/*
- * 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 (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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/>.
*/
package jalview.analysis;
{
names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
// add in any interesting identifiers
- if (seqs[i].getDBRef()!=null)
+ if (seqs[i].getDBRef() != null)
{
DBRefEntry dbr[] = seqs[i].getDBRef();
- SeqIdName sid=null;
- for (int r=0;r<dbr.length;r++)
+ SeqIdName sid = null;
+ for (int r = 0; r < dbr.length; r++)
{
sid = new SeqIdName(dbr[r].getAccessionId());
if (!names.contains(sid))
* matches to the names hash.
*
* @param candName
- * SeqIdName
+ * SeqIdName
* @param matches
- * Vector of SequenceI objects
+ * Vector of SequenceI objects
* @return SequenceI closest SequenceI to SeqIdName
*/
private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
* get SequenceI with closest SequenceI.getName() to seq.getName()
*
* @param seq
- * SequenceI
+ * SequenceI
* @return SequenceI
*/
- SequenceI findIdMatch(SequenceI seq)
+ public SequenceI findIdMatch(SequenceI seq)
{
SeqIdName nam = new SeqIdName(seq.getName());
return findIdMatch(nam);
}
- SequenceI findIdMatch(String seqnam)
+ public SequenceI findIdMatch(String seqnam)
{
SeqIdName nam = new SeqIdName(seqnam);
return findIdMatch(nam);
* same Id as a given set of different sequence objects
*
* @param seqs
- * SequenceI[]
+ * SequenceI[]
* @return SequenceI[]
*/
- SequenceI[] findIdMatch(SequenceI[] seqs)
+ public SequenceI[] findIdMatch(SequenceI[] seqs)
{
SequenceI[] namedseqs = null;
int i = 0;
* core findIdMatch search method
*
* @param nam
- * SeqIdName
+ * SeqIdName
* @return SequenceI
*/
private SequenceI findIdMatch(
* todo: (JBPNote) Set separator characters appropriately
*
* @param s
- * SeqIdName
+ * SeqIdName
* @return boolean
*/
public boolean equals(SeqIdName s)