X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=494530622c90e72e8c8e20dfaacc9cfba2c2f3bf;hb=581e7e5a0736b3b5e5ade54656c194b399b2a3ec;hp=2001338ce0bc244cf88df9d18b4cd602df2b5ced;hpb=b13f521553582ef2fbfd7815ae25e23284babdea;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 2001338..4945306 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -5,14 +5,14 @@ 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.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;
 
 import java.awt.Color;
 import java.io.BufferedReader;
@@ -26,7 +26,7 @@ import com.json.JSONException;
 
 public class BioJsHTMLOutput
 {
-  private AlignViewport av;
+  private AlignmentViewport av;
 
   private jalview.api.FeatureRenderer fr;
 
@@ -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);
     }