X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=8146be0314bd1be23d4188153ce7c6111886cd20;hb=e1124a62486322d2d28482529d2d6b850ce1719b;hp=444b6bbb0f4bc6cf0104a468ec2add8689984497;hpb=019042a9f87d94260b3060cdf45ab93ca714a46d;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 444b6bb..8146be0 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -203,6 +203,8 @@ public class SeqPanel extends JPanel
             });
     }
 
+    int startWrapBlock=-1;
+    int wrappedBlock=-1;
     int findRes(MouseEvent evt)
    {
      int res = 0;
@@ -216,10 +218,10 @@ public class SeqPanel extends JPanel
 
         int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
         int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
-        int block = y/chunkHeight;
-        block += av.getStartRes()/cwidth;
+        wrappedBlock = y/chunkHeight;
+        wrappedBlock += av.getStartRes()/cwidth;
 
-        res = block*cwidth   +   x / av.getCharWidth();
+        res = wrappedBlock*cwidth   +   x / av.getCharWidth();
     }
     else
     {
@@ -284,6 +286,9 @@ public class SeqPanel extends JPanel
       int seq = findSeq(evt);
       int res = findRes(evt);
 
+      if(seq<0 || res<0)
+        return;
+
         if ((seq < av.getAlignment().getHeight()) &&
                 (res < av.getAlignment().getSequenceAt(seq).getLength()))
         {
@@ -580,97 +585,8 @@ public class SeqPanel extends JPanel
         ap.alignFrame.updateEditMenuBar();
       }
 
-      av.updateConservation();
-      av.updateConsensus();
-
-      //Does the edit affect any groups?
-      //////////////////////////////
-      Vector groupsToUpdate = new Vector();
-      SequenceGroup sg = av.getSelectionGroup();
-
-      int s, g, gSize = av.alignment.getGroups().size();
-      if (sg != null)
-      {
-        groupsToUpdate.addElement(av.getSelectionGroup());
-        int sSize = sg.getSize();
-        for (s = 0; s < sSize; s++)
-        {
-          SequenceI seq = sg.getSequenceAt(s);
-
-          for (g = 0; g < gSize; g++)
-          {
-            SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().
-                elementAt(
-                    g);
-            if (sg2.sequences.contains(seq))
-            {
-              if (!groupsToUpdate.contains(sg2))
-                groupsToUpdate.addElement(sg2);
-              continue;
-            }
-          }
-        }
-      }
-      else
-      {
-        SequenceI seq = av.alignment.getSequenceAt(startseq);
-        for (g = 0; g < gSize; g++)
-        {
-          SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt(
-              g);
-          if (sg2.sequences.contains(seq))
-          {
-            if (!groupsToUpdate.contains(sg2))
-              groupsToUpdate.addElement(sg2);
-            continue;
-          }
-        }
-      }
-
-      gSize = groupsToUpdate.size();
-      for (g = 0; g < gSize; g++)
-      {
-        ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation();
-      }
-      ////End of updating groups
-      //////////////////////////////////////////
-
-        // Y O Y CLUSTALX
-        ColourSchemeI cs = av.getGlobalColourScheme();
-        if(cs!=null)
-        {
-          if (cs.conservationApplied())
-          {
-            Conservation c = new Conservation("All",
-                                              ResidueProperties.propHash, 3,
-                                              av.alignment.getSequences(),
-                                              0, av.alignment.getWidth() - 1);
-            c.calculate();
-            c.verdict(false, av.ConsPercGaps);
-
-            if (cs instanceof ClustalxColourScheme)
-            {
-              ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
-              cxs.resetClustalX(av.alignment.getSequences(),
-                                av.alignment.getWidth());
-              cs.setConservation(c);
-              av.setGlobalColourScheme(cs);
-            }
-            else
-            {
-              cs.setConservation(c);
-              av.setGlobalColourScheme(cs);
-            }
+      av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
 
-          }
-
-          if (cs instanceof ClustalxColourScheme)
-          {
-            ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
-                                                       av.alignment.getWidth());
-            av.setGlobalColourScheme(cs);
-          }
-        }
     }
 
     /**
@@ -684,6 +600,11 @@ public class SeqPanel extends JPanel
       int seq = findSeq(evt);
       oldSeq = seq;
 
+      startWrapBlock=wrappedBlock;
+
+      if(seq<0 || res<0)
+        return;
+
         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
         if ((sequence == null) || (res > sequence.getLength()))
@@ -831,6 +752,9 @@ public class SeqPanel extends JPanel
       int res = findRes(evt);
       int y = findSeq(evt);
 
+      if(wrappedBlock!=startWrapBlock)
+        return;
+
       if (stretchGroup == null)
       {
             return;