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 9a4f2c4..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;
@@ -123,6 +124,30 @@ public class TreePanel extends GTreePanel
     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();