Merge branch 'JAL-957_jbake' into Release_2_8_Branch

[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
new file mode 100644 (file)
index 0000000..20504d8
--- /dev/null
+++ b/examples-jbake/templates/jvl_embeddedWJmol_hdr.ftl
@@ -0,0 +1,91 @@
+<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>