/*
- * 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
// 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++)
{
}
}
+ @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);