//--><!]]>
</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>
<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;
jvfollower = document.getElementById("jvA");
setConsole(document.getElementById("stdout"));
- sep = jvfollower.getSeparator();
+ // sep = jvfollower.getSeparator();
//jvapp.setSeparator(""+jvapp.getSeparator());
linkJvJmol(jvfollower, "jmolView", modeltofiles);
};
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',
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
var jmbinding=_jvjmols.get(jmolView);
if (!jmbinding)
{
--- /dev/null
+/* \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
+\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: "HTML5", // could be JAVA or HTML5\r
+ // the serverURL path is only used to load binary files in Safari, Chrome, and MSIE\r
+ serverURL: "http://your.server.here/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
try
{
- content = doc.getElementById("seqData");
+ boolean contentFromDiv = true;
+ // search for BioJSON data in div element with id seqData
+ content = doc.select("div[id=seqData]").first();
+ if (content == null)
+ {
+ contentFromDiv = false;
+ // search for BioJSON data in input element with id seqData
+ content = doc.getElementById("seqData");
+ }
+
if (content == null)
{
errormessage = "The html document is not embedded with BioJSON data";
throw new IOException(errormessage);
}
- JSONFile jsonFile = new JSONFile().parse(new StringReader(content
+ JSONFile jsonFile = new JSONFile().parse(new StringReader(
+ contentFromDiv ? content.text() : content
.val()));
this.seqs = jsonFile.getSeqs();
this.seqGroups = jsonFile.getSeqGroups();
htmlSvg.append("<html>\n");
if (jsonData != null)
{
- htmlSvg.append("<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button>");
- htmlSvg.append("<input type=\"hidden\" name=\"seqData\" id=\"seqData\" value='"
- + jsonData + "'>");
+ htmlSvg.append("<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> ");
+ htmlSvg.append("<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
+ htmlSvg.append("<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
+ + jsonData + "</div>");
+ htmlSvg.append("<br/> ");
}
htmlSvg.append("\n<style type=\"text/css\"> "
+ "div.parent{ width:100%;<!-- overflow: auto; -->}\n"
+ "div.titlex{ width:11%; float: left; }\n"
+ "div.align{ width:89%; float: right; }\n"
+ + "div.main-container{ border: 2px solid blue; border: 2px solid blue; width: 99%; min-height: 99%; }\n"
+ ".sub-category-container {overflow-y: scroll; overflow-x: hidden; width: 100%; height: 100%;}\n"
- + "object {pointer-events: none;}"
- + "</style>");
- htmlSvg.append("<div>");
- htmlSvg.append(
-"<div class=\"titlex\">");
- htmlSvg.append(
-"<div class=\"sub-category-container\"> ")
- .append(titleSvg)
- .append("</div>")
- .append("</div>\n\n<!-- ========================================================================================== -->\n\n");
- htmlSvg.append(
-"<div class=\"align\" >");
+ + "object {pointer-events: none;}");
+ if (jsonData != null)
+ {
+ // facebox style sheet for displaying raw BioJSON data
+ htmlSvg.append("#facebox { position: absolute; top: 0; left: 0; z-index: 100; text-align: left; }\n"
+ + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
+ + "-moz-border-radius:5px; border-radius:5px; -webkit-box-shadow:0 0 18px rgba(0,0,0,0.4); -moz-box-shadow:0 0 18px rgba(0,0,0,0.4);"
+ + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
+ + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
+ + " border-radius:4px; }\n"
+ + "#facebox .content > p:first-child{ margin-top:0; }\n"
+ + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
+ + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
+ + "#facebox .close img{ opacity:0.3; }\n"
+ + "#facebox .close:hover img{ opacity:1.0; }\n"
+ + "#facebox .loading { text-align: center; }\n"
+ + "#facebox .image { text-align: center;}\n"
+ + "#facebox img { border: 0; margin: 0; }\n"
+ + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
+ + ".facebox_hide { z-index:-100; }\n"
+ + ".facebox_overlayBG { background-color: #000; z-index: 99; }");
+ }
+
+ htmlSvg.append("</style>");
+ htmlSvg.append("<div class=\"main-container\" \n>");
+ htmlSvg.append("<div class=\"titlex\">\n");
+ htmlSvg.append("<div class=\"sub-category-container\"> \n");
+ htmlSvg.append(titleSvg);
+ htmlSvg.append("</div>");
+ htmlSvg.append("</div>\n\n<!-- ========================================================================================== -->\n\n");
+ htmlSvg.append("<div class=\"align\" >");
htmlSvg.append(
"<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
.append(alignmentSvg)
htmlSvg.append("</div>");
htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
- + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"//ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
+ + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
+ "<script>\n"
+ "var subCatContainer = $(\".sub-category-container\");\n"
+ "subCatContainer.scroll(\nfunction() {\n"
htmlSvg.append("<script language=\"JavaScript\">\n");
htmlSvg.append("function openJalviewUsingCurrentUrl(){\n");
- htmlSvg.append(" var json = JSON.parse(document.getElementById(\"seqData\").value);\n");
+ htmlSvg.append(" var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
htmlSvg.append(" var jalviewVersion = json['appSettings'].version;\n");
htmlSvg.append(" var url = json['appSettings'].webStartUrl;\n");
htmlSvg.append(" var myForm = document.createElement(\"form\");\n\n");
htmlSvg.append(" myForm.submit() ;\n");
htmlSvg.append(" document.body.removeChild(myForm);\n");
htmlSvg.append("}\n");
+
+ // jquery facebox for displaying raw BioJSON data");
+ if (jsonData != null)
+ {
+ htmlSvg.append("/* Facebox (for jQuery)\n");
+ htmlSvg.append("* version: 1.3\n");
+ htmlSvg.append(" * @requires jQuery v1.2 or later\n");
+ htmlSvg.append(" * @homepage https://github.com/defunkt/facebox\n");
+ htmlSvg.append(" * Licensed under the MIT:\n");
+ htmlSvg.append(" * http://www.opensource.org/licenses/mit-license.php\n");
+ htmlSvg.append(" * Copyright Forever Chris Wanstrath, Kyle Neath\n");
+ htmlSvg.append(" * Usage:\n");
+ htmlSvg.append(" * jQuery(document).ready(function() {\n");
+ htmlSvg.append(" * jQuery('a[rel*=facebox]').facebox()\n");
+ htmlSvg.append(" * })\n");
+ htmlSvg.append(" * <a href=\"#terms\" rel=\"facebox\">Terms</a>\n");
+ htmlSvg.append(" * Loads the #terms div in the box\n");
+ htmlSvg.append(" * <a href=\"terms.html\" rel=\"facebox\">Terms</a>\n");
+ htmlSvg.append(" * Loads the terms.html page in the box\n");
+ htmlSvg.append(" * <a href=\"terms.png\" rel=\"facebox\">Terms</a>\n");
+ htmlSvg.append(" * Loads the terms.png image in the box\n");
+ htmlSvg.append(" * You can also use it programmatically:\n");
+ htmlSvg.append(" * jQuery.facebox('some html')\n");
+ htmlSvg.append(" * jQuery.facebox('some html', 'my-groovy-style')\n");
+ htmlSvg.append(" * The above will open a facebox with \"some html\" as the content.\n");
+ htmlSvg.append(" * jQuery.facebox(function($) {\n");
+ htmlSvg.append(" * $.get('blah.html', function(data) { $.facebox(data) })\n");
+ htmlSvg.append(" * })\n");
+ htmlSvg.append(" * The above will show a loading screen before the passed function is called,\n");
+ htmlSvg.append(" * allowing for a better ajaxy experience.\n");
+ htmlSvg.append(" * The facebox function can also display an ajax page, an image, or the contents of a div:\n");
+ htmlSvg.append(" * jQuery.facebox({ ajax: 'remote.html' })\n");
+ htmlSvg.append(" * jQuery.facebox({ ajax: 'remote.html' }, 'my-groovy-style')\n");
+ htmlSvg.append(" * jQuery.facebox({ image: 'stairs.jpg' })\n");
+ htmlSvg.append(" * jQuery.facebox({ image: 'stairs.jpg' }, 'my-groovy-style')\n");
+ htmlSvg.append(" * jQuery.facebox({ div: '#box' })\n");
+ htmlSvg.append(" * jQuery.facebox({ div: '#box' }, 'my-groovy-style')\n");
+ htmlSvg.append(" * Want to close the facebox? Trigger the 'close.facebox' document event:\n");
+ htmlSvg.append(" * jQuery(document).trigger('close.facebox')\n");
+ htmlSvg.append(" * Facebox also has a bunch of other hooks:\n");
+ htmlSvg.append(" * loading.facebox\n");
+ htmlSvg.append(" * beforeReveal.facebox\n");
+ htmlSvg.append(" * reveal.facebox (aliased as 'afterReveal.facebox')\n");
+ htmlSvg.append(" * init.facebox\n");
+ htmlSvg.append(" * afterClose.facebox\n");
+ htmlSvg.append(" * Simply bind a function to any of these hooks:\n");
+ htmlSvg.append(" * $(document).bind('reveal.facebox', function() { ...stuff to do after the facebox and contents are revealed... })\n");
+ htmlSvg.append(" *\n");
+ htmlSvg.append(" */\n");
+ htmlSvg.append("(function($) {\n");
+ htmlSvg.append(" $.facebox = function(data, klass) {\n");
+ htmlSvg.append(" $.facebox.loading()\n");
+ htmlSvg.append(" if (data.ajax) fillFaceboxFromAjax(data.ajax, klass)\n");
+ htmlSvg.append(" else if (data.image) fillFaceboxFromImage(data.image, klass)\n");
+ htmlSvg.append(" else if (data.div) fillFaceboxFromHref(data.div, klass)\n");
+ htmlSvg.append(" else if ($.isFunction(data)) data.call($)\n");
+ htmlSvg.append(" else $.facebox.reveal(data, klass)\n");
+ htmlSvg.append(" }\n");
+
+ htmlSvg.append(" $.extend($.facebox, {\n");
+ htmlSvg.append(" settings: {\n");
+ htmlSvg.append(" opacity : 0.2,\n");
+ htmlSvg.append(" overlay : true,\n");
+ htmlSvg.append(" loadingImage : 'https://raw.githubusercontent.com/jalview/biojson/gh-pages/images/loading.gif',\n");
+ htmlSvg.append(" closeImage : 'https://raw.githubusercontent.com/jalview/biojson/gh-pages/images/cancel.png',\n");
+ htmlSvg.append(" imageTypes : [ 'png', 'jpg', 'jpeg', 'gif' ],\n");
+ htmlSvg.append(" faceboxHtml : '<div id=\"facebox\" style=\"display:none; width: 95%; height: 85%; overflow: auto;\"> ");
+ htmlSvg.append(" <div class=\"popup\"> ");
+ htmlSvg.append(" <div class=\"content\"> ");
+ htmlSvg.append(" </div> ");
+ htmlSvg.append(" <a href=\"#\" class=\"close\"></a> ");
+ htmlSvg.append(" </div> ");
+ htmlSvg.append(" </div>'\n");
+ htmlSvg.append(" }, \n");
+ htmlSvg.append(" loading: function() {\n");
+ htmlSvg.append(" init()\n");
+ htmlSvg.append(" if ($('#facebox .loading').length == 1) return true\n");
+ htmlSvg.append(" showOverlay() \n");
+ htmlSvg.append(" $('#facebox .content').empty().\n");
+ htmlSvg.append(" append('<div class=\"loading\"><img src=\"'+$.facebox.settings.loadingImage+'\"/></div>')\n");
+ htmlSvg.append(" $('#facebox').show().css({\n");
+ htmlSvg.append(" top: getPageScroll()[1] + (getPageHeight() / 10),\n");
+ htmlSvg.append(" left: $(window).width() / 2 - ($('#facebox .popup').outerWidth() / 2)\n");
+ htmlSvg.append(" }) \n");
+ htmlSvg.append(" $(document).bind('keydown.facebox', function(e) {\n");
+ htmlSvg.append(" if (e.keyCode == 27) $.facebox.close()\n");
+ htmlSvg.append(" return true\n");
+ htmlSvg.append(" })\n");
+ htmlSvg.append(" $(document).trigger('loading.facebox')\n");
+ htmlSvg.append(" },\n");
+ htmlSvg.append(" reveal: function(data, klass) {\n");
+ htmlSvg.append(" $(document).trigger('beforeReveal.facebox')\n");
+ htmlSvg.append(" if (klass) $('#facebox .content').addClass(klass)\n");
+ htmlSvg.append(" $('#facebox .content').empty().append('<pre><code>'+JSON.stringify(JSON.parse(data),null,4)+'</pre></code>')\n");
+ htmlSvg.append(" $('#facebox .popup').children().fadeIn('normal')\n");
+ htmlSvg.append(" $('#facebox').css('left', $(window).width() / 2 - ($('#facebox .popup').outerWidth() / 2))\n");
+ htmlSvg.append(" $(document).trigger('reveal.facebox').trigger('afterReveal.facebox')\n");
+ htmlSvg.append(" }, \n");
+ htmlSvg.append(" close: function() {\n");
+ htmlSvg.append(" $(document).trigger('close.facebox')\n");
+ htmlSvg.append(" return false\n");
+ htmlSvg.append(" }\n");
+ htmlSvg.append(" })\n");
+ htmlSvg.append(" $.fn.facebox = function(settings) {\n");
+ htmlSvg.append(" if ($(this).length == 0) return \n");
+ htmlSvg.append(" init(settings) \n");
+ htmlSvg.append(" function clickHandler() {\n");
+ htmlSvg.append(" $.facebox.loading(true) \n");
+ htmlSvg.append(" // support for rel=\"facebox.inline_popup\" syntax, to add a class\n");
+ htmlSvg.append(" // also supports deprecated \"facebox[.inline_popup]\" syntax\n");
+ htmlSvg.append(" var klass = this.rel.match(/facebox\\[?\\.(\\w+)\\]?/)\n");
+ htmlSvg.append(" if (klass) klass = klass[1]\n");
+ htmlSvg.append(" fillFaceboxFromHref(this.href, klass)\n");
+ htmlSvg.append(" return false\n");
+ htmlSvg.append(" } \n");
+ htmlSvg.append(" return this.bind('click.facebox', clickHandler)\n");
+ htmlSvg.append(" }\n");
+ htmlSvg.append(" // called one time to setup facebox on this page\n");
+ htmlSvg.append(" function init(settings) {\n");
+ htmlSvg.append(" if ($.facebox.settings.inited) return true\n");
+ htmlSvg.append(" else $.facebox.settings.inited = true\n");
+ htmlSvg.append(" $(document).trigger('init.facebox')\n");
+ htmlSvg.append(" makeCompatible()\n");
+ htmlSvg.append(" var imageTypes = $.facebox.settings.imageTypes.join('|')\n");
+ htmlSvg.append(" $.facebox.settings.imageTypesRegexp = new RegExp('\\\\.(' + imageTypes + ')(\\\\?.*)?$', 'i')\n");
+
+ htmlSvg.append(" if (settings) $.extend($.facebox.settings, settings)\n");
+ htmlSvg.append(" $('body').append($.facebox.settings.faceboxHtml)\n");
+
+ htmlSvg.append(" var preload = [ new Image(), new Image() ]\n");
+ htmlSvg.append(" preload[0].src = $.facebox.settings.closeImage\n");
+ htmlSvg.append(" preload[1].src = $.facebox.settings.loadingImage\n");
+
+ htmlSvg.append(" $('#facebox').find('.b:first, .bl').each(function() {\n");
+ htmlSvg.append(" preload.push(new Image())\n");
+ htmlSvg.append(" preload.slice(-1).src = $(this).css('background-image').replace(/url\\((.+)\\)/, '$1')\n");
+ htmlSvg.append(" })\n");
+
+ htmlSvg.append(" $('#facebox .close')\n");
+ htmlSvg.append(" .click($.facebox.close)\n");
+ htmlSvg.append(" .append('<img src=\"'\n");
+ htmlSvg.append(" + $.facebox.settings.closeImage\n");
+ htmlSvg.append(" + '\" class=\"close_image\" title=\"close\">')\n");
+ htmlSvg.append(" }\n");
+
+ htmlSvg.append(" // getPageScroll() by quirksmode.com\n");
+ htmlSvg.append(" function getPageScroll() {\n");
+ htmlSvg.append(" var xScroll, yScroll;\n");
+ htmlSvg.append(" if (self.pageYOffset) {\n");
+ htmlSvg.append(" yScroll = self.pageYOffset;\n");
+ htmlSvg.append(" xScroll = self.pageXOffset;\n");
+ htmlSvg.append(" } else if (document.documentElement && document.documentElement.scrollTop) { // Explorer 6 Strict\n");
+ htmlSvg.append(" yScroll = document.documentElement.scrollTop;\n");
+ htmlSvg.append(" xScroll = document.documentElement.scrollLeft;\n");
+ htmlSvg.append(" } else if (document.body) {// all other Explorers\n");
+ htmlSvg.append(" yScroll = document.body.scrollTop;\n");
+ htmlSvg.append(" xScroll = document.body.scrollLeft;\n");
+ htmlSvg.append(" }\n");
+ htmlSvg.append(" return new Array(xScroll,yScroll)\n");
+ htmlSvg.append(" }\n");
+
+ // Adapted from getPageSize() by quirksmode.com");
+ htmlSvg.append(" function getPageHeight() {\n");
+ htmlSvg.append(" var windowHeight\n");
+ htmlSvg.append(" if (self.innerHeight) { // all except Explorer\n");
+ htmlSvg.append(" windowHeight = self.innerHeight;\n");
+ htmlSvg.append(" } else if (document.documentElement && document.documentElement.clientHeight) { // Explorer 6 Strict Mode\n");
+ htmlSvg.append(" windowHeight = document.documentElement.clientHeight;\n");
+ htmlSvg.append(" } else if (document.body) { // other Explorers\n");
+ htmlSvg.append(" windowHeight = document.body.clientHeight;\n");
+ htmlSvg.append(" }\n");
+ htmlSvg.append(" return windowHeight\n");
+ htmlSvg.append(" }\n");
+
+ htmlSvg.append(" // Backwards compatibility\n");
+ htmlSvg.append(" function makeCompatible() {\n");
+ htmlSvg.append(" var $s = $.facebox.settings \n");
+ htmlSvg.append(" $s.loadingImage = $s.loading_image || $s.loadingImage\n");
+ htmlSvg.append(" $s.closeImage = $s.close_image || $s.closeImage\n");
+ htmlSvg.append(" $s.imageTypes = $s.image_types || $s.imageTypes\n");
+ htmlSvg.append(" $s.faceboxHtml = $s.facebox_html || $s.faceboxHtml\n");
+ htmlSvg.append(" }\n");
+
+ htmlSvg.append(" // Figures out what you want to display and displays it\n");
+ htmlSvg.append(" // formats are:\n");
+ htmlSvg.append(" // div: #id\n");
+ htmlSvg.append(" // image: blah.extension\n");
+ htmlSvg.append(" // ajax: anything else\n");
+ htmlSvg.append(" function fillFaceboxFromHref(href, klass) {\n");
+ htmlSvg.append(" // div\n");
+ htmlSvg.append(" if (href.match(/#/)) {\n");
+ htmlSvg.append(" var url = window.location.href.split('#')[0]\n");
+ htmlSvg.append(" var target = href.replace(url,'')\n");
+ htmlSvg.append(" if (target == '#') return\n");
+ htmlSvg.append(" $.facebox.reveal($(target).html(), klass)\n");
+
+ htmlSvg.append(" // image\n");
+ htmlSvg.append(" } else if (href.match($.facebox.settings.imageTypesRegexp)) {\n");
+ htmlSvg.append(" fillFaceboxFromImage(href, klass)\n");
+ htmlSvg.append(" // ajax\n");
+ htmlSvg.append(" } else {\n");
+ htmlSvg.append(" fillFaceboxFromAjax(href, klass)\n");
+ htmlSvg.append(" }\n");
+ htmlSvg.append(" }\n");
+
+ htmlSvg.append(" function fillFaceboxFromImage(href, klass) {\n");
+ htmlSvg.append(" var image = new Image()\n");
+ htmlSvg.append(" image.onload = function() {\n");
+ htmlSvg.append(" $.facebox.reveal('<div class=\"image\"><img src=\"' + image.src + '\" /></div>', klass)\n");
+ htmlSvg.append(" }\n");
+ htmlSvg.append(" image.src = href\n");
+ htmlSvg.append(" }\n");
+
+ htmlSvg.append(" function fillFaceboxFromAjax(href, klass) {\n");
+ htmlSvg.append(" $.facebox.jqxhr = $.get(href, function(data) { $.facebox.reveal(data, klass) })\n");
+ htmlSvg.append(" }\n");
+
+ htmlSvg.append(" function skipOverlay() {\n");
+ htmlSvg.append(" return $.facebox.settings.overlay == false || $.facebox.settings.opacity === null\n");
+ htmlSvg.append(" }\n");
+
+ htmlSvg.append(" function showOverlay() {\n");
+ htmlSvg.append(" if (skipOverlay()) return\n");
+
+ htmlSvg.append(" if ($('#facebox_overlay').length == 0)\n");
+ htmlSvg.append(" $(\"body\").append('<div id=\"facebox_overlay\" class=\"facebox_hide\"></div>')\n");
+
+ htmlSvg.append(" $('#facebox_overlay').hide().addClass(\"facebox_overlayBG\")\n");
+ htmlSvg.append(" .css('opacity', $.facebox.settings.opacity)\n");
+ htmlSvg.append(" .click(function() { $(document).trigger('close.facebox') })\n");
+ htmlSvg.append(" .fadeIn(200)\n");
+ htmlSvg.append(" return false\n");
+ htmlSvg.append(" }\n");
+
+ htmlSvg.append(" function hideOverlay() {\n");
+ htmlSvg.append(" if (skipOverlay()) return \n");
+ htmlSvg.append(" $('#facebox_overlay').fadeOut(200, function(){\n");
+ htmlSvg.append(" $(\"#facebox_overlay\").removeClass(\"facebox_overlayBG\")\n");
+ htmlSvg.append(" $(\"#facebox_overlay\").addClass(\"facebox_hide\")\n");
+ htmlSvg.append(" $(\"#facebox_overlay\").remove()\n");
+ htmlSvg.append(" }) \n");
+ htmlSvg.append(" return false\n");
+ htmlSvg.append(" }\n");
+
+ htmlSvg.append(" $(document).bind('close.facebox', function() {\n");
+ htmlSvg.append(" if ($.facebox.jqxhr) {\n");
+ htmlSvg.append(" $.facebox.jqxhr.abort()\n");
+ htmlSvg.append(" $.facebox.jqxhr = null\n");
+ htmlSvg.append(" }\n");
+ htmlSvg.append(" $(document).unbind('keydown.facebox')\n");
+ htmlSvg.append(" $('#facebox').fadeOut(function() {\n");
+ htmlSvg.append(" $('#facebox .content').removeClass().addClass('content')\n");
+ htmlSvg.append(" $('#facebox .loading').remove()\n");
+ htmlSvg.append(" $(document).trigger('afterClose.facebox')\n");
+ htmlSvg.append(" })\n");
+ htmlSvg.append(" hideOverlay()\n");
+ htmlSvg.append(" })\n");
+
+ htmlSvg.append("})(jQuery);\n");
+
+ }
+
htmlSvg.append("</script>\n");
htmlSvg.append("</hmtl>");
return htmlSvg.toString();
git://source.jalview.org / jalview.git / commitdiff