JAL-4134 display tree for columns - selecting an internal node selects column in...

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 2d446d9..6a07a4e 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -53,6 +53,7 @@ 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;
@@ -105,7 +106,7 @@ public class TreePanel extends GTreePanel
           SimilarityParamsI options)
   {
     super();
-    this.setFrameIcon(WindowIcons.treeIcon);
+    this.setFrameIcon(null);
     this.similarityParams = options;
     initTreePanel(ap, type, modelName, null, null);
 
@@ -118,10 +119,35 @@ 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)
+  {
+    this(alignPanel, fin, title, null);
+    columnWise=true;
+    assocAnnotation = aa;
+    
+
+  }
+  boolean columnWise=false;
+  AlignmentAnnotation assocAnnotation=null;
+  public boolean getColumnWise()
+  {
+    return columnWise;
+  }
+
   public AlignmentI getAlignment()
   {
     return getTreeCanvas().getViewport().getAlignment();
@@ -720,7 +746,7 @@ 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 +788,7 @@ 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);
           }
         }
       }