From e5e2f56bca0fbb7e989df50e0c33dc92df14b773 Mon Sep 17 00:00:00 2001
From: Charles Ofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 7 Nov 2014 12:08:22 +0000
Subject: [PATCH] Updated BioJsTemplate to not show the menu by default and
 implemented a toggle button for the menu, also the LableId
 was disabled by default

---
 resources/templates/BioJSTemplate.txt |   55 ++++++++++++++++++++++++++++++---
 1 file changed, 51 insertions(+), 4 deletions(-)

diff --git a/resources/templates/BioJSTemplate.txt b/resources/templates/BioJSTemplate.txt
index 972aa0b..88ade1a 100644
--- a/resources/templates/BioJSTemplate.txt
+++ b/resources/templates/BioJSTemplate.txt
@@ -121,7 +121,6 @@
 <!-- <link type=text/css rel=stylesheet href=https://s3-eu-west-1.amazonaws.com/biojs/msa/latest/msa.css /> -->
   
   
-<div id="menuDiv"></div>
 <div id="yourDiv">press "Run with JS"</div>
 <input type='hidden' id='seqData' name='seqData' value='#sequenceData#'/>
 </br>
@@ -133,6 +132,7 @@
 </br>
 
 <button onclick="javascipt:openJalviewUsingCurrentUrl();">Launch in Jalview</button>
+<input type="button" name="divToggleButton" id="divToggleButton" onclick="javascipt:toggleMenuVisibility();" value="Show BioJs Menu"></input>
 
 </body>
 </html>
@@ -140,6 +140,52 @@
 
 
 <script>
+
+function toggleMenuVisibility(){
+	//alert("toggleMenuVisibility called!");
+	
+	var menu = document.getElementsByClassName("biojs_msa_menubar");
+	var divToggleButton = document.getElementById("divToggleButton");
+	if(menu[0].style.display == 'block'){
+          menu[0].style.display = 'none';
+          divToggleButton.value="Show BioJs Menu";
+       }else{
+          menu[0].style.display = 'block'; 
+          divToggleButton.value="Hide BioJs 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";
   	var myForm = document.createElement("form");
@@ -9082,7 +9128,6 @@ function Nets(uri, opts, cb) {
 
 // this is a way how you use a bundled file parser
 biojs.io.clustal.read("#", function(seqs){
-
 var opts = {};
 
 // set your custom properties
@@ -9091,7 +9136,7 @@ var opts = {};
 opts.seqs = JSON.parse(document.getElementById("seqData").value); 
 
 opts.el = document.getElementById("yourDiv");
-opts.vis = {conserv: false, overviewbox: false, labelid: false};
+opts.vis = {conserv: false, overviewbox: false, labelId: false};
 opts.zoomer = {alignmentHeight: 225, labelWidth: 130,labelFontsize: "13px",labelIdLength: 20,   menuFontsize: "12px",menuMarginLeft: "3px", menuPadding: "3px 4px 3px 4px", menuItemFontsize: "14px", menuItemLineHeight: "14px"};
 
 
@@ -9110,6 +9155,8 @@ m.addView("menu", defMenu);
 
 // call render at the end to display the whole MSA
 m.render();
-  
+ 
+toggleMenuVisibility(); 
+toggleMenuVisibility(); 
 });
 </script>
\ No newline at end of file
-- 
1.7.10.2