X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Fjavascript%2Fjalview.js;h=7995ddb787a766958c851102572ac3ec8e5614a0;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=293b73a0da00ce277828df6f53688076e5fecdab;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/examples/javascript/jalview.js b/examples/javascript/jalview.js
index 293b73a..7995ddb 100644
--- 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);
+  };
+