X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=32589f711df95d6c44896e01f258a8aac4caa707;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=9704170c41883e94370e115239802e21c99eec90;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java index 9704170..32589f7 100755 --- a/src/jalview/util/DBRefUtils.java +++ b/src/jalview/util/DBRefUtils.java @@ -1,38 +1,67 @@ /* - * 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 2.9) + * 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 . + * 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 canonicalSourceNameLookup = new HashMap(); + + private static Map dasCoordinateSystemsLookup = new HashMap(); + + 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, @@ -46,8 +75,8 @@ public class DBRefUtils { return dbrefs; } - Hashtable srcs = new Hashtable(); - Vector res = new Vector(); + Map srcs = new HashMap(); + ArrayList res = new ArrayList(); for (int i = 0; i < sources.length; i++) { @@ -57,18 +86,14 @@ public class DBRefUtils { 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! @@ -79,43 +104,25 @@ public class DBRefUtils * 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) + if (string == null || dBRefEntry == 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) - { - 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 @@ -127,34 +134,27 @@ public class DBRefUtils */ 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 + *
    + *
  • database sources are the same
    • + *
  • accession ids are the same
    • + *
  • both have no mapping, or the mappings are the same
    • + *
* * @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) @@ -163,30 +163,36 @@ public class DBRefUtils 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 rfs = new ArrayList(); + 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); } @@ -301,14 +307,16 @@ public class DBRefUtils { 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; @@ -362,6 +370,8 @@ public class DBRefUtils { 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.":".")); if (refa.getSource() != null && refb.getSource() != null && refb.getSource().equals(refa.getSource())) { @@ -380,9 +390,9 @@ public class DBRefUtils && (refb.getMap().getMap() == null && refa.getMap() .getMap() == null) || (refb.getMap().getMap() != null - && refa.getMap().getMap() != null && refb - .getMap().getMap().equals(refa.getMap().getMap()))) - { + && refa.getMap().getMap() != null && (refb + .getMap().getMap().equals(refa.getMap().getMap())))) + { // getMap().getMap().containsEither(false,refa.getMap().getMap()) return true; } } @@ -392,14 +402,17 @@ public class DBRefUtils }; /** - * 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. + *

+ * 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, @@ -408,19 +421,25 @@ public class DBRefUtils 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 = "_"; @@ -429,8 +448,16 @@ public class DBRefUtils 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 {