From c56392962706a7a93001d9aeb4e541f7e7d044e3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 8 Nov 2005 11:39:18 +0000
Subject: [PATCH] Preliminary storeJalview

---
 src/jalview/io/VamsasDatastore.java |   29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java
index 69213af..efc13da 100755
--- a/src/jalview/io/VamsasDatastore.java
+++ b/src/jalview/io/VamsasDatastore.java
@@ -24,6 +24,8 @@ import org.vamsas.objects.core.*;
 import jalview.gui.*;
 import java.io.*;
 import java.util.jar.*;
+import org.exolab.castor.xml.*;
+import org.exolab.castor.mapping.Mapping;
 
 /*
 
@@ -50,6 +52,33 @@ public class VamsasDatastore
           storeVAMSAS(file);
         }
 
+        public void storeJalview(String file, AlignFrame af)
+        {
+          try
+          {
+            // 1. Load the mapping information from the file
+            Mapping map = new Mapping(getClass().getClassLoader());
+            java.net.URL url = getClass().getResource("/jalview_mapping.xml");
+            map.loadMapping(url);
+
+            // 2. Unmarshal the data
+            // Unmarshaller unmar = new Unmarshaller();
+            //unmar.setIgnoreExtraElements(true);
+            //unmar.setMapping(map);
+            // uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
+
+            // 3. marshal the data with the total price back and print the XML in the console
+              Marshaller marshaller = new Marshaller( new FileWriter(file) );
+
+             marshaller.setMapping(map);
+             marshaller.marshal(af);
+          }
+          catch (Exception e)
+          {
+            e.printStackTrace();
+          }
+        }
+
 
 
         public VAMSAS storeVAMSAS(String file)
-- 
1.7.10.2