X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=b11838ce2473dbee03b7add60370998a907b96ec;hb=29f633ca27df2db2790b81b1ca346d6692d4936c;hp=cdff8a3a65f5cd2af3698584dfe2df65819db439;hpb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index cdff8a3..b11838c 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -81,8 +81,6 @@ public class AlignmentPanel
     annotationScroller.setViewportView(annotationPanel);
     annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
 
-    fontChanged();
-
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
 
@@ -109,6 +107,7 @@ public class AlignmentPanel
       }
     });
 
+    fontChanged();
     adjustAnnotationHeight();
 
   }
@@ -117,14 +116,10 @@ public class AlignmentPanel
   {
     av.alignmentChanged(this);
 
-    if (overviewPanel != null)
-    {
-      overviewPanel.updateOverviewImage();
-    }
-
     alignFrame.updateEditMenuBar();
 
-    repaint();
+    paintAlignment(true);
+
   }
 
   /**
@@ -243,6 +238,8 @@ public class AlignmentPanel
         scrollToWrappedVisible(start);
       }
     }
+
+    paintAlignment(true);
   }
 
   void scrollToWrappedVisible(int res)
@@ -300,14 +297,20 @@ public class AlignmentPanel
 
     int height = annotationPanel.adjustPanelHeight();
 
+    if (hscroll.isVisible())
+    {
+      height += hscroll.getPreferredSize().height;
+    }
     if (height > alignFrame.getHeight() / 2)
     {
       height = alignFrame.getHeight() / 2;
     }
 
+    hscroll.addNotify();
+
     annotationScroller.setPreferredSize(
-        new Dimension(annotationScroller.getWidth(),
-                      height));
+        new Dimension(annotationScroller.getWidth(), height));
+
 
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
         annotationSpaceFillerHolder.getWidth(),
@@ -915,7 +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())