X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=76931429f326be2c619a4492e83df234f090f836;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=9f8fb82bde033a6fa1b46bb906fef830489b91e7;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 9f8fb82..7693142 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -283,11 +283,14 @@ public class DBRefFetcher implements Runnable
   {
     if (dbSources == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_must_init_dbsources"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_must_init_dbsources"));
     }
     running = true;
     long startTime = System.currentTimeMillis();
-    af.setProgressBar(MessageManager.getString("status.fetching_db_refs"), startTime);
+    af.setProgressBar(MessageManager.getString("status.fetching_db_refs"),
+            startTime);
     try
     {
       if (Cache.getDefault("DBREFFETCH_USEPICR", false))
@@ -393,8 +396,8 @@ public class DBRefFetcher implements Runnable
             {
               SequenceI sequence = dataset[seqIndex];
               DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-                      sequence.getDBRef(), new String[]
-                      { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+                      sequence.getDBRef(),
+                      new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
               // });
               // check for existing dbrefs to use
               if (uprefs != null && uprefs.length > 0)
@@ -517,8 +520,7 @@ public class DBRefFetcher implements Runnable
       Vector sequenceMatches = new Vector();
       // look for corresponding accession ids
       DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
-              entry.getDBRef(), new String[]
-              { dbSource });
+              entry.getDBRef(), new String[] { dbSource });
       if (entryRefs == null)
       {
         System.err
@@ -616,11 +618,10 @@ public class DBRefFetcher implements Runnable
           // absStart = 0;
           // create valid mapping between matching region of local sequence and
           // the mapped sequence
-          mp = new Mapping(null, new int[]
-          { sequence.getStart() + absStart,
+          mp = new Mapping(null, new int[] {
+              sequence.getStart() + absStart,
               sequence.getStart() + absStart + entrySeq.length() - 1 },
-                  new int[]
-                  { entry.getStart(),
+                  new int[] { entry.getStart(),
                       entry.getStart() + entrySeq.length() - 1 }, 1, 1);
           updateRefFrame = false; // mapping is based on current start/end so
           // don't modify start and end