X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDasSequenceFeatureFetcher.java;h=30fe7253f1ee69f5490ce771217d0d0ac8d07b15;hb=3bd894ddb06a8d9a1efd29c1705235031174e391;hp=ab02baf672889a24e6ae7f51f77f7cb5848793ca;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index ab02baf..30fe725 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -22,6 +22,9 @@ import java.util.*;
 
 import javax.swing.*;
 
+import org.biodas.jdas.client.SourcesClient;
+import org.biodas.jdas.schema.sources.SOURCE;
+import org.biodas.jdas.schema.sources.SOURCES;
 import org.biojava.dasobert.das.*;
 import org.biojava.dasobert.das2.*;
 import org.biojava.dasobert.das2.io.*;
@@ -240,8 +243,7 @@ public class DasSequenceFeatureFetcher
         }
       } catch (Exception ex)
       {
-        debug(
-                "Exception whilst setting default feature sources from registry and local preferences.",
+        debug("Exception whilst setting default feature sources from registry and local preferences.",
                 ex);
       }
     }
@@ -511,8 +513,8 @@ public class DasSequenceFeatureFetcher
           for (int i = 0; i < features.length; i++)
           {
             // standard DAS feature-> jalview sequence feature transformation
-            SequenceFeature f = newSequenceFeature(features[i], source
-                    .getNickname());
+            SequenceFeature f = newSequenceFeature(features[i],
+                    source.getNickname());
             if (!parseSeqFeature(seq, f, features[i], source))
             {
               if (dbref.getMap() != null && f.getBegin() > 0
@@ -615,8 +617,8 @@ public class DasSequenceFeatureFetcher
             for (int i = 0; i < features.length; i++)
             {
               // standard DAS feature-> jalview sequence feature transformation
-              SequenceFeature f = newSequenceFeature(features[i], source
-                      .getNickname());
+              SequenceFeature f = newSequenceFeature(features[i],
+                      source.getNickname());
               if (!parseSeqFeature(seq, f, features[i], source))
               {
                 // just add as a simple sequence feature
@@ -805,8 +807,9 @@ public class DasSequenceFeatureFetcher
       {
       }
 
-      SequenceFeature f = new SequenceFeature((String) dasfeature
-              .get("TYPE"), desc, start, end, score, nickname);
+      SequenceFeature f = new SequenceFeature(
+              (String) dasfeature.get("TYPE"), desc, start, end, score,
+              nickname);
 
       if (dasfeature.containsKey("LINK"))
       {
@@ -840,7 +843,7 @@ public class DasSequenceFeatureFetcher
    * 
    * @return list of sources
    */
-  public static DasSource[] getDASSources()
+  public static SOURCE[] getDASSources()
   {
 
     String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
@@ -854,38 +857,19 @@ public class DasSequenceFeatureFetcher
    * @param registryURL
    *          return sources from registryURL
    */
-  public static DasSource[] getDASSources(String registryURL)
+  public static SOURCE[] getDASSources(String registryURL)
   {
-    DasSourceReaderImpl reader = new DasSourceReaderImpl();
-
+    
     try
     {
       URL url = new URL(registryURL);
+      org.biodas.jdas.client.SourcesClientInterface client = new SourcesClient();
+      
+      SOURCES sources = client.fetchData(registryURL);
 
-      DasSource[] sources = reader.readDasSource(url);
-
-      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);
-        }
-      }
+      List<SOURCE> dassources = sources.getSOURCE();
 
-      return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources
-              .size()]);
+      return dassources.toArray(new SOURCE[dassources.size()]);
     } catch (Exception ex)
     {
       System.err.println("Failed to contact DAS1 registry at "