JAL-3855 auto select clusters and fix up colouring/propagation on calculation & tree...

[jalview.git] / src / jalview / gui / TreePanel.java

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 6a07a4e..2eff542 100755 (executable)
--- 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();
@@ -169,7 +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();
@@ -354,9 +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);
@@ -721,8 +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);
+    }
   }
 
   /**