fixed column selection cut/paste and self paste.

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index b3f44df..f6b56f9 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -116,14 +116,10 @@ public class AlignmentPanel
   {\r
     av.alignmentChanged(this);\r
 \r
-    if (overviewPanel != null)\r
-    {\r
-      overviewPanel.updateOverviewImage();\r
-    }\r
-\r
     alignFrame.updateEditMenuBar();\r
 \r
-    repaint();\r
+    paintAlignment(true);\r
+\r
   }\r
 \r
   /**\r
@@ -299,9 +295,12 @@ public class AlignmentPanel
       System.out.println("NEEDS FIXING");\r
     }\r
 \r
-    int height = annotationPanel.adjustPanelHeight() +\r
-        hscroll.getPreferredSize().height;\r
+    int height = annotationPanel.adjustPanelHeight();\r
 \r
+    if (hscroll.isVisible())\r
+    {\r
+      height += hscroll.getPreferredSize().height;\r
+    }\r
     if (height > alignFrame.getHeight() / 2)\r
     {\r
       height = alignFrame.getHeight() / 2;\r
@@ -310,8 +309,7 @@ public class AlignmentPanel
     hscroll.addNotify();\r
 \r
     annotationScroller.setPreferredSize(\r
-        new Dimension(annotationScroller.getWidth(),\r
-                      height + hscroll.getHeight()));\r
+        new Dimension(annotationScroller.getWidth(), height));\r
 \r
 \r
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r