X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=675325a52b6f2a642ba0987384d75556e8eec886;hb=0452450533728e478ef8c893ea2cb3483c740fb3;hp=bc9adfea44964eae35149f7a60b9315cdf53cc9e;hpb=dbcfef03ad3d2853eda62c727978a160fc347f58;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index bc9adfe..675325a 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -366,7 +366,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         SequenceGroup sg = av.selectionGroup;
         //Find the top and bottom of this group
         int min = av.alignment.getHeight(), max = 0;
-        for(int i=0; i<sg.getSize(false); i++)
+        for(int i=0; i<sg.getSize(); i++)
         {
           int index = av.alignment.findIndex( sg.getSequenceAt(i) );
           if(index > max)
@@ -402,7 +402,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         else
         {
           // Now add any sequences between min and max
-          sg.getSequences(false).clear();
+          sg.getSequences(null).clear();
           for (int i = min; i < max; i++)
           {
             sg.addSequence(av.alignment.getSequenceAt(i), false);
@@ -809,24 +809,20 @@ public class SeqPanel extends JPanel implements MouseListener,
       boolean fixedColumns = false;
       SequenceGroup sg = av.getSelectionGroup();
 
+      SequenceI seq = av.alignment.getSequenceAt(startseq);
 
+      //No group, but the sequence may represent a group
         if (!groupEditing && av.hasHiddenRows)
         {
-          if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
+          if (av.hiddenRepSequences!=null
+              && av.hiddenRepSequences.containsKey(seq))
           {
+            sg = (SequenceGroup)av.hiddenRepSequences.get(seq);
             groupEditing = true;
           }
         }
 
-        //No group, but the sequence may represent a group
-        if (groupEditing
-            && sg == null
-            && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
-        {
-          groupEditing = false;
-        }
 
-        SequenceI seq = av.alignment.getSequenceAt(startseq);
         StringBuffer message = new StringBuffer();
         if (groupEditing)
         {
@@ -855,7 +851,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
         //Are we editing within a selection group?
         if (groupEditing
-            || (sg != null && sg.getSequences(true).contains(seq)))
+            || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
         {
           fixedColumns = true;
 
@@ -863,9 +859,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           //but the sequence represents a group
           if (sg == null)
           {
-            sg = new SequenceGroup(null, null, false, false, false, 0,
-                                   av.alignment.getWidth()-1);
-            sg.addSequence(av.alignment.getSequenceAt(startseq), false);
+            sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
           }
 
           fixedLeft = sg.getStartRes();
@@ -924,7 +918,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
         if (groupEditing)
         {
-          Vector vseqs = sg.getSequences(true);
+          Vector vseqs = sg.getSequences(av.hiddenRepSequences);
           int g, groupSize = vseqs.size();
           SequenceI[] groupSeqs = new SequenceI[groupSize];
           for (g = 0; g < groupSeqs.length; g++)
@@ -972,7 +966,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             if (!blank)
             {
-              if(sg.getSize(false) == av.alignment.getHeight()  )
+              if(sg.getSize() == av.alignment.getHeight()  )
               {
                 if((av.hasHiddenColumns
                     && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
@@ -1221,7 +1215,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );
       if(evt.getClickCount()>1)
       {
-        if (av.getSelectionGroup().getSize(false) == 1
+        if (av.getSelectionGroup().getSize() == 1
             && av.getSelectionGroup().getEndRes()
             - av.getSelectionGroup().getStartRes() < 2)
           av.setSelectionGroup(null);
@@ -1327,7 +1321,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                 stretchGroup = null;
             }
         }
-        else if (!stretchGroup.getSequences(false).contains(sequence) ||
+        else if (!stretchGroup.getSequences(null).contains(sequence) ||
                 (stretchGroup.getStartRes() > res) ||
                 (stretchGroup.getEndRes() < res))
         {
@@ -1442,7 +1436,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           if (stretchGroup.cs instanceof ClustalxColourScheme)
           {
             ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
-                stretchGroup.getSequences(true),
+                stretchGroup.getSequences(av.hiddenRepSequences),
                 stretchGroup.getWidth());
           }
 
@@ -1549,7 +1543,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-            if (stretchGroup.getSequences(false).contains(nextSeq))
+            if (stretchGroup.getSequences(null).contains(nextSeq))
             {
                 stretchGroup.deleteSequence(seq, false);
             }