X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=f708c482f9497054a931acc05f355196caed5226;hb=9d465da4f21e403c20b835264929906b538c0c9b;hp=6a07a4e075c69a9898433793fe1fd05a305ed87b;hpb=c2e6335a319d61b641fb6fcbb0a4a5dc88a58014;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 6a07a4e..f708c48 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -24,6 +24,8 @@ import java.awt.Font;
 import java.awt.Graphics;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.io.File;
@@ -67,6 +69,7 @@ import jalview.gui.ImageExporter.ImageWriterI;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
 import jalview.jbgui.GTreePanel;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
@@ -135,19 +138,28 @@ public class TreePanel extends GTreePanel
   public TreePanel(AlignmentPanel alignPanel, NewickFile fin,
           AlignmentAnnotation aa, String title)
   {
-    this(alignPanel, fin, title, null);
-    columnWise=true;
+    super();
+    columnWise = true;
     assocAnnotation = aa;
-    
-
+    this.setFrameIcon(null);
+    this.treeTitle = title;
+    initTreePanel(alignPanel, null, null, fin, null);
   }
-  boolean columnWise=false;
-  AlignmentAnnotation assocAnnotation=null;
-  public boolean getColumnWise()
+
+  boolean columnWise = false;
+
+  AlignmentAnnotation assocAnnotation = null;
+
+  public boolean isColumnWise()
   {
     return columnWise;
   }
 
+  public AlignmentAnnotation getAssocAnnotation()
+  {
+    return assocAnnotation;
+  }
+
   public AlignmentI getAlignment()
   {
     return getTreeCanvas().getViewport().getAlignment();
@@ -170,6 +182,31 @@ public class TreePanel extends GTreePanel
     treeCanvas = new TreeCanvas(this, ap, scrollPane);
     scrollPane.setViewportView(treeCanvas);
 
+    if (columnWise)
+    {
+      bootstrapMenu.setVisible(false);
+      placeholdersMenu.setState(false);
+      placeholdersMenu.setVisible(false);
+      fitToWindow.setState(false);
+      sortAssocViews.setVisible(false);
+    }
+
+    addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent e)
+      {
+        switch (e.getKeyCode())
+        {
+        case 27: // escape
+          treeCanvas.clearSelectedLeaves();
+          e.consume();
+          break;
+
+        }
+
+      }
+    });
     PaintRefresher.Register(this, ap.av.getSequenceSetId());
 
     buildAssociatedViewMenu();
@@ -223,7 +260,7 @@ public class TreePanel extends GTreePanel
         {
           if (tree == null)
           {
-            System.out.println("tree is null");
+            jalview.bin.Console.outPrintln("tree is null");
             // TODO: deal with case when a change event is received whilst a
             // tree is still being calculated - should save reference for
             // processing message later.
@@ -231,7 +268,7 @@ public class TreePanel extends GTreePanel
           }
           if (evt.getNewValue() == null)
           {
-            System.out.println(
+            jalview.bin.Console.outPrintln(
                     "new alignment sequences vector value is null");
           }
 
@@ -354,9 +391,9 @@ public class TreePanel extends GTreePanel
                 ? new NJTree(av, sm, similarityParams)
                 : new AverageDistanceTree(av, sm, similarityParams);
         tree = new TreeModel(njtree);
-        showDistances(true);
+        // don't display distances for columnwise trees
       }
-
+      showDistances(!columnWise);
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
       treeCanvas.setTree(tree);
@@ -721,8 +758,16 @@ public class TreePanel extends GTreePanel
     String tree = MessageManager.getString("label.tree");
     ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
             tree);
-    exporter.doExport(null, this, width, height,
-            tree.toLowerCase(Locale.ROOT));
+    try
+    {
+      exporter.doExport(null, this, width, height,
+              tree.toLowerCase(Locale.ROOT));
+    } catch (ImageOutputException ioex)
+    {
+      Console.error(
+              "Unexpected error whilst writing " + imageFormat.toString(),
+              ioex);
+    }
   }
 
   /**
@@ -854,7 +899,7 @@ public class TreePanel extends GTreePanel
       pg.close();
     } catch (Exception ex)
     {
-      System.err.println("Error writing tree as EPS");
+      jalview.bin.Console.errPrintln("Error writing tree as EPS");
       ex.printStackTrace();
     }
   }