X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=94bc5da5b471315224b2d57477dea24d612dda70;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=d3788ea1ead1a96fa555c0956214a805c591f7ba;hpb=0d6e36143a2d7471edb7ef386d0b79095e0cd63e;p=jalview.git diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java index d3788ea..94bc5da 100755 --- a/src/jalview/util/DBRefUtils.java +++ b/src/jalview/util/DBRefUtils.java @@ -1,72 +1,475 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 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 java.util.*; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; +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.List; +import java.util.Map; +import com.stevesoft.pat.Regex; public class DBRefUtils { - /** - * 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; - Hashtable srcs = new Hashtable(); - Vector res=new Vector(); - - for (int i=0; i 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(); - if (res.size()>0) + 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())) { - DBRefEntry [] reply = new DBRefEntry[res.size()]; - for(int i=0; i 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 + * + * @param string + * String + * @param 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) + 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() { - if (DasCoordinateSystemsLookup==null) - { // Initialise - DasCoordinateSystemsLookup = new Hashtable(); - DasCoordinateSystemsLookup.put("pdbresnum", - jalview.datamodel.DBRefSource.PDB); - DasCoordinateSystemsLookup.put("uniprot", - jalview.datamodel.DBRefSource.UNIPROT); - } - - String coordsys = (String) DasCoordinateSystemsLookup.get(string.toLowerCase()); - if (coordsys!=null) - return coordsys.equals(dBRefEntry.getSource()); - return false; + 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; } + }