/* * 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.Arrays; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Set; import com.stevesoft.pat.Regex; /** * Utilities for handling DBRef objects and their collections. */ public class DBRefUtils { /* * lookup from lower-case form of a name to its canonical (standardised) form */ 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); // Ensembl values for dbname in xref REST service: canonicalSourceNameLookup.put("uniprot/sptrembl", DBRefSource.UNIPROT); canonicalSourceNameLookup.put("uniprot/swissprot", DBRefSource.UNIPROT); canonicalSourceNameLookup.put("pdb", DBRefSource.PDB); canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL); // Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served // from ENA. canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL); canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL); // Make sure we have lowercase entries for all canonical string lookups Set keys = canonicalSourceNameLookup.keySet(); for (String k : keys) { canonicalSourceNameLookup.put(k.toLowerCase(), canonicalSourceNameLookup.get(k)); } dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB); dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT); dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBL); // dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBLCDS); } /** * Returns those DBRefEntry objects whose source identifier (once converted to * Jalview's canonical form) is in the list of sources to search for. Returns * null if no matches found. * * @param dbrefs * DBRefEntry objects to search * @param sources * array of sources to select * @return */ public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs, String[] sources) { if (dbrefs == null || sources == null) { return dbrefs; } HashSet srcs = new HashSet(); for (String src : sources) { srcs.add(src.toUpperCase()); } List res = new ArrayList(); for (DBRefEntry dbr : dbrefs) { String source = getCanonicalName(dbr.getSource()); if (srcs.contains(source.toUpperCase())) { res.add(dbr); } } if (res.size() > 0) { DBRefEntry[] reply = new DBRefEntry[res.size()]; return res.toArray(reply); } 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 a (possibly empty) list of those references that match the given * entry. 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 List searchRefs(DBRefEntry[] ref, DBRefEntry entry) { return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList); } /** * Returns a list of those references that match the given accession id *
    *
  • database sources are the same
  • *
  • accession ids are the same
  • *
  • both have no mapping, or the mappings are the same
  • *
* * @param refs * Set of references to search * @param accId * accession id to match * @return */ public static List searchRefs(DBRefEntry[] refs, String accId) { return searchRefs(refs, new DBRefEntry("", "", accId), matchId); } /** * Returns a (possibly empty) list of those references that match the given * entry, according to the given comparator. * * @param refs * an array of database references to search * @param entry * an entry to compare against * @param comparator * @return */ static List searchRefs(DBRefEntry[] refs, DBRefEntry entry, DbRefComp comparator) { List rfs = new ArrayList(); if (refs == null || entry == null) { return rfs; } for (int i = 0; i < refs.length; i++) { if (comparator.matches(entry, refs[i])) { rfs.add(refs[i]); } } return rfs; } interface DbRefComp { public boolean matches(DBRefEntry refa, DBRefEntry refb); } /** * match on all non-null fields in refa */ // TODO unused - remove? public static DbRefComp matchNonNullonA = new DbRefComp() { @Override public boolean matches(DBRefEntry refa, DBRefEntry refb) { if (refa.getSource() == null || DBRefUtils.getCanonicalName(refb.getSource()).equals( DBRefUtils.getCanonicalName(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. */ // TODO unused - remove? public static DbRefComp matchEitherNonNull = new DbRefComp() { @Override public boolean matches(DBRefEntry refa, DBRefEntry refb) { if (nullOrEqualSource(refa.getSource(), refb.getSource()) && nullOrEqual(refa.getVersion(), refb.getVersion()) && nullOrEqual(refa.getAccessionId(), refb.getAccessionId()) && nullOrEqual(refa.getMap(), refb.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?) */ // TODO unused - remove? public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp() { @Override public boolean matches(DBRefEntry refa, DBRefEntry refb) { if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource()).equals( DBRefUtils.getCanonicalName(refa.getSource()))) { // We dont care about version if (refa.getAccessionId() != null && refb.getAccessionId() != null // FIXME should be && not || here? || 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. */ // TODO unused - remove? public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp() { @Override public boolean matches(DBRefEntry refa, DBRefEntry refb) { if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource()).equals( DBRefUtils.getCanonicalName(refa.getSource()))) { // We dont care about version 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. */ // TODO unused - remove? public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp() { @Override public boolean matches(DBRefEntry refa, DBRefEntry refb) { if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource()).equals( DBRefUtils.getCanonicalName(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, or null on a. 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() { @Override public boolean matches(DBRefEntry refa, DBRefEntry refb) { if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource()).equals( DBRefUtils.getCanonicalName(refa.getSource()))) { // We dont care about version if (refa.getAccessionId() == null || refa.getAccessionId().equals(refb.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 only must be identical. */ public static DbRefComp matchId = new DbRefComp() { @Override public boolean matches(DBRefEntry refa, DBRefEntry refb) { if (refa.getAccessionId() != null && refb.getAccessionId() != null && refb.getAccessionId().equals(refa.getAccessionId())) { 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.setChainCode(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; } /** * Returns true if either object is null, or they are equal * * @param o1 * @param o2 * @return */ public static boolean nullOrEqual(Object o1, Object o2) { if (o1 == null || o2 == null) { return true; } return o1.equals(o2); } /** * canonicalise source string before comparing. null is always wildcard * * @param o1 * - null or source string to compare * @param o2 * - null or source string to compare * @return true if either o1 or o2 are null, or o1 equals o2 under * DBRefUtils.getCanonicalName * (o1).equals(DBRefUtils.getCanonicalName(o2)) */ public static boolean nullOrEqualSource(String o1, String o2) { if (o1 == null || o2 == null) { return true; } return DBRefUtils.getCanonicalName(o1).equals( DBRefUtils.getCanonicalName(o2)); } /** * Selects just the DNA or protein references from a set of references * * @param selectDna * if true, select references to 'standard' DNA databases, else to * 'standard' peptide databases * @param refs * a set of references to select from * @return */ public static DBRefEntry[] selectDbRefs(boolean selectDna, DBRefEntry[] refs) { return selectRefs(refs, selectDna ? DBRefSource.DNACODINGDBS : DBRefSource.PROTEINDBS); // could attempt to find other cross // refs here - ie PDB xrefs // (not dna, not protein seq) } /** * Returns the (possibly empty) list of those supplied dbrefs which have the * specified source database, with a case-insensitive match of source name * * @param dbRefs * @param source * @return */ public static List searchRefsForSource(DBRefEntry[] dbRefs, String source) { List matches = new ArrayList(); if (dbRefs != null && source != null) { for (DBRefEntry dbref : dbRefs) { if (source.equalsIgnoreCase(dbref.getSource())) { matches.add(dbref); } } } return matches; } /** * promote direct database references to primary for nucleotide or protein * sequences if they have an appropriate primary ref * * * * * * * * * * * * * * * * * * * * * *
Seq TypePrimary DBDirect which will be promoted
peptidesEnsemblUniprot
peptidesEnsemblUniprot
dnaEnsemblENA
* * @param sequence */ public static void ensurePrimaries(SequenceI sequence) { List pr = sequence.getPrimaryDBRefs(); if (pr.size() == 0) { // nothing to do return; } List selfs = new ArrayList(); { DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(), sequence.getDBRefs()); if (selfArray == null || selfArray.length == 0) { // nothing to do return; } selfs.addAll(Arrays.asList(selfArray)); } // filter non-primary refs for (DBRefEntry p : pr) { while (selfs.contains(p)) { selfs.remove(p); } } List toPromote = new ArrayList(); for (DBRefEntry p : pr) { List promType = new ArrayList(); if (sequence.isProtein()) { switch (getCanonicalName(p.getSource())) { case DBRefSource.UNIPROT: // case DBRefSource.UNIPROTKB: // case DBRefSource.UP_NAME: // search for and promote ensembl promType.add(DBRefSource.ENSEMBL); break; case DBRefSource.ENSEMBL: // search for and promote Uniprot promType.add(DBRefSource.UNIPROT); break; } } else { // TODO: promote transcript refs } // collate candidates and promote them DBRefEntry[] candidates = selectRefs( selfs.toArray(new DBRefEntry[0]), promType.toArray(new String[0])); if (candidates != null) { for (DBRefEntry cand : candidates) { if (cand.hasMap()) { if (cand.getMap().getTo() != null && cand.getMap().getTo() != sequence) { // can't promote refs with mappings to other sequences continue; } if (cand.getMap().getMap().getFromLowest() != sequence .getStart() && cand.getMap().getMap().getFromHighest() != sequence .getEnd()) { // can't promote refs with mappings from a region of this sequence // - eg CDS continue; } } // and promote cand.setVersion(p.getVersion() + " (promoted)"); selfs.remove(cand); toPromote.add(cand); if (!cand.isPrimaryCandidate()) { System.out.println("Warning: Couldn't promote dbref " + cand.toString() + " for sequence " + sequence.toString()); } } } } } }