/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * 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 Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.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 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 * @param sources * String[] array of source DBRef IDs to retrieve * @return Vector */ public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs, String[] sources) { if (dbrefs == null) { return null; } if (sources == null) { return dbrefs; } Map srcs = new HashMap(); ArrayList res = new ArrayList(); for (int i = 0; i < sources.length; i++) { srcs.put(new String(sources[i]), new Integer(i)); } for (int i = 0, j = dbrefs.length; i < j; i++) { if (srcs.containsKey(dbrefs[i].getSource())) { res.add(dbrefs[i]); } } if (res.size() > 0) { DBRefEntry[] reply = new DBRefEntry[res.size()]; return res.toArray(reply); } res = null; // there are probable memory leaks in the hashtable! return null; } /** * isDasCoordinateSystem * * @param string * String * @param dBRefEntry * DBRefEntry * @return boolean true if Source DBRefEntry is compatible with DAS * CoordinateSystem name */ public static boolean isDasCoordinateSystem(String string, DBRefEntry dBRefEntry) { if (string == null || dBRefEntry == null) { return false; } String coordsys = dasCoordinateSystemsLookup.get(string .toLowerCase()); return coordsys == null ? false : coordsys.equals(dBRefEntry .getSource()); } /** * 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 * no canonical form. * * @param source * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) * or original source */ public static String getCanonicalName(String source) { if (source == null) { return null; } String canonical = canonicalSourceNameLookup.get(source .toLowerCase()); return canonical == null ? source : canonical; } /** * 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 * @param entry * pattern to match * @return */ public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry) { return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList); } /** * 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 (refs == null || entry == null) { return null; } List rfs = new ArrayList(); for (int i = 0; i < refs.length; i++) { if (comparator.matches(entry, refs[i])) { rfs.add(refs[i]); } } return rfs.size() == 0 ? null : rfs.toArray(new DBRefEntry[rfs.size()]); } interface DbRefComp { public boolean matches(DBRefEntry refa, DBRefEntry refb); } /** * match on all non-null fields in refa */ public static DbRefComp matchNonNullonA = new DbRefComp() { public boolean matches(DBRefEntry refa, DBRefEntry refb) { if (refa.getSource() == null || refb.getSource().equals(refa.getSource())) { if (refa.getVersion() == null || refb.getVersion().equals(refa.getVersion())) { if (refa.getAccessionId() == null || refb.getAccessionId().equals(refa.getAccessionId())) { if (refa.getMap() == null || (refb.getMap() != null && refb.getMap().equals( refa.getMap()))) { return true; } } } } return false; } }; /** * either field is null or field matches for all of source, version, accession * id and map. */ public static DbRefComp matchEitherNonNull = new DbRefComp() { public boolean matches(DBRefEntry refa, DBRefEntry refb) { if ((refa.getSource() == null || refb.getSource() == null) || refb.getSource().equals(refa.getSource())) { if ((refa.getVersion() == null || refb.getVersion() == null) || refb.getVersion().equals(refa.getVersion())) { if ((refa.getAccessionId() == null || refb.getAccessionId() == null) || refb.getAccessionId().equals(refa.getAccessionId())) { if ((refa.getMap() == null || refb.getMap() == null) || (refb.getMap() != null && refb.getMap().equals( refa.getMap()))) { return true; } } } } return false; } }; /** * accession ID and DB must be identical. Version is ignored. Map is either * not defined or is a match (or is compatible?) */ public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp() { public boolean matches(DBRefEntry refa, DBRefEntry refb) { if (refa.getSource() != null && refb.getSource() != null && refb.getSource().equals(refa.getSource())) { // We dont care about version // if ((refa.getVersion()==null || refb.getVersion()==null) // || refb.getVersion().equals(refa.getVersion())) // { if (refa.getAccessionId() != null && refb.getAccessionId() != null || refb.getAccessionId().equals(refa.getAccessionId())) { if ((refa.getMap() == null || refb.getMap() == null) || (refa.getMap() != null && refb.getMap() != null && refb .getMap().equals(refa.getMap()))) { return true; } } } return false; } }; /** * accession ID and DB must be identical. Version is ignored. 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. */ public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp() { public boolean matches(DBRefEntry refa, DBRefEntry refb) { if (refa.getSource() != null && refb.getSource() != null && refb.getSource().equals(refa.getSource())) { // We dont care about version // if ((refa.getVersion()==null || refb.getVersion()==null) // || refb.getVersion().equals(refa.getVersion())) // { if (refa.getAccessionId() != null && refb.getAccessionId() != null || refb.getAccessionId().equals(refa.getAccessionId())) { 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()))) { return true; } } } } return false; } }; /** * accession ID and DB must be identical. Version is ignored. 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. */ public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp() { public boolean matches(DBRefEntry refa, DBRefEntry refb) { if (refa.getSource() != null && refb.getSource() != null && refb.getSource().equals(refa.getSource())) { // We dont care about version // if ((refa.getVersion()==null || refb.getVersion()==null) // || refb.getVersion().equals(refa.getVersion())) // { if (refa.getAccessionId() != null && refb.getAccessionId() != null || refb.getAccessionId().equals(refa.getAccessionId())) { if (refa.getMap() == null && refb.getMap() == null) { return true; } if (refa.getMap() != null && refb.getMap() != null && ((refb.getMap().getMap() == null && refa.getMap() .getMap() == null) || (refb.getMap().getMap() != null && refa.getMap().getMap() != null && refb .getMap().getMap().equals(refa.getMap().getMap())))) { return true; } } } return false; } }; /** * accession ID and DB must be identical. Version is ignored. 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. */ public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp() { 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())) { // We dont care about version // if ((refa.getVersion()==null || refb.getVersion()==null) // || refb.getVersion().equals(refa.getVersion())) // { if (refa.getAccessionId() != null && refb.getAccessionId() != null && refb.getAccessionId().equals(refa.getAccessionId())) { if (refa.getMap() == null || refb.getMap() == null) { return true; } if ((refa.getMap() != null && refb.getMap() != null) && (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()) return true; } } } return false; } }; /** * 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 annotate with reference * @return parsed version of entry that was added to seq (if any) */ public static DBRefEntry parseToDbRef(SequenceI seq, String dbname, String version, String acn) { DBRefEntry ref = null; if (dbname != null) { String locsrc = DBRefUtils.getCanonicalName(dbname); if (locsrc.equals(DBRefSource.PDB)) { /* * 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); if (chaincode==null) { chaincode = " "; } // String mapstart = r.stringMatched(3); // String mapend = r.stringMatched(4); if (chaincode.equals(" ")) { chaincode = "_"; } // construct pdb ref. 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 { // default: ref = new DBRefEntry(locsrc, version, acn); } } if (ref != null) { seq.addDBRef(ref); } return ref; } }