JAL-4315 allow feature settings to be loaded from a file or input stream without...

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 5ccd68d..0a0c1b8 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -179,17 +179,18 @@ 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()
     {
@@ -260,7 +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.
@@ -268,7 +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");
           }
 
@@ -391,9 +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);
@@ -895,7 +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();
     }
   }