JAL-516 JAL-759 JAL-1066 group & group colourscheme always gets notified when group...

[jalview.git] / src / jalview / appletgui / SeqPanel.java

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index b9c5cf0..a7345db 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1411,27 +1411,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       return;
     }
 
+    stretchGroup.recalcConservation(); // always do this - annotation has own
+                                       // state
     if (stretchGroup.cs != null)
     {
-      if (stretchGroup.cs instanceof ClustalxColourScheme)
-      {
-        ((ClustalxColourScheme) stretchGroup.cs).alignmentChanged(
-stretchGroup,av.getHiddenRepSequences());
-      }
-
-      if (stretchGroup.cs instanceof Blosum62ColourScheme
-              || stretchGroup.cs instanceof PIDColourScheme
-              || stretchGroup.cs.conservationApplied()
-              || stretchGroup.cs.getThreshold() > 0)
-      {
-        stretchGroup.recalcConservation();
-      }
-
+      stretchGroup.cs.alignmentChanged(stretchGroup,av.getHiddenRepSequences());
+      
       if (stretchGroup.cs.conservationApplied())
       {
         SliderPanel.setConservationSlider(ap, stretchGroup.cs,
                 stretchGroup.getName());
-        stretchGroup.recalcConservation();
       }
       else
       {
@@ -1780,7 +1769,7 @@ stretchGroup,av.getHiddenRepSequences());
     
     row = row<0 ? ap.av.startSeq : row;
     column = column<0 ? ap.av.startRes : column;
-    ap.scrollTo(row, row, column, true, true);
+    ap.scrollTo(column, column, row, true, true);
   }
   /**
    * scroll to the given row - or nearest visible location
@@ -1790,7 +1779,7 @@ stretchGroup,av.getHiddenRepSequences());
   {
     
     row = row<0 ? ap.av.startSeq : row;
-    ap.scrollTo(row, row, ap.av.startRes, true, true);
+    ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
   }
   /**
    * scroll to the given column - or nearest visible location
@@ -1800,7 +1789,7 @@ stretchGroup,av.getHiddenRepSequences());
   {
     
     column = column<0 ? ap.av.startRes : column;
-    ap.scrollTo(ap.av.startRes, ap.av.startRes, column, true, true);
+    ap.scrollTo( column, column, ap.av.startSeq, true, true);
   }
 
 }