From 3e63bb86ad0e6f4bc86197053f921cb67b341567 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 18 Mar 2005 16:56:21 +0000
Subject: [PATCH] Load and Save trees.

---
 src/jalview/gui/TreePanel.java |   53 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 52 insertions(+), 1 deletion(-)

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 58c668f..73ef46b 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -66,6 +66,38 @@ public class TreePanel extends GTreePanel
     scrollPane.setViewportView(treeCanvas);
 
   }
+  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
+                   String type, String pwtype)
+    {
+      super();
+      // These are probably only  arbitrary strings reflecting source of tree
+      this.type = type;
+      this.pwtype = pwtype;
+
+      start = 0;
+      end = seqVector.size();
+
+      String longestName = "";
+      seq = new Sequence [seqVector.size()];
+      for (int i=0;i < seqVector.size();i++)
+      {
+        seq[i] = (Sequence) seqVector.elementAt(i);
+        if(seq[i].getName().length()>longestName.length())
+          longestName = seq[i].getName();
+      }
+      // This constructor matches sequence names to treenodes and sets up the tree layouts.
+      tree = new NJTree(seq, newtree);
+      av.setCurrentTree(tree);
+
+      propertiesInit();
+
+      tree.reCount(tree.getTopNode());
+      tree.findHeight(tree.getTopNode());
+
+      treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+      scrollPane.setViewportView(treeCanvas);
+
+    }
 
 
 public void drawPostscript(PostscriptProperties pp) {
@@ -256,7 +288,26 @@ public void propertiesInit() {
 
   protected void saveMenu_actionPerformed(ActionEvent e)
   {
-
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save tree as newick file");
+    chooser.setToolTipText("Save");
+    int value = chooser.showSaveDialog(null);
+    if (value == JalviewFileChooser.APPROVE_OPTION) {
+      String choice =  chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",  choice);
+      try{
+        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+        String output = fout.print(false,true); // distances only
+        java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
+        out.println(output);
+        out.close();
+      }
+      catch (Exception ex) {
+        ex.printStackTrace();
+      }
+    }
   }
 
   protected void printMenu_actionPerformed(ActionEvent e)
-- 
1.7.10.2