JAL-1926 JAL-2106 fix name for flag controlling addition of secondary structure annot...

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

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 16bbfe6..65179a2 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -21,7 +21,7 @@
 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;
@@ -39,9 +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
@@ -59,11 +57,8 @@ 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);
@@ -71,8 +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)
     {