X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=e6a48531f322ac5e80ffe03e1d18789544700216;hb=2b0142bf85bf5b3d20612c01433e7ce29b633ec4;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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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);