/* * 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.Mapping; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import java.util.ArrayList; import java.util.BitSet; 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<>(); public final static int DB_SOURCE = 1; public final static int DB_VERSION = 2; public final static int DB_ID = 4; public final static int DB_MAP = 8; public final static int SEARCH_MODE_NO_MAP_NO_VERSION = DB_SOURCE | DB_ID; public final static int SEARCH_MODE_FULL = DB_SOURCE | DB_VERSION | DB_ID | DB_MAP; 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); // guarantee we always have lowercase entries for canonical string lookups for (String k : canonicalSourceNameLookup.keySet()) { canonicalSourceNameLookup.put(k.toLowerCase(), canonicalSourceNameLookup.get(k)); } } /** * 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 List selectRefs(List dbrefs, String[] sources) { if (dbrefs == null || sources == null) { return dbrefs; } // BH TODO (what?) HashSet srcs = new HashSet(); for (String src : sources) { srcs.add(src.toUpperCase()); } int nrefs = dbrefs.size(); List res = new ArrayList(); for (int ib = 0; ib < nrefs; ib++) { DBRefEntry dbr = dbrefs.get(ib); String source = getCanonicalName(dbr.getSource()); if (srcs.contains(source.toUpperCase())) { res.add(dbr); } } if (res.size() > 0) { // List reply = new DBRefEntry[res.size()]; return res;// .toArray(reply); } return null; } private static boolean selectRefsBS(List dbrefs, int sourceKeys, BitSet bsSelect) { if (dbrefs == null || sourceKeys == 0) { return false; } for (int i = 0, n = dbrefs.size(); i < n; i++) { DBRefEntry dbr = dbrefs.get(i); if ((dbr.getSourceKey() & sourceKeys) != 0) { bsSelect.clear(i); } } return !bsSelect.isEmpty(); } /** * 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; } /** * 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 * @param mode SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional * @return */ public static List searchRefs(List ref, DBRefEntry entry, int mode) { return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList, mode); } /** * 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(List refs, String accId) { List rfs = new ArrayList(); if (refs == null || accId == null) { return rfs; } for (int i = 0, n = refs.size(); i < n; i++) { DBRefEntry e = refs.get(i); if (accId.equals(e.getAccessionId())) { rfs.add(e); } } return rfs; // return searchRefs(refs, new DBRefEntry("", "", accId), matchId, SEARCH_MODE_FULL); } /** * 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 * @param mode SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION * optional * @return */ static List searchRefs(List refs, DBRefEntry entry, DbRefComp comparator, int mode) { List rfs = new ArrayList(); if (refs == null || entry == null) { return rfs; } for (int i = 0, n = refs.size(); i < n; i++) { DBRefEntry e = refs.get(i); if (comparator.matches(entry, e, SEARCH_MODE_FULL)) { rfs.add(e); } } return rfs; } interface DbRefComp { default public boolean matches(DBRefEntry refa, DBRefEntry refb) { return matches(refa, refb, SEARCH_MODE_FULL); }; public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode); } /** * match on all non-null fields in refa */ // TODO unused - remove? would be broken by equating "" with null public static DbRefComp matchNonNullonA = new DbRefComp() { @Override public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) { if ((mode & DB_SOURCE) != 0 && (refa.getSource() == null || DBRefUtils.getCanonicalName(refb.getSource()) .equals(DBRefUtils.getCanonicalName(refa.getSource())))) { if ((mode & DB_VERSION) != 0 && (refa.getVersion() == null || refb.getVersion().equals(refa.getVersion()))) { if ((mode & DB_ID) != 0 && (refa.getAccessionId() == null || refb.getAccessionId().equals(refa.getAccessionId()))) { if ((mode & DB_MAP) != 0 && (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, int mode) { 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, int mode) { 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, int mode) { 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, int mode) { 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, int mode) { 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; } }; /** * 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; } /** * 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 List selectDbRefs(boolean selectDna, List 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(List 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) { if (pr.size() == 0) { // nothing to do return; } int sstart = sequence.getStart(); int send = sequence.getEnd(); boolean isProtein = sequence.isProtein(); BitSet bsSelect = new BitSet(); // List selfs = new ArrayList(); // { // List selddfs = selectDbRefs(!isprot, sequence.getDBRefs()); // if (selfs == null || selfs.size() == 0) // { // // nothing to do // return; // } List dbrefs = sequence.getDBRefs(); bsSelect.set(0, dbrefs.size()); if (!selectRefsBS(dbrefs, isProtein ? DBRefSource.PROTEIN_MASK : DBRefSource.DNA_CODING_MASK, bsSelect)) return; // selfs.addAll(selfArray); // } // filter non-primary refs for (int ip = pr.size(); --ip >= 0;) { DBRefEntry p = pr.get(ip); for (int i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect.nextSetBit(i + 1)) { if (dbrefs.get(i) == p) bsSelect.clear(i); } // while (selfs.contains(p)) // { // selfs.remove(p); // } } // List toPromote = new ArrayList(); for (int ip = pr.size(), keys = 0; --ip >= 0 && keys != DBRefSource.PRIMARY_MASK;) { DBRefEntry p = pr.get(ip); if (isProtein) { switch (getCanonicalName(p.getSource())) { case DBRefSource.UNIPROT: keys |= DBRefSource.UNIPROT_MASK; break; case DBRefSource.ENSEMBL: keys |= DBRefSource.ENSEMBL_MASK; break; } } else { // TODO: promote transcript refs ?? } if (keys == 0 || !selectRefsBS(dbrefs, keys, bsSelect)) return; // if (candidates != null) { for (int ic = bsSelect.nextSetBit(0); ic >= 0; ic = bsSelect.nextSetBit(ic + 1)) // for (int ic = 0, n = candidates.size(); ic < n; ic++) { DBRefEntry cand = dbrefs.get(ic);// candidates.get(ic); if (cand.hasMap()) { Mapping map = cand.getMap(); SequenceI cto = map.getTo(); if (cto != null && cto != sequence) { // can't promote refs with mappings to other sequences continue; } MapList mlist = map.getMap(); if (mlist.getFromLowest() != sstart && mlist.getFromHighest() != send) { // can't promote refs with mappings from a region of this sequence // - eg CDS continue; } } // and promote - not that version must be non-null here, // as p must have passed isPrimaryCandidate() cand.setVersion(p.getVersion() + " (promoted)"); bsSelect.clear(ic); // selfs.remove(cand); // toPromote.add(cand); if (!cand.isPrimaryCandidate()) { System.out.println("Warning: Couldn't promote dbref " + cand.toString() + " for sequence " + sequence.toString()); } } } } } }