X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=3bc9bc56f33848ec04e901519cc1d0199fb423fd;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=55bec56139156b54db198696e1010d9c89542289;hpb=99cb058c4b312055ca758890b10d41428105dabe;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 55bec56..3bc9bc5 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -115,8 +115,7 @@ public class SeqPanel extends JPanel
 
     seqEditOccurred = -1;
 
-    ap.RefreshPanels();
-    repaint();
+    ap.repaint();
 
   }
 
@@ -175,8 +174,6 @@ public class SeqPanel extends JPanel
       y %= chunkHeight;
       seq =     y / av.getCharHeight() + av.getStartSeq();
 
-      //   chunkHeight =  (da.getHeight() + 2)*charHeight;
-      //  startx += chunkWidth;
     }
     else
     {
@@ -250,7 +247,9 @@ 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 +359,8 @@ 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 +383,10 @@ public class SeqPanel extends JPanel
     if(stretchGroup == null)
      {
        stretchGroup = av.alignment.findGroup( sequence );
-       av.setSelectionGroup( stretchGroup );
+       if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
+         av.setSelectionGroup(stretchGroup);
+       else
+         stretchGroup = null;
      }
 
     else if(!stretchGroup.sequences.contains(sequence)
@@ -430,14 +419,9 @@ public class SeqPanel extends JPanel
       stretchGroup = sg;
 
       if(av.getConservationSelected())
-        Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");
-      else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())
-      {
-        ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();
-        int threshold = rcs.getThreshold();
-        if (threshold > 0)
-          Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
-      }
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
+      if(av.getAbovePIDThreshold())
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
 
     }
     else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
@@ -457,7 +441,6 @@ public class SeqPanel extends JPanel
       changeStartRes = true;
 
 
-    seqCanvas.paintFlag = true;
     repaint();
 
   }
@@ -478,28 +461,15 @@ public class SeqPanel extends JPanel
     if(stretchGroup.cs instanceof ClustalxColourScheme)
     {
       stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
-      seqCanvas.paintFlag = true;
       repaint();
     }
 
     else if(stretchGroup.cs instanceof ConservationColourScheme)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
-
-      Conservation c = new Conservation("Group",
-                                        ResidueProperties.propHash, 3, stretchGroup.sequences, 0,
-                                        av.alignment.getWidth() );
-
-       c.calculate();
-       c.verdict(false, 100);
-       ccs = new ConservationColourScheme(c, ccs.cs);
-
+       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
        stretchGroup.cs = ccs;
+       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
 
-
-       Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;
-
-       seqCanvas.paintFlag = true;
        repaint();
     }
     else
@@ -507,9 +477,7 @@ public class SeqPanel extends JPanel
       if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
       {
         ResidueColourScheme rcs =  (ResidueColourScheme) stretchGroup.cs;
-        int threshold = rcs.getThreshold();
-        if(threshold>0)
-          Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
       }
 
     }
@@ -531,6 +499,10 @@ public class SeqPanel extends JPanel
     if(stretchGroup==null)
       return;
 
+    if(res>av.alignment.getWidth())
+      res = av.alignment.getWidth()-1;
+
+
     if(stretchGroup.getEndRes()==res)
       // Edit end res position of selected group
       changeEndRes = true;
@@ -562,7 +534,7 @@ 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.
@@ -578,6 +550,7 @@ public class SeqPanel extends JPanel
       }
       else
       {
+       if(seq!=null)
         stretchGroup.addSequence(seq);
         stretchGroup.addSequence(nextSeq);
       }
@@ -587,7 +560,6 @@ public class SeqPanel extends JPanel
     if(scrollThread!=null)
       scrollThread.setEvent(evt);
 
-    seqCanvas.paintFlag = true;
     repaint();
   }
 
@@ -648,7 +620,6 @@ public class SeqPanel extends JPanel
             running = ap.scrollRight(false);
         }
 
-        ap.repaint();
         try
         {
           Thread.sleep(75);