JAL-2154 patch the hack (Jalview2XML tests pass)

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index eeb4214..1a82a68 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());
         }
       }
 
@@ -899,10 +898,10 @@ public class Jalview2XML
       for (AlignedCodonFrame acf : jac)
       {
         AlcodonFrame alc = new AlcodonFrame();
-        vamsasSet.addAlcodonFrame(alc);
         if (acf.getProtMappings() != null
                 && acf.getProtMappings().length > 0)
         {
+          boolean hasMap = false;
           SequenceI[] dnas = acf.getdnaSeqs();
           jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
           for (int m = 0; m < pmaps.length; m++)
@@ -912,6 +911,11 @@ public class Jalview2XML
             alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
                     false));
             alc.addAlcodMap(alcmap);
+            hasMap = true;
+          }
+          if (hasMap)
+          {
+            vamsasSet.addAlcodonFrame(alc);
           }
         }
         // TODO: delete this ? dead code from 2.8.3->2.9 ?
@@ -2662,7 +2666,7 @@ public class Jalview2XML
     // LOAD SEQUENCES
 
     List<SequenceI> hiddenSeqs = null;
-    jalview.datamodel.Sequence jseq;
+
 
     List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
 
@@ -2674,21 +2678,24 @@ public class Jalview2XML
     {
       String seqId = jseqs[i].getId();
 
-      if (seqRefIds.get(seqId) != null)
+      SequenceI tmpSeq = seqRefIds.get(seqId);
+      if (tmpSeq != null)
       {
-        tmpseqs.add(seqRefIds.get(seqId));
+        tmpSeq.setStart(jseqs[i].getStart());
+        tmpSeq.setEnd(jseqs[i].getEnd());
+        tmpseqs.add(tmpSeq);
         multipleView = true;
       }
       else
       {
-        jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
+        tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
                 vamsasSeq[vi].getSequence());
-        jseq.setDescription(vamsasSeq[vi].getDescription());
-        jseq.setStart(jseqs[i].getStart());
-        jseq.setEnd(jseqs[i].getEnd());
-        jseq.setVamsasId(uniqueSetSuffix + seqId);
-        seqRefIds.put(vamsasSeq[vi].getId(), jseq);
-        tmpseqs.add(jseq);
+        tmpSeq.setDescription(vamsasSeq[vi].getDescription());
+        tmpSeq.setStart(jseqs[i].getStart());
+        tmpSeq.setEnd(jseqs[i].getEnd());
+        tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
+        seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
+        tmpseqs.add(tmpSeq);
         vi++;
       }
 
@@ -2704,7 +2711,7 @@ public class Jalview2XML
           hiddenSeqs = new ArrayList<SequenceI>();
         }
 
-        hiddenSeqs.add(seqRefIds.get(seqId));
+        hiddenSeqs.add(tmpSeq);
       }
     }
 
@@ -2714,7 +2721,7 @@ public class Jalview2XML
     SequenceI[] orderedSeqs = tmpseqs
             .toArray(new SequenceI[tmpseqs.size()]);
 
-    Alignment al = new Alignment(orderedSeqs);
+    AlignmentI al = new Alignment(orderedSeqs);
 
     if (referenceseqForView != null)
     {
@@ -2856,8 +2863,8 @@ public class Jalview2XML
                   mapping });
             }
           }
+          al.addCodonFrame(cf);
         }
-        al.addCodonFrame(cf);
       }
     }
 
@@ -4097,7 +4104,7 @@ 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)
   {
@@ -4145,25 +4152,25 @@ 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);
@@ -4450,7 +4457,7 @@ 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;
@@ -4574,7 +4581,7 @@ 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
@@ -4729,10 +4736,11 @@ 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)
     {
@@ -4882,15 +4890,15 @@ 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))
@@ -4900,11 +4908,11 @@ 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);
   }
@@ -4915,7 +4923,7 @@ public class Jalview2XML
    * @param dataset
    * @return
    */
-  private String getDatasetIdRef(Alignment dataset)
+  private String getDatasetIdRef(AlignmentI dataset)
   {
     if (dataset.getDataset() != null)
     {
@@ -4927,7 +4935,7 @@ public class Jalview2XML
       // make a new datasetId and record it
       if (dataset2Ids == null)
       {
-        dataset2Ids = new IdentityHashMap<Alignment, String>();
+        dataset2Ids = new IdentityHashMap<AlignmentI, String>();
       }
       else
       {