Merge branch 'develop' into features/JAL-2110_crossRefDuplications

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 01e60d4..ac85aad 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2713,7 +2713,7 @@ public class Jalview2XML
     SequenceI[] orderedSeqs = tmpseqs
             .toArray(new SequenceI[tmpseqs.size()]);
 
-    Alignment al = new Alignment(orderedSeqs);
+    AlignmentI al = new Alignment(orderedSeqs);
 
     if (referenceseqForView != null)
     {
@@ -4096,7 +4096,7 @@ public class Jalview2XML
   }
 
   AlignFrame loadViewport(String file, JSeq[] JSEQ,
-          List<SequenceI> hiddenSeqs, Alignment al,
+          List<SequenceI> hiddenSeqs, AlignmentI al,
           JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
           String viewId, List<JvAnnotRow> autoAlan)
   {
@@ -4144,25 +4144,25 @@ public class Jalview2XML
     {
       for (int s = 0; s < JSEQ.length; s++)
       {
-        jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
-
+        SequenceGroup hidden = new SequenceGroup();
+        boolean isRepresentative = false;
         for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
         {
-          hidden.addSequence(
-                  al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
+          isRepresentative = true;
+          SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s]
+                  .getHiddenSequences(r));
+          hidden.addSequence(sequenceToHide, false);
+          // remove from hiddenSeqs list so we don't try to hide it twice
+          hiddenSeqs.remove(sequenceToHide);
+        }
+        if (isRepresentative)
+        {
+          SequenceI representativeSequence = al.getSequenceAt(s);
+          hidden.addSequence(representativeSequence, false);
+          af.viewport.hideRepSequences(representativeSequence, hidden);
         }
-        af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
       }
 
-      // jalview.datamodel.SequenceI[] hseqs = new
-      // jalview.datamodel.SequenceI[hiddenSeqs
-      // .size()];
-      //
-      // for (int s = 0; s < hiddenSeqs.size(); s++)
-      // {
-      // hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
-      // }
-
       SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
               .size()]);
       af.viewport.hideSequence(hseqs);
@@ -4449,7 +4449,7 @@ public class Jalview2XML
   }
 
   private ColourSchemeI constructAnnotationColour(
-          AnnotationColours viewAnnColour, AlignFrame af, Alignment al,
+          AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
           JalviewModelSequence jms, boolean checkGroupAnnColour)
   {
     boolean propagateAnnColour = false;
@@ -4573,7 +4573,7 @@ public class Jalview2XML
     return cs;
   }
 
-  private void reorderAutoannotation(AlignFrame af, Alignment al,
+  private void reorderAutoannotation(AlignFrame af, AlignmentI al,
           List<JvAnnotRow> autoAlan)
   {
     // copy over visualization settings for autocalculated annotation in the
@@ -4728,10 +4728,11 @@ public class Jalview2XML
     }
   }
 
-  private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
+  private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
           boolean ignoreUnrefed)
   {
-    jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
+    jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet
+            .getDatasetId());
     Vector dseqs = null;
     if (ds == null)
     {
@@ -4881,15 +4882,15 @@ public class Jalview2XML
    * TODO use AlignmentI here and in related methods - needs
    * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
    */
-  Hashtable<String, Alignment> datasetIds = null;
+  Hashtable<String, AlignmentI> datasetIds = null;
 
-  IdentityHashMap<Alignment, String> dataset2Ids = null;
+  IdentityHashMap<AlignmentI, String> dataset2Ids = null;
 
-  private Alignment getDatasetFor(String datasetId)
+  private AlignmentI getDatasetFor(String datasetId)
   {
     if (datasetIds == null)
     {
-      datasetIds = new Hashtable<String, Alignment>();
+      datasetIds = new Hashtable<String, AlignmentI>();
       return null;
     }
     if (datasetIds.containsKey(datasetId))
@@ -4899,11 +4900,11 @@ public class Jalview2XML
     return null;
   }
 
-  private void addDatasetRef(String datasetId, Alignment dataset)
+  private void addDatasetRef(String datasetId, AlignmentI dataset)
   {
     if (datasetIds == null)
     {
-      datasetIds = new Hashtable<String, Alignment>();
+      datasetIds = new Hashtable<String, AlignmentI>();
     }
     datasetIds.put(datasetId, dataset);
   }
@@ -4914,7 +4915,7 @@ public class Jalview2XML
    * @param dataset
    * @return
    */
-  private String getDatasetIdRef(Alignment dataset)
+  private String getDatasetIdRef(AlignmentI dataset)
   {
     if (dataset.getDataset() != null)
     {
@@ -4926,7 +4927,7 @@ public class Jalview2XML
       // make a new datasetId and record it
       if (dataset2Ids == null)
       {
-        dataset2Ids = new IdentityHashMap<Alignment, String>();
+        dataset2Ids = new IdentityHashMap<AlignmentI, String>();
       }
       else
       {