Merge branch 'develop' into features/JAL-1705_ensembl

[jalview.git] / examples-jbake / templates / jvl_embeddedWJmol_hdr.ftl

diff --git a/examples-jbake/templates/jvl_embeddedWJmol_hdr.ftl b/examples-jbake/templates/jvl_embeddedWJmol_hdr.ftl
deleted file mode 100644 (file)
index 20504d8..0000000
--- a/examples-jbake/templates/jvl_embeddedWJmol_hdr.ftl
+++ /dev/null
@@ -1,91 +0,0 @@
-<script src="javascript/deployJava.js"></script>
-<script src="jmol/Jmol.js"></script>
-<script src="javascript/jquery-1.4.4.min.js"></script>
-<script src="javascript/jquery.timer.js"></script>
-<script src="javascript/jquery.blockUI.js"></script>
-<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
-<!-- <script src="archive-min.js" language="javascript"></script>
--->
-<script src="javascript/jalview.js" language="javascript"></script>
-<script language="JavaScript">
-// instead of this, we use a custom JmolApplet spec
-// jmolInitialize('jmol');
-jmolInitialize("","${content.jmol}");
-function genHref()
-{
- var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
- for(i=0; i<11; i++)
- { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); 
- }
- window.location=href;
-}
-</script>
-<script>
- var loglevel=1;
- function dbg(lvl,string) {
-  if (_console && lvl<=loglevel) {_console.value += string + "\n";}
- }
- var _lastTime=new Date();
- var _path;
- var _datazip;
- var _zip;
- var alignA;
- var alignB;
- var featuresA;
- var featuresB;
- var pairs;
- var atompairs;
- var structdata;
- var jmolview;
- var jvstructassoc;
- var modeltofiles = new Array();
-
- function lJvA() {
-  jvfollower = document.getElementById("jvA");
-  setConsole(document.getElementById("stdout"));
-  
-  sep = jvfollower.getSeparator();
-  //jvapp.setSeparator(""+jvapp.getSeparator());
-  linkJvJmol(jvfollower, "jmolView", modeltofiles);
- };
-
- var _jvA=new Object();
- _jvA.attributes = {
-  code : 'jalview.bin.JalviewLite',
-  archive : '${content.jvl}',
-  width : '500',
-  height : '350',
-  mayscript : 'True',
-  scriptable: 'True',
-  id : 'jvA'
- };
- _jvA.parameters = {
-   java_arguments : "-Xmx256m",
-  externalstructureviewer : "true",
-   oninit : "lJvA",
-  automaticScrolling : "true",
-//  <!-- defaultColour : "Strand Propensity", -->
-  file : "uniref50_mz.fa",
-  
-  relaxedidmatch : "true",
-  debug : "true",
-  wrap : "false",
-  // separator : "^",
-  showAnnotation : "false",
-  embedded : "true",
-  showFullId : "false",
-  RGB : "F2F2FF",
-  linkLabel_1 : "EMBL-EBI Search",
-  linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
-  ,
-  linkLabel_2 : "Uniprot"
-  ,
-  linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
-  APPLICATION_URL : "http://www.jalview.org/services/launchApp",
-  PDBfile : "1gaq.txt FER1_MAIZE",
-  permissions : "sandbox"
- };
- jmolSetCallback("hoverCallback","_jmolhover");
-  jmolSetCallback("pickCallback","_jmolpick");
-  modeltofiles+="1gaq.txt";
-</script>