From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 29 Feb 2012 16:16:58 +0000 (+0000)
Subject: refactored das sequence source creation code to the implementor of the das source... 
X-Git-Tag: Jalview_2_9~532^2~31^2~11
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9d2628ef9266d6c7a953c8fd6e5539069e5997b3;p=jalview.git

refactored das sequence source creation code to the implementor of the das source api and das registry api
---

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 4f9e0ab..8c9e08f 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -17,23 +17,19 @@
  */
 package jalview.ws;
 
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.Vector;
-
-import org.biojava.dasobert.das2.Das2Source;
-import org.biojava.dasobert.dasregistry.Das1Source;
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-import org.biojava.dasobert.dasregistry.DasSource;
-
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
-import jalview.ws.dbsources.DasSequenceSource;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
 /**
  * This is the the concrete implementation of the sequence retrieval interface
  * and abstract class in jalview.ws.seqfetcher. This implements the run-time
@@ -75,7 +71,7 @@ public class SequenceFetcher extends ASequenceFetcher
     for (int i = 0; i < srcs.length; i++)
     {
       String nm = getSourceProxy(srcs[i]).getDbName();
-      if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.DasSequenceSource)
+      if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
       {
         if (nm.startsWith("das:"))
         {
@@ -317,91 +313,18 @@ public class SequenceFetcher extends ASequenceFetcher
    */
   public void registerDasSequenceSources()
   {
-    DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher
-            .getDASSources();
-    if (sources != null)
-    {
-      for (int s = 0; sources != null && s < sources.length; s++)
-      {
-        addDasSequenceSource(sources[s]);
-      }
-    }
-
-    Vector localsources = jalview.bin.Cache.getLocalDasSources();
-    if (localsources != null)
-    {
-      for (Enumeration ls = localsources.elements(); ls.hasMoreElements();)
-      {
-        addDasSequenceSource((DasSource) ls.nextElement());
-      }
-    }
-  }
-
-  /**
-   * Try to create and add a DasSequenceSource to the list of sources.
-   * 
-   * @param source
-   * @return null if no source was added, or the new DasSequenceSource created
-   */
-  DasSequenceSource addDasSequenceSource(DasSource source)
-  {
-    DasSequenceSource ds = null;
-    Das1Source d1s = null;
-    if (source.hasCapability("sequence"))
-    {
-      if (source instanceof Das2Source)
-      {
-        if (((Das2Source) source).hasDas1Capabilities())
-        {
-          try
-          {
-            d1s = org.biojava.dasobert.das2.DasSourceConverter
-                    .toDas1Source((Das2Source) source);
-          } catch (Exception e)
-          {
-            System.err.println("Ignoring DAS2 sequence source "
-                    + source.getNickname()
-                    + " - couldn't map to Das1Source.\n");
-            e.printStackTrace();
-          }
-        }
-      }
-      else
-      {
-        if (source instanceof Das1Source)
-        {
-          d1s = (Das1Source) source;
-        }
-      }
-    }
-    if (d1s != null)
+    // TODO: define a context as a registry provider (either desktop,
+    // jalview.bin.cache, or something else).
+    for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry().getSources())
     {
-      DasCoordinateSystem[] css = d1s.getCoordinateSystem();
-      if (css == null || css.length == 0)
+      if (source.isSequenceSource())
       {
-        // TODO: query das source directly to identify coordinate system... or
-        // have to make up a coordinate system
-        css = new DasCoordinateSystem[]
-        { new DasCoordinateSystem() };
-        css[0].setName(d1s.getNickname());
-        css[0].setUniqueId(d1s.getNickname());
-      }
-      for (int c = 0; c < css.length; c++)
-      {
-        try
+        List<DbSourceProxy> dassources = source.getSequenceSourceProxies();
+        for (DbSourceProxy seqsrc : dassources)
         {
-          addDbRefSourceImpl(ds = new DasSequenceSource("das:"
-                  + d1s.getNickname() + " (" + css[c].getName() + ")",
-                  css[c].getName(), d1s, css[c]));
-        } catch (Exception e)
-        {
-          System.err.println("Ignoring sequence coord system " + c + " ("
-                  + css[c].getName() + ") for source " + d1s.getNickname()
-                  + "- threw exception when constructing fetcher.\n");
-          e.printStackTrace();
+          addDbRefSourceImpl(seqsrc);
         }
       }
     }
-    return ds;
   }
 }