2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 import jalview.datamodel.*;
25 public class DBRefUtils
28 * Utilities for handling DBRef objects and their collections.
32 * @param dbrefs Vector of DBRef objects to search
33 * @param sources String[] array of source DBRef IDs to retrieve
36 public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs, String[] sources)
46 Hashtable srcs = new Hashtable();
47 Vector res = new Vector();
49 for (int i = 0; i < sources.length; i++)
51 srcs.put(new String(sources[i]), new Integer(i));
53 for (int i = 0, j = dbrefs.length; i < j; i++)
55 if (srcs.containsKey(dbrefs[i].getSource()))
57 res.addElement(dbrefs[i]);
63 DBRefEntry[] reply = new DBRefEntry[res.size()];
64 for (int i = 0; i < res.size(); i++)
66 reply[i] = (DBRefEntry) res.elementAt(i);
71 // there are probable memory leaks in the hashtable!
76 * isDasCoordinateSystem
78 * @param string String
79 * @param dBRefEntry DBRefEntry
80 * @return boolean true if Source DBRefEntry is compatible with DAS CoordinateSystem name
82 public static Hashtable DasCoordinateSystemsLookup = null;
83 public static boolean isDasCoordinateSystem(String string,
84 DBRefEntry dBRefEntry)
86 if (DasCoordinateSystemsLookup == null)
88 // TODO: Make a DasCoordinateSystemsLookup properties resource
90 DasCoordinateSystemsLookup = new Hashtable();
91 DasCoordinateSystemsLookup.put("pdbresnum",
92 jalview.datamodel.DBRefSource.PDB);
93 DasCoordinateSystemsLookup.put("uniprot",
94 jalview.datamodel.DBRefSource.UNIPROT);
95 DasCoordinateSystemsLookup.put("EMBL",
96 jalview.datamodel.DBRefSource.EMBL);
97 //DasCoordinateSystemsLookup.put("EMBL",
98 // jalview.datamodel.DBRefSource.EMBLCDS);
101 String coordsys = (String) DasCoordinateSystemsLookup.get(string.
103 if (coordsys != null)
105 return coordsys.equals(dBRefEntry.getSource());
109 public static Hashtable CanonicalSourceNameLookup=null;
111 * look up source in an internal list of database reference sources
112 * and return the canonical jalview name for the source, or the original
113 * string if it has no canonical form.
115 * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) or original source
117 public static String getCanonicalName(String source)
119 if (CanonicalSourceNameLookup==null) {
120 CanonicalSourceNameLookup = new Hashtable();
121 CanonicalSourceNameLookup.put("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT);
122 CanonicalSourceNameLookup.put("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT);
123 CanonicalSourceNameLookup.put("pdb", jalview.datamodel.DBRefSource.PDB);
125 String canonical = (String) CanonicalSourceNameLookup.get(source.
134 * find RefEntry corresponding to a particular pattern
135 * the equals method of each entry is used, from String attributes right down to Mapping attributes.
136 * @param ref Set of references to search
137 * @param entry pattern to collect - null any entry for wildcard match
140 public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
142 return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList);
144 public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry, DbRefComp comparator)
146 if (ref==null || entry==null)
148 Vector rfs = new Vector();
149 for (int i=0; i<ref.length;i++)
151 if (comparator.matches(entry, ref[i]))
153 rfs.addElement(ref[i]);
156 // TODO Auto-generated method stub
159 DBRefEntry[] rf = new DBRefEntry[rfs.size()];
165 public interface DbRefComp {
166 public boolean matches(DBRefEntry refa, DBRefEntry refb);
169 * match on all non-null fields in refa
171 public static DbRefComp matchNonNullonA = new DbRefComp()
173 public boolean matches(DBRefEntry refa, DBRefEntry refb)
175 if (refa.getSource()==null || refb.getSource().equals(refa.getSource()))
177 if (refa.getVersion()==null || refb.getVersion().equals(refa.getVersion()))
179 if (refa.getAccessionId()==null || refb.getAccessionId().equals(refa.getAccessionId()))
181 if (refa.getMap()==null || (refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
192 * either field is null or field matches for all of source, version, accession id and map.
194 public static DbRefComp matchEitherNonNull = new DbRefComp()
196 public boolean matches(DBRefEntry refa, DBRefEntry refb)
198 if ((refa.getSource()==null || refb.getSource()==null)
199 || refb.getSource().equals(refa.getSource()))
201 if ((refa.getVersion()==null || refb.getVersion()==null)
202 || refb.getVersion().equals(refa.getVersion()))
204 if ((refa.getAccessionId()==null || refb.getAccessionId()==null)
205 || refb.getAccessionId().equals(refa.getAccessionId()))
207 if ((refa.getMap()==null || refb.getMap()==null)
208 || (refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
219 * accession ID and DB must be identical. Version is ignored. Map is either not defined or is a match (or is compatible?)
221 public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp()
223 public boolean matches(DBRefEntry refa, DBRefEntry refb)
225 if (refa.getSource()!=null && refb.getSource()!=null
226 && refb.getSource().equals(refa.getSource()))
228 // We dont care about version
229 //if ((refa.getVersion()==null || refb.getVersion()==null)
230 // || refb.getVersion().equals(refa.getVersion()))
232 if (refa.getAccessionId()!=null && refb.getAccessionId()!=null
233 || refb.getAccessionId().equals(refa.getAccessionId()))
235 if ((refa.getMap()==null || refb.getMap()==null)
236 || (refa.getMap()!=null && refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
246 * accession ID and DB must be identical. Version is ignored.
247 * No map on either or map but no maplist on either or maplist of map on a is the complement of maplist of map on b.
249 public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp()
251 public boolean matches(DBRefEntry refa, DBRefEntry refb)
253 if (refa.getSource()!=null && refb.getSource()!=null
254 && refb.getSource().equals(refa.getSource()))
256 // We dont care about version
257 //if ((refa.getVersion()==null || refb.getVersion()==null)
258 // || refb.getVersion().equals(refa.getVersion()))
260 if (refa.getAccessionId()!=null && refb.getAccessionId()!=null
261 || refb.getAccessionId().equals(refa.getAccessionId()))
263 if ((refa.getMap()==null && refb.getMap()==null)
264 || (refa.getMap()!=null && refb.getMap()!=null))
265 if ((refb.getMap().getMap()==null && refa.getMap().getMap()==null)
266 || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
267 && refb.getMap().getMap().getInverse().equals(refa.getMap().getMap())))
277 * accession ID and DB must be identical. Version is ignored.
278 * No map on both or or map but no maplist on either or maplist of map on a is equivalent to the maplist of map on b.
280 public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp()
282 public boolean matches(DBRefEntry refa, DBRefEntry refb)
284 if (refa.getSource()!=null && refb.getSource()!=null
285 && refb.getSource().equals(refa.getSource()))
287 // We dont care about version
288 //if ((refa.getVersion()==null || refb.getVersion()==null)
289 // || refb.getVersion().equals(refa.getVersion()))
291 if (refa.getAccessionId()!=null && refb.getAccessionId()!=null
292 || refb.getAccessionId().equals(refa.getAccessionId()))
294 if (refa.getMap()==null && refb.getMap()==null)
298 if (refa.getMap()!=null && refb.getMap()!=null
299 && ((refb.getMap().getMap()==null && refa.getMap().getMap()==null)
300 || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
301 && refb.getMap().getMap().equals(refa.getMap().getMap()))))
311 * accession ID and DB must be identical. Version is ignored.
312 * No map on either or map but no maplist on either or maplist of map on a is equivalent to the maplist of map on b.
314 public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
316 public boolean matches(DBRefEntry refa, DBRefEntry refb)
318 if (refa.getSource()!=null && refb.getSource()!=null
319 && refb.getSource().equals(refa.getSource()))
321 // We dont care about version
322 //if ((refa.getVersion()==null || refb.getVersion()==null)
323 // || refb.getVersion().equals(refa.getVersion()))
325 if (refa.getAccessionId()!=null && refb.getAccessionId()!=null
326 && refb.getAccessionId().equals(refa.getAccessionId()))
328 if (refa.getMap()==null || refb.getMap()==null)
332 if ((refa.getMap()!=null && refb.getMap()!=null)
333 && (refb.getMap().getMap()==null && refa.getMap().getMap()==null)
334 || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
335 && refb.getMap().getMap().equals(refa.getMap().getMap())))
345 * used by file parsers to generate DBRefs from annotation within file (eg stockholm)
349 * @param seq where to anotate with reference
350 * @return parsed version of entry that was added to seq (if any)
352 public static DBRefEntry parseToDbRef(SequenceI seq, String dbname, String version,
355 DBRefEntry ref = null;
358 String locsrc = jalview.util.DBRefUtils
359 .getCanonicalName(dbname);
360 if (locsrc.equals(jalview.datamodel.DBRefSource.PDB))
362 // check for chaincode and mapping
363 // PFAM style stockhom PDB citation
364 com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex("([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;([0-9]+)-([0-9]+)");
365 if (r.search(acn.trim()))
367 String pdbid = r.stringMatched(1);
368 String chaincode = r.stringMatched(2);
369 String mapstart = r.stringMatched(3);
370 String mapend = r.stringMatched(4);
371 if (chaincode.equals(" "))
375 // construct pdb ref.
376 ref = new DBRefEntry(locsrc, version, pdbid+chaincode);
377 PDBEntry pdbr = new PDBEntry();
383 ref = new DBRefEntry(locsrc, version, acn);