Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 30e4305..0a0c1b8 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;
@@ -136,20 +139,24 @@ public class TreePanel extends GTreePanel
           AlignmentAnnotation aa, String title)
   {
     super();
-    columnWise=true;
+    columnWise = true;
     assocAnnotation = aa;
     this.setFrameIcon(null);
     this.treeTitle = title;
     initTreePanel(alignPanel, null, null, fin, null);
   }
-  
-  boolean columnWise=false;
-  AlignmentAnnotation assocAnnotation=null;
+
+  boolean columnWise = false;
+
+  AlignmentAnnotation assocAnnotation = null;
+
   public boolean isColumnWise()
   {
     return columnWise;
   }
-  public AlignmentAnnotation getAssocAnnotation() {
+
+  public AlignmentAnnotation getAssocAnnotation()
+  {
     return assocAnnotation;
   }
 
@@ -172,18 +179,35 @@ public class TreePanel extends GTreePanel
     this.treeType = type;
     this.scoreModelName = modelName;
 
+    treeCanvas = new TreeCanvas(this, ap, scrollPane);
+    scrollPane.setViewportView(treeCanvas);
+    
     if (columnWise)
     {
       bootstrapMenu.setVisible(false);
-      placeholdersMenu.setSelected(false);
+      placeholdersMenu.setState(false);
       placeholdersMenu.setVisible(false);
-      fitToWindow.setSelected(false);
+      fitToWindow.setState(false);
       sortAssocViews.setVisible(false);
     }
 
-    treeCanvas = new TreeCanvas(this, ap, scrollPane);
-    scrollPane.setViewportView(treeCanvas);
 
+    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();
@@ -237,7 +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.
@@ -245,7 +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");
           }
 
@@ -368,9 +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);
@@ -735,8 +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);
+    }
   }
 
   /**
@@ -868,7 +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();
     }
   }