X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9aa8733e36920b13d36d5fe58c6e533b1cee57d1;hb=HEAD;hp=958ebcc4f0130cc7a609b0503c4c37472188a7e1;hpb=f6d1305378fa256a42caf7d284b13d5a084bc471;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 958ebcc..9aa8733 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3572,8 +3572,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
             showHidden);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
-            frame.getHeight(), true, true);
+
+    alignPanel.setOverviewPanel(overview);
+    alignPanel.setOverviewTitle(this);
+
+    Desktop.addInternalFrame(frame, overview.getTitle(), true,
+            frame.getWidth(), frame.getHeight(), true, true);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     final AlignmentPanel thePanel = this.alignPanel;
@@ -3593,9 +3597,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       frame.addKeyListener(getKeyListeners()[0]);
     }
 
-    alignPanel.setOverviewPanel(overview);
-    alignPanel.setOverviewTitle(this);
-
     return overview;
   }
 
@@ -4864,7 +4865,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
                   mtch = idm.findAllIdMatches(pdbfn);
                 }
-                FileFormatI type=null;
+                FileFormatI type = null;
                 if (mtch != null)
                 {
                   try
@@ -4882,7 +4883,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
                 // File wasn't named like one of the sequences or wasn't a PDB
                 // file.
-                filesnotmatched.add(new Object[] { file, protocol, type});
+                filesnotmatched.add(new Object[] { file, protocol, type });
               }
             }
             int assocfiles = 0;
@@ -4936,7 +4937,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                  */
                 for (Object[] o : filesmatched)
                 {
-                  filesnotmatched.add(new Object[] { o[0], o[1]});
+                  filesnotmatched.add(new Object[] { o[0], o[1] });
                 }
               }
             }
@@ -4960,7 +4961,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               }
               for (Object[] fn : filesnotmatched)
               {
-                loadJalviewDataFile(fn[0], (DataSourceType) fn[1], (FileFormatI)fn[2], null);
+                loadJalviewDataFile(fn[0], (DataSourceType) fn[1],
+                        (FileFormatI) fn[2], null);
               }
 
             }
@@ -5636,9 +5638,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
   {
-    AlignmentI al = viewport.getAlignment();
-    al.justify(false);
-    viewport.firePropertyChange("alignment", null, al);
+    avc.justify_Region(true);
   }
 
   /**
@@ -5647,9 +5647,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
   {
-    AlignmentI al = viewport.getAlignment();
-    al.justify(true);
-    viewport.firePropertyChange("alignment", null, al);
+    avc.justify_Region(false);
   }
 
   @Override
@@ -5854,6 +5852,9 @@ 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();
   }