JAL-1541 Modified BioJs exporter to take advantage of the abstracted JSONFile export...

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

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 4945306..86b4c28 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,59 +1,33 @@
 package jalview.io;
 
-import jalview.api.FeaturesDisplayedI;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
 import jalview.exceptions.NoFileSelectedException;
+import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.FeatureRenderer;
-import jalview.json.binding.v1.AlignmentPojo;
-import jalview.json.binding.v1.SequenceFeaturesPojo;
-import jalview.json.binding.v1.SequencePojo;
-import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
 
-import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.PrintWriter;
 import java.net.URL;
-import java.util.ArrayList;
-
-import com.json.JSONException;
 
 public class BioJsHTMLOutput
 {
-  private AlignmentViewport av;
-
-  private jalview.api.FeatureRenderer fr;
-
-  private String globalColorScheme;
-
-  private FeaturesDisplayedI displayedFeatures;
+  private AlignViewport av;
 
-  private String jalviewVersion;
-
-  private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
 
   public BioJsHTMLOutput(AlignmentPanel ap,
           FeatureRenderer fr1)
   {
 
-    jalviewVersion = jalview.bin.Cache.getProperty("VERSION");
-    webStartLaunchServletUrl = jalview.bin.Cache.getDefault(
-            "www.jalview.org", "http://www.jalview.org")
-            + "/services/launchApp";
     if (ap != null)
     {
+
       this.av = ap.av;
-      this.globalColorScheme = ColourSchemeProperty.getColourName(av
-              .getGlobalColourScheme());
-      this.fr = ap.cloneFeatureRenderer();
-      displayedFeatures = av.getFeaturesDisplayed();
+      av.setFeatureRenderer(new FeatureRenderer(ap));
     }
+    exportJalviewAlignmentAsBioJsHtmlFile();
   }
 
   private void exportJalviewAlignmentAsBioJsHtmlFile()
@@ -61,8 +35,7 @@ public class BioJsHTMLOutput
     try
     {
       String outputFile = getOutputFile();
-      String jalviewAlignmentJson = getJalviewAlignmentAsJsonString(av
-              .getAlignment());
+      String jalviewAlignmentJson = JSONFile.getJSONData(av);
       String bioJSTemplateString = getBioJsTemplateAsString(this);
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
               .replaceAll(
@@ -110,63 +83,9 @@ public class BioJsHTMLOutput
     {
       throw new NoFileSelectedException("No file was selected.");
     }
-
     return selectedFile;
   }
 
-  public String getJalviewAlignmentAsJsonString(AlignmentI alignment)
-          throws IOException, JSONException
-  {
-    AlignmentPojo bjsAlignment = new AlignmentPojo();
-
-    // bjsAlignment.setGlobalColorScheme(getGlobalColorScheme());
-    // bjsAlignment.setJalviewVersion(jalviewVersion);
-    // bjsAlignment.setWebStartUrl(webStartLaunchServletUrl);
-
-    int count = 0;
-    for (SequenceI seq : alignment.getSequences())
-    {
-      StringBuilder name = new StringBuilder();
-      name.append(seq.getName()).append("/").append(seq.getStart())
-              .append("-").append(seq.getEnd());
-
-      SequencePojo seqPojo = new SequencePojo();
-      seqPojo.setId(String.valueOf(++count));
-      seqPojo.setEnd(seq.getEnd());
-      seqPojo.setStart(seq.getStart());
-      seqPojo.setName(name.toString());
-      seqPojo.setSeq(seq.getSequenceAsString());
-
-      SequenceFeature[] seqFeatures = seq.getSequenceFeatures();
-      if (seqFeatures != null)
-      {
-        ArrayList<SequenceFeaturesPojo> bjsSeqFeatures = new ArrayList<SequenceFeaturesPojo>();
-        for (SequenceFeature sf : seqFeatures)
-        {
-          if (displayedFeatures != null
-                  && displayedFeatures.isVisible(sf.getType()))
-          {
-
-            // TODO: translate graduated/complex colourschemes to biojs model
-            String featureColour = jalview.util.Format.getHexString(fr
-                    .findFeatureColour(Color.white, seq,
-                            seq.findIndex(sf.getBegin())));
-            // SequenceFeaturesPojo bjsFeature = new SequenceFeaturesPojo();
-            // bjsFeature.setFillColor(featureColour);
-            // bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
-            // bjsFeature.setXend(seq.findIndex(sf.getEnd()));
-            // bjsFeature.setType(sf.getType());
-            // bjsSeqFeatures.add(bjsFeature);
-          }
-        }
-        // seqPojo.setFeatures(bjsSeqFeatures);
-      }
-      bjsAlignment.getSeqs().add(seqPojo);
-    }
-
-    return new com.json.JSONObject(bjsAlignment).toString()
-            .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd");
-  }
 
   public static String getBioJsTemplateAsString(Object currentObj)
           throws IOException
@@ -207,15 +126,4 @@ public class BioJsHTMLOutput
     }
     return sb.toString();
   }
-
-  public String getGlobalColorScheme()
-  {
-    return globalColorScheme;
-  }
-
-  public void setGlobalColorScheme(String globalColorScheme)
-  {
-    this.globalColorScheme = globalColorScheme;
-  }
-
 }