javadoc

[jalview.git] / src / jalview / analysis / SequenceIdMatcher.java

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 240f9cf..56b760a 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -55,6 +55,20 @@ public class SequenceIdMatcher
     for (int i = 0; i < seqs.length; i++)
     {
       names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
+      // add in any interesting identifiers
+      if (seqs[i].getDBRef()!=null)
+      {
+        DBRefEntry dbr[] = seqs[i].getDBRef();
+        SeqIdName sid=null;
+        for (int r=0;r<dbr.length;r++)
+        {
+          sid = new SeqIdName(dbr[r].getAccessionId());
+          if (!names.contains(sid))
+          {
+            names.put(sid, seqs[i]);
+          }
+        }
+      }
     }
   }