doco writing.

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index fea4704..1b01606 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -38,7 +38,6 @@ import java.util.*;
 \r
 import javax.imageio.*;\r
 \r
 \r
 import javax.imageio.*;\r
 \r

-import javax.swing.*;\r

 import java.beans.PropertyChangeEvent;\r
 \r
 \r
 import java.beans.PropertyChangeEvent;\r
 \r
 \r

@@ -57,6 +56,7 @@ public class TreePanel extends GTreePanel
     int end;\r
     TreeCanvas treeCanvas;\r
     NJTree tree;\r
     int end;\r
     TreeCanvas treeCanvas;\r
     NJTree tree;\r

+    AlignViewport av;\r

 \r
     /**\r
      * Creates a new TreePanel object.\r
 \r
     /**\r
      * Creates a new TreePanel object.\r

@@ -94,6 +94,11 @@ 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

@@ -130,6 +135,8 @@ public class TreePanel extends GTreePanel
         }\r
       });\r
 \r
         }\r
       });\r
 \r

+      this.av = av;\r
+\r

 \r
       TreeLoader tl = new TreeLoader(newTree);\r
       tl.start();\r
 \r
       TreeLoader tl = new TreeLoader(newTree);\r
       tl.start();\r

@@ -165,6 +172,8 @@ public class TreePanel extends GTreePanel
 \r
         treeCanvas.repaint();\r
 \r
 \r
         treeCanvas.repaint();\r
 \r

+        av.setCurrentTree(tree);\r
+\r

       }\r
     }\r
 \r
       }\r
     }\r
 \r

@@ -232,7 +241,7 @@ 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

@@ -259,7 +268,7 @@ 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