/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
-import java.util.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Vector;
public class DBRefUtils
{
/**
*
* @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,
{
return dbrefs;
}
- Hashtable srcs = new Hashtable();
- Vector res = new Vector();
+ Map<String, Integer> srcs = new HashMap<String, Integer>();
+ ArrayList<DBRefEntry> res = new ArrayList<DBRefEntry>();
for (int i = 0; i < sources.length; i++)
{
{
if (srcs.containsKey(dbrefs[i].getSource()))
{
- res.addElement(dbrefs[i]);
+ res.add(dbrefs[i]);
}
}
if (res.size() > 0)
{
DBRefEntry[] reply = new DBRefEntry[res.size()];
- for (int i = 0; i < res.size(); i++)
- {
- reply[i] = (DBRefEntry) res.elementAt(i);
- }
- return reply;
+ return res.toArray(reply);
}
res = null;
// there are probable memory leaks in the hashtable!
* 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)
DbRefComp comparator)
{
if (ref == null || entry == null)
+ {
return null;
+ }
Vector rfs = new Vector();
for (int i = 0; i < ref.length; i++)
{
{
if ((refa.getMap() == null && refb.getMap() == null)
|| (refa.getMap() != null && refb.getMap() != null))
+ {
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;
}
+ }
}
}
return false;
{
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,
// check for chaincode and mapping
// PFAM style stockhom PDB citation
com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
- "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;([0-9]+)-([0-9]+)");
+ "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
if (r.search(acn.trim()))
{
String pdbid = r.stringMatched(1);
String chaincode = r.stringMatched(2);
+ if (chaincode==null)
+ {
+ chaincode = " ";
+ }
String mapstart = r.stringMatched(3);
String mapend = r.stringMatched(4);
if (chaincode.equals(" "))
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
+ pdbr.setProperty(new Hashtable());
+ pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
+ } else {
+ System.err.println("Malformed PDB DR line:"+acn);
}
}
else