X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=65179a212a794e98216280561b4b878c1114c6fc;hb=36dceb54710feb97a81f4bd69ad051f316141dc3;hp=a5300dba881361ada6257af5ff96a4af18e704f8;hpb=ae014811dc190f0d4532728fcffa58264d288b6b;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index a5300db..65179a2 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -20,10 +20,8 @@
  */
 package jalview.ws;
 
-import jalview.ext.ensembl.EnsemblCdna;
-import jalview.ext.ensembl.EnsemblCds;
-import jalview.ext.ensembl.EnsemblGenome;
-import jalview.ext.ensembl.EnsemblProtein;
+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;
@@ -41,9 +39,7 @@ 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
@@ -61,10 +57,8 @@ public class SequenceFetcher extends ASequenceFetcher
 
   public SequenceFetcher(boolean addDas)
   {
-    addDBRefSourceImpl(EnsemblProtein.class);
-    addDBRefSourceImpl(EnsemblCds.class);
-    addDBRefSourceImpl(EnsemblGenome.class);
-    addDBRefSourceImpl(EnsemblCdna.class);
+    addDBRefSourceImpl(EnsemblGene.class);
+    addDBRefSourceImpl(EnsemblGenomes.class);
     addDBRefSourceImpl(EmblSource.class);
     addDBRefSourceImpl(EmblCdsSource.class);
     addDBRefSourceImpl(Uniprot.class);
@@ -72,8 +66,6 @@ public class SequenceFetcher extends ASequenceFetcher
     addDBRefSourceImpl(Pdb.class);
     addDBRefSourceImpl(PfamFull.class);
     addDBRefSourceImpl(PfamSeed.class);
-    // ensures Seed alignment is 'default' for PFAM
-    addDBRefSourceImpl(RfamFull.class);
     addDBRefSourceImpl(RfamSeed.class);
     if (addDas)
     {