X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=aca8baa099d9199478b475e02cbda36123d20e3b;hb=1140532d01b32b648e7e5b17ea717ae790625f8f;hp=00bd4f9f04863b7ac705544e96b2065ccea74353;hpb=d4eb0781b285bc64fbc9b040c9bfc1eb5f6d8267;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 00bd4f9..aca8baa 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -95,6 +95,7 @@ import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
+import jalview.bin.groovy.JalviewObjectI;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -503,7 +504,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @Override
       public void focusGained(FocusEvent e)
       {
-        Jalview.setCurrentAlignFrame(AlignFrame.this);
+        Jalview.getInstance().setCurrentAlignFrame(AlignFrame.this);
       }
     });
 
@@ -5841,6 +5842,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
     }
     alignPanel.validateAnnotationDimensions(true);
+    // TODO this triggers relayout of annotation panel - otherwise annotation label height is different to panel height
+    alignPanel.fontChanged();
     alignPanel.alignmentChanged();
   }
 
@@ -5963,12 +5966,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void runGroovy_actionPerformed()
   {
-    Jalview.setCurrentAlignFrame(this);
+    Jalview.getInstance().setCurrentAlignFrame(this);
     groovy.console.ui.Console console = Desktop.getGroovyConsole();
     if (console != null)
     {
       try
       {
+        console.setVariable(JalviewObjectI.currentAlFrameName, this);
         console.runScript();
       } catch (Exception ex)
       {