From 49236af7c1d2b9e2cd5f4ffca47922fdeb12cbbe Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 15 Jun 2006 14:06:00 +0000
Subject: [PATCH] Not using AxisDasRegistry

---
 src/jalview/io/DasSequenceFeatureFetcher.java |   49 +++++++++++++++++++------
 1 file changed, 37 insertions(+), 12 deletions(-)

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 9dd2d1e..0c9681a 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -30,8 +30,13 @@ import org.biojava.dasobert.das.FeatureThread;
 import org.biojava.dasobert.dasregistry.Das1Source;
 import org.biojava.dasobert.eventmodel.FeatureEvent;
 import org.biojava.dasobert.eventmodel.FeatureListener;
-import org.biojava.services.das.registry.DasRegistryAxisClient;
-import org.biojava.services.das.registry.DasSource;
+import org.biojava.dasobert.dasregistry.DasSource;
+
+import org.biojava.dasobert.das2.io.DasSourceReaderImpl;
+import org.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.das2.Das2Source;
+import org.biojava.dasobert.das2.DasSourceConverter;
 
 
 import jalview.bin.Cache;
@@ -246,7 +251,7 @@ public class DasSequenceFeatureFetcher implements Runnable
               for (int j = 0, k = uprefs.size(); j < k; j++)
               {
                 // Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end
-                org.biojava.services.das.registry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
+                org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
                 for (int l=0; l<cs.length; l++) {
                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)
                       uprefs.get(j)))
@@ -296,27 +301,47 @@ public class DasSequenceFeatureFetcher implements Runnable
   }
 
 
- public static DasSource[] getDASSources()
+  public static DasSource[] getDASSources()
   {
-    try
-    {
-      String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
-          "http://servlet.sanger.ac.uk/dasregistry/services/das_registry");
+    DasSourceReaderImpl reader = new DasSourceReaderImpl();
 
+    String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
+        "http://servlet.sanger.ac.uk/dasregistry/services/das_registry");
 
+    try
+    {
       URL url = new URL(registryURL);
 
-      DasRegistryAxisClient client = new DasRegistryAxisClient(url);
+      DasSource[] sources = reader.readDasSource(url);
 
-      DasSource[] services = client.listServices();
+      List das1sources = new ArrayList();
+      for (int i = 0; i < sources.length; i++)
+      {
+        DasSource ds = sources[i];
+        if (ds instanceof Das2Source)
+        {
+          Das2Source d2s = (Das2Source) ds;
+          if (d2s.hasDas1Capabilities())
+          {
+            Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
+            das1sources.add(d1s);
+          }
+
+          //
+        }
+        else if (ds instanceof Das1Source)
+        {
+          das1sources.add( (Das1Source) ds);
+        }
+      }
 
-      return services;
+      return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);
     }
     catch (Exception ex)
     {
       ex.printStackTrace();
+      return null;
     }
-    return null;
 
   }
 }
-- 
1.7.10.2