X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=bccb877e88d0ac0718339da63e2fabd4ea033e44;hb=76b5c58c65413e8b239dbf71999f500600ef0f95;hp=fde4d90e18bbf9f5c2b1e09f3aac7850c817c9a6;hpb=7570956d4b58f313d402cdd0507737c0628f1544;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fde4d90..bccb877 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1118,22 +1118,55 @@ public class AlignViewport
         colSel.hideColumns(start);
       else
         colSel.hideColumns(start, end);
-      setSelectionGroup(null);
+
       hasHiddenColumns = true;
     }
 
+    public void hideAllSelectedSeqs()
+    {
+      if (selectionGroup == null)
+        return;
+
+      SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
+
+      for (int i = 0; i < seqs.length; i++)
+      {
+        alignment.getHiddenSequences().hideSequence(seqs[i]);
+      }
+      firePropertyChange("alignment", null, alignment.getSequences());
+      hasHiddenRows = true;
+      setSelectionGroup(null);
+    }
+
     public void hideSequence(SequenceI seq)
     {
       if(seq!=null)
       {
         alignment.getHiddenSequences().hideSequence(seq);
         hasHiddenRows = true;
+        firePropertyChange("alignment", null, alignment.getSequences());
       }
     }
 
     public void showSequence(int index)
     {
-      alignment.getHiddenSequences().showSequence(index);
+      Vector tmp = alignment.getHiddenSequences().showSequence(index);
+      if(tmp.size()>0)
+      {
+        if(selectionGroup==null)
+        {
+          selectionGroup = new SequenceGroup();
+          selectionGroup.setEndRes(alignment.getWidth()-1);
+        }
+
+        for (int t = 0; t < tmp.size(); t++)
+        {
+          selectionGroup.addSequence(
+              (SequenceI) tmp.elementAt(t), false
+              );
+        }
+        firePropertyChange("alignment", null, alignment.getSequences());
+      }
 
       if(alignment.getHiddenSequences().getSize()<1)
         hasHiddenRows = false;
@@ -1156,11 +1189,39 @@ public class AlignViewport
     {
       if(alignment.getHiddenSequences().getSize()>0)
       {
-        alignment.getHiddenSequences().showAll();
+        if(selectionGroup==null)
+        {
+          selectionGroup = new SequenceGroup();
+          selectionGroup.setEndRes(alignment.getWidth()-1);
+        }
+        Vector tmp = alignment.getHiddenSequences().showAll();
+        for(int t=0; t<tmp.size(); t++)
+        {
+          selectionGroup.addSequence(
+              (SequenceI)tmp.elementAt(t), false
+              );
+        }
+        firePropertyChange("alignment", null, alignment.getSequences());
         hasHiddenRows = false;
       }
     }
 
+    public void invertColumnSelection()
+    {
+      int column;
+      for(int i=0; i<alignment.getWidth(); i++)
+      {
+        column = i;
+
+        if(colSel.contains(column))
+          colSel.removeElement(column);
+        else
+          colSel.addElement(column);
+
+      }
+
+    }
+
     public int adjustForHiddenSeqs(int alignmentIndex)
     {
       return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);