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 df076d9..ac85aad 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -680,9 +680,8 @@ public class Jalview2XML
     Set<String> calcIdSet = new HashSet<String>();
 
     // SAVE SEQUENCES
-    for (int i = 0; i < rjal.getHeight(); i++)
+    for (final SequenceI jds : rjal.getSequences())
     {
-      final SequenceI jds = rjal.getSequenceAt(i);
       final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
               : jds.getDatasetSequence();
       String id = seqHash(jds);
@@ -725,15 +724,15 @@ public class Jalview2XML
           jseq.setHidden(av.getAlignment().getHiddenSequences()
                   .isHidden(jds));
 
-          if (av.isHiddenRepSequence(rjal.getSequenceAt(i)))
+          if (av.isHiddenRepSequence(jds))
           {
             jalview.datamodel.SequenceI[] reps = av
-                    .getRepresentedSequences(rjal.getSequenceAt(i))
+                    .getRepresentedSequences(jds)
                     .getSequencesInOrder(rjal);
 
             for (int h = 0; h < reps.length; h++)
             {
-              if (reps[h] != rjal.getSequenceAt(i))
+              if (reps[h] != jds)
               {
                 jseq.addHiddenSequences(rjal.findIndex(reps[h]));
               }
@@ -743,7 +742,7 @@ public class Jalview2XML
         // mark sequence as reference - if it is the reference for this view
         if (jal.hasSeqrep())
         {
-          jseq.setViewreference(rjal.getSequenceAt(i) == jal.getSeqrep());
+          jseq.setViewreference(jds == jal.getSeqrep());
         }
       }
 
@@ -4145,25 +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);