X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=b11838ce2473dbee03b7add60370998a907b96ec;hb=266c4e2544701f88a8d21294b4a4f4cc42cf76cc;hp=b3f44dff8af2173ff45ce048049fefef62e6f872;hpb=6f0db27f863a935a73b78a14ba8466671171616d;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index b3f44df..b11838c 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -116,14 +116,10 @@ public class AlignmentPanel
   {
     av.alignmentChanged(this);
 
-    if (overviewPanel != null)
-    {
-      overviewPanel.updateOverviewImage();
-    }
-
     alignFrame.updateEditMenuBar();
 
-    repaint();
+    paintAlignment(true);
+
   }
 
   /**
@@ -299,9 +295,12 @@ public class AlignmentPanel
       System.out.println("NEEDS FIXING");
     }
 
-    int height = annotationPanel.adjustPanelHeight() +
-        hscroll.getPreferredSize().height;
+    int height = annotationPanel.adjustPanelHeight();
 
+    if (hscroll.isVisible())
+    {
+      height += hscroll.getPreferredSize().height;
+    }
     if (height > alignFrame.getHeight() / 2)
     {
       height = alignFrame.getHeight() / 2;
@@ -310,8 +309,7 @@ public class AlignmentPanel
     hscroll.addNotify();
 
     annotationScroller.setPreferredSize(
-        new Dimension(annotationScroller.getWidth(),
-                      height + hscroll.getHeight()));
+        new Dimension(annotationScroller.getWidth(), height));
 
 
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
@@ -920,7 +918,8 @@ public class AlignmentPanel
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
     }
 
-    int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+    int height = ( (av.alignment.getHeight() + 1) * av.charHeight)
+        + scalePanel.getHeight();
     int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
 
     if (av.getWrapAlignment())