X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=e6a48531f322ac5e80ffe03e1d18789544700216;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=d2bdaa2859f5e44e0b548608819fb14f4d3d76db;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index d2bdaa2..e6a4853 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,25 +1,31 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
-import java.util.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
 
 /**
  * Routines for approximate Sequence Id resolution by name using string
@@ -39,10 +45,15 @@ public class SequenceIdMatcher
       // TODO: deal with ID collisions - SequenceI should be appended to list
       // associated with this key.
       names.put(new SeqIdName(seqs[i].getDisplayId(true)), seqs[i]);
+      SequenceI dbseq = seqs[i];
+      while (dbseq.getDatasetSequence()!=null)
+      {
+        dbseq = dbseq.getDatasetSequence();
+      }
       // add in any interesting identifiers
-      if (seqs[i].getDBRef() != null)
+      if (dbseq.getDBRef() != null)
       {
-        DBRefEntry dbr[] = seqs[i].getDBRef();
+        DBRefEntry dbr[] = dbseq.getDBRef();
         SeqIdName sid = null;
         for (int r = 0; r < dbr.length; r++)
         {
@@ -250,14 +261,20 @@ public class SequenceIdMatcher
       }
     }
 
+    @Override
     public int hashCode()
     {
       return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
               .hashCode());
     }
 
+    @Override
     public boolean equals(Object s)
     {
+      if (s == null)
+      {
+        return false;
+      }
       if (s instanceof SeqIdName)
       {
         return this.equals((SeqIdName) s);