X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=b11838ce2473dbee03b7add60370998a907b96ec;hb=ea7870f9bf9ae81876afbe3fdd4d9bd9022b4014;hp=62c0d09ee0ac9113e62d280bf4ab3d9c251fb5dc;hpb=59337999169ff8987c3f8ffc4ae30ca8cf1e56aa;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 62c0d09..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);
+
   }
 
   /**
@@ -242,6 +238,8 @@ public class AlignmentPanel
         scrollToWrappedVisible(start);
       }
     }
+
+    paintAlignment(true);
   }
 
   void scrollToWrappedVisible(int res)
@@ -297,9 +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;
@@ -308,8 +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(
@@ -918,7 +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())