From 452f3c23b6cea9565a13fa39e606a3e9ea29e035 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 11 May 2005 10:40:48 +0000
Subject: [PATCH] reads in treeFile from applet parameter

---
 src/jalview/appletgui/AlignFrame.java |   27 +++++++++++++++++++
 src/jalview/appletgui/TreePanel.java  |   48 +++++++++++++++++++++++++++++++++
 2 files changed, 75 insertions(+)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 28b7cb5..e73854f 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -45,6 +45,33 @@ public class AlignFrame extends GAlignFrame
     alignPanel = new AlignmentPanel(this, viewport);
     add(alignPanel);
     alignPanel.validate();
+
+    String treeFile = applet.getParameter("treeFile");
+    TreePanel treepanel = null;
+    if (treeFile != null)
+    {
+      try
+      {
+        treeFile = treeFile;
+        jalview.io.NewickFile fin = new jalview.io.NewickFile( applet.getCodeBase()+treeFile, "URL");
+        fin.parse();
+
+        if (fin.getTree() != null)
+        {
+          TreePanel tp = null;
+          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                             fin, "FromFile", applet.getCodeBase()+treeFile);
+          jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+          addTreeMenuItem(tp, treeFile);
+        }
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+
+
   }
 
   public void inputText_actionPerformed(ActionEvent e)
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 89ff20f..2aeeaed 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -5,6 +5,7 @@ import jalview.analysis.*;
 import jalview.jbappletgui.GTreePanel;
 import java.awt.event.*;
 import java.util.*;
+import jalview.io.NewickFile;
 
 
 public class TreePanel extends GTreePanel
@@ -52,6 +53,41 @@ public class TreePanel extends GTreePanel
 
   }
 
+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);
+
+  tree.reCount(tree.getTopNode());
+  tree.findHeight(tree.getTopNode());
+
+  treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+  treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+  bootstrapMenu.setState(newtree.HasBootstrap());
+  treeCanvas.setShowDistances(newtree.HasDistances());
+  distanceMenu.setState(newtree.HasDistances());
+  scrollPane.add(treeCanvas);
+
+}
+
+
 
 public String getText(String format) {
   return null;
@@ -63,6 +99,18 @@ public String getText(String format) {
     repaint();
   }
 
+  public void newickOutput_actionPerformed(ActionEvent actionEvent)
+  {
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+    String output = fout.print(false, true);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    cap.setText(output);
+    java.awt.Frame frame = new java.awt.Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,500);
+  }
+
+
 
   protected void fontSize_actionPerformed(ActionEvent e)
   {
-- 
1.7.10.2