From 6fa2247c40e66f9d90ebb9967da5ef6cd96edfa0 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 28 May 2014 15:15:21 +0100
Subject: [PATCH] fix for JAL-1510 - workaround for IE9

---
 examples-jbake/assets/javascript/jalview.js |   26 +++++++++++++++++++-------
 examples/javascript/jalview.js              |   26 +++++++++++++++++++-------
 2 files changed, 38 insertions(+), 14 deletions(-)

diff --git a/examples-jbake/assets/javascript/jalview.js b/examples-jbake/assets/javascript/jalview.js
index 293b73a..c9e5d1e 100644
--- a/examples-jbake/assets/javascript/jalview.js
+++ b/examples-jbake/assets/javascript/jalview.js
@@ -27,6 +27,21 @@ 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;
 }
@@ -147,7 +162,7 @@ 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 +205,8 @@ 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 +311,7 @@ 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;
diff --git a/examples/javascript/jalview.js b/examples/javascript/jalview.js
index 293b73a..c9e5d1e 100644
--- a/examples/javascript/jalview.js
+++ b/examples/javascript/jalview.js
@@ -27,6 +27,21 @@ 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;
 }
@@ -147,7 +162,7 @@ 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 +205,8 @@ 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 +311,7 @@ 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;
-- 
1.7.10.2