X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=a0b77deff937aa8ef2ef395515a87e2a210904b4;hb=fa2bb8831f34064277273dd27c64ad2beee70bd8;hp=007c85cf0ffcbe8f167de3439d3ad302ab6756e4;hpb=c406d789d51e6ac1ff45e3568d37e9ed53025f03;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 007c85c..a0b77de 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -21,15 +21,14 @@
 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;
@@ -38,9 +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
@@ -58,21 +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();
@@ -86,7 +78,8 @@ public class SequenceFetcher extends ASequenceFetcher
   public String[] getOrderedSupportedSources()
   {
     String[] srcs = this.getSupportedDb();
-    ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
+    ArrayList<String> dassrc = new ArrayList<String>(),
+            nondas = new ArrayList<String>();
     for (int i = 0; i < srcs.length; i++)
     {
       boolean das = false, skip = false;
@@ -102,7 +95,8 @@ public class SequenceFetcher extends ASequenceFetcher
         else
         {
           nm = dbs.getDbName();
-          if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+          if (getSourceProxy(
+                  srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
           {
             if (nm.startsWith("das:"))
             {
@@ -126,8 +120,8 @@ public class SequenceFetcher extends ASequenceFetcher
         nondas.add(srcs[i]);
       }
     }
-    String[] tosort = nondas.toArray(new String[0]), sorted = nondas
-            .toArray(new String[0]);
+    String[] tosort = nondas.toArray(new String[0]),
+            sorted = nondas.toArray(new String[0]);
     for (int j = 0, jSize = sorted.length; j < jSize; j++)
     {
       tosort[j] = tosort[j].toLowerCase();