JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / examples / javascript / jalview.js

diff --git a/examples/javascript/jalview.js b/examples/javascript/jalview.js
index 293b73a..7995ddb 100644 (file)
--- a/examples/javascript/jalview.js
+++ b/examples/javascript/jalview.js
@@ -1,6 +1,6 @@
 /**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -17,6 +17,14 @@
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 
+
+
+
+
+
+
+
+
 // default console to report messages
 var _console = document.getElementById("stdout");
 var _jvapps = new Array();
@@ -27,6 +35,21 @@ var _modeltofiles = new Array();
 // counter for jmol structures
 var mnum = 1;
 
+function getDocumentBase() {
+       var dburi = document.baseURI;
+       // IE does not support document.baseURI
+       // logic from patch to TYPO3:
+       // http://forge.typo3.org/projects/typo3cms-core/repository/revisions/f61358afad28adb6dcaeb270ba480e998dfb0b79/diff/typo3/sysext/rtehtmlarea/htmlarea/htmlarea.js
+       if (!dburi) {
+               var baseTags = document.getElementsByTagName('base');
+               if (baseTags.length > 0) {
+                       dburi = baseTags[0].href;
+               } else {
+                       dburi = document.URL;
+               }
+       }
+       return dburi.substring(0, dburi.lastIndexOf("/") + 1);
+}
 function setConsole(console) {
        _console = console;
 }
@@ -130,7 +153,7 @@ function linkJvJmol(applet, jmolView, modeltofiles) {
                var sep = applet.getSeparator();
                var oldjm=jmolView;
                // recover full id of Jmol applet
-               jmolView=_jmolGetApplet(jmolView).id;
+               jmolView=jmolFindTarget(jmolView)._id; // Jmol 14.2.14
                var jmbinding=_jvjmols.get(jmolView);
                if (!jmbinding)
                {       
@@ -147,7 +170,7 @@ function linkJvJmol(applet, jmolView, modeltofiles) {
                jmbinding._jmol=jmolView;
                // now update structureListener list
                mtf="";
-               var dbase = document.baseURI.substring(0,document.baseURI.lastIndexOf("/")+1);
+               var dbase = getDocumentBase();
                for (m in jmbinding._modelstofiles)
                { if (m>0) { mtf+=sep; }
                mtf+=jmbinding._modelstofiles[m];
@@ -190,10 +213,8 @@ function _structure(list1, list2, list3, list4) {
                                ("" + list4));
                // 1 is pdb file, 2 is residue number, 3 is chain
                // list1 = new Object(list1);
-               var base = list[1].indexOf(document.baseURI
-                               .substring(0, document.baseURI.lastIndexOf('/'))
-                               ); // .indexOf(_path);
-               if (base==0) { base = document.baseURI.lastIndexOf('/'); }
+               var base = list[1].indexOf(getDocumentBase()); // .indexOf(_path);
+               if (base==0) { base = getDocumentBase(); }
                var sid = list[1]; // .substring(base);
                base = list[1].substring(0, base);
                if (_console) {
@@ -298,8 +319,7 @@ function _jmolhover(jmid, atomlabel, atomidx) {
        // use atomlabel[5] to look up model filename so we can highlight associated positions in any jalviews
        for (ap in _jvapps) {
                _jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3],
-                               document.baseURI
-                                               .substring(0, document.baseURI.lastIndexOf('/'))
+                               getDocumentBase()
                                                + "/" + 
                                                modeltofiles[atomlabel[5]]);
                msg = _jmolhovermsg;
@@ -326,3 +346,37 @@ function _jmolMessagecallback(jmid, statmess) {
 
        }
 }
+
+
+  function lJvApp() {
+    setTimeout(function() {
+       //alert("in lJvApp");
+       var jvapp = document.getElementById("jvapp");
+       var jvfollower = document.getElementById("jvfollower");
+       //console.log(">>>>>>>> lJvApp" + jvapp);
+       linkJvJmol(jvapp);
+    }, 200);
+    setConsole(document.getElementById("stdout"));
+  };
+
+  function lJvFollow() {
+    setTimeout(function() {
+       //alert("in lJvFollow");
+       var jvapp = document.getElementById("jvapp");
+       var jvfollower = document.getElementById("jvfollower");
+       console.log(">>>>>>> lJvFollow" + jvfollower);
+       linkJvJmol(jvfollower);
+    }, 200);
+  };
+
+  function lJvA() {
+    setTimeout(function() {
+      //alert("lJvA");
+      jvfollower = document.getElementById("jvA");
+      setConsole(document.getElementById("stdout"));  
+      //sep = jvfollower.getSeparator();
+      //jvapp.setSeparator(""+jvapp.getSeparator());
+      linkJvJmol(jvfollower, "jmolView", modeltofiles);
+    }, 100);
+  };
+