From 8b4b5ed1b7165be4cc2efac0326c3b7ef3a3f3a4 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 9 Dec 2005 11:13:18 +0000
Subject: [PATCH] Only load the tree file once, for first alignment

---
 src/jalview/bin/JalviewLite.java |   29 +++++++++++++++++++++++++++--
 1 file changed, 27 insertions(+), 2 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index d5801df..be4675f 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -28,6 +28,7 @@ import java.applet.*;
 
 import java.awt.*;
 import java.awt.event.*;
+import jalview.appletgui.TreePanel;
 
 
 /**
@@ -243,6 +244,32 @@ public class JalviewLite extends Applet
                 if(featuresFile!=null)
                   currentAlignFrame.parseFeaturesFile(featuresFile);
 
+                String treeFile = applet.getParameter("treeFile");
+                if (treeFile != null)
+                {
+                  try
+                  {
+                    jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
+                        getCodeBase() + treeFile, "URL");
+                    fin.parse();
+
+                    if (fin.getTree() != null)
+                    {
+                      TreePanel tp = null;
+                      tp = new TreePanel(currentAlignFrame.viewport,
+                                         currentAlignFrame.viewport.getAlignment().getSequences(),
+                                         fin, "FromFile", applet.getCodeBase() + treeFile);
+                      jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+                      currentAlignFrame.addTreeMenuItem(tp, treeFile);
+                    }
+                  }
+                  catch (Exception ex)
+                  {
+                    ex.printStackTrace();
+                  }
+              }
+
+
                 String pdbfile = applet.getParameter("PDBFILE");
                 if(pdbfile!=null)
                 {
@@ -256,8 +283,6 @@ public class JalviewLite extends Applet
                     new MCview.AppletPDBViewer(pdbfile, "URL",
                                                (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
                                                currentAlignFrame.getSeqcanvas());
-
-
                   }
 
                 }
-- 
1.7.10.2