperty(sKey,sValue); } japroto._evaluate = function(molecularMath) { //carries out molecular math on a model var result = "" + this._getPropertyAsJavaObject("evaluate", molecularMath); var s = result.replace(/\-*\d+/, ""); if(s == "" && !isNaN(parseInt(result))) return parseInt(result); var s = result.replace(/\-*\d*\.\d*/, "") if(s == "" && !isNaN(parseFloat(result))) return parseFloat(result); return result; } japroto._saveOrientation = function(id) { return this._savedOrientations[id] = this._getPropertyAsArray("orientationInfo","info").moveTo; } japroto._restoreOrientation = function(id) { var s = this._savedOrientations[id]; if(!s || s == "") return s = s.replace(/1\.0/, "0"); return this._scriptWait(s); } japroto._restoreOrientationDelayed = function(id,delay) { arguments.length < 1 && ( delay = 1); var s = this._savedOrientations[id]; if(!s || s == "") return s = s.replace(/1\.0/, delay); return this._scriptWait(s); } japroto._resizeApplet = function(size) { // See _jmolGetAppletSize() for the formats accepted as size [same used by jmolApplet()] // Special case: an empty value for width or height is accepted, meaning no change in that dimension. /* * private functions */ function _getAppletSize(size, units) { /* Accepts single number, 2-value array, or object with width and height as mroperties, each one can be one of: percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.) [width, height] array of strings is returned, with units added if specified. Percent is relative to container div or element (which should have explicitly set size). */ var width, height; if(( typeof size) == "object" && size != null) { width = size[0]||size.width; height = size[1]||size.height; } else { width = height = size; } return [_fixDim(width, units), _fixDim(height, units)]; } function _fixDim(x, units) { var sx = "" + x; return (sx.length == 0 ? (units ? "" : Jmol._allowedJmolSize[2]) : sx.indexOf("%") == sx.length - 1 ? sx : (x = parseFloat(x)) <= 1 && x > 0 ? x * 100 + "%" : (isNaN(x = Math.floor(x)) ? Jmol._allowedJmolSize[2] : x < Jmol._allowedJmolSize[0] ? Jmol._allowedJmolSize[0] : x > Jmol._allowedJmolSize[1] ? Jmol._allowedJmolSize[1] : x) + (units ? units : "") ); } var sz = _getAppletSize(size, "px"); var d = Jmol._getElement(this, "appletinfotablediv"); d.style.width = sz[0]; d.style.height = sz[1]; this._containerWidth = sz[0]; this._containerHeight = sz[1]; if (this._is2D) Jmol._repaint(this, true); } japroto._loadFile = function(fileName, params){ this._showInfo(false); params || (params = ""); this._thisJmolModel = "" + Math.random(); this._fileName = fileName; if (!Jmol._scriptLoad(this, fileName, params, this._isSigned)) { var self = this; Jmol._loadFileData(this, fileName, function(data){self._loadModel(data, params)}); } } japroto._searchDatabase = function(query, database, script){ if (this._2dapplet && this._2dapplet._isEmbedded && Jmol.$(this, "2dappletdiv:visible")[0]) return this._2dapplet._searchDatabase(query, database, script); this._showInfo(false); if (query.indexOf("?") >= 0) { Jmol._getInfoFromDatabase(this, database, query.split("?")[0]); return; } script || (script = Jmol._getScriptForDatabase(database)); var dm = database + query; if (Jmol.db._DirectDatabaseCalls[database]) { this._loadFile(dm, script); return; } script = ";" + script; if (!Jmol._scriptLoad(this, dm, script, this._isSigned)) { // need to do the postLoad here as well var self = this; Jmol._getRawDataFromServer( database, query, function(data){self._loadModel(data, script)} ); } } japroto._isDeferred = function () { return this._cover && this._isCovered && this._deferApplet } japroto._checkDeferred = function(script) { if (this._isDeferred()) { this._coverScript = script; this._cover(false); return true; } return false; } // _Image -- an alternative to _Applet Jmol._Image = function(id, Info, checkOnly){ this._jmolType = "image"; if (checkOnly) return this; this._create(id, Info); return this; } Jmol._Image.prototype._create = function(id, Info) { Jmol._setObject(this, id, Info); this._src || (this._src = ""); var t = Jmol._getWrapper(this, true) + '' + Jmol._getWrapper(this, false) + (Info.addSelectionOptions ? Jmol._getGrabberOptions(this) : ""); if (Jmol._debugAlert) alert(t); this._code = Jmol._documentWrite(t); this._ready = false; if (Jmol._document) this._readyCallback(id, null, this._ready = true, null); } Jmol._Applet._setCommonMethods(Jmol._Image.prototype); Jmol._Image.prototype._canScript = function(script) { var slc = script.toLowerCase().replace(/[\",\']/g, ''); var ipt = slc.length; return (script.indexOf("#alt:LOAD") >= 0 || slc.indexOf(";") < 0 && slc.indexOf("\n") < 0 && (slc.indexOf("script ") == 0 || slc.indexOf("load ") == 0) && (slc.indexOf(".png") == ipt - 4 || slc.indexOf(".jpg") == ipt - 4)); } Jmol._Image.prototype._script = function(script) { var slc = script.toLowerCase().replace(/[\",\']/g, ''); // single command only // "script ..." or "load ..." only // PNG or PNGJ or JPG only // automatically switches to .all.png(j) from .min.png(j) var ipt = slc.length; if (slc.indexOf(";") < 0 && slc.indexOf("\n") < 0 && (slc.indexOf("script ") == 0 || slc.indexOf("load ") == 0) && (slc.indexOf(".png") == ipt - 4 || slc.indexOf(".pngj") == ipt - 5 || slc.indexOf(".jpg") == ipt - 4)) { var imageFile = script.substring(script.indexOf(" ") + 1); ipt = imageFile.length; for (var i = 0; i < ipt; i++) { switch (imageFile.charAt(i)) { case " ": continue; case '"': imageFile = imageFile.substring(i + 1, imageFile.indexOf('"', i + 1)) i = ipt; continue; case "'": imageFile = imageFile.substring(i + 1, imageFile.indexOf("'", i + 1)) i = ipt; continue; default: imageFile = imageFile.substring(i) i = ipt; continue; } } imageFile = imageFile.replace(/\.min\.png/,".all.png") document.getElementById(this._id + "_image").src = imageFile } else if (script.indexOf("#alt:LOAD ") >= 0) { imageFile = script.split("#alt:LOAD ")[1] if (imageFile.indexOf("??") >= 0) { var db = imageFile.split("??")[0]; imageFile = prompt(imageFile.split("??")[1], ""); if (!imageFile) return; if (!Jmol.db._DirectDatabaseCalls[imageFile.substring(0,1)]) imageFile = db + imageFile; } this._loadFile(imageFile); } } Jmol._Image.prototype._show = function(tf) { Jmol._getElement(this, "appletdiv").style.display = (tf ? "block" : "none"); } Jmol._Image.prototype._loadFile = function(fileName, params){ this._showInfo(false); this._thisJmolModel = "" + Math.random(); params = (params ? params : ""); var database = ""; if (Jmol._isDatabaseCall(fileName)) { database = fileName.substring(0, 1); fileName = Jmol._getDirectDatabaseCall(fileName, false); } else if (fileName.indexOf("://") < 0) { var ref = document.location.href var pt = ref.lastIndexOf("/"); fileName = ref.substring(0, pt + 1) + fileName; } var src = Jmol._serverUrl + "?call=getImageForFileLoad" + "&file=" + escape(fileName) + "&width=" + this._width + "&height=" + this._height + "¶ms=" + encodeURIComponent(params + ";frank off;"); Jmol._getElement(this, "image").src = src; } Jmol._Image.prototype._searchDatabase = function(query, database, script){ if (query.indexOf("?") == query.length - 1) { Jmol._getInfoFromDatabase(this, database, query.split("?")[0]); return; } this._showInfo(false); script || (script = Jmol._getScriptForDatabase(database)); var src = Jmol._serverUrl + "?call=getImageFromDatabase" + "&database=" + database + "&query=" + query + "&width=" + this._width + "&height=" + this._height + "&script=" + encodeURIComponent(script + ";frank off;"); Jmol._getElement(this, "image").src = src; } })(Jmol, document);
\n" + Jmol._Applet._noJavaMsg + "