Hidden representatives moved from sequence to viewport

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 05ba166..be7f8f4 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -120,6 +120,8 @@ public class AlignViewport
 
     boolean rightAlignIds = false;
 
+    Hashtable hiddenRepSequences;
+
 
     /**
      * Creates a new AlignViewport object.
@@ -1262,6 +1264,33 @@ public class AlignViewport
       hasHiddenColumns = true;
     }
 
+    public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+    {
+      int sSize = sg.getSize();
+      if(sSize < 2)
+        return;
+
+      if(hiddenRepSequences==null)
+        hiddenRepSequences = new Hashtable();
+
+       hiddenRepSequences.put(repSequence, sg);
+
+      //Hide all sequences except the repSequence
+      SequenceI [] seqs = new SequenceI[sSize-1];
+      int index = 0;
+      for(int i=0; i<sSize; i++)
+        if(sg.getSequenceAt(i)!=repSequence)
+        {
+          if(index==sSize-1)
+            return;
+
+          seqs[index++] = sg.getSequenceAt(i);
+        }
+
+      hideSequence(seqs);
+
+    }
+
     public void hideAllSelectedSeqs()
     {
       if (selectionGroup == null)
@@ -1279,8 +1308,9 @@ public class AlignViewport
       if(seq!=null)
       {
         for (int i = 0; i < seq.length; i++)
+        {
           alignment.getHiddenSequences().hideSequence(seq[i]);
-
+        }
         hasHiddenRows = true;
         firePropertyChange("alignment", null, alignment.getSequences());
       }
@@ -1288,7 +1318,8 @@ public class AlignViewport
 
     public void showSequence(int index)
     {
-      Vector tmp = alignment.getHiddenSequences().showSequence(index);
+      Vector tmp = alignment.getHiddenSequences().showSequence(index
+          , hiddenRepSequences);
       if(tmp.size()>0)
       {
         if(selectionGroup==null)
@@ -1332,7 +1363,7 @@ public class AlignViewport
           selectionGroup = new SequenceGroup();
           selectionGroup.setEndRes(alignment.getWidth()-1);
         }
-        Vector tmp = alignment.getHiddenSequences().showAll();
+        Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
         for(int t=0; t<tmp.size(); t++)
         {
           selectionGroup.addSequence(
@@ -1341,9 +1372,12 @@ public class AlignViewport
         }
         firePropertyChange("alignment", null, alignment.getSequences());
         hasHiddenRows = false;
+        hiddenRepSequences = null;
       }
     }
 
+
+
     public void invertColumnSelection()
     {
       for(int i=0; i<alignment.getWidth(); i++)
@@ -1357,9 +1391,7 @@ public class AlignViewport
             colSel.addElement(i);
           }
         }
-
       }
-
     }
 
     public int adjustForHiddenSeqs(int alignmentIndex)
@@ -1400,7 +1432,7 @@ public class AlignViewport
       int start = 0, end = 0;
       if(selectedRegionOnly && selectionGroup!=null)
       {
-        iSize = selectionGroup.getSize(false);
+        iSize = selectionGroup.getSize();
         seqs = selectionGroup.getSequencesInOrder(alignment);
         start = selectionGroup.getStartRes();
         end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
@@ -1495,7 +1527,7 @@ public class AlignViewport
       int start = 0, end = 0;
       if(selectedRegionOnly && selectionGroup!=null)
       {
-        iSize = selectionGroup.getSize(false);
+        iSize = selectionGroup.getSize();
         seqs = selectionGroup.getSequencesInOrder(alignment);
         start = selectionGroup.getStartRes();
         end = selectionGroup.getEndRes()+1;
@@ -1605,7 +1637,7 @@ public class AlignViewport
         if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
         {
           ((ClustalxColourScheme)sg.cs).resetClustalX(
-              sg.getSequences(true), sg.getWidth());
+              sg.getSequences(hiddenRepSequences), sg.getWidth());
         }
         sg.recalcConservation();
       }