X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=6a612a0602665d356b50b18cf8c150dd2905bf4a;hb=2dcd2b8cfb1b38575c8b2246d59ba1c1a2fb59cd;hp=c182dfa8f901519a763250d2da8afa10da5d9488;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index c182dfa..6a612a0 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 2.8.2b1)
- * 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.
  * 
@@ -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)
@@ -169,13 +167,11 @@ public class SequenceFetcher extends ASequenceFetcher
           {
             nm = nm.substring(4);
           }
-          dassrc.add(new String[]
-          { srcs[i], nm.toUpperCase() });
+          dassrc.add(new String[] { srcs[i], nm.toUpperCase() });
         }
         else
         {
-          nondas.add(new String[]
-          { srcs[i], nm.toUpperCase() });
+          nondas.add(new String[] { srcs[i], nm.toUpperCase() });
         }
       }
     }
@@ -285,7 +281,9 @@ 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
@@ -331,9 +329,8 @@ public class SequenceFetcher extends ASequenceFetcher
             }
             else
             {
-              noProds.addElement((dna ? new Object[]
-              { al, al } : new Object[]
-              { al }));
+              noProds.addElement((dna ? new Object[] { al, al }
+                      : new Object[] { al }));
             }
 
           }
@@ -348,9 +345,13 @@ 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
         {
@@ -365,8 +366,7 @@ public class SequenceFetcher extends ASequenceFetcher
             }
             if (ds == null)
             {
-              ds = new Alignment(new SequenceI[]
-              { sq });
+              ds = new Alignment(new SequenceI[] { sq });
 
             }
             else