JAL-1641 cherry-picked changes into develop compatible branch

[jalview.git] / src / jalview / io / BioJsHTMLOutput.java

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index d2c4a7f..4945306 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -7,9 +7,9 @@ import jalview.datamodel.SequenceI;
 import jalview.exceptions.NoFileSelectedException;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.FeatureRenderer;
-import jalview.json.binding.v1.BioJsAlignmentPojo;
-import jalview.json.binding.v1.BioJsFeaturePojo;
-import jalview.json.binding.v1.BioJsSeqPojo;
+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;
@@ -117,11 +117,11 @@ public class BioJsHTMLOutput
   public String getJalviewAlignmentAsJsonString(AlignmentI alignment)
           throws IOException, JSONException
   {
-    BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
+    AlignmentPojo bjsAlignment = new AlignmentPojo();
 
-    bjsAlignment.setGlobalColorScheme(getGlobalColorScheme());
-    bjsAlignment.setJalviewVersion(jalviewVersion);
-    bjsAlignment.setWebStartUrl(webStartLaunchServletUrl);
+    // bjsAlignment.setGlobalColorScheme(getGlobalColorScheme());
+    // bjsAlignment.setJalviewVersion(jalviewVersion);
+    // bjsAlignment.setWebStartUrl(webStartLaunchServletUrl);
 
     int count = 0;
     for (SequenceI seq : alignment.getSequences())
@@ -130,7 +130,7 @@ public class BioJsHTMLOutput
       name.append(seq.getName()).append("/").append(seq.getStart())
               .append("-").append(seq.getEnd());
 
-      BioJsSeqPojo seqPojo = new BioJsSeqPojo();
+      SequencePojo seqPojo = new SequencePojo();
       seqPojo.setId(String.valueOf(++count));
       seqPojo.setEnd(seq.getEnd());
       seqPojo.setStart(seq.getStart());
@@ -140,7 +140,7 @@ public class BioJsHTMLOutput
       SequenceFeature[] seqFeatures = seq.getSequenceFeatures();
       if (seqFeatures != null)
       {
-        ArrayList<BioJsFeaturePojo> bjsSeqFeatures = new ArrayList<BioJsFeaturePojo>();
+        ArrayList<SequenceFeaturesPojo> bjsSeqFeatures = new ArrayList<SequenceFeaturesPojo>();
         for (SequenceFeature sf : seqFeatures)
         {
           if (displayedFeatures != null
@@ -151,15 +151,15 @@ public class BioJsHTMLOutput
             String featureColour = jalview.util.Format.getHexString(fr
                     .findFeatureColour(Color.white, seq,
                             seq.findIndex(sf.getBegin())));
-            BioJsFeaturePojo bjsFeature = new BioJsFeaturePojo();
-            bjsFeature.setFillColor(featureColour);
-            bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
-            bjsFeature.setXend(seq.findIndex(sf.getEnd()));
-            bjsFeature.setText(sf.getType());
-            bjsSeqFeatures.add(bjsFeature);
+            // 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);
+        // seqPojo.setFeatures(bjsSeqFeatures);
       }
       bjsAlignment.getSeqs().add(seqPojo);
     }