X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=88a0b0f6a528dfe41ab1489bbc702df33ba02b4d;hb=0452450533728e478ef8c893ea2cb3483c740fb3;hp=ad7113aad1015e73f240a560f6656b77feed78ac;hpb=dbcfef03ad3d2853eda62c727978a160fc347f58;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index ad7113a..88a0b0f 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -111,6 +111,8 @@ public class AlignViewport
 
   String sequenceSetID;
 
+  Hashtable hiddenRepSequences;
+
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     this.applet = applet;
@@ -951,6 +953,33 @@ 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)
@@ -997,7 +1026,7 @@ 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(
@@ -1006,7 +1035,8 @@ public class AlignViewport
       }
       firePropertyChange("alignment", null, alignment.getSequences());
       hasHiddenRows = false;
-    }
+      hiddenRepSequences = null;
+      }
   }
 
   public int adjustForHiddenSeqs(int alignmentIndex)
@@ -1047,7 +1077,7 @@ 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
@@ -1142,7 +1172,7 @@ 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;
@@ -1310,7 +1340,7 @@ 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();
     }