From 4712d64e31201c2bc156dd88d88e95a1c66f4bbd Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 4 Apr 2006 09:30:50 +0000
Subject: [PATCH] For archive only

---
 src/jalview/gui/Jalview2XML.java |   68 ++++++++++++++++++++++++++++----------
 1 file changed, 51 insertions(+), 17 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 893846c..5a4b03a 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -18,10 +18,11 @@
  */
 package jalview.gui;
 
-import jalview.io.*;
 
 import jalview.schemes.*;
 
+import jalview.gui.*;
+
 import java.io.*;
 
 import java.net.*;
@@ -32,7 +33,11 @@ import java.util.jar.*;
 
 import javax.swing.*;
 
-import jalview.binding.*;
+import org.exolab.castor.xml.*;
+
+import jalview.schemabinding.version2.*;
+
+
 
 
 /**
@@ -44,7 +49,7 @@ import jalview.binding.*;
 public class Jalview2XML
 {
     // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
-    public static void SaveState(File statefile)
+    public void SaveState(File statefile)
     {
         long creation = System.currentTimeMillis();
         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -116,7 +121,7 @@ public class Jalview2XML
     }
 
     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-    public static void SaveAlignment(AlignFrame af, String jarFile,
+    public void SaveAlignment(AlignFrame af, String jarFile,
         String fileName)
     {
         try
@@ -148,7 +153,7 @@ public class Jalview2XML
      * @param jout DOCUMENT ME!
      * @param out DOCUMENT ME!
      */
-    public static void SaveState(AlignFrame af, long timeStamp,
+    public void SaveState(AlignFrame af, long timeStamp,
         String fileName, JarOutputStream jout, PrintWriter out)
     {
         Vector seqids = new Vector();
@@ -157,7 +162,7 @@ public class Jalview2XML
         AlignViewport av = af.viewport;
 
         JalviewModel object = new JalviewModel();
-        object.setVamsasModel(new jalview.binding.VamsasModel());
+        object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 
         object.setCreationDate(new java.util.Date(timeStamp));
         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
@@ -316,6 +321,9 @@ public class Jalview2XML
                   an.setGraph(true);
                   an.setGraphType(aa[i].graph);
                 }
+                else
+                  an.setGraph(false);
+
                 an.setLabel(aa[i].label);
 
                 AnnotationElement ae;
@@ -461,7 +469,8 @@ public class Jalview2XML
 
         if(av.featuresDisplayed!=null)
         {
-          jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
+          jalview.schemabinding.version2.FeatureSettings fs
+              = new jalview.schemabinding.version2.FeatureSettings();
 
           Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
           while (e.hasMoreElements())
@@ -508,7 +517,7 @@ public class Jalview2XML
         }
     }
 
-    static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+    String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
         Vector userColours, JalviewModelSequence jms)
     {
         String id = null;
@@ -519,12 +528,12 @@ public class Jalview2XML
             userColours.add(ucs);
 
             java.awt.Color[] colours = ucs.getColours();
-            jalview.binding.UserColours uc = new jalview.binding.UserColours();
-            jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();
+            jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
+            jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
 
             for (int i = 0; i < colours.length; i++)
             {
-                jalview.binding.Colour col = new jalview.binding.Colour();
+                jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
                 jbucs.addColour(col);
             }
@@ -538,7 +547,7 @@ public class Jalview2XML
         return id;
     }
 
-    static jalview.schemes.UserColourScheme GetUserColourScheme(
+   jalview.schemes.UserColourScheme GetUserColourScheme(
         JalviewModelSequence jms, String id)
     {
         UserColours[] uc = jms.getUserColours();
@@ -571,9 +580,9 @@ public class Jalview2XML
      *
      * @param file DOCUMENT ME!
      */
-    public static AlignFrame LoadJalviewAlign(String file)
+    public AlignFrame LoadJalviewAlign(String file)
     {
-        JalviewModel object = new JalviewModel();
+
         jalview.gui.AlignFrame af = null;
 
         try
@@ -604,12 +613,28 @@ public class Jalview2XML
                 for (int i = 0; i < entryCount; i++)
                 {
                     jarentry = jin.getNextJarEntry();
-                }
+
+                  }
+
+
+                  class NoDescIDResolver implements IDResolver
+                  {
+                    public Object resolve(String idref)
+                    {
+                      System.out.println(idref+" used");
+                      return null;
+                    }
+                  }
+
 
                 if (jarentry != null)
                 {
                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-                    object = (JalviewModel) object.unmarshal(in);
+                    JalviewModel object = new JalviewModel();
+
+                    Unmarshaller unmar = new Unmarshaller(object);
+                    object = (JalviewModel) unmar.unmarshal( in );
+
                     af = LoadFromObject(object);
                     entryCount++;
                 }
@@ -629,6 +654,14 @@ public class Jalview2XML
         }
         catch (Exception ex)
         {
+          //Is Version 1 Jar file?
+          af =  new Jalview2XML_V1().LoadJalviewAlign(file);
+
+          if(af!=null)
+          {
+            System.out.println("Successfuly loaded archive file");
+            return af;
+          }
           ex.printStackTrace();
             System.err.println("Exception whilst loading jalview XML file : " +
                 ex + "\n");
@@ -642,7 +675,7 @@ public class Jalview2XML
         return af;
     }
 
-    static AlignFrame LoadFromObject(JalviewModel object)
+    AlignFrame LoadFromObject(JalviewModel object)
     {
         Vector seqids = new Vector();
         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
@@ -963,3 +996,4 @@ public class Jalview2XML
         return af;
     }
 }
+
-- 
1.7.10.2