removed excess imports

[jalview.git] / src / jalview / ws / DasSequenceFeatureFetcher.java

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 6b5abad..30fe725 100644 (file)
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,6 +1,6 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
  * \r
  * This file is part of Jalview.\r
  * \r
@@ -22,6 +22,9 @@ import java.util.*;
 \r
 import javax.swing.*;\r
 \r
+import org.biodas.jdas.client.SourcesClient;\r
+import org.biodas.jdas.schema.sources.SOURCE;\r
+import org.biodas.jdas.schema.sources.SOURCES;\r
 import org.biojava.dasobert.das.*;\r
 import org.biojava.dasobert.das2.*;\r
 import org.biojava.dasobert.das2.io.*;\r
@@ -240,8 +243,7 @@ public class DasSequenceFeatureFetcher
         }\r
       } catch (Exception ex)\r
       {\r
-        debug(\r
-                "Exception whilst setting default feature sources from registry and local preferences.",\r
+        debug("Exception whilst setting default feature sources from registry and local preferences.",\r
                 ex);\r
       }\r
     }\r
@@ -511,8 +513,8 @@ public class DasSequenceFeatureFetcher
           for (int i = 0; i < features.length; i++)\r
           {\r
             // standard DAS feature-> jalview sequence feature transformation\r
-            SequenceFeature f = newSequenceFeature(features[i], source\r
-                    .getNickname());\r
+            SequenceFeature f = newSequenceFeature(features[i],\r
+                    source.getNickname());\r
             if (!parseSeqFeature(seq, f, features[i], source))\r
             {\r
               if (dbref.getMap() != null && f.getBegin() > 0\r
@@ -615,8 +617,8 @@ public class DasSequenceFeatureFetcher
             for (int i = 0; i < features.length; i++)\r
             {\r
               // standard DAS feature-> jalview sequence feature transformation\r
-              SequenceFeature f = newSequenceFeature(features[i], source\r
-                      .getNickname());\r
+              SequenceFeature f = newSequenceFeature(features[i],\r
+                      source.getNickname());\r
               if (!parseSeqFeature(seq, f, features[i], source))\r
               {\r
                 // just add as a simple sequence feature\r
@@ -805,8 +807,9 @@ public class DasSequenceFeatureFetcher
       {\r
       }\r
 \r
-      SequenceFeature f = new SequenceFeature((String) dasfeature\r
-              .get("TYPE"), desc, start, end, score, nickname);\r
+      SequenceFeature f = new SequenceFeature(\r
+              (String) dasfeature.get("TYPE"), desc, start, end, score,\r
+              nickname);\r
 \r
       if (dasfeature.containsKey("LINK"))\r
       {\r
@@ -840,7 +843,7 @@ public class DasSequenceFeatureFetcher
    * \r
    * @return list of sources\r
    */\r
-  public static DasSource[] getDASSources()\r
+  public static SOURCE[] getDASSources()\r
   {\r
 \r
     String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
@@ -854,38 +857,19 @@ public class DasSequenceFeatureFetcher
    * @param registryURL\r
    *          return sources from registryURL\r
    */\r
-  public static DasSource[] getDASSources(String registryURL)\r
+  public static SOURCE[] getDASSources(String registryURL)\r
   {\r
-    DasSourceReaderImpl reader = new DasSourceReaderImpl();\r
-\r
+    \r
     try\r
     {\r
       URL url = new URL(registryURL);\r
+      org.biodas.jdas.client.SourcesClientInterface client = new SourcesClient();\r
+      \r
+      SOURCES sources = client.fetchData(registryURL);\r
 \r
-      DasSource[] sources = reader.readDasSource(url);\r
-\r
-      List das1sources = new ArrayList();\r
-      for (int i = 0; i < sources.length; i++)\r
-      {\r
-        DasSource ds = sources[i];\r
-        if (ds instanceof Das2Source)\r
-        {\r
-          Das2Source d2s = (Das2Source) ds;\r
-          if (d2s.hasDas1Capabilities())\r
-          {\r
-            Das1Source d1s = DasSourceConverter.toDas1Source(d2s);\r
-            das1sources.add(d1s);\r
-          }\r
-\r
-        }\r
-        else if (ds instanceof Das1Source)\r
-        {\r
-          das1sources.add((Das1Source) ds);\r
-        }\r
-      }\r
+      List<SOURCE> dassources = sources.getSOURCE();\r
 \r
-      return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources\r
-              .size()]);\r
+      return dassources.toArray(new SOURCE[dassources.size()]);\r
     } catch (Exception ex)\r
     {\r
       System.err.println("Failed to contact DAS1 registry at "\r