X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=e6a48531f322ac5e80ffe03e1d18789544700216;hb=a4780f236ded1ae07824254bca59b2aa0ea539ba;hp=f14afb2a958d5d959789f1eab9a25252d2151e01;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index f14afb2..e6a4853 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
  * 
@@ -20,9 +20,12 @@
  */
 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
@@ -42,10 +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++)
         {
@@ -253,14 +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);