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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 1d197c3..9c1e42e 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -93,6 +93,11 @@ public class TreePanel extends GTreePanel
       initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
     }\r
 \r
       initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
     }\r
 \r

+    public AlignmentI getAlignment()\r
+    {\r
+      return treeCanvas.av.getAlignment();\r
+    }\r
+\r

 \r
     void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
                        String pwtype, int s, int e, NewickFile newTree)\r
 \r
     void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
                        String pwtype, int s, int e, NewickFile newTree)\r

@@ -231,7 +236,7 @@ public class TreePanel extends GTreePanel
         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
 \r
         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
 \r
         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r

-        cap.setText(fout.print(false, true));\r
+        cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));\r

     }\r
 \r
     /**\r
     }\r
 \r
     /**\r

@@ -258,7 +263,7 @@ public class TreePanel extends GTreePanel
             try\r
             {\r
                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
             try\r
             {\r
                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r

-                String output = fout.print(false, true); // distances only\r
+                String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());\r

                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
                             choice));\r
                 out.println(output);\r
                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
                             choice));\r
                 out.println(output);\r