/*
- * 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 2.9)
+ * Copyright (C) 2015 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.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
-import jalview.datamodel.*;
+import com.stevesoft.pat.Regex;
public class DBRefUtils
{
+ private static Map<String, String> canonicalSourceNameLookup = new HashMap<String, String>();
+
+ private static Map<String, String> dasCoordinateSystemsLookup = new HashMap<String, String>();
+
+ static
+ {
+ // TODO load these from a resource file?
+ canonicalSourceNameLookup.put("uniprotkb/swiss-prot",
+ DBRefSource.UNIPROT);
+ canonicalSourceNameLookup.put("uniprotkb/trembl", DBRefSource.UNIPROT);
+ canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
+
+ dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB);
+ dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT);
+ dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBL);
+ // dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBLCDS);
+ }
+
/**
* Utilities for handling DBRef objects and their collections.
*/
/**
*
* @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
*/
- public static Hashtable DasCoordinateSystemsLookup = null;
public static boolean isDasCoordinateSystem(String string,
DBRefEntry dBRefEntry)
{
- if (DasCoordinateSystemsLookup == null)
- {
- // TODO: Make a DasCoordinateSystemsLookup properties resource
- // Initialise
- DasCoordinateSystemsLookup = new Hashtable();
- DasCoordinateSystemsLookup.put("pdbresnum",
- jalview.datamodel.DBRefSource.PDB);
- DasCoordinateSystemsLookup.put("uniprot",
- jalview.datamodel.DBRefSource.UNIPROT);
- DasCoordinateSystemsLookup.put("EMBL",
- jalview.datamodel.DBRefSource.EMBL);
- // DasCoordinateSystemsLookup.put("EMBL",
- // jalview.datamodel.DBRefSource.EMBLCDS);
- }
-
- String coordsys = (String) DasCoordinateSystemsLookup.get(string
- .toLowerCase());
- if (coordsys != null)
+ if (string == null || dBRefEntry == null)
{
- return coordsys.equals(dBRefEntry.getSource());
+ return false;
}
- return false;
+ String coordsys = dasCoordinateSystemsLookup.get(string.toLowerCase());
+ return coordsys == null ? false : coordsys.equals(dBRefEntry
+ .getSource());
}
- public static Hashtable CanonicalSourceNameLookup = null;
-
/**
* look up source in an internal list of database reference sources and return
* the canonical jalview name for the source, or the original string if it has
*/
public static String getCanonicalName(String source)
{
- if (CanonicalSourceNameLookup == null)
- {
- CanonicalSourceNameLookup = new Hashtable();
- CanonicalSourceNameLookup.put("uniprotkb/swiss-prot",
- jalview.datamodel.DBRefSource.UNIPROT);
- CanonicalSourceNameLookup.put("uniprotkb/trembl",
- jalview.datamodel.DBRefSource.UNIPROT);
- CanonicalSourceNameLookup.put("pdb",
- jalview.datamodel.DBRefSource.PDB);
- }
- String canonical = (String) CanonicalSourceNameLookup.get(source
- .toLowerCase());
- if (canonical == null)
+ if (source == null)
{
- return source;
+ return null;
}
- return canonical;
+ String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
+ return canonical == null ? source : canonical;
}
/**
- * find RefEntry corresponding to a particular pattern the equals method of
- * each entry is used, from String attributes right down to Mapping
- * attributes.
+ * Returns an array of those references that match the given entry, or null if
+ * no matches. Currently uses a comparator which matches if
+ * <ul>
+ * <li>database sources are the same</li>
+ * <li>accession ids are the same</li>
+ * <li>both have no mapping, or the mappings are the same</li>
+ * </ul>
*
* @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 match
* @return
*/
public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
matchDbAndIdAndEitherMapOrEquivalentMapList);
}
- public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry,
+ /**
+ * Returns an array of those references that match the given entry, according
+ * to the given comparator. Returns null if no matches.
+ *
+ * @param refs
+ * an array of database references to search
+ * @param entry
+ * an entry to compare against
+ * @param comparator
+ * @return
+ */
+ static DBRefEntry[] searchRefs(DBRefEntry[] refs, DBRefEntry entry,
DbRefComp comparator)
{
- if (ref == null || entry == null)
+ if (refs == null || entry == null)
+ {
return null;
- Vector rfs = new Vector();
- for (int i = 0; i < ref.length; i++)
+ }
+ List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+ for (int i = 0; i < refs.length; i++)
{
- if (comparator.matches(entry, ref[i]))
+ if (comparator.matches(entry, refs[i]))
{
- rfs.addElement(ref[i]);
+ rfs.add(refs[i]);
}
}
- // TODO Auto-generated method stub
- if (rfs.size() > 0)
- {
- DBRefEntry[] rf = new DBRefEntry[rfs.size()];
- rfs.copyInto(rf);
- return rf;
- }
- return null;
+ return rfs.size() == 0 ? null : rfs.toArray(new DBRefEntry[rfs.size()]);
}
- public interface DbRefComp
+ interface DbRefComp
{
public boolean matches(DBRefEntry refa, DBRefEntry refb);
}
{
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;
}
}
};
/**
- * used by file parsers to generate DBRefs from annotation within file (eg
- * stockholm)
+ * Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
+ * database is PDB.
+ * <p>
+ * Used by file parsers to generate DBRefs from annotation within file (eg
+ * Stockholm)
*
* @param dbname
* @param version
* @param acn
* @param seq
- * where to anotate with reference
+ * where to annotate with reference
* @return parsed version of entry that was added to seq (if any)
*/
public static DBRefEntry parseToDbRef(SequenceI seq, String dbname,
DBRefEntry ref = null;
if (dbname != null)
{
- String locsrc = jalview.util.DBRefUtils.getCanonicalName(dbname);
- if (locsrc.equals(jalview.datamodel.DBRefSource.PDB))
+ String locsrc = DBRefUtils.getCanonicalName(dbname);
+ if (locsrc.equals(DBRefSource.PDB))
{
- // 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]+)");
+ /*
+ * Check for PFAM style stockhom PDB accession id citation e.g.
+ * "1WRI A; 7-80;"
+ */
+ Regex r = new com.stevesoft.pat.Regex(
+ "([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);
- String mapstart = r.stringMatched(3);
- String mapend = r.stringMatched(4);
+ if (chaincode == null)
+ {
+ chaincode = " ";
+ }
+ // String mapstart = r.stringMatched(3);
+ // String mapend = r.stringMatched(4);
if (chaincode.equals(" "))
{
chaincode = "_";
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
+ pdbr.setType(PDBEntry.Type.PDB);
+ pdbr.setProperty(new Hashtable());
+ pdbr.setChainCode(chaincode);
+ // pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
}
+ else
+ {
+ System.err.println("Malformed PDB DR line:" + acn);
+ }
}
else
{
git://source.jalview.org / jalview.git / blobdiff