JAL-1369 mark reference sequence & view state and restore it

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a3604d6..2509f15 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -634,11 +634,15 @@ public class Jalview2XML
     object.setVersion(jalview.bin.Cache.getDefault("VERSION",
             "Development Build"));
 
-    jalview.datamodel.AlignmentI jal = av.getAlignment();
+    /**
+     * rjal is full height alignment, jal is actual alignment with full metadata
+     * but excludes hidden sequences.
+     */
+    jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
 
     if (av.hasHiddenRows())
     {
-      jal = jal.getHiddenSequences().getFullAlignment();
+      rjal = jal.getHiddenSequences().getFullAlignment();
     }
 
     SequenceSet vamsasSet = new SequenceSet();
@@ -655,6 +659,7 @@ public class Jalview2XML
       {
         // switch jal and the dataset
         jal = jal.getDataset();
+        rjal = jal;
       }
     }
     if (jal.getProperties() != null)
@@ -674,9 +679,9 @@ public class Jalview2XML
     Set<String> calcIdSet = new HashSet<String>();
 
     // SAVE SEQUENCES
-    for (int i = 0; i < jal.getHeight(); i++)
+    for (int i = 0; i < rjal.getHeight(); i++)
     {
-      final SequenceI jds = jal.getSequenceAt(i);
+      final SequenceI jds = rjal.getSequenceAt(i);
       final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
               : jds.getDatasetSequence();
       String id = seqHash(jds);
@@ -715,26 +720,34 @@ public class Jalview2XML
         // Store any sequences this sequence represents
         if (av.hasHiddenRows())
         {
+          // use rjal, contains the full height alignment
           jseq.setHidden(av.getAlignment().getHiddenSequences()
                   .isHidden(jds));
 
-          if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
+          if (av.isHiddenRepSequence(rjal.getSequenceAt(i)))
           {
             jalview.datamodel.SequenceI[] reps = av
-                    .getRepresentedSequences(jal.getSequenceAt(i))
-                    .getSequencesInOrder(jal);
+                    .getRepresentedSequences(rjal.getSequenceAt(i))
+                    .getSequencesInOrder(rjal);
 
             for (int h = 0; h < reps.length; h++)
             {
-              if (reps[h] != jal.getSequenceAt(i))
+              if (reps[h] != rjal.getSequenceAt(i))
               {
-                jseq.addHiddenSequences(jal.findIndex(reps[h]));
+                jseq.addHiddenSequences(rjal.findIndex(reps[h]));
               }
             }
           }
         }
+        // mark sequence as reference - if it is the reference for this view
+        if (jal.hasSeqrep())
+        {
+          jseq.setViewreference(rjal.getSequenceAt(i) == jal.getSeqrep());
+        }
       }
 
+      // TODO: omit sequence features from each alignment view's XML dump if we
+      // are storing dataset
       if (jds.getSequenceFeatures() != null)
       {
         jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
@@ -900,7 +913,7 @@ public class Jalview2XML
             alc.addAlcodMap(alcmap);
           }
         }
-
+        // TODO: delete this ? dead code from 2.8.3->2.9 ?
         // {
         // AlcodonFrame alc = new AlcodonFrame();
         // vamsasSet.addAlcodonFrame(alc);
@@ -2654,7 +2667,7 @@ public class Jalview2XML
     List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
 
     boolean multipleView = false;
-
+    SequenceI referenceseqForView = null;
     JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
     int vi = 0; // counter in vamsasSeq array
     for (int i = 0; i < jseqs.length; i++)
@@ -2679,6 +2692,11 @@ public class Jalview2XML
         vi++;
       }
 
+      if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
+      {
+        referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
+      }
+
       if (jseqs[i].getHidden())
       {
         if (hiddenSeqs == null)
@@ -2688,7 +2706,6 @@ public class Jalview2XML
 
         hiddenSeqs.add(seqRefIds.get(seqId));
       }
-
     }
 
     // /
@@ -2699,6 +2716,10 @@ public class Jalview2XML
 
     Alignment al = new Alignment(orderedSeqs);
 
+    if (referenceseqForView != null)
+    {
+      al.setSeqrep(referenceseqForView);
+    }
     // / Add the alignment properties
     for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
     {
@@ -4092,6 +4113,12 @@ public class Jalview2XML
               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
     }
 
+    if (al.hasSeqrep())
+    {
+      af.getViewport().setColourByReferenceSeq(true);
+      af.getViewport().setDisplayReferenceSeq(true);
+    }
+
     af.viewport.setGatherViewsHere(view.getGatheredViews());
 
     if (view.getSequenceSetId() != null)