From 06b5f3c06a09ad8e32431be9eb560ec68e7f3770 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 14 Jun 2005 10:41:25 +0000
Subject: [PATCH] Load/Save trees

---
 src/jalview/gui/Jalview2XML.java |   91 +++++++++++++++++++++++++++++++++++---
 1 file changed, 85 insertions(+), 6 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index addba63..34502f1 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -53,6 +53,7 @@ public class Jalview2XML
           "UTF-8"));
 
       Vector shortNames = new Vector();
+      int treeCount=1;
 
       //REVERSE ORDER
       for (int i = frames.length - 1; i > -1; i--)
@@ -103,8 +104,9 @@ public class Jalview2XML
     }
   }
 
+
   // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-  public static void SaveState(AlignFrame af, String jarFile, String fileName)
+  public static void SaveAlignment(AlignFrame af, String jarFile, String fileName)
   {
     try
     {
@@ -175,9 +177,39 @@ public class Jalview2XML
     }
 
     //SAVE TREES
+    ///////////////////////////////////
     if (af.viewport.currentTree != null)
     {
-      object.getVamsasModel().addTree(af.viewport.currentTree.toString());
+      // FIND ANY ASSOCIATED TREES
+      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+      for(int t=0; t<frames.length; t++)
+      {
+        if (frames[t] instanceof TreePanel)
+        {
+          TreePanel tp = (TreePanel) frames[t];
+          if(tp.treeCanvas.av.alignment==jal)
+          {
+            Tree tree = new Tree();
+            tree.setTitle(tp.getTitle());
+            tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));
+            tree.setNewick(tp.getTree().toString());
+            tree.setThreshold(tp.treeCanvas.threshold);
+
+            tree.setFitToWindow(tp.fitToWindow.getState());
+            tree.setFontSize(tp.treeCanvas.fontSize);
+            tree.setMarkUnlinked( tp.placeholdersMenu.getState() );
+            tree.setShowBootstrap( tp.bootstrapMenu.getState() );
+            tree.setShowDistances( tp.distanceMenu.getState() );
+
+            tree.setHeight(tp.getHeight());
+            tree.setWidth(tp.getWidth());
+            tree.setXpos(tp.getX());
+            tree.setYpos(tp.getY());
+
+            jms.addTree(tree);
+          }
+        }
+      }
     }
 
     //SAVE ANNOTATIONS
@@ -702,13 +734,60 @@ public class Jalview2XML
        al.featuresAdded = true;
     }
 
-    //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE
-    if (object.getVamsasModel().getTreeCount() > 0)
+    //LOAD TREES
+    ///////////////////////////////////////
+ /*   JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+for(int t=0; t<frames.length; t++)
+{
+  if (frames[t] instanceof TreePanel)
+  {
+    TreePanel tp = (TreePanel) frames[t];
+    if(tp.treeCanvas.av.alignment==jal)
+    {
+      Tree tree = new Tree();
+      tree.setTitle(tp.getTitle());
+      tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));
+      tree.setNewick(tp.getTree().toString());
+      tree.setThreshold(tp.treeCanvas.threshold);
+
+      tree.setHeight(tp.getHeight());
+      tree.setWidth(tp.getWidth());
+      tree.setXpos(tp.getX());
+      tree.setYpos(tp.getY());
+
+      jms.addTree(tree);
+    }
+*/
+    if (jms.getTreeCount() > 0)
     {
       try
       {
-        af.ShowNewickTree(new jalview.io.NewickFile(
-            (String) object.getVamsasModel().getTree(0)), "Tree");
+        for(int t = 0; t<jms.getTreeCount(); t++)
+        {
+          Tree tree = jms.getTree(t);
+
+          TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
+                  tree.getNewick()), tree.getTitle());
+
+          tp.setBounds( tree.getXpos(),
+                        tree.getYpos(),
+                        tree.getWidth(),
+                        tree.getHeight());
+
+          tp.fitToWindow.setState(tree.getFitToWindow());
+          tp.fitToWindow_actionPerformed(null);
+          tp.treeCanvas.fontSize = tree.getFontSize();
+          tp.fontSize.setText("Font Size - "+tree.getFontSize());
+          tp.placeholdersMenu.setState(tree.getMarkUnlinked());
+          tp.placeholdersMenu_actionPerformed(null);
+          tp.bootstrapMenu.setState(tree.getShowBootstrap());
+          tp.bootstrapMenu_actionPerformed(null);
+          tp.distanceMenu.setState(tree.getShowDistances());
+          tp.distanceMenu_actionPerformed(null);
+          tp.treeCanvas.threshold = tree.getThreshold();
+          if(tree.getCurrentTree());
+             af.viewport.setCurrentTree(tp.getTree());
+        }
       }
       catch (Exception ex)
       {
-- 
1.7.10.2