-/* \r
-\r
-Jmol2.js (JSmol version)\r
-author: Bob Hanson hansonr@stolaf.edu 5/24/2013 12:06:25 PM\r
-\r
-Script replacement for legacy Jmol.js that uses JSmol instead.\r
-Can be used to turn most legacy Jmol.js-based sites to JSmol.\r
-\r
-BH 1/16/2014 10:33:46 PM adding serverURL indication, more notes\r
-BH 1/13/2014 11:14:12 AM incorrect default for missing jmolInitialize() (should be ".")\r
-BH 1/8/2014 5:56:15 AM simplified instructions; removed option for self.Info\r
-BH 11/12/2013 6:34:22 AM adds jmolAppletInline()\r
-BH 9/23/2013 10:07:16 PM adds set of loadInline functions\r
-BH 9/19/2013 7:09:41 AM fixed jmolSetTarget() to accept "0" as a suffix; use of undefined --> null\r
-\r
-Summary:\r
-\r
-You should not have to change any of your HTML pages.\r
-You are going to replace Jmol.js, wherever that is, with this file.\r
-You are going to replace all your JAR file with the ones in this distribution.\r
-You are going to add about 1000 files in the jsmol/j2s directory to your website. \r
- Don't worry; only a few will be called. But you won't know which ones.\r
-You will be able to switch from HTML5 to JAVA using ?_USE=SIGNED in the URL\r
-\r
-Procedure:\r
-\r
-1a) If you want to use HTML5, copy all jsmol/j2s/* files into a j2s subdirectory \r
- in the directory that contains Jmol.js and your old Jmol jar files.\r
-\r
-1b) If you are not using HTML5, change the "use" parameter below from "HTML5" to "JAVA" and save this file.\r
- Copy all the jsmol/java/* files into the directory containing your current JAR files. This adds\r
- four JNLP files as well and will replace all your JAR files.\r
-\r
-2) Rename your current Jmol.js file Jmol_old.js in case you want to undo this.\r
-\r
-3) Concatenate Jmol.min.js if you are not using jQuery (or Jmol.min.nojq.js if you are)\r
- with this file to form a new file (Jmol.min.js first, then Jmol2.js) and replace your\r
- current Jmol.js with it. Note that if you are using your own version of jQuery, it\r
- must be version 1.9 or higher, and note that 2.0 or higher will not work with MSIE\r
- used locally but accessing remote resources. See http://bugs.jquery.com/ticket/14876\r
- \r
-4) Try your page and see how it goes. You may still have some problems, because not all of the \r
- methods in the original Jmol.js are included here. Let me know if that's the case.\r
-\r
-If you wish to change the directories your j2s or JAR files and override the default settings\r
-(old JAR file location; j2s directory in the directory of those JAR files) and thus override\r
-your current settings in your HTML files, then you can to that three ways:\r
-\r
-a) You can change the parameters below to override what your pages already use by uncommenting\r
- one or the other of the jarPath and j2sPath definitions. This will override jmolInitialize\r
- in ALL your HTML files. \r
- \r
-b) You can change your jmolInitialization call in an individual HTML file. This sets both \r
- the JAR path and the j2s path (as [jarPath]/j2s) together.\r
-\r
-c) You can add lines to an individual HTML file along the lines of:\r
-\r
- Jmol.Info.jarPath = "../../Jmol"\r
- Jmol.Info.j2sPath = "../../JSmol"\r
-\r
- or whatever. This will override jmolInitialize in that specific HTML file only. \r
- \r
-Note that: \r
-\r
- -- FireFox works great. You will be able to read binary files from your local machine\r
- -- Chrome can only read local files if started with the --allow-file-access-from-files flag\r
- and even then the files must be ASCII, not binary.\r
- -- MSIE and Safari cannot work with local pages\r
-\r
-*/\r
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-"px",left:a._mousePageX+"px"})},b.mouseMove=function(b){if(this.isDragging&&a._mouseOwner==this){this.timestamp=System.currentTimeMillis();var c=this.pageX0+(b.pageX-this.pageX);b=this.pageY0+(b.pageY-this.pageY);a._mousePageX=c;a._mousePageY=b;this.container.css({top:b+"px",left:c+"px"})}},b.dragBind=function(b){this.applet._ignoreMouse=!b;this.container.unbind("mousemoveoutjsmol");this.container.unbind("touchmoveoutjsmol");this.container.unbind("mouseupoutjsmol");this.container.unbind("touchendoutjsmol");\r
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-"checked",!!b.selected)};r.setSelectedIndex=function(b){a.$prop(b.id,"selectedIndex",b.selectedIndex)};r.setText=function(b){a.$prop(b.id,"value",b.text)};r.setVisible=function(b){a.$setVisible(b.id,b.visible)};r.setEnabled=function(b){a.$setEnabled(b.id,b.enabled)};r.click=function(b,d){var c=r.htDialogs[b.id];if(c){var k=c.toString();if(0<=k.indexOf("JCheck"))c.selected=b.checked;else if(0<=k.indexOf("JCombo"))c.selectedIndex=b.selectedIndex;else if(null!=c.text&&(c.text=b.value,d&&13!=(d.charCode||\r
-d.keyCode)))return}k=r.htDialogs[a.$getAncestorDiv(b.id,"JDialog").id];k.manager.actionPerformed(c?c.name:k.registryKey+"/"+b.id)};r.setFront=function(b){var d=b.manager.vwr.html5Applet;b.zIndex!=a._getZ(d,"dialog")&&(b.zIndex=a._incrZ(d,"dialog"));b.container&&((b.container[0]||b.container).style.zIndex=b.zIndex)};r.hideMenus=function(a){if(a=a._menus)for(var d in a)a[d].visible&&r.hideMenu(a[d])};r.windowClosing=function(b){b=r.htDialogs[a.$getAncestorDiv(b.id,"JDialog").id];b.registryKey?b.manager.processWindowClosing(b.registryKey):\r
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-k+"]"):[];setTimeout(function(){d._currentView==h&&b.updateAtomPick(d,n)},10);a.User.viewUpdatedCallback&&a.User.viewUpdatedCallback(d,"updateFromSync")}};b.updateAtomPick=function(b,c){var d=b._currentView;if(null!=d){for(var k in d)"info"!=k&&d[k].applet!=b&&d[k].applet._updateAtomPick(c);a.User.viewUpdatedCallback&&a.User.viewUpdatedCallback(b,"updateAtomPick")}};b.dumpViews=function(a){var c=b.sets[a];if(c){var d="View set "+a+":\n";a=b.applets[a];for(var k in a)d+="\napplet "+a[k]._id+" currentView="+\r
-(a[k]._currentView?a[k]._currentView.info.viewID:null);for(k=c.length;0<=--k;){a=c[k];var d=d+("\n\n<b>view="+k+" viewID="+a.info.viewID+" chemID="+a.info.chemID+"</b>\n"),h,n;for(n in a)"info"!=n&&(d+="\nview="+k+" type="+n+" applet="+((h=a[n]).applet?h.applet._id:null)+" SMILES="+h.smiles+"\n atomMap="+JSON.stringify(h.atomMap)+"\n data=\n"+h.data+"\n")}return d}};b.__init=function(a){var c=a._viewSet,d=b.applets;d[c]||(d[c]={});d[c][a._viewType]=a};b.__findView=function(a,c){var d=b.sets[a];null==\r
-d&&(d=b.sets[a]=[]);for(var k=d.length;0<=--k;){var h=d[k];if(c.viewID){if(h.info.viewID==c.viewID)return h}else{if(null!=c.chemID&&c.chemID==h.info.chemID)return h;for(var n in h)if("info"!=n&&(null!=c.data&&null!=h[n].data?c.data==h[n].data:c.type==n))return h}}return null};b.__createViewSet=function(d,c,k){b.count++;c={info:{chemID:c,viewID:k||"model_"+b.count}};for(var h in a._applets)k=a._applets[h],k._viewSet==d&&(c[k._viewType]={applet:k,data:null});b.sets[d].push(c);return c};b.__setView=\r
-function(a,b,d){for(var k in a)if("info"!=k){var h=a[k],n=h.applet,s=d||null!=n&&"<modified>"==n._molData;if(!(null==n||n==b&&!s)){var l=null==h.data,r=null!=n._currentView;n._currentView=a;if(!r||!(a[k].data==h.data&&!l&!s))if(n._loadModelFromView(a),l)break}}}})(a.View);a.Cache={fileCache:{}};a.Cache.get=function(b){return a.Cache.fileCache[b]};a.Cache.put=function(b,d){a.Cache.fileCache[b]=d};a.Cache.setDragDrop=function(b){a.$appEvent(b,"appletdiv","dragover",function(a){a=a.originalEvent;a.stopPropagation();\r
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-!1);"JSV"==b._viewType||h.endsWith(".jdx")?a.Cache.put(h,c):b._appletPanel.cachePut(h,c);(c=a._jsGetXY(b._canvas,d))&&(!b._appletPanel.setStatusDragDropped||b._appletPanel.setStatusDragDropped(0,c[0],c[1],h))&&b._appletPanel.openFileAsyncSpecial(h,1)}},c.readAsArrayBuffer(k)})}})(Jmol,jQuery);Jmol._debugCode=!1;\r
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-function(){}),LoadClazz=null,b.__Info.uncompressed&&Clazz.loadClass(),Clazz._Loader.onGlobalLoaded=function(){Clazz._LoaderProgressMonitor.showStatus("Application loaded.",!0);if(!a._debugCode||!a.haveCore)a.haveCore=!0,r()},Clazz._Loader.loadPackageClasspath("java",null,!0,r))},e=function(a,b){Clazz._Loader.loadClass(b,function(){r()})};a.showExecLog=function(){return k.join("\n")};a._addExec=function(a){a[1]||(a[1]=e);var b="JSmol load "+a[0]._id+" "+a[3];self.console&&console.log(b+"...");k.push(b);\r
-h.push(a)};a._addCoreFile=function(b,d,e){b=b.toLowerCase().split(".")[0];if(!(0<=n.join("").indexOf(b))){n.push(b);n.sort();a._coreFiles=[d+"/core/core"+n.join("")+".z.js"];if(e&&(e=e.split(" ")))for(b=0;b<e.length;b++)0>s.join("").indexOf(e[b])&&s.push(d+"/core/core"+e[b]+".z.js");for(b=0;b<s.length;b++)a._coreFiles.push(s[b])}};a._Canvas2D=function(b,d,e,k){this._uniqueId=(""+Math.random()).substring(3);this._id=b;this._is2D=!0;this._isJava=!1;this._jmolType="Jmol._Canvas2D ("+e+")";this._isLayered=\r
-d._isLayered||!1;this._isSwing=d._isSwing||!1;this._isJSV=d._isJSV||!1;this._isAstex=d._isAstex||!1;this._platform=d._platform||"";if(k)return this;window[b]=this;this._createCanvas(b,d);if(!a._document||this._deferApplet)return this;this._init();return this};a._setAppletParams=function(b,d,e,k){for(var h in e)if(!b||0<=b.indexOf(";"+h.toLowerCase()+";"))null==e[h]||"language"==h&&!a.featureDetection.supportsLocalization()||(k?d.put(h,!0===e[h]?Boolean.TRUE:!1===e[h]?Boolean.FALSE:e[h]):d[h]=e[h])};\r
-a._jsSetPrototype=function(c){c._init=function(){this._setupJS();this._showInfo(!0);this._disableInitialConsole&&this._showInfo(!1)};c._createCanvas=function(b,c,d){a._setObject(this,b,c);d&&(this._GLmol=d,this._GLmol.applet=this,this._GLmol.id=this._id);d=a._getWrapper(this,!0);this._deferApplet||(a._document?(a._documentWrite(d),this._newCanvas(!1),d=""):(this._deferApplet=!0,d+='<script type="text/javascript">'+b+"._cover(false)\x3c/script>"));d+=a._getWrapper(this,!1);c.addSelectionOptions&&(d+=\r
-a._getGrabberOptions(this));a._debugAlert&&!a._document&&alert(d);this._code=a._documentWrite(d)};c._newCanvas=function(a){this._is2D?this._createCanvas2d(a):this._GLmol.create()};c._getHtml5Canvas=function(){return this._canvas};c._getWidth=function(){return this._canvas.width};c._getHeight=function(){return this._canvas.height};c._getContentLayer=function(){return a.$(this,"contentLayer")[0]};c._repaintNow=function(){a._repaint(this,!1)};c._createCanvas2d=function(){var b=a.$(this,"appletdiv");\r
-try{b[0].removeChild(this._canvas),this._canvas.frontLayer&&b[0].removeChild(this._canvas.frontLayer),this._canvas.rearLayer&&b[0].removeChild(this._canvas.rearLayer),this._canvas.contentLayer&&b[0].removeChild(this._canvas.contentLayer),a._jsUnsetMouse(this._mouseInterface)}catch(c){}var d=Math.round(b.width()),e=Math.round(b.height()),k=document.createElement("canvas");k.applet=this;this._canvas=k;k.style.width="100%";k.style.height="100%";k.width=d;k.height=e;k.id=this._id+"_canvas2d";b.append(k);\r
-a._$(k.id).css({"z-index":a._getZ(this,"main")});if(this._isLayered){var h=document.createElement("div");k.contentLayer=h;h.id=this._id+"_contentLayer";b.append(h);a._$(h.id).css({zIndex:a._getZ(this,"image"),position:"absolute",left:"0px",top:"0px",width:(this._isSwing?d:0)+"px",height:(this._isSwing?e:0)+"px",overflow:"hidden"});this._isSwing?(b=document.createElement("div"),b.id=this._id+"_swingdiv",a._$(this._id+"_appletinfotablediv").append(b),a._$(b.id).css({zIndex:a._getZ(this,"rear"),position:"absolute",\r
-left:"0px",top:"0px",width:d+"px",height:e+"px",overflow:"hidden"}),this._mouseInterface=k.contentLayer,k.contentLayer.applet=this):this._mouseInterface=this._getLayer("front",b,d,e,!1)}else this._mouseInterface=k;a._jsSetMouse(this._mouseInterface)};c._getLayer=function(b,c,d,e,k){var h=document.createElement("canvas");this._canvas[b+"Layer"]=h;h.style.width="100%";h.style.height="100%";h.id=this._id+"_"+b+"Layer";h.width=d;h.height=e;c.append(h);h.applet=this;a._$(h.id).css({background:k?"rgb(0,0,0,1)":\r
-"rgb(0,0,0,0.001)","z-index":a._getZ(this,b),position:"absolute",left:"0px",top:"0px",overflow:"hidden"});return h};c._setupJS=function(){window["j2s.lib"]={base:this._j2sPath+"/",alias:".",console:this._console,monitorZIndex:a._getZ(this,"monitorZIndex")};0==h.length&&a._addExec([this,b,null,"loadClazz"]);this._addCoreFiles();a._addExec([this,this.__startAppletJS,null,"start applet"]);this._isSigned=!0;this._ready=!1;this._applet=null;this._canScript=function(){return!0};this._savedOrientations=\r
-[];d&&clearTimeout(d);d=setTimeout(r,100)};c.__startAppletJS=function(b){0==a._version.indexOf("$Date: ")&&(a._version=(a._version.substring(7)+" -").split(" -")[0]+" (JSmol/j2s)");var c=Clazz._4Name("java.util.Hashtable").newInstance();a._setAppletParams(b._availableParams,c,b.__Info,!0);c.put("appletReadyCallback","Jmol._readyCallback");c.put("applet",!0);c.put("name",b._id);c.put("syncId",a._syncId);a._isAsync&&c.put("async",!0);b._color&&c.put("bgcolor",b._color);b._startupScript&&c.put("script",\r
-b._startupScript);a._syncedApplets.length&&c.put("synccallback","Jmol._mySyncCallback");c.put("signedApplet","true");c.put("platform",b._platform);b._is2D&&c.put("display",b._id+"_canvas2d");c.put("documentBase",document.location.href);var d=b._j2sPath+"/";if(0>d.indexOf("://")){var e=document.location.href.split("#")[0].split("?")[0].split("/");0==d.indexOf("/")?e=[e[0],d.substring(1)]:e[e.length-1]=d;d=e.join("/")}c.put("codePath",d);a._registerApplet(b._id,b);try{b._newApplet(c)}catch(k){System.out.println((a._isAsync?\r
-"normal async abort from ":"")+k);return}b._jsSetScreenDimensions();r()};c._restoreState||(c._restoreState=function(){});c._jsSetScreenDimensions=function(){if(this._appletPanel){var b=a._getElement(this,this._is2D?"canvas2d":"canvas");this._appletPanel.setScreenDimension(b.width,b.height)}};c._show=function(b){a.$setVisible(a.$(this,"appletdiv"),b);b&&a._repaint(this,!0)};c._canScript=function(){return!0};c.equals=function(a){return this==a};c.clone=function(){return this};c.hashCode=function(){return parseInt(this._uniqueId)};\r
-c._processGesture=function(a){return this._appletPanel.processTwoPointGesture(a)};c._processEvent=function(a,b){this._appletPanel.processMouseEvent(a,b[0],b[1],b[2],System.currentTimeMillis())};c._resize=function(){var b="__resizeTimeout_"+this._id;a[b]&&clearTimeout(a[b]);var c=this;a[b]=setTimeout(function(){a._repaint(c,!0);a[b]=null},100)};return c};a._repaint=function(b,d){if(b&&b._appletPanel){var e=a.$(b,"appletdiv"),k=Math.round(e.width()),e=Math.round(e.height());if(b._is2D&&(b._canvas.width!=\r
-k||b._canvas.height!=e))b._newCanvas(!0),b._appletPanel.setDisplay(b._canvas);b._appletPanel.setScreenDimension(k,e);k=function(){b._appletPanel.paint?b._appletPanel.paint(null):b._appletPanel.update(null)};d?setTimeout(k):k()}};a._getHiddenCanvas=function(a,b,d,e){b=a._id+"_"+b;a=document.createElement("canvas");a.width=a.style.width=d;a.height=a.style.height=e;a.id=b;return a};a._loadImage=function(b,d,e,k,h){var n=d[1];if(null==h&&(h=new Image,null==e?h.onload=function(){a._loadImage(b,d,null,\r
-k,h)}:(e=JU.Base64.getBase64(e).toString(),n=n.substring(n.lastIndexOf("/")+1),n="data:"+(0<=n.indexOf(".png")?"image/png":0<=n.indexOf(".jpg")?"image/jpg":"")+";base64,"+e),h.src=n,null==e))return;e=h.width;var s=h.height,l="echo_"+d[0],r=a._getHiddenCanvas(b.vwr.html5Applet,l,e,s,!0);r.imageWidth=e;r.imageHeight=s;r.id=l;r.image=h;a._setCanvasImage(r,e,s);k(r,n)};a._setCanvasImage=function(a,b,d){a.buf32=null;a.width=b;a.height=d;a.getContext("2d").drawImage(a.image,0,0,b,d)}})(Jmol);\r
-(function(a,l){a._Applet=function(d,k,h){window[d]=this;this._jmolType="Jmol._Applet"+(k.isSigned?" (signed)":"");this._viewType="Jmol";this._isJava=!0;this._syncKeyword="Select:";this._availableParams=";progressbar;progresscolor;boxbgcolor;boxfgcolor;allowjavascript;boxmessage;\t\t\t\t\t\t\t\t\t;messagecallback;pickcallback;animframecallback;appletreadycallback;atommovedcallback;\t\t\t\t\t\t\t\t\t;echocallback;evalcallback;hovercallback;language;loadstructcallback;measurecallback;\t\t\t\t\t\t\t\t\t;minimizationcallback;resizecallback;scriptcallback;statusform;statustext;statustextarea;\t\t\t\t\t\t\t\t\t;synccallback;usecommandthread;syncid;appletid;startupscript;menufile;";\r
-if(h)return this;this._isSigned=k.isSigned;this._readyFunction=k.readyFunction;this._ready=!1;this._isJava=!0;this._isInfoVisible=!1;this._applet=null;this._memoryLimit=k.memoryLimit||512;this._canScript=function(){return!0};this._savedOrientations=[];this._initialize=function(d,b){var e=!1;a._jarFile&&(b=a._jarFile);if(this._jarFile){var c=this._jarFile;0<=c.indexOf("/")?(alert("This web page URL is requesting that the applet used be "+c+". 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."),\r
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-k._noJavaMsg+"</p></object>\n":"<applet "+e+" code='"+s.code+"' codebase='"+d._jarPath+"' archive='"+r+"' mayscript='true'>\n"+c+"<table bgcolor='yellow'><tr><td align='center' valign='middle' "+b+">\n"+k._noJavaMsg+"</td></tr></table></applet>\n";d._deferApplet&&(d._javaCode=c,c="");c=a._getWrapper(d,!0)+c+a._getWrapper(d,!1)+(h.addSelectionOptions?a._getGrabberOptions(d):"");a._debugAlert&&alert(c);d._code=a._documentWrite(c)};h._newApplet=function(a){this._is2D||a.put("script",(a.get("script")||\r
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-h._loadModelFromView=function(d){this._currentView=d;var k=d.Jmol;null!=k.data?this.__loadModel(k.data,null,d.info.chemID):null!=d.info.chemID?a._searchMol(this,d.info.chemID,null,!1):(k=d.JME)&&k.applet._show2d(!1,this)};h._updateView=function(){null!=this._viewSet&&this._applet&&(chemID=""+this._getPropertyAsJavaObject("variableInfo","script('show chemical inchiKey')"),chemID=36>chemID.length()?null:chemID.substring(36).split("\n")[0],a.View.updateView(this,{chemID:chemID,data:""+this._getPropertyAsJavaObject("evaluate",\r
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-l._addScript(c,h);h='<span id="span_'+b+'"'+(e?' title="'+e+'"':"")+"><input name='"+r+"' id='"+b+"' type='radio' onclick='Jmol.controls._click(this);return true;' onmouseover='Jmol.controls._mouseOver(this);return true;' onmouseout='Jmol.controls._mouseOut()' "+(n?"checked='true' ":"")+l._radioCssText+" />";0<=d.toLowerCase().indexOf("<td>")&&(h+=a,a="");return h+('<label for="'+b+'">'+d+"</label>"+a+s)};l._scriptExecute=function(k,h){var d=a._applets[h[0]],l=h[1];if("object"==typeof l)l[0](k,l,\r
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-0==D.linesCount||1>c.childNodes.length)l=document.createElement("DIV"),c.appendChild(l),l.style.whiteSpace="nowrap",D.linesCount++;else try{l=c.childNodes[c.childNodes.length-1]}catch(n){l=document.createElement("DIV"),c.appendChild(l),l.style.whiteSpace="nowrap",D.linesCount++}var q=document.createElement("SPAN");l.appendChild(q);q.style.whiteSpace="nowrap";b&&(q.style.color=b);l=h[d];0==l.length&&(l=X);q.appendChild(document.createTextNode(l));D.pinning||(c.scrollTop+=100);D.metLineBreak=d!=k||\r
-e}d=c.parentNode.className;!D.pinning&&(d&&-1!=d.indexOf("composite"))&&(c.parentNode.scrollTop=c.parentNode.scrollHeight);D.lastOutputTime=(new Date).getTime()};D.clear=function(){try{D.metLineBreak=!0;var a=window["j2s.lib"],b=a&&a.console;if(b&&(b=document.getElementById(b))){for(var c=b.childNodes,d=c.length;0<=--d;)b.removeChild(c[d]);D.linesCount=0}}catch(e){}};a.alert=function(a){D.consoleOutput(a+"\r\n")};W.out.print=function(a){D.consoleOutput(a)};W.out.println=function(a){D.consoleOutput("undefined"==\r
-typeof a?"\r\n":null==a?"null\r\n":a+"\r\n")};W.out.write=function(a,b,c){W.out.print(String.instantialize(a).substring(b,b+c))};W.err.__CLASS_NAME__="java.io.PrintStream";W.err.print=function(a){D.consoleOutput(a,"red")};W.err.println=function(a){D.consoleOutput("undefined"==typeof a?"\r\n":null==a?"null\r\n":a+"\r\n","red")};W.err.write=function(a,b,c){W.err.print(String.instantialize(a).substring(b,b+c))}}(Clazz,Jmol))};Jmol.___JmolDate="$Date: 2015-06-10 23:34:03 -0500 (Wed, 10 Jun 2015) $";\r
-Jmol.___fullJmolProperties="src/org/jmol/viewer/Jmol.properties";Jmol.___JmolVersion="14.2.14_2015.06.11";\r
-\r
-Jmol.Info = { \r
- // uncomment one or more of these next lines only if you want to override jmolInitialize()\r
- //jarPath: "java", \r
- //jarFile: "JmolAppletSigned0.jar", \r
- //j2sPath: "j2s", \r
- use: "JAVA", // could be JAVA or HTML5\r
- // the serverURL path is only used to load binary files in Safari, Chrome, and MSIE\r
- serverURL: "http://www.jalview.org/jsmol.php", // required for binary file loading (Spartan, .gz, .map, etc.)\r
- disableJ2SLoadMonitor: false,\r
- disableInitialConsole: true\r
-\r
-}\r
-\r
-////////// private functions /////////////\r
-\r
-var _jmol = {\r
- appletCount: 0,\r
- applets: {},\r
- allowedJmolSize: [25, 2048, 300], // min, max, default (pixels)\r
- codebase: ".",\r
- targetSuffix: 0,\r
- target: "jmolApplet0",\r
- buttonCount: 0,\r
- checkboxCount: 0,\r
- linkCount: 0,\r
- cmdCount: 0,\r
- menuCount: 0,\r
- radioCount: 0,\r
- radioGroupCount: 0,\r
- initialized: false,\r
- initChecked: false,\r
- archivePath: "JmolAppletSigned0.jar"\r
-}\r
-\r
-function _jmolApplet(size, inlineModel, script, nameSuffix) {\r
- nameSuffix == null && (nameSuffix = _jmol.appletCount);\r
- var id = "jmolApplet" + nameSuffix;\r
- jmolSetTarget(nameSuffix);\r
- ++_jmol.appletCount;\r
- script || (script = "select *");\r
- inlineModel && (script = 'load DATA "inline"\n' + inlineModel + '\nEND "inline";' + script); \r
- var Info = {}\r
- for (var i in Jmol.Info)\r
- Info[i] = Jmol.Info[i]\r
- Info.jarFile || (Info.jarFile = _jmol.archivePath);\r
- Info.jarPath || (Info.jarPath = _jmol.codebase);\r
- Info.j2sPath || (Info.j2sPath = Info.jarPath + "/j2s"); \r
- var sz = _jmolGetAppletSize(size);\r
- Info.width || (Info.width = sz[0]);\r
- Info.height || (Info.height = sz[1]); \r
- Info.script || (Info.script = script);\r
- Info.isSigned == null && (Info.isSigned = (Info.jarFile.indexOf("Signed") >= 0));\r
- for (var i in _jmol.params)\r
- if(_jmol.params[i]!="")\r
- Info[i] || (Info[i] = _jmol.params[i]);\r
-// alert(JSON.stringify(Info).replace(/\,/g,"\n\n\n\n"))\r
- return _jmol.applets[id] = Jmol.getApplet(id, Info)\r
-}\r
-\r
-function _jmolGetJarFilename(fileNameOrFlag) {\r
- _jmol.archivePath =\r
- (typeof(fileNameOrFlag) == "string" ? fileNameOrFlag : (fileNameOrFlag ? "JmolAppletSigned" : "JmolApplet") + "0.jar");\r
-}\r
-\r
-////////////////////////////////////////////////////////////////\r
-// Legacy Scripting API\r
-////////////////////////////////////////////////////////////////\r
-\r
-function jmolSetParameter(key,value) {\r
- Jmol.Info[key] = value;\r
-}\r
-\r
-function jmolSetXHTML(id) {\r
- Jmol.setXHTML(id);\r
-}\r
-\r
-function jmolSetTranslation(TF) {\r
- // n/a\r
-}\r
-\r
-function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {\r
- if (_jmol.initialized)\r
- return;\r
- _jmol.initialized = true;\r
- if(_jmol.jmoljar) {\r
- var f = _jmol.jmoljar;\r
- if (f.indexOf("/") >= 0) {\r
- 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.")\r
- var ok = prompt("Do you want to use applet " + f + "? ","yes or no")\r
- if (ok == "yes") {\r
- codebaseDirectory = f.substring(0, f.lastIndexOf("/"));\r
- fileNameOrUseSignedApplet = f.substring(f.lastIndexOf("/") + 1);\r
- } else {\r
- _jmolGetJarFilename(fileNameOrUseSignedApplet);\r
- alert("The web page URL was ignored. Continuing using " + _jmol.archivePath + ' in directory "' + codebaseDirectory + '"');\r
- }\r
- } else {\r
- fileNameOrUseSignedApplet = f;\r
- }\r
- }\r
- _jmol.codebase = codebaseDirectory;\r
- _jmolGetJarFilename(fileNameOrUseSignedApplet);\r
-}\r
-\r
-function jmolSetDocument(doc) {\r
- _jmol.currentDocument = doc;\r
-}\r
-\r
-function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {\r
- Jmol.Info.color = boxbgcolor ? boxbgcolor : "black";\r
-}\r
-\r
-function jmolSetAppletWindow(w) {\r
- _jmol.appletWindow = w;\r
-}\r
-\r
-function jmolApplet(size, script, nameSuffix) {\r
- return _jmolApplet(size, null, script, nameSuffix);\r
-}\r
-\r
-function jmolAppletInline(size, inlineModel, script, nameSuffix) {\r
- return _jmolApplet(size, inlineModel, script, nameSuffix);\r
-}\r
-\r
-\r
-\r
-////////////////////////////////////////////////////////////////\r
-// Basic controls\r
-////////////////////////////////////////////////////////////////\r
-\r
-function jmolButton(script, label, id, title) {\r
- return Jmol.jmolButton(_jmol.target, script, label, id, title);\r
-}\r
-\r
-function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked, labelHtml, isChecked, id, title) {\r
- return Jmol.jmolCheckbox(_jmol.target, scriptWhenChecked, scriptWhenUnchecked, labelHtml, isChecked, id, title)\r
-}\r
-\r
-function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {\r
- return Jmol.jmolRadioGroup(_jmol.target, arrayOfRadioButtons, separatorHtml, groupName, id, title)\r
-}\r
-\r
-\r
-function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {\r
- return Jmol.jmolRadio(_jmol.target, script, labelHtml, isChecked, separatorHtml, groupName, id, title)\r
-}\r
-\r
-function jmolLink(script, label, id, title) {\r
- return Jmol.jmolLink(_jmol.target, script, label, id, title)\r
-}\r
-\r
-function jmolCommandInput(label, size, id, title) {\r
- return Jmol.jmolCommandInput(_jmol.target, label, size, id, title);\r
-}\r
-\r
-function jmolMenu(arrayOfMenuItems, size, id, title) {\r
- return Jmol.jmolMenu(_jmol.target, arrayOfMenuItems, size, id, title);\r
-}\r
-\r
-function jmolHtml(html) {\r
- return Jmol._documentWrite(html);\r
-}\r
-\r
-function jmolBr() {\r
- return Jmol._documentWrite("<br />");\r
-}\r
-\r
-////////////////////////////////////////////////////////////////\r
-// advanced scripting functions\r
-////////////////////////////////////////////////////////////////\r
-\r
-function jmolDebugAlert(enableAlerts) {\r
- // n/a\r
-}\r
-\r
-\r
-function jmolLoadInline(model, targetSuffix) {\r
- return jmolLoadInlineScript(model, null, targetSuffix, false)\r
-}\r
-\r
-function jmolLoadInlineArray(ModelArray, script, targetSuffix) {\r
- return jmolLoadInlineScript(ModelArray.join("\n"), script, targetSuffix, false)\r
-}\r
-\r
-function jmolAppendInlineArray(ModelArray, script, targetSuffix) {\r
- return jmolLoadInlineScript(ModelArray.join("\n"), script, targetSuffix, true)\r
-}\r
-\r
-function jmolAppendInlineScript(model, script, targetSuffix) {\r
- return jmolLoadInlineScript(model, script, targetSuffix, true)\r
-}\r
-\r
-function jmolLoadInlineScript(model, script, targetSuffix, isAppend) {\r
- Jmol.script(jmolFindTarget(targetSuffix),\r
- "load " \r
- + (isAppend ? "APPEND " : "") \r
- + "DATA 'mydata'\n" + model.replace(/\"/g,'\\"') + "\nEND 'mydata'\n")\r
-}\r
-\r
-function jmolSetTarget(targetSuffix) {\r
- targetSuffix == null || (_jmol.targetSuffix = targetSuffix);\r
- return _jmol.target = "jmolApplet" + _jmol.targetSuffix;\r
-}\r
-\r
-function jmolFindTarget(targetSuffix) {\r
- return _jmol.applets[jmolSetTarget(targetSuffix)];\r
-}\r
-\r
-function jmolScript(script, targetSuffix) {\r
- Jmol.script(jmolFindTarget(targetSuffix), script)\r
-}\r
-\r
-function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {\r
- // unnecessary\r
-}\r
-\r
-////////////////////////////////////////////////////////////////\r
-// Cascading Style Sheet Class support\r
-////////////////////////////////////////////////////////////////\r
-\r
-function jmolSetAppletCssClass(appletCssClass) {\r
- Jmol.setAppletCss(appletCssClass)\r
-}\r
-\r
-function jmolSetButtonCssClass(s) {\r
- Jmol.setButtonCss(s)\r
-}\r
-\r
-function jmolSetCheckboxCssClass(s) {\r
- Jmol.setCheckboxCss(s)\r
-}\r
-\r
-function jmolSetRadioCssClass(s) {\r
- Jmol.setRadioCss(s)\r
-}\r
-\r
-function jmolSetLinkCssClass(s) {\r
- Jmol.setLinkCss(s)\r
-}\r
-\r
-function jmolSetMenuCssClass(s) {\r
- Jmol.setMenuCss(s)\r
-}\r
-\r
-function jmolSetMemoryMb(nMb) {\r
- // n/a\r
-}\r
-\r
-\r
-function jmolSetCallback(callbackName,funcName) {\r
-//if(!self[funcName])alert(funcName + " is not defined yet in jmolSetCallback")\r
- Jmol.Info[callbackName] = funcName\r
- //document.title=("jmolSetCallback " + callbackName + "/" + funcName + " must be included in Info definition")\r
-}\r
-\r
-function jmolSetSyncId(n) {\r
- alert("jmolSetSyncId " + n + " must be included in Info definition")\r
-}\r
-\r
-function jmolSetLogLevel(n) {\r
- Jmol.script(_jmol.target, "set loglevel " + n)\r
-}\r
-\r
-function _jmolGetAppletSize(size, units) {\r
- var width, height;\r
- if ( (typeof size) == "object" && size != null ) {\r
- width = size[0]; height = size[1];\r
- } else {\r
- width = height = size;\r
- }\r
- return [_jmolFixDim(width, units), _jmolFixDim(height, units)];\r
-}\r
-\r
-function _jmolFixDim(x, units) {\r
- var sx = "" + x;\r
- return (sx.length == 0 ? (units ? "" : _jmol.allowedJmolSize[2])\r
- : sx.indexOf("%") == sx.length-1 ? sx\r
- : (x = parseFloat(x)) <= 1 && x > 0 ? x * 100 + "%"\r
- : (isNaN(x = Math.floor(x)) ? _jmol.allowedJmolSize[2]\r
- : x < _jmol.allowedJmolSize[0] ? _jmol.allowedJmolSize[0]\r
- : x > _jmol.allowedJmolSize[1] ? _jmol.allowedJmolSize[1]\r
- : x) + (units ? units : ""));\r
-}\r
-\r
-//////////user property/status functions/////////\r
-\r
-function jmolGetStatus(strStatus,targetSuffix){\r
- return Jmol.getStatus(jmolFindTarget(targetSuffix), strStatus)\r
-}\r
-\r
-function jmolGetPropertyAsArray(sKey,sValue,targetSuffix) {\r
- return Jmol.getPropertyAsArray(jmolFindTarget(targetSuffix), sKey, sValue)\r
-}\r
-\r
-function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {\r
- return Jmol.getPropertyAsString(jmolFindTarget(targetSuffix), sKey, sValue)\r
-}\r
-\r
-function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {\r
- return Jmol.getPropertyAsJSON(jmolFindTarget(targetSuffix), sKey, sValue)\r
-}\r
-\r
-function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {\r
- return Jmol.getPropertyAsJavaObject(jmolFindTarget(targetSuffix), sKey, sValue)\r
-}\r
-\r
-///////// synchronous scripting ////////\r
-\r
-function jmolScriptWait(script, targetSuffix) {\r
- return Jmol.scriptWait(jmolFindTarget(targetSuffix), script)\r
-}\r
-\r
-function jmolScriptWaitOutput(script, targetSuffix) {\r
- return Jmol.scriptWaitOutput(jmolFindTarget(targetSuffix), script)\r
-}\r
-\r
-function jmolEvaluate(molecularMath, targetSuffix) {\r
- return Jmol.evaluate(jmolFindTarget(targetSuffix), molecularMath)\r
-}\r
-\r
-function jmolScriptEcho(script, targetSuffix) {\r
- return Jmol.scriptEcho(jmolFindTarget(targetSuffix), script)\r
-}\r
-\r
-\r
-function jmolScriptMessage(script, targetSuffix) {\r
- return Jmol.scriptMessage(jmolFindTarget(targetSuffix), script)\r
-}\r
-\r
-\r
-function jmolScriptWaitAsArray(script, targetSuffix) {\r
- return Jmol.scriptWait(jmolFindTarget(targetSuffix), script)\r
-}\r
-\r
-\r
-\r
-//////////// save/restore orientation /////////////\r
-\r
-function jmolSaveOrientation(id, targetSuffix) {\r
- return Jmol.saveOrientation(jmolFindTarget(targetSuffix), id)\r
-}\r
-\r
-function jmolRestoreOrientation(id, targetSuffix) {\r
- return Jmol.restoreOrientation(jmolFindTarget(targetSuffix), id)\r
-}\r
-\r
-function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {\r
- return Jmol.restoreOrientationDelayed(jmolFindTarget(targetSuffix), id, delay)\r
-}\r
-\r
-function jmolResizeApplet(size, targetSuffix) {\r
- return Jmol.resizeApplet(jmolFindTarget(targetSuffix), size);\r
-}\r
-\r
-\r
-//////////// add parameter /////////////\r
-\r
-function jmolAppletAddParam(appletCode,name,value){\r
- alert ("use Info to add a parameter: " + name + "/" + value)\r
-}\r
-\r
+/*
+
+Jmol2.js (JSmol version)
+author: Bob Hanson hansonr@stolaf.edu 5/24/2013 12:06:25 PM
+
+Script replacement for legacy Jmol.js that uses JSmol instead.
+Can be used to turn most legacy Jmol.js-based sites to JSmol.
+
+BH 1/16/2014 10:33:46 PM adding serverURL indication, more notes
+BH 1/13/2014 11:14:12 AM incorrect default for missing jmolInitialize() (should be ".")
+BH 1/8/2014 5:56:15 AM simplified instructions; removed option for self.Info
+BH 11/12/2013 6:34:22 AM adds jmolAppletInline()
+BH 9/23/2013 10:07:16 PM adds set of loadInline functions
+BH 9/19/2013 7:09:41 AM fixed jmolSetTarget() to accept "0" as a suffix; use of undefined --> null
+
+Summary:
+
+You should not have to change any of your HTML pages.
+You are going to replace Jmol.js, wherever that is, with this file.
+You are going to replace all your JAR file with the ones in this distribution.
+You are going to add about 1000 files in the jsmol/j2s directory to your website.
+ Don't worry; only a few will be called. But you won't know which ones.
+You will be able to switch from HTML5 to JAVA using ?_USE=SIGNED in the URL
+
+Procedure:
+
+1a) If you want to use HTML5, copy all jsmol/j2s/* files into a j2s subdirectory
+ in the directory that contains Jmol.js and your old Jmol jar files.
+
+1b) If you are not using HTML5, change the "use" parameter below from "HTML5" to "JAVA" and save this file.
+ Copy all the jsmol/java/* files into the directory containing your current JAR files. This adds
+ four JNLP files as well and will replace all your JAR files.
+
+2) Rename your current Jmol.js file Jmol_old.js in case you want to undo this.
+
+3) Concatenate Jmol.min.js if you are not using jQuery (or Jmol.min.nojq.js if you are)
+ with this file to form a new file (Jmol.min.js first, then Jmol2.js) and replace your
+ current Jmol.js with it. Note that if you are using your own version of jQuery, it
+ must be version 1.9 or higher, and note that 2.0 or higher will not work with MSIE
+ used locally but accessing remote resources. See http://bugs.jquery.com/ticket/14876
+
+4) Try your page and see how it goes. You may still have some problems, because not all of the
+ methods in the original Jmol.js are included here. Let me know if that's the case.
+
+If you wish to change the directories your j2s or JAR files and override the default settings
+(old JAR file location; j2s directory in the directory of those JAR files) and thus override
+your current settings in your HTML files, then you can to that three ways:
+
+a) You can change the parameters below to override what your pages already use by uncommenting
+ one or the other of the jarPath and j2sPath definitions. This will override jmolInitialize
+ in ALL your HTML files.
+
+b) You can change your jmolInitialization call in an individual HTML file. This sets both
+ the JAR path and the j2s path (as [jarPath]/j2s) together.
+
+c) You can add lines to an individual HTML file along the lines of:
+
+ Jmol.Info.jarPath = "../../Jmol"
+ Jmol.Info.j2sPath = "../../JSmol"
+
+ or whatever. This will override jmolInitialize in that specific HTML file only.
+
+Note that:
+
+ -- FireFox works great. You will be able to read binary files from your local machine
+ -- Chrome can only read local files if started with the --allow-file-access-from-files flag
+ and even then the files must be ASCII, not binary.
+ -- MSIE and Safari cannot work with local pages
+
+*/
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+f,j){var c=j&&Na(a);return V(a,f,j?aa(a,b,j,v.boxSizing()&&"border-box"===g.css(a,"boxSizing",!1,c),c):0)}}});v.opacity||(g.cssHooks.opacity={get:function(a,b){return Ed.test((b&&a.currentStyle?a.currentStyle.filter:a.style.filter)||"")?0.01*parseFloat(RegExp.$1)+"":b?"1":""},set:function(a,b){var j=a.style,c=a.currentStyle,e=g.isNumeric(b)?"alpha(opacity="+100*b+")":"",d=c&&c.filter||j.filter||"";j.zoom=1;if((1<=b||""===b)&&""===g.trim(d.replace(ec,""))&&j.removeAttribute)if(j.removeAttribute("filter"),
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+"input"))a.defaultValue=b;else return eb&&eb.set(a,b,j)}};Ua||(eb={set:function(a,b,j){var c=a.getAttributeNode(j);c||a.setAttributeNode(c=a.ownerDocument.createAttribute(j));c.value=b+="";if("value"===j||b===a.getAttribute(j))return b}},Ha.id=Ha.name=Ha.coords=function(a,b,j){var c;if(!j)return(c=a.getAttributeNode(b))&&""!==c.value?c.value:null},g.valHooks.button={get:function(a,b){var j=a.getAttributeNode(b);if(j&&j.specified)return j.value},set:eb.set},g.attrHooks.contenteditable={set:function(a,
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+void 0,delete this[a]}catch(b){}})}});g.extend({propFix:{"for":"htmlFor","class":"className"},prop:function(a,b,j){var c,e,d;d=a.nodeType;if(a&&!(3===d||8===d||2===d)){if(d=1!==d||!g.isXMLDoc(a))b=g.propFix[b]||b,e=g.propHooks[b];return void 0!==j?e&&"set"in e&&void 0!==(c=e.set(a,j,b))?c:a[b]=j:e&&"get"in e&&null!==(c=e.get(a,b))?c:a[b]}},propHooks:{tabIndex:{get:function(a){var b=g.find.attr(a,"tabindex");return b?parseInt(b,10):Ld.test(a.nodeName)||Md.test(a.nodeName)&&a.href?0:-1}}}});v.hrefNormalized||
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+function(a,b,d){for(var k in a)if("info"!=k){var h=a[k],n=h.applet,s=d||null!=n&&"<modified>"==n._molData;if(!(null==n||n==b&&!s)){var l=null==h.data,r=null!=n._currentView;n._currentView=a;if(!r||!(a[k].data==h.data&&!l&!s))if(n._loadModelFromView(a),l)break}}}})(a.View);a.Cache={fileCache:{}};a.Cache.get=function(b){return a.Cache.fileCache[b]};a.Cache.put=function(b,d){a.Cache.fileCache[b]=d};a.Cache.setDragDrop=function(b){a.$appEvent(b,"appletdiv","dragover",function(a){a=a.originalEvent;a.stopPropagation();
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+left:"0px",top:"0px",width:d+"px",height:e+"px",overflow:"hidden"}),this._mouseInterface=k.contentLayer,k.contentLayer.applet=this):this._mouseInterface=this._getLayer("front",b,d,e,!1)}else this._mouseInterface=k;a._jsSetMouse(this._mouseInterface)};c._getLayer=function(b,c,d,e,k){var h=document.createElement("canvas");this._canvas[b+"Layer"]=h;h.style.width="100%";h.style.height="100%";h.id=this._id+"_"+b+"Layer";h.width=d;h.height=e;c.append(h);h.applet=this;a._$(h.id).css({background:k?"rgb(0,0,0,1)":
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+c._processGesture=function(a){return this._appletPanel.processTwoPointGesture(a)};c._processEvent=function(a,b){this._appletPanel.processMouseEvent(a,b[0],b[1],b[2],System.currentTimeMillis())};c._resize=function(){var b="__resizeTimeout_"+this._id;a[b]&&clearTimeout(a[b]);var c=this;a[b]=setTimeout(function(){a._repaint(c,!0);a[b]=null},100)};return c};a._repaint=function(b,d){if(b&&b._appletPanel){var e=a.$(b,"appletdiv"),k=Math.round(e.width()),e=Math.round(e.height());if(b._is2D&&(b._canvas.width!=
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+k._setCommonMethods=function(a){a._showInfo=h._showInfo;a._search=h._search;a._getName=h._getName;a._readyCallback=h._readyCallback};k._createApplet=function(d,h,s){d._initialize(h.jarPath,h.jarFile);var r=d._jarFile;a._isFile&&(r=r.replace(/0\.jar/,".jar"));var b=0<=d._containerWidth.indexOf("px")?d._containerWidth:"100%",e=0<=d._containerHeight.indexOf("px")?d._containerHeight:"100%",b=' style="width:'+b+";height:"+e+'" ',e="name='"+d._id+"_object' id='"+d._id+"_object' \n"+b+"\n";s.codebase=d._jarPath;
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+0<a?a:999999};D.maxLatency=40;D.setMaxLatency=function(a){D.maxLatency=0<a?a:40};D.pinning=!1;D.enablePinning=function(a){D.pinning=a};D.linesCount=0;D.metLineBreak=!1;D.createConsoleWindow=function(){var a=document.createElement("DIV");a.style.cssText="font-family:monospace, Arial, sans-serif;";document.body.appendChild(a);return a};var X=String.fromCharCode(160),X=X+(X+X+X);D.consoleOutput=function(a,b){var c=window["j2s.lib"];(c=c&&c.console)&&"string"==typeof c&&(c=document.getElementById(c));
+if(!c)return!1;if(D.linesCount>D.maxTotalLines){for(var d=0;d<D.linesCount-D.maxTotalLines;d++)c&&0<c.childNodes.length&&c.removeChild(c.childNodes[0]);D.linesCount=D.maxTotalLines}var e=!1;a=("undefined"==typeof a?"":null==a?"null":""+a).replace(/\t/g,X);if(0<a.length)switch(a.charAt(a.length-1)){case "\n":case "\r":a=1<a.length?a.substring(0,a.length-("\r"==a.charAt(a.length-2)?2:1)):"",e=!0}var h=null;a=a.replace(/\t/g,X);for(var h=a.split(/\r\n|\r|\n/g),d=0,k=h.length-1;d<=k;d++){var l=null;if(D.metLineBreak||
+0==D.linesCount||1>c.childNodes.length)l=document.createElement("DIV"),c.appendChild(l),l.style.whiteSpace="nowrap",D.linesCount++;else try{l=c.childNodes[c.childNodes.length-1]}catch(n){l=document.createElement("DIV"),c.appendChild(l),l.style.whiteSpace="nowrap",D.linesCount++}var q=document.createElement("SPAN");l.appendChild(q);q.style.whiteSpace="nowrap";b&&(q.style.color=b);l=h[d];0==l.length&&(l=X);q.appendChild(document.createTextNode(l));D.pinning||(c.scrollTop+=100);D.metLineBreak=d!=k||
+e}d=c.parentNode.className;!D.pinning&&(d&&-1!=d.indexOf("composite"))&&(c.parentNode.scrollTop=c.parentNode.scrollHeight);D.lastOutputTime=(new Date).getTime()};D.clear=function(){try{D.metLineBreak=!0;var a=window["j2s.lib"],b=a&&a.console;if(b&&(b=document.getElementById(b))){for(var c=b.childNodes,d=c.length;0<=--d;)b.removeChild(c[d]);D.linesCount=0}}catch(e){}};a.alert=function(a){D.consoleOutput(a+"\r\n")};W.out.print=function(a){D.consoleOutput(a)};W.out.println=function(a){D.consoleOutput("undefined"==
+typeof a?"\r\n":null==a?"null\r\n":a+"\r\n")};W.out.write=function(a,b,c){W.out.print(String.instantialize(a).substring(b,b+c))};W.err.__CLASS_NAME__="java.io.PrintStream";W.err.print=function(a){D.consoleOutput(a,"red")};W.err.println=function(a){D.consoleOutput("undefined"==typeof a?"\r\n":null==a?"null\r\n":a+"\r\n","red")};W.err.write=function(a,b,c){W.err.print(String.instantialize(a).substring(b,b+c))}}(Clazz,Jmol))};Jmol.___JmolDate="$Date: 2015-06-10 23:34:03 -0500 (Wed, 10 Jun 2015) $";
+Jmol.___fullJmolProperties="src/org/jmol/viewer/Jmol.properties";Jmol.___JmolVersion="14.2.14_2015.06.11";
+
+Jmol.Info = {
+ // uncomment one or more of these next lines only if you want to override jmolInitialize()
+ //jarPath: "java",
+ //jarFile: "JmolAppletSigned0.jar",
+ //j2sPath: "j2s",
+ use: "JAVA", // could be JAVA or HTML5
+ // the serverURL path is only used to load binary files in Safari, Chrome, and MSIE
+ serverURL: "http://www.jalview.org/jsmol.php", // required for binary file loading (Spartan, .gz, .map, etc.)
+ disableJ2SLoadMonitor: false,
+ disableInitialConsole: true
+
+}
+
+////////// private functions /////////////
+
+var _jmol = {
+ appletCount: 0,
+ applets: {},
+ allowedJmolSize: [25, 2048, 300], // min, max, default (pixels)
+ codebase: ".",
+ targetSuffix: 0,
+ target: "jmolApplet0",
+ buttonCount: 0,
+ checkboxCount: 0,
+ linkCount: 0,
+ cmdCount: 0,
+ menuCount: 0,
+ radioCount: 0,
+ radioGroupCount: 0,
+ initialized: false,
+ initChecked: false,
+ archivePath: "JmolAppletSigned0.jar"
+}
+
+function _jmolApplet(size, inlineModel, script, nameSuffix) {
+ nameSuffix == null && (nameSuffix = _jmol.appletCount);
+ var id = "jmolApplet" + nameSuffix;
+ jmolSetTarget(nameSuffix);
+ ++_jmol.appletCount;
+ script || (script = "select *");
+ inlineModel && (script = 'load DATA "inline"\n' + inlineModel + '\nEND "inline";' + script);
+ var Info = {}
+ for (var i in Jmol.Info)
+ Info[i] = Jmol.Info[i]
+ Info.jarFile || (Info.jarFile = _jmol.archivePath);
+ Info.jarPath || (Info.jarPath = _jmol.codebase);
+ Info.j2sPath || (Info.j2sPath = Info.jarPath + "/j2s");
+ var sz = _jmolGetAppletSize(size);
+ Info.width || (Info.width = sz[0]);
+ Info.height || (Info.height = sz[1]);
+ Info.script || (Info.script = script);
+ Info.isSigned == null && (Info.isSigned = (Info.jarFile.indexOf("Signed") >= 0));
+ for (var i in _jmol.params)
+ if(_jmol.params[i]!="")
+ Info[i] || (Info[i] = _jmol.params[i]);
+// alert(JSON.stringify(Info).replace(/\,/g,"\n\n\n\n"))
+ return _jmol.applets[id] = Jmol.getApplet(id, Info)
+}
+
+function _jmolGetJarFilename(fileNameOrFlag) {
+ _jmol.archivePath =
+ (typeof(fileNameOrFlag) == "string" ? fileNameOrFlag : (fileNameOrFlag ? "JmolAppletSigned" : "JmolApplet") + "0.jar");
+}
+
+////////////////////////////////////////////////////////////////
+// Legacy Scripting API
+////////////////////////////////////////////////////////////////
+
+function jmolSetParameter(key,value) {
+ Jmol.Info[key] = value;
+}
+
+function jmolSetXHTML(id) {
+ Jmol.setXHTML(id);
+}
+
+function jmolSetTranslation(TF) {
+ // n/a
+}
+
+function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
+ if (_jmol.initialized)
+ return;
+ _jmol.initialized = true;
+ if(_jmol.jmoljar) {
+ var f = _jmol.jmoljar;
+ 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") {
+ codebaseDirectory = f.substring(0, f.lastIndexOf("/"));
+ fileNameOrUseSignedApplet = f.substring(f.lastIndexOf("/") + 1);
+ } else {
+ _jmolGetJarFilename(fileNameOrUseSignedApplet);
+ alert("The web page URL was ignored. Continuing using " + _jmol.archivePath + ' in directory "' + codebaseDirectory + '"');
+ }
+ } else {
+ fileNameOrUseSignedApplet = f;
+ }
+ }
+ _jmol.codebase = codebaseDirectory;
+ _jmolGetJarFilename(fileNameOrUseSignedApplet);
+}
+
+function jmolSetDocument(doc) {
+ _jmol.currentDocument = doc;
+}
+
+function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
+ Jmol.Info.color = boxbgcolor ? boxbgcolor : "black";
+}
+
+function jmolSetAppletWindow(w) {
+ _jmol.appletWindow = w;
+}
+
+function jmolApplet(size, script, nameSuffix) {
+ return _jmolApplet(size, null, script, nameSuffix);
+}
+
+function jmolAppletInline(size, inlineModel, script, nameSuffix) {
+ return _jmolApplet(size, inlineModel, script, nameSuffix);
+}
+
+
+
+////////////////////////////////////////////////////////////////
+// Basic controls
+////////////////////////////////////////////////////////////////
+
+function jmolButton(script, label, id, title) {
+ return Jmol.jmolButton(_jmol.target, script, label, id, title);
+}
+
+function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked, labelHtml, isChecked, id, title) {
+ return Jmol.jmolCheckbox(_jmol.target, scriptWhenChecked, scriptWhenUnchecked, labelHtml, isChecked, id, title)
+}
+
+function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {
+ return Jmol.jmolRadioGroup(_jmol.target, arrayOfRadioButtons, separatorHtml, groupName, id, title)
+}
+
+
+function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
+ return Jmol.jmolRadio(_jmol.target, script, labelHtml, isChecked, separatorHtml, groupName, id, title)
+}
+
+function jmolLink(script, label, id, title) {
+ return Jmol.jmolLink(_jmol.target, script, label, id, title)
+}
+
+function jmolCommandInput(label, size, id, title) {
+ return Jmol.jmolCommandInput(_jmol.target, label, size, id, title);
+}
+
+function jmolMenu(arrayOfMenuItems, size, id, title) {
+ return Jmol.jmolMenu(_jmol.target, arrayOfMenuItems, size, id, title);
+}
+
+function jmolHtml(html) {
+ return Jmol._documentWrite(html);
+}
+
+function jmolBr() {
+ return Jmol._documentWrite("<br />");
+}
+
+////////////////////////////////////////////////////////////////
+// advanced scripting functions
+////////////////////////////////////////////////////////////////
+
+function jmolDebugAlert(enableAlerts) {
+ // n/a
+}
+
+
+function jmolLoadInline(model, targetSuffix) {
+ return jmolLoadInlineScript(model, null, targetSuffix, false)
+}
+
+function jmolLoadInlineArray(ModelArray, script, targetSuffix) {
+ return jmolLoadInlineScript(ModelArray.join("\n"), script, targetSuffix, false)
+}
+
+function jmolAppendInlineArray(ModelArray, script, targetSuffix) {
+ return jmolLoadInlineScript(ModelArray.join("\n"), script, targetSuffix, true)
+}
+
+function jmolAppendInlineScript(model, script, targetSuffix) {
+ return jmolLoadInlineScript(model, script, targetSuffix, true)
+}
+
+function jmolLoadInlineScript(model, script, targetSuffix, isAppend) {
+ Jmol.script(jmolFindTarget(targetSuffix),
+ "load "
+ + (isAppend ? "APPEND " : "")
+ + "DATA 'mydata'\n" + model.replace(/\"/g,'\\"') + "\nEND 'mydata'\n")
+}
+
+function jmolSetTarget(targetSuffix) {
+ targetSuffix == null || (_jmol.targetSuffix = targetSuffix);
+ return _jmol.target = "jmolApplet" + _jmol.targetSuffix;
+}
+
+function jmolFindTarget(targetSuffix) {
+ return _jmol.applets[jmolSetTarget(targetSuffix)];
+}
+
+function jmolScript(script, targetSuffix) {
+ Jmol.script(jmolFindTarget(targetSuffix), script)
+}
+
+function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {
+ // unnecessary
+}
+
+////////////////////////////////////////////////////////////////
+// Cascading Style Sheet Class support
+////////////////////////////////////////////////////////////////
+
+function jmolSetAppletCssClass(appletCssClass) {
+ Jmol.setAppletCss(appletCssClass)
+}
+
+function jmolSetButtonCssClass(s) {
+ Jmol.setButtonCss(s)
+}
+
+function jmolSetCheckboxCssClass(s) {
+ Jmol.setCheckboxCss(s)
+}
+
+function jmolSetRadioCssClass(s) {
+ Jmol.setRadioCss(s)
+}
+
+function jmolSetLinkCssClass(s) {
+ Jmol.setLinkCss(s)
+}
+
+function jmolSetMenuCssClass(s) {
+ Jmol.setMenuCss(s)
+}
+
+function jmolSetMemoryMb(nMb) {
+ // n/a
+}
+
+
+function jmolSetCallback(callbackName,funcName) {
+//if(!self[funcName])alert(funcName + " is not defined yet in jmolSetCallback")
+ Jmol.Info[callbackName] = funcName
+ //document.title=("jmolSetCallback " + callbackName + "/" + funcName + " must be included in Info definition")
+}
+
+function jmolSetSyncId(n) {
+ alert("jmolSetSyncId " + n + " must be included in Info definition")
+}
+
+function jmolSetLogLevel(n) {
+ Jmol.script(_jmol.target, "set loglevel " + n)
+}
+
+function _jmolGetAppletSize(size, units) {
+ var width, height;
+ if ( (typeof size) == "object" && size != null ) {
+ width = size[0]; height = size[1];
+ } else {
+ width = height = size;
+ }
+ return [_jmolFixDim(width, units), _jmolFixDim(height, units)];
+}
+
+function _jmolFixDim(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 : ""));
+}
+
+//////////user property/status functions/////////
+
+function jmolGetStatus(strStatus,targetSuffix){
+ return Jmol.getStatus(jmolFindTarget(targetSuffix), strStatus)
+}
+
+function jmolGetPropertyAsArray(sKey,sValue,targetSuffix) {
+ return Jmol.getPropertyAsArray(jmolFindTarget(targetSuffix), sKey, sValue)
+}
+
+function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {
+ return Jmol.getPropertyAsString(jmolFindTarget(targetSuffix), sKey, sValue)
+}
+
+function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {
+ return Jmol.getPropertyAsJSON(jmolFindTarget(targetSuffix), sKey, sValue)
+}
+
+function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {
+ return Jmol.getPropertyAsJavaObject(jmolFindTarget(targetSuffix), sKey, sValue)
+}
+
+///////// synchronous scripting ////////
+
+function jmolScriptWait(script, targetSuffix) {
+ return Jmol.scriptWait(jmolFindTarget(targetSuffix), script)
+}
+
+function jmolScriptWaitOutput(script, targetSuffix) {
+ return Jmol.scriptWaitOutput(jmolFindTarget(targetSuffix), script)
+}
+
+function jmolEvaluate(molecularMath, targetSuffix) {
+ return Jmol.evaluate(jmolFindTarget(targetSuffix), molecularMath)
+}
+
+function jmolScriptEcho(script, targetSuffix) {
+ return Jmol.scriptEcho(jmolFindTarget(targetSuffix), script)
+}
+
+
+function jmolScriptMessage(script, targetSuffix) {
+ return Jmol.scriptMessage(jmolFindTarget(targetSuffix), script)
+}
+
+
+function jmolScriptWaitAsArray(script, targetSuffix) {
+ return Jmol.scriptWait(jmolFindTarget(targetSuffix), script)
+}
+
+
+
+//////////// save/restore orientation /////////////
+
+function jmolSaveOrientation(id, targetSuffix) {
+ return Jmol.saveOrientation(jmolFindTarget(targetSuffix), id)
+}
+
+function jmolRestoreOrientation(id, targetSuffix) {
+ return Jmol.restoreOrientation(jmolFindTarget(targetSuffix), id)
+}
+
+function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {
+ return Jmol.restoreOrientationDelayed(jmolFindTarget(targetSuffix), id, delay)
+}
+
+function jmolResizeApplet(size, targetSuffix) {
+ return Jmol.resizeApplet(jmolFindTarget(targetSuffix), size);
+}
+
+
+//////////// add parameter /////////////
+
+function jmolAppletAddParam(appletCode,name,value){
+ alert ("use Info to add a parameter: " + name + "/" + value)
+}
+