X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=29d4ec790de4508477b4d0325d7dd2d5b5c1e98c;hb=20a4d7ddb86ee996f2b6617a0470922b83354c35;hp=007c85cf0ffcbe8f167de3439d3ad302ab6756e4;hpb=c406d789d51e6ac1ff45e3568d37e9ed53025f03;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 007c85c..29d4ec7 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -21,26 +21,21 @@
 package jalview.ws;
 
 import jalview.ext.ensembl.EnsemblGene;
+import jalview.ext.ensembl.EnsemblGenomes;
 import jalview.ws.dbsources.EmblCdsSource;
 import jalview.ws.dbsources.EmblSource;
 import jalview.ws.dbsources.Pdb;
 import jalview.ws.dbsources.PfamFull;
 import jalview.ws.dbsources.PfamSeed;
-import jalview.ws.dbsources.RfamFull;
 import jalview.ws.dbsources.RfamSeed;
 import jalview.ws.dbsources.Uniprot;
-import jalview.ws.dbsources.UniprotName;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.ArrayList;
-import java.util.List;
 
 /**
- * This is the the concrete implementation of the sequence retrieval interface
- * and abstract class in jalview.ws.seqfetcher. This implements the run-time
- * discovery of sequence database clientss.
+ * This implements the run-time discovery of sequence database clients.
  * 
  */
 public class SequenceFetcher extends ASequenceFetcher
@@ -53,44 +48,28 @@ public class SequenceFetcher extends ASequenceFetcher
    */
   public SequenceFetcher()
   {
-    this(true);
-  }
-
-  public SequenceFetcher(boolean addDas)
-  {
-    // addDBRefSourceImpl(EnsemblProtein.class);
-    // addDBRefSourceImpl(EnsemblCds.class);
-    // addDBRefSourceImpl(EnsemblGenome.class);
     addDBRefSourceImpl(EnsemblGene.class);
-    // addDBRefSourceImpl(EnsemblCdna.class);
+    addDBRefSourceImpl(EnsemblGenomes.class);
     addDBRefSourceImpl(EmblSource.class);
     addDBRefSourceImpl(EmblCdsSource.class);
     addDBRefSourceImpl(Uniprot.class);
-    addDBRefSourceImpl(UniprotName.class);
     addDBRefSourceImpl(Pdb.class);
     addDBRefSourceImpl(PfamFull.class);
     addDBRefSourceImpl(PfamSeed.class);
-    // ensures Seed alignment is 'default' for PFAM
-    addDBRefSourceImpl(RfamFull.class);
     addDBRefSourceImpl(RfamSeed.class);
-    if (addDas)
-    {
-      registerDasSequenceSources();
-    }
   }
 
   /**
-   * return an ordered list of database sources where non-das database classes
-   * appear before das database classes
+   * return an ordered list of database sources excluding alignment only databases
    */
   public String[] getOrderedSupportedSources()
   {
     String[] srcs = this.getSupportedDb();
-    ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
+    ArrayList<String> src = new ArrayList<>();
+
     for (int i = 0; i < srcs.length; i++)
     {
-      boolean das = false, skip = false;
-      String nm;
+      boolean skip = false;
       for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
       {
         // Skip the alignment databases for the moment - they're not useful for
@@ -99,85 +78,28 @@ public class SequenceFetcher extends ASequenceFetcher
         {
           skip = true;
         }
-        else
-        {
-          nm = dbs.getDbName();
-          if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
-          {
-            if (nm.startsWith("das:"))
-            {
-              nm = nm.substring(4);
-              das = true;
-            }
-            break;
-          }
-        }
       }
       if (skip)
       {
         continue;
       }
-      if (das)
       {
-        dassrc.add(srcs[i]);
-      }
-      else
-      {
-        nondas.add(srcs[i]);
+        src.add(srcs[i]);
       }
     }
-    String[] tosort = nondas.toArray(new String[0]), sorted = nondas
-            .toArray(new String[0]);
+    String[] tosort = src.toArray(new String[0]),
+            sorted = src.toArray(new String[0]);
     for (int j = 0, jSize = sorted.length; j < jSize; j++)
     {
       tosort[j] = tosort[j].toLowerCase();
     }
     jalview.util.QuickSort.sort(tosort, sorted);
     // construct array with all sources listed
-
-    srcs = new String[sorted.length + dassrc.size()];
     int i = 0;
     for (int j = sorted.length - 1; j >= 0; j--, i++)
     {
       srcs[i] = sorted[j];
-      sorted[j] = null;
-    }
-
-    sorted = dassrc.toArray(new String[0]);
-    tosort = dassrc.toArray(new String[0]);
-    for (int j = 0, jSize = sorted.length; j < jSize; j++)
-    {
-      tosort[j] = tosort[j].toLowerCase();
-    }
-    jalview.util.QuickSort.sort(tosort, sorted);
-    for (int j = sorted.length - 1; j >= 0; j--, i++)
-    {
-      srcs[i] = sorted[j];
     }
     return srcs;
   }
-
-  /**
-   * query the currently defined DAS source registry for sequence sources and
-   * add a DasSequenceSource instance for each source to the SequenceFetcher
-   * source list.
-   */
-  public void registerDasSequenceSources()
-  {
-    // TODO: define a context as a registry provider (either desktop,
-    // jalview.bin.cache, or something else).
-    for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry()
-            .getSources())
-    {
-      if (source.isSequenceSource())
-      {
-        List<DbSourceProxy> dassources = source.getSequenceSourceProxies();
-        for (DbSourceProxy seqsrc : dassources)
-        {
-          addDbRefSourceImpl(seqsrc);
-        }
-      }
-    }
-  }
-
 }