From 0b29b2f4d9bfb2c9dd551637cf6fd7b6dd59715e Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 4 Sep 2015 16:03:38 +0100
Subject: [PATCH] JAL-1859 embedded Jmol applet example updated for Jmol 14.2
 javascript

---
 examples/embeddedWJmol.html    |   16 +-
 examples/javascript/jalview.js |    4 +-
 examples/jmol/Jmol2.js         |  432 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 439 insertions(+), 13 deletions(-)
 create mode 100644 examples/jmol/Jmol2.js

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index e8c9df3..bf050c0 100644
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -85,7 +85,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
 //--><!]]>
   </script>
 <script src="javascript/deployJava.js"></script>
-<script src="jmol/Jmol.js"></script>
+<script src="jmol/Jmol2.js"></script>
 <script src="javascript/jquery-1.4.4.min.js"></script>
 <script src="javascript/jquery.timer.js"></script>
 <script src="javascript/jquery.blockUI.js"></script>
@@ -96,15 +96,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
 <script language="JavaScript">
 // instead of this, we use a custom JmolApplet spec
 // jmolInitialize('jmol');
-jmolInitialize("","JmolApplet-12.2.4.jar");
-function genHref()
-{
- var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
- for(i=0; i<11; i++)
- { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); 
- }
- window.location=href;
-}
+jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
 </script>
 <script>
  var loglevel=1;
@@ -130,7 +122,7 @@ function genHref()
   jvfollower = document.getElementById("jvA");
   setConsole(document.getElementById("stdout"));
   
-  sep = jvfollower.getSeparator();
+ // sep = jvfollower.getSeparator();
   //jvapp.setSeparator(""+jvapp.getSeparator());
   linkJvJmol(jvfollower, "jmolView", modeltofiles);
  };
@@ -138,7 +130,7 @@ function genHref()
  var _jvA=new Object();
  _jvA.attributes = {
   code : 'jalview.bin.JalviewLite',
-  archive : 'jalviewApplet.jar,JmolApplet-12.2.4.jar',
+  archive : 'jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar',
   width : '500',
   height : '350',
   mayscript : 'True',
diff --git a/examples/javascript/jalview.js b/examples/javascript/jalview.js
index dfe8c26..c33be19 100644
--- a/examples/javascript/jalview.js
+++ b/examples/javascript/jalview.js
@@ -145,7 +145,9 @@ function linkJvJmol(applet, jmolView, modeltofiles) {
 		var sep = applet.getSeparator();
 		var oldjm=jmolView;
 		// recover full id of Jmol applet
-		jmolView=_jmolGetApplet(jmolView).id;
+//		jmolView=_jmolGetApplet(jmolView).id; // Jmol 12.4
+		jmolView=JmolFindTarget(jmolView).id; // Jmol 14.2.14
+		alert("FoundTarget " + jmolView.id);
 		var jmbinding=_jvjmols.get(jmolView);
 		if (!jmbinding)
 		{	
diff --git a/examples/jmol/Jmol2.js b/examples/jmol/Jmol2.js
new file mode 100644
index 0000000..6312657
--- /dev/null
+++ b/examples/jmol/Jmol2.js
@@ -0,0 +1,432 @@
+/* 
+
+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("<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)
+}
+
-- 
1.7.10.2