better vamsas tree io (for when there are no nodemappings)

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index cdff8a3..b11838c 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -81,8 +81,6 @@ public class AlignmentPanel
     annotationScroller.setViewportView(annotationPanel);\r
     annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
 \r
-    fontChanged();\r
-\r
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
 \r
@@ -109,6 +107,7 @@ public class AlignmentPanel
       }\r
     });\r
 \r
+    fontChanged();\r
     adjustAnnotationHeight();\r
 \r
   }\r
@@ -117,14 +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
@@ -243,6 +238,8 @@ public class AlignmentPanel
         scrollToWrappedVisible(start);\r
       }\r
     }\r
+\r
+    paintAlignment(true);\r
   }\r
 \r
   void scrollToWrappedVisible(int res)\r
@@ -300,14 +297,20 @@ public class AlignmentPanel
 \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
     }\r
 \r
+    hscroll.addNotify();\r
+\r
     annotationScroller.setPreferredSize(\r
-        new Dimension(annotationScroller.getWidth(),\r
-                      height));\r
+        new Dimension(annotationScroller.getWidth(), height));\r
+\r
 \r
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
         annotationSpaceFillerHolder.getWidth(),\r
@@ -915,7 +918,8 @@ public class AlignmentPanel
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);\r
     }\r
 \r
-    int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
+    int height = ( (av.alignment.getHeight() + 1) * av.charHeight)\r
+        + scalePanel.getHeight();\r
     int width = getVisibleIdWidth() + (maxwidth * av.charWidth);\r
 \r
     if (av.getWrapAlignment())\r