X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=06298ba09555a541e8083dc939f813b1bacf8034;hb=80b889f0cca49103e1b20ed806755a0719789906;hp=2d02e7958513194675c6aef3cb7a39d0e72c95a2;hpb=8288438dd58cfc2d1fe18a060afda0d647b85c32;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2d02e79..06298ba 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3440,8 +3440,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
-    boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
-                false);
+    boolean showHiddenRegions = Cache
+            .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false);
     openOverviewPanel(showHiddenRegions);
   }
 
@@ -3452,14 +3452,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return alignPanel.overviewPanel;
     }
     JInternalFrame frame = new JInternalFrame();
-    final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden);
+    final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
+            showHidden);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(),
-            true, true);
+    Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
+            frame.getHeight(), true, true);
     frame.setFrameIcon(null);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    final AlignmentPanel thePanel = this.alignPanel; 
+    final AlignmentPanel thePanel = this.alignPanel;
     frame.addInternalFrameListener(
             new javax.swing.event.InternalFrameAdapter()
             {
@@ -3478,7 +3479,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     alignPanel.setOverviewPanel(overview);
     alignPanel.setOverviewTitle(this);
-    
+
     return overview;
   }
 
@@ -4133,7 +4134,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return showNewickTree(nf, treeTitle, null, w, h, x, y);
   }
 
-
   /**
    * Add a treeviewer for the tree extracted from a Newick file object to the
    * current alignment view
@@ -4184,13 +4184,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return tp;
   }
 
-
   public void showContactMapTree(AlignmentAnnotation aa,
           PAEContactMatrix cm)
   {
     int x = 4, y = 5;
     int w = 400, h = 500;
-    
+
     try
     {
       NewickFile fin = new NewickFile(
@@ -4198,42 +4197,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       String title = "PAE Matrix Tree for "
               + cm.getReferenceSeq().getDisplayId(false);
 
-      showColumnWiseTree(fin, aa, title, w,h, x,y);
+      showColumnWiseTree(fin, aa, title, w, h, x, y);
     } catch (Throwable xx)
     {
       Console.error("Unexpected exception showing tree for contact matrix",
               xx);
     }
   }
-  public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, String treeTitle,
-           int w, int h, int x, int y)
+
+  public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa,
+          String treeTitle, int w, int h, int x, int y)
   {
-      try
+    try
+    {
+      nf.parse();
+      if (nf.getTree() == null)
       {
-        nf.parse();
-        if (nf.getTree() == null)
-        {
-          return null;
-        }
-        TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
-
-        tp.setSize(w, h);
+        return null;
+      }
+      TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
 
-        if (x > 0 && y > 0)
-        {
-          tp.setLocation(x, y);
-        }
+      tp.setSize(w, h);
 
-        Desktop.addInternalFrame(tp, title, w, h);
-        return tp;
-      } catch (Throwable xx)
+      if (x > 0 && y > 0)
       {
-        Console.error("Unexpected exception showing tree for contact matrix",
-                xx);
+        tp.setLocation(x, y);
       }
-      return null;
+
+      Desktop.addInternalFrame(tp, title, w, h);
+      return tp;
+    } catch (Throwable xx)
+    {
+      Console.error("Unexpected exception showing tree for contact matrix",
+              xx);
+    }
+    return null;
   }
-  
+
   private boolean buildingMenu = false;
 
   /**
@@ -5027,7 +5027,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
        * to add view name "Original" if necessary
        */
       alignPanel.setOverviewTitle(this);
-      
+
       /*
        * switch panels and set Overview title (if there is one
        * because it was opened automatically)