X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=37946b1f38d2a104d286e1b867d1b3ffb74629fa;hb=bf2dd2a4708bdec06517605f9c6e69bfdc53d5ee;hp=16bbfe6642fff5fef381b7ecf701886e7f51bdad;hpb=ef9282b464dc189faf9ce40a4b7420a204266668;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 16bbfe6..37946b1 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -21,16 +21,14 @@
 package jalview.ws;
 
 import jalview.ext.ensembl.EnsemblGene;
-import jalview.ext.ensembl.EnsemblProtein;
+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;
@@ -39,9 +37,7 @@ 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
@@ -59,21 +55,16 @@ public class SequenceFetcher extends ASequenceFetcher
 
   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();