X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=0a0c1b80dac1005d7ddff4e223cf23a9154569d2;hb=8dca84768d848bc368985a8f0938a6c7ac059952;hp=fd85779fd54b75d805e69130cdae9ca7e24ea352;hpb=c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index fd85779..0a0c1b8 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;
@@ -53,6 +55,7 @@ import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.BinaryNode;
@@ -66,6 +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;
@@ -118,10 +122,44 @@ public class TreePanel extends GTreePanel
           String theTitle, AlignmentView inputData)
   {
     super();
+    this.setFrameIcon(null);
     this.treeTitle = theTitle;
     initTreePanel(alignPanel, null, null, newtree, inputData);
   }
 
+  /**
+   * columnwise tree associated with positions in aa
+   * 
+   * @param alignPanel
+   * @param fin
+   * @param title
+   * @param aa
+   */
+  public TreePanel(AlignmentPanel alignPanel, NewickFile fin,
+          AlignmentAnnotation aa, String title)
+  {
+    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 isColumnWise()
+  {
+    return columnWise;
+  }
+
+  public AlignmentAnnotation getAssocAnnotation()
+  {
+    return assocAnnotation;
+  }
+
   public AlignmentI getAlignment()
   {
     return getTreeCanvas().getViewport().getAlignment();
@@ -143,7 +181,33 @@ 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();
@@ -197,7 +261,7 @@ 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.
@@ -205,7 +269,7 @@ public class TreePanel extends GTreePanel
           }
           if (evt.getNewValue() == null)
           {
-            System.out.println(
+            jalview.bin.Console.outPrintln(
                     "new alignment sequences vector value is null");
           }
 
@@ -328,9 +392,9 @@ 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);
@@ -695,8 +759,12 @@ public class TreePanel extends GTreePanel
     String tree = MessageManager.getString("label.tree");
     ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
             tree);
+    try {
     exporter.doExport(null, this, width, height,
             tree.toLowerCase(Locale.ROOT));
+    } catch (ImageOutputException ioex) {
+      Console.error("Unexpected error whilst writing "+imageFormat.toString(),ioex);
+    }
   }
 
   /**
@@ -720,7 +788,7 @@ public class TreePanel extends GTreePanel
                 && !((SequenceNode) node).isDummy())
         {
           String newname = null;
-          SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+          SequenceI sq = (SequenceI) ((BinaryNode) node).element();
           if (sq != null)
           {
             // search dbrefs, features and annotation
@@ -762,7 +830,7 @@ public class TreePanel extends GTreePanel
           {
             // String oldname = ((SequenceNode) node).getName();
             // TODO : save oldname in the undo object for this modification.
-            ((SequenceNode) node).setName(newname);
+            ((BinaryNode) node).setName(newname);
           }
         }
       }
@@ -828,7 +896,7 @@ 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();
     }
   }