X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=a0b77deff937aa8ef2ef395515a87e2a210904b4;hb=9f118a08c0f093fb30a51a2459e2609b3c959614;hp=902ce27aaacc7b23162b714f03e8db46d5980432;hpb=b8058f3f849f44740a695c83e96bdca3a197af5c;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 902ce27..a0b77de 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -27,10 +27,8 @@ 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
@@ -64,13 +60,11 @@ public class SequenceFetcher extends ASequenceFetcher
     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();
@@ -84,7 +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;
@@ -100,7 +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:"))
             {
@@ -124,8 +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();