X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=3bfc7db208167d24399600f1dc45066af77ad169;hb=1340920fd1b15c9bc8cd2284def7ec176a4989d5;hp=8e7141be41852f6a4f0b5db85d3191f82a79c3ef;hpb=f602f5590ae442664ecd8024087a62f71f00d82c;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 8e7141b..3bfc7db 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -175,8 +175,6 @@ public class SeqPanel extends JPanel
       y %= chunkHeight;
       seq =     y / av.getCharHeight() + av.getStartSeq();
 
-      //   chunkHeight =  (da.getHeight() + 2)*charHeight;
-      //  startx += chunkWidth;
     }
     else
     {
@@ -250,7 +248,9 @@ public class SeqPanel extends JPanel
 	// Group editing
 	if (evt.isAltDown() || evt.isControlDown())
         {
-	  SequenceGroup sg = av.getAlignment().findGroup(startseq);
+	  SequenceGroup sg = av.getSelectionGroup();
+          if(sg==null)
+            av.getAlignment().findGroup(startseq);
           if (sg != null)
           {
             boolean deleteAllowed = false;
@@ -360,21 +360,8 @@ public class SeqPanel extends JPanel
 
   void updateConservation(int i)
   {
-  /*  Alignment al = (Alignment) av.getAlignment();
-    SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
-    if(sg==null || !(sg.cs instanceof ConservationColourScheme))
-      return;
-
-    Conservation c = sg.getConservation();
-
-    c = new Conservation("All", al.cons,
-                         ResidueProperties.propHash, 3, sg.sequences, 0,
-                         al.getWidth());
-    c.calculate();
-    c.verdict(false, 100);
-    sg.setConservation(c);
-    ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-    ccs.conserve = c;*/
+    av.updateConservation();
+    av.updateConsensus();
   }
 
 //////////////////////////////////////////
@@ -397,7 +384,7 @@ public class SeqPanel extends JPanel
     if(stretchGroup == null)
      {
        stretchGroup = av.alignment.findGroup( sequence );
-       if(res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
+       if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
          av.setSelectionGroup(stretchGroup);
        else
          stretchGroup = null;
@@ -460,7 +447,6 @@ public class SeqPanel extends JPanel
       changeStartRes = true;
 
 
-    seqCanvas.paintFlag = true;
     repaint();
 
   }
@@ -481,7 +467,6 @@ public class SeqPanel extends JPanel
     if(stretchGroup.cs instanceof ClustalxColourScheme)
     {
       stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
-      seqCanvas.paintFlag = true;
       repaint();
     }
 
@@ -495,7 +480,6 @@ public class SeqPanel extends JPanel
 
        Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;
 
-       seqCanvas.paintFlag = true;
        repaint();
     }
     else
@@ -527,6 +511,10 @@ public class SeqPanel extends JPanel
     if(stretchGroup==null)
       return;
 
+    if(res>av.alignment.getWidth()-2)
+      res = av.alignment.getWidth()-2;
+
+
     if(stretchGroup.getEndRes()==res)
       // Edit end res position of selected group
       changeEndRes = true;
@@ -558,7 +546,7 @@ public class SeqPanel extends JPanel
     else if (y < oldSeq)
       dragDirection = -1;
 
-    while (y != oldSeq && oldSeq>0)
+    while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
     {
       // This routine ensures we don't skip any sequences, as the
       // selection is quite slow.
@@ -574,6 +562,7 @@ public class SeqPanel extends JPanel
       }
       else
       {
+       if(seq!=null)
         stretchGroup.addSequence(seq);
         stretchGroup.addSequence(nextSeq);
       }
@@ -583,7 +572,6 @@ public class SeqPanel extends JPanel
     if(scrollThread!=null)
       scrollThread.setEvent(evt);
 
-    seqCanvas.paintFlag = true;
     repaint();
   }
 
@@ -644,7 +632,6 @@ public class SeqPanel extends JPanel
             running = ap.scrollRight(false);
         }
 
-        ap.repaint();
         try
         {
           Thread.sleep(75);