X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;fp=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=ff2ffbb5a92a7c8cabf674e7f683349bbc39ac71;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=c700635fd8ad3e82e1bfd5acdb9d158c6ebd01ec;hpb=98558735e9208afa98bb155bd5350ad0a680ca24;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index c700635..ff2ffbb 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -214,7 +214,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     alignFrame.updateEditMenuBar();
 
-    paintAlignment(true);
+    // no idea if we need to update structure
+    paintAlignment(true, true);
 
   }
 
@@ -481,7 +482,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       scrollNeeded = vpRanges.scrollToWrappedVisible(start);
     }
 
-    paintAlignment(redrawOverview);
+    paintAlignment(redrawOverview, false);
 
     return scrollNeeded;
   }
@@ -538,7 +539,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     validateAnnotationDimensions(true);
     addNotify();
-    paintAlignment(true);
+    // TODO: many places call this method and also paintAlignment with various
+    // different settings. this means multiple redraws are triggered...
+    paintAlignment(true, false);
   }
 
   /**
@@ -837,12 +840,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
     repaint();
   }
 
-  /**
-   * Repaint the alignment including the annotations and overview panels (if
-   * shown).
+  /* (non-Javadoc)
+   * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
    */
   @Override
-  public void paintAlignment(boolean updateOverview)
+  public void paintAlignment(boolean updateOverview,
+          boolean updateStructures)
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
@@ -850,10 +853,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
             av.getSortAnnotationsBy());
     repaint();
 
-    if (updateOverview)
+    if (updateStructures)
     {
-      // TODO: determine if this paintAlignment changed structure colours
       av.getStructureSelectionManager().sequenceColoursChanged(this);
+    }
+    if (updateOverview)
+    {
 
       if (overviewPanel != null)
       {
@@ -1866,7 +1871,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (adjustHeight)
     {
       // sort, repaint, update overview
-      paintAlignment(true);
+      paintAlignment(true, false);
     }
     else
     {