X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=9c42f0a0e7c00e352b8c8a833f7c47b06d22067f;hb=061a05484ccda133e2e77b19454238fb0ba8f11d;hp=caf5b5e5209a5a2b8d191864dcc28e2aa287a757;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index caf5b5e..9c42f0a 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,11 @@
  */
 package jalview.ws;
 
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
@@ -28,11 +33,6 @@ import jalview.ws.dbsources.das.api.jalviewSourceI;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.Vector;
-
 /**
  * This is the the concrete implementation of the sequence retrieval interface
  * and abstract class in jalview.ws.seqfetcher. This implements the run-time
@@ -61,10 +61,8 @@ public class SequenceFetcher extends ASequenceFetcher
     addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
     addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
     addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed
-    // alignment is
-    // 'default' for
-    // PFAM
+    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class);
+    // ensures Seed alignment is 'default' for PFAM
     addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
     addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
     if (addDas)
@@ -285,7 +283,9 @@ public class SequenceFetcher extends ASequenceFetcher
       String db = dbSources[dbsource];
       // skip me
       if (db.equals(DBRefSource.PDB))
+      {
         continue;
+      }
       for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
       {
         System.out.println("Source: " + sp.getDbName() + " (" + db
@@ -348,9 +348,13 @@ public class SequenceFetcher extends ASequenceFetcher
           System.out.println("ERROR:No alignment retrieved.");
           StringBuffer raw = sp.getRawRecords();
           if (raw != null)
+          {
             System.out.println(raw.toString());
+          }
           else
+          {
             System.out.println("ERROR:No Raw results.");
+          }
         }
         else
         {