/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
*
- * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.util;
/**
*
* @param dbrefs
- * Vector of DBRef objects to search
+ * Vector of DBRef objects to search
* @param sources
- * String[] array of source DBRef IDs to retrieve
+ * String[] array of source DBRef IDs to retrieve
* @return Vector
*/
public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs,
* isDasCoordinateSystem
*
* @param string
- * String
+ * String
* @param dBRefEntry
- * DBRefEntry
+ * DBRefEntry
* @return boolean true if Source DBRefEntry is compatible with DAS
* CoordinateSystem name
*/
* attributes.
*
* @param ref
- * Set of references to search
+ * Set of references to search
* @param entry
- * pattern to collect - null any entry for wildcard match
+ * pattern to collect - null any entry for wildcard match
* @return
*/
public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
|| (refb.getMap().getMap() != null
&& refa.getMap().getMap() != null && refb
- .getMap().getMap().getInverse().equals(
- refa.getMap().getMap())))
+ .getMap().getMap().getInverse()
+ .equals(refa.getMap().getMap())))
{
return true;
}
{
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
-// System.err.println("Comparing A: "+refa.getSrcAccString()+(refa.hasMap()?" has map.":"."));
-// System.err.println("Comparing B: "+refb.getSrcAccString()+(refb.hasMap()?" has map.":"."));
+ // System.err.println("Comparing A: "+refa.getSrcAccString()+(refa.hasMap()?" has map.":"."));
+ // System.err.println("Comparing B: "+refb.getSrcAccString()+(refb.hasMap()?" has map.":"."));
if (refa.getSource() != null && refb.getSource() != null
&& refb.getSource().equals(refa.getSource()))
{
&& (refb.getMap().getMap() == null && refa.getMap()
.getMap() == null)
|| (refb.getMap().getMap() != null
- && refa.getMap().getMap() != null &&
- (refb
- .getMap().getMap().equals(refa.getMap().getMap())))) { // getMap().getMap().containsEither(false,refa.getMap().getMap())
+ && refa.getMap().getMap() != null && (refb
+ .getMap().getMap().equals(refa.getMap().getMap()))))
+ { // getMap().getMap().containsEither(false,refa.getMap().getMap())
return true;
}
}
* @param version
* @param acn
* @param seq
- * where to anotate with reference
+ * where to anotate with reference
* @return parsed version of entry that was added to seq (if any)
*/
public static DBRefEntry parseToDbRef(SequenceI seq, String dbname,
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
+ pdbr.getProperty().put("CHAIN",chaincode);
seq.addPDBId(pdbr);
}
}