From: tcofoegbu Date: Tue, 8 Sep 2015 11:56:04 +0000 (+0100) Subject: commited jmol/Jmol2.js diff with origin shows no change, seems to be an issue with... X-Git-Tag: Release_2_10_0~469 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=689acdc2cd646be253e48413f1fc544824294bf5;p=jalview.git commited jmol/Jmol2.js diff with origin shows no change, seems to be an issue with line endings as git gave the following warning: 'CRLF will be replaced by LF' --- diff --git a/examples/jmol/Jmol2.js b/examples/jmol/Jmol2.js index e0dcb92..664bcf7 100644 --- a/examples/jmol/Jmol2.js +++ b/examples/jmol/Jmol2.js @@ -1,871 +1,871 @@ -/* - -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. 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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= -function(a,b,d){for(var k in a)if("info"!=k){var h=a[k],n=h.applet,s=d||null!=n&&""==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.$appEvent(b,"appletdiv","dragover",function(a){a=a.originalEvent;a.stopPropagation(); -a.preventDefault();a.dataTransfer.dropEffect="copy"});a.$appEvent(b,"appletdiv","drop",function(d){var c=d.originalEvent;c.stopPropagation();c.preventDefault();var k=c.dataTransfer.files[0];if(null==k)try{k=""+c.dataTransfer.getData("text"),(0==k.indexOf("file:/")||0==k.indexOf("http:/"))&&b._scriptLoad(k)}catch(h){}else c=new FileReader,c.onloadend=function(c){if(c.target.readyState==FileReader.DONE){var h="cache://DROP_"+k.name;c=a._toBytes(c.target.result);h.endsWith(".spt")||b._appletPanel.cacheFileByName("cache://DROP_*", -!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; -(function(a){a._isAsync=!1;a._asyncCallbacks={};a._coreFiles=[];var l=!1,k=[],h=[],d=0,n=[],s=[],r=function(b){arguments.length||(b=!0);delete d;for(var e;0s.join("").indexOf(e[b])&&s.push(d+"/core/core"+e[b]+".z.js");for(b=0;b'+b+"._cover(false)\x3c/script>"));d+=a._getWrapper(this,!1);c.addSelectionOptions&&(d+= 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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); -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", -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._$(h.id).css({background:k?"rgb(0,0,0,1)": -"rgb(0,0,0,0.001)","z-index":a._getZ(this,b),position:"absolute",left:"0px",top:"0px",overflow:"hidden"});return h};c._setupJS=function(){window["j2s.lib"]={base:this._j2sPath+"/",alias:".",console:this._console,monitorZIndex:a._getZ(this,"monitorZIndex")};0==h.length&&a._addExec([this,b,null,"loadClazz"]);this._addCoreFiles();a._addExec([this,this.__startAppletJS,null,"start applet"]);this._isSigned=!0;this._ready=!1;this._applet=null;this._canScript=function(){return!0};this._savedOrientations= -[];d&&clearTimeout(d);d=setTimeout(r,100)};c.__startAppletJS=function(b){0==a._version.indexOf("$Date: ")&&(a._version=(a._version.substring(7)+" -").split(" -")[0]+" 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e=a.$(b,"appletdiv"),k=Math.round(e.width()),e=Math.round(e.height());if(b._is2D&&(b._canvas.width!= -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, -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 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"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 + "? 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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("
"); -} - -//////////////////////////////////////////////////////////////// -// 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) -} - +/* + +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. 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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= +function(a,b,d){for(var k in a)if("info"!=k){var h=a[k],n=h.applet,s=d||null!=n&&""==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(); +a.preventDefault();a.dataTransfer.dropEffect="copy"});a.$appEvent(b,"appletdiv","drop",function(d){var c=d.originalEvent;c.stopPropagation();c.preventDefault();var k=c.dataTransfer.files[0];if(null==k)try{k=""+c.dataTransfer.getData("text"),(0==k.indexOf("file:/")||0==k.indexOf("http:/"))&&b._scriptLoad(k)}catch(h){}else c=new FileReader,c.onloadend=function(c){if(c.target.readyState==FileReader.DONE){var h="cache://DROP_"+k.name;c=a._toBytes(c.target.result);h.endsWith(".spt")||b._appletPanel.cacheFileByName("cache://DROP_*", +!1);"JSV"==b._viewType||h.endsWith(".jdx")?a.Cache.put(h,c):b._appletPanel.cachePut(h,c);(c=a._jsGetXY(b._canvas,d))&&(!b._appletPanel.setStatusDragDropped||b._appletPanel.setStatusDragDropped(0,c[0],c[1],h))&&b._appletPanel.openFileAsyncSpecial(h,1)}},c.readAsArrayBuffer(k)})}})(Jmol,jQuery);Jmol._debugCode=!1; +(function(a){a._isAsync=!1;a._asyncCallbacks={};a._coreFiles=[];var l=!1,k=[],h=[],d=0,n=[],s=[],r=function(b){arguments.length||(b=!0);delete d;for(var e;0s.join("").indexOf(e[b])&&s.push(d+"/core/core"+e[b]+".z.js");for(b=0;b'+b+"._cover(false)\x3c/script>"));d+=a._getWrapper(this,!1);c.addSelectionOptions&&(d+= 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d=Math.round(b.width()),e=Math.round(b.height()),k=document.createElement("canvas");k.applet=this;this._canvas=k;k.style.width="100%";k.style.height="100%";k.width=d;k.height=e;k.id=this._id+"_canvas2d";b.append(k); +a._$(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._$(b.id).css({zIndex:a._getZ(this,"rear"),position:"absolute", +left:"0px",top:"0px",width:d+"px",height:e+"px",overflow:"hidden"}),this._mouseInterface=k.contentLayer,k.contentLayer.applet=this):this._mouseInterface=this._getLayer("front",b,d,e,!1)}else this._mouseInterface=k;a._jsSetMouse(this._mouseInterface)};c._getLayer=function(b,c,d,e,k){var h=document.createElement("canvas");this._canvas[b+"Layer"]=h;h.style.width="100%";h.style.height="100%";h.id=this._id+"_"+b+"Layer";h.width=d;h.height=e;c.append(h);h.applet=this;a._$(h.id).css({background:k?"rgb(0,0,0,1)": +"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= +[];d&&clearTimeout(d);d=setTimeout(r,100)};c.__startAppletJS=function(b){0==a._version.indexOf("$Date: ")&&(a._version=(a._version.substring(7)+" -").split(" -")[0]+" 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e=a.$(b,"appletdiv"),k=Math.round(e.width()),e=Math.round(e.height());if(b._is2D&&(b._canvas.width!= +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, +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 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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."), +"yes"==prompt("Do you want to use applet "+c+"? ","yes or no")?(d=c.substring(0,c.lastIndexOf("/")),b=c.substring(c.lastIndexOf("/")+1)):e=!0):b=c;this_isSigned=k.isSigned=0<=b.indexOf("Signed")}this._jarPath=k.jarPath=d||".";this._jarFile=k.jarFile="string"==typeof b?b:(b?"JmolAppletSigned":"JmolApplet")+"0.jar";e&&alert("The web page URL was ignored. Continuing using "+this._jarFile+' in directory "'+this._jarPath+'"');void 0==a.controls||a.controls._onloadResetForms()};this._create(d,k);return this}; +var k=a._Applet,h=a._Applet.prototype;k._get=function(d,h,l){l||(l=!1);h||(h={});a._addDefaultInfo(h,{color:"#FFFFFF",width:300,height:300,addSelectionOptions:!1,serverURL:"http://your.server.here/jsmol.php",defaultModel:"",script:null,src:null,readyFunction:null,use:"HTML5",jarPath:"java",jarFile:"JmolApplet0.jar",isSigned:!1,j2sPath:"j2s",coverImage:null,coverTitle:"",coverCommand:"",deferApplet:!1,deferUncover:!1,disableJ2SLoadMonitor:!1,disableInitialConsole:!1,debug:!1});a._debugAlert=h.debug; +h.serverURL&&(a._serverUrl=h.serverURL);for(var r=!1,b=null,e=h.use.toUpperCase().split("#")[0].split(" "),c=0;cs.codePath.indexOf("://")){var c=l.location.href.split("#")[0].split("?")[0].split("/");c[c.length-1]=s.codePath;s.codePath=c.join("/")}s.archive=r;s.mayscript="true";s.java_arguments="-Xmx"+Math.round(h.memoryLimit||d._memoryLimit)+"m";s.permissions=d._isSigned?"all-permissions":"sandbox";s.documentLocation=l.location.href;s.documentBase=l.location.href.split("#")[0].split("?")[0];s.jarPath=h.jarPath;a._syncedApplets.length&&(s.synccallback="Jmol._mySyncCallback"); +d._startupScript&&(s.script=d._startupScript);var c="\n",q;for(q in s)s[q]&&(c+=" \n");c=a.featureDetection.useIEObject||a.featureDetection.useHtml4Object?"":" type='application/x-java-applet'>")+c+"

\n"+ +k._noJavaMsg+"

\n":"\n"+c+"
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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("
"); +} + +//////////////////////////////////////////////////////////////// +// 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) +} +