Merge branch 'feature/JAL-1244stretchStatusMsg' into merge/JAL-1244

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 87e655b..7292499 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -731,7 +731,7 @@ public class SeqPanel extends JPanel
       // over residue to change abruptly, causing highlighted residue in panel 2
       // to change, causing a scroll in panel 1 etc)
       ap.setToScrollComplementPanel(false);
-      wasScrolled = ap.scrollToPosition(results, false);
+      wasScrolled = ap.scrollToPosition(results);
       if (wasScrolled)
       {
         seqCanvas.revalidate();
@@ -2015,8 +2015,11 @@ public class SeqPanel extends JPanel
             && afterDrag;
     if (stretchGroup.cs != null)
     {
-      stretchGroup.cs.alignmentChanged(stretchGroup,
-              av.getHiddenRepSequences());
+      if (afterDrag)
+      {
+        stretchGroup.cs.alignmentChanged(stretchGroup,
+                av.getHiddenRepSequences());
+      }
 
       ResidueShaderI groupColourScheme = stretchGroup
               .getGroupColourScheme();
@@ -2449,7 +2452,7 @@ public class SeqPanel extends JPanel
     HiddenColumns hs = new HiddenColumns();
     MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
     av.setColumnSelection(cs);
-    av.getAlignment().setHiddenColumns(hs);
+    boolean hiddenChanged = av.getAlignment().setHiddenColumns(hs);
 
     // lastly, update any dependent dialogs
     if (ap.getCalculationDialog() != null)
@@ -2457,7 +2460,11 @@ public class SeqPanel extends JPanel
       ap.getCalculationDialog().validateCalcTypes();
     }
 
-    PaintRefresher.Refresh(this, av.getSequenceSetId());
+    /*
+     * repaint alignment, and also Overview or Structure
+     * if hidden column selection has changed
+     */
+    ap.paintAlignment(hiddenChanged, hiddenChanged);
 
     return true;
   }