X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=3bc9bc56f33848ec04e901519cc1d0199fb423fd;hb=efe332764f9f789f6b18b421a8586b174d4ad4e4;hp=c39396efa5dc4ec0708b52d440ca2f5388b596ce;hpb=9f9494f3319ec24f962437826e7db705bc0c4665;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index c39396e..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
     {
@@ -422,14 +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))
@@ -449,7 +441,6 @@ public class SeqPanel extends JPanel
       changeStartRes = true;
 
 
-    seqCanvas.paintFlag = true;
     repaint();
 
   }
@@ -470,21 +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;
-
-
+       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
@@ -492,9 +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());
       }
 
     }
@@ -516,6 +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;
@@ -547,7 +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.
@@ -563,6 +550,7 @@ public class SeqPanel extends JPanel
       }
       else
       {
+       if(seq!=null)
         stretchGroup.addSequence(seq);
         stretchGroup.addSequence(nextSeq);
       }