JAL-2745 stderr rather than stdout for unexpected HTTP response

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

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 74bf56f..a0b77de 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -20,19 +20,15 @@
  */
 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;
 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;
@@ -41,9 +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
@@ -61,24 +55,16 @@ public class SequenceFetcher extends ASequenceFetcher
 
   public SequenceFetcher(boolean addDas)
   {
-    addDBRefSourceImpl(EnsemblProtein.class);
-    // EnsemblTranscript would just replace EnsemblProtein as the proxy for
-    // { DbSource="ENSEMBL", DbName="ENSEMBL (Protein)" }
-    // addDBRefSourceImpl(EnsemblTranscript.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);
-    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();
@@ -92,7 +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;
@@ -108,7 +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:"))
             {
@@ -132,8 +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();