Merge branch 'features/JAL-1541_BioJsMSA' into develop

[jalview.git] / resources / templates / BioJSTemplate.txt

diff --git a/resources/templates/BioJSTemplate.txt b/resources/templates/BioJSTemplate.txt
index bf780bb..c47b059 100644 (file)
--- a/resources/templates/BioJSTemplate.txt
+++ b/resources/templates/BioJSTemplate.txt
@@ -44,9 +44,9 @@ function toggleMenuVisibility(){
 
 
 function openJalviewUsingCurrentUrl(){
-       var jalviewData = JSON.parse(document.getElementById("seqData").value)
-    var jalviewVersion = jalviewData['jalviewVersion'];
-    var url = jalviewData['webStartUrl'];
+       var json = JSON.parse(document.getElementById("seqData").value)
+    var jalviewVersion = json['jalviewSettings'].jalviewVersion;
+    var url = json['jalviewSettings'].webStartUrl;
        var myForm = document.createElement("form");
        myForm.action = url;
        
@@ -9009,12 +9009,28 @@ opts.zoomer = {alignmentHeight: 225, labelWidth: 130,labelFontsize: "13px",label
 // init msa
 var m = new msa.msa(opts);
 
-m.g.colorscheme.set("scheme", jalviewData['globalColorScheme']);
+m.g.colorscheme.set("scheme", jalviewData['jalviewSettings'].globalColorScheme);
 
 var x = 0;
-jalviewData.seqs.forEach( function (seq)
+//jalviewData.seqs.forEach( function (seq)
+//{
+//m.seqs.at(x++).set("features", new msa.model.featurecol(seq.features));
+//});
+
+//console.debug(">>>>>>>>>>>>>" + m.seqs.length);
+//console.debug(">>>>>>>>>>>>> Found features : " + jalviewData.seqFeatures.length);
+m.seqs.forEach( function (seq )
 {
-m.seqs.at(x++).set("features", new msa.model.featurecol(seq.features));
+       var seqFeats = [];              
+       for (i = 0; i < jalviewData.seqFeatures.length; i++) { 
+               console.debug('comparing >>>>>>>> '+ seq.id)
+               if(jalviewData.seqFeatures[i].sequenceRef === seq.id){
+                       // console.debug('>>>>>>>> '+jalviewData.seqFeatures[i].sequenceRef+' | '+ seq.id)
+                       seqFeats.push(jalviewData.seqFeatures[i]);                              
+               }
+       } 
+console.debug('matched features count : '+seqFeats.length);
+seq.set("features", new msa.model.featurecol(seqFeats));
 });
 
 // the menu is independent to the MSA container