JAL-4134 store/restore Newick tree for PAE annotation row

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 6a07a4e..30e4305 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -135,18 +135,23 @@ public class TreePanel extends GTreePanel
   public TreePanel(AlignmentPanel alignPanel, NewickFile fin,
           AlignmentAnnotation aa, String title)
   {
-    this(alignPanel, fin, title, null);
+    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()
+  public boolean isColumnWise()
   {
     return columnWise;
   }
+  public AlignmentAnnotation getAssocAnnotation() {
+    return assocAnnotation;
+  }
 
   public AlignmentI getAlignment()
   {
@@ -167,6 +172,15 @@ public class TreePanel extends GTreePanel
     this.treeType = type;
     this.scoreModelName = modelName;
 
+    if (columnWise)
+    {
+      bootstrapMenu.setVisible(false);
+      placeholdersMenu.setSelected(false);
+      placeholdersMenu.setVisible(false);
+      fitToWindow.setSelected(false);
+      sortAssocViews.setVisible(false);
+    }
+
     treeCanvas = new TreeCanvas(this, ap, scrollPane);
     scrollPane.setViewportView(treeCanvas);