From 2420d32d1800074e7357587af270358c63b8c1bc Mon Sep 17 00:00:00 2001
From: Charles Ofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 14 Nov 2014 16:05:31 +0000
Subject: [PATCH] updated BioJsTemplate.txt

---
 resources/templates/BioJSTemplate.txt |   35 ++-------------------------------
 1 file changed, 2 insertions(+), 33 deletions(-)

diff --git a/resources/templates/BioJSTemplate.txt b/resources/templates/BioJSTemplate.txt
index d86fa65..af0e4d2 100644
--- a/resources/templates/BioJSTemplate.txt
+++ b/resources/templates/BioJSTemplate.txt
@@ -43,37 +43,7 @@ function toggleMenuVisibility(){
           divToggleButton.value="Hide Menu";
           }
 }
-function openJalviewUsingCurrentUrl2(){
-var jnpl = "<!--"+
-"Hi!"+
-"If you have downloaded this file after pressing \"Launch Full Application\" from Jalview on a web page and you don't know what to do with this file, you must install Java from http://www.java.sun.com then try opening this file again."+
-" \n"+
-"	JNLP generated by /jalviewServlet/services/launchAppDev"+
-"	JNLP generated from http://www.jalview.org/builds/develop/webstart/jalview.jnlp"+
-"Available servlet parameters (please URLEncode):"+
-"	open=<alignment file URL>"+
-"	jvm-max-heap=heap size in M or G"+
-"	features maps to	'-features'"+
-"	treeFile maps to	'-tree'"+
-"	tree maps to	'-tree'"+
-"	annotations maps to	'-annotations'"+
-"	colour maps to	'-colour'"+
-" "+
-"-->"+
-"<?xml version=\"1.0\" encoding=\"UTF-8\"?><jnlp spec=\"1.0+\" codebase=\"http://www.jalview.org/builds/develop/webstart\">	<information>		<title>Jalview</title>		<vendor>The Barton Group</vendor>		<homepage href=\"http://www.jalview.org\"/>		<description>Jalview Multiple Alignment Editor</description>		<description kind=\"short\">Jalview</description>		<icon href=\"JalviewLogo_big.png\"/>		<offline-allowed/>	</information>	<security>		<all-permissions/>	</security>	<resources>		<j2se version=\"1.7+\" initial-heap-size=\"10M\" max-heap-size=\"2G\"/>		<jar href=\"jalview.jar\"/>		<jar href=\"JGoogleAnalytics_0.3.jar\"/>		<jar href=\"Jmol-12.2.4.jar\"/>		<jar href=\"VARNAv3-91.jar\"/>		<jar href=\"activation.jar\"/>		<jar href=\"apache-mime4j-0.6.jar\"/>		<jar href=\"axis.jar\"/>		<jar href=\"castor-1.1-cycle-xml.jar\"/>		<jar href=\"commons-codec-1.3.jar\"/>		<jar href=\"commons-discovery.jar\"/>		<jar href=\"commons-logging-1.1.1.jar\"/>		<jar href=\"groovy-all-1.8.2.jar\"/>		<jar href=\"httpclient-4.0.3.jar\"/>		<jar href=\"httpcore-4.0.1.jar\"/>		<jar href=\"httpmime-4.0.3.jar\"/>		<jar href=\"jalview_jnlp_vm.jar\"/>		<jar href=\"jaxrpc.jar\"/>		<jar href=\"jdas-1.0.4.jar\"/>		<jar href=\"jhall.jar\"/>		<jar href=\"json_simple-1.1.jar\"/>		<jar href=\"jsoup-1.8.1.jar\"/>		<jar href=\"jswingreader-0.3.jar\"/>		<jar href=\"log4j-to-slf4j-2.0-rc2.jar\"/>		<jar href=\"mail.jar\"/>		<jar href=\"miglayout-4.0-swing.jar\"/>		<jar href=\"min-jabaws-client-2.1.0.jar\"/>		<jar href=\"regex.jar\"/>		<jar href=\"saaj.jar\"/>		<jar href=\"slf4j-api-1.7.7.jar\"/>		<jar href=\"slf4j-log4j12-1.7.7.jar\"/>		<jar href=\"spring-core-3.0.5.RELEASE.jar\"/>		<jar href=\"spring-web-3.0.5.RELEASE.jar\"/>		<jar href=\"vamsas-client.jar\"/>		<jar href=\"wsdl4j.jar\"/>		<jar href=\"xercesImpl.jar\"/>		<jar href=\"xml-apis.jar\"/>		<property name=\"jalview.version\" value=\"Development Branch Build\"/>	</resources>"+
-"<application-desc main-class=\"jalview.bin.Jalview\">"+
-"<argument>-open</argument>"+
-"<argument>file:///Users/tcnofoegbu/Documents/workspace/java/dev/jalview/examples/example_biojs.html</argument>"+
-"</application-desc>"+
-"	<security>"+
-"		<all-permissions/>"+
-"	</security>"+
-"</jnlp>"
-
-var encodedUri = encodeURI(jnpl);
-window.open(encodedUri)
-//alert(jnpl)
-}
+
 
 function openJalviewUsingCurrentUrl(){
 	var url = "http://webservices.compbio.dundee.ac.uk:38080/jalviewServlet/services/launchAppDev";
@@ -88,8 +58,7 @@ function openJalviewUsingCurrentUrl(){
     var myInput1 = document.createElement("input") ;
     myInput1.setAttribute("name", "open") ;
     myInput1.setAttribute("value", document.URL);
-    myForm.appendChild(myInput1) ;
-    
+    myForm.appendChild(myInput1) ;    
 
   	document.body.appendChild(myForm) ;
   	myForm.submit() ;
-- 
1.7.10.2