X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=0b84fa53172fd7531db253bd4349e5cfc64507d1;hb=8548008f4fbd321b445c7e69fbdffda26e21f457;hp=3e47f4b91169d714a675ba17e7dba59c6399162e;hpb=6f3b2d39f15649cfa5808e18edbe8d5e876dc011;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3e47f4b..0b84fa5 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))
@@ -474,13 +466,9 @@ public class SeqPanel extends JPanel
 
     else if(stretchGroup.cs instanceof ConservationColourScheme)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
-
-
+       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
        stretchGroup.cs = ccs;
-
-
-       Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;
+       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
 
        repaint();
     }
@@ -489,9 +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());
       }
 
     }
@@ -513,6 +499,10 @@ 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;
@@ -544,7 +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.
@@ -560,6 +550,7 @@ public class SeqPanel extends JPanel
       }
       else
       {
+       if(seq!=null)
         stretchGroup.addSequence(seq);
         stretchGroup.addSequence(nextSeq);
       }