X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=examples%2Fjmol%2FJmol2.js;h=664bcf7821a369f1fb4b283266340c34bb240734;hb=refs%2Fheads%2Ffeatures%2FJAL-4219_extended_fasta_rna_ss;hp=631265797475d9ef3855bd5bcca91cb9c3857c52;hpb=0b29b2f4d9bfb2c9dd551637cf6fd7b6dd59715e;p=jalview.git
diff --git a/examples/jmol/Jmol2.js b/examples/jmol/Jmol2.js
index 6312657..664bcf7 100644
--- a/examples/jmol/Jmol2.js
+++ b/examples/jmol/Jmol2.js
@@ -1,432 +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. 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
-
-*/
-
-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: "HTML5", // could be JAVA or HTML5
- // the serverURL path is only used to load binary files in Safari, Chrome, and MSIE
- serverURL: "http://your.server.here/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)
-}
-
+/*
+
+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
+
+*/
+(function(a,l){"object"===typeof module&&"object"===typeof module.exports?module.exports=a.document?l(a,!0):function(a){if(!a.document)throw Error("jQuery requires a window with a document");return l(a)}:l(a)})("undefined"!==typeof window?window:this,function(a,l){function k(f){var w=f.length,a=g.type(f);return"function"===a||g.isWindow(f)?!1:1===f.nodeType&&w?!0:"array"===a||0===w||"number"===typeof w&&0")).appendTo(a.documentElement),a=(fb[0].contentWindow||fb[0].contentDocument).document,a.write(),a.close(),p=za(f,a),fb.detach();nc[f]=p}return p}function pa(f,
+a){return{get:function(){var p=f();if(null!=p)if(p)delete this.get;else return(this.get=a).apply(this,arguments)}}}function gb(f,a){if(a in f)return a;for(var p=a.charAt(0).toUpperCase()+a.slice(1),x=a,g=oc.length;g--;)if(a=oc[g]+p,a in f)return a;return x}function A(f,a){for(var p,x,b,j=[],c=0,e=f.length;ca;a+=2)"margin"===p&&(j+=g.css(f,p+Ma[a],!0,b)),x?("content"===p&&(j-=g.css(f,"padding"+Ma[a],!0,b)),"margin"!==p&&(j-=g.css(f,"border"+
+Ma[a]+"Width",!0,b))):(j+=g.css(f,"padding"+Ma[a],!0,b),"padding"!==p&&(j+=g.css(f,"border"+Ma[a]+"Width",!0,b)));return j}function fa(f,a,p){var x=!0,b="width"===a?f.offsetWidth:f.offsetHeight,j=Na(f),c=v.boxSizing()&&"border-box"===g.css(f,"boxSizing",!1,j);if(0>=b||null==b){b=Oa(f,a,j);if(0>b||null==b)b=f.style[a];if(sb.test(b))return b;x=c&&(v.boxSizingReliable()||b===f.style[a]);b=parseFloat(b)||0}return b+aa(f,a,p||(c?"border":"content"),x,j)+"px"}function C(f,a,p,x,b){return new C.prototype.init(f,
+a,p,x,b)}function ua(){setTimeout(function(){Xa=void 0});return Xa=g.now()}function qa(f,a){var p,x={height:f},b=0;for(a=a?1:0;4>b;b+=2-a)p=Ma[b],x["margin"+p]=x["padding"+p]=f;a&&(x.opacity=x.width=f);return x}function ib(f,a,p){for(var b,g=(jb[a]||[]).concat(jb["*"]),j=0,c=g.length;jw&&b)return a;d.resolveWith(f,[m]);return!1},m=d.promise({elem:f,props:g.extend({},a),opts:g.extend(!0,{specialEasing:{}},p),originalProperties:a,originalOptions:p,startTime:Xa||ua(),duration:p.duration,tweens:[],createTween:function(a,w){var p=g.Tween(f,m.opts,a,w,m.opts.specialEasing[a]||m.opts.easing);m.tweens.push(p);return p},stop:function(a){var w=0,p=a?m.tweens.length:0;if(j)return this;for(j=
+!0;w