X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=4d5a0250b24c403591ae80f5b6b6e6bddb1924f0;hb=c17981672620e0b780a2338bd0c74e55cf9ddec2;hp=75927485b8df6aa86d0e38aebc7e4d3834c6e6b6;hpb=b318e1301843732eabd1b34ce391828887c883df;p=jalview.git diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java index 7592748..4d5a025 100755 --- a/src/jalview/util/DBRefUtils.java +++ b/src/jalview/util/DBRefUtils.java @@ -1,394 +1,705 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * 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 + * 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. - * - * 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 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 jalview.datamodel.*; +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 { - /** - * Utilities for handling DBRef objects and their collections. + /* + * lookup from lower-case form of a name to its canonical (standardised) form */ - /** - * - * @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) + private static Map canonicalSourceNameLookup = new HashMap<>(); + + + static { - if (dbrefs == null) + // 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) { - return null; + canonicalSourceNameLookup.put(k.toLowerCase(), + canonicalSourceNameLookup.get(k)); } - if (sources == null) + + } + + /** + * 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; } - Hashtable srcs = new Hashtable(); - Vector res = new Vector(); - - for (int i = 0; i < sources.length; i++) + HashSet srcs = new HashSet<>(); + for (String src : sources) { - srcs.put(new String(sources[i]), new Integer(i)); + srcs.add(src.toUpperCase()); } - for (int i = 0, j = dbrefs.length; i < j; i++) + + List res = new ArrayList<>(); + for (DBRefEntry dbr : dbrefs) { - if (srcs.containsKey(dbrefs[i].getSource())) + String source = getCanonicalName(dbr.getSource()); + if (srcs.contains(source.toUpperCase())) { - res.addElement(dbrefs[i]); + res.add(dbr); } } 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! return null; } /** - * isDasCoordinateSystem - * - * @param string String - * @param dBRefEntry DBRefEntry - * @return boolean true if Source DBRefEntry is compatible with DAS CoordinateSystem name + * 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 Hashtable DasCoordinateSystemsLookup = null; - public static boolean isDasCoordinateSystem(String string, - DBRefEntry dBRefEntry) + public static String getCanonicalName(String source) { - if (DasCoordinateSystemsLookup == 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) + if (source == null) { - return coordsys.equals(dBRefEntry.getSource()); + return null; } - return false; + String canonical = canonicalSourceNameLookup.get(source.toLowerCase()); + return canonical == null ? source : canonical; } - 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 no canonical form. - * @param source - * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) or original source + * 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 String getCanonicalName(String source) + public static List searchRefs(DBRefEntry[] ref, + DBRefEntry entry) { - 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) - { - return source; - } - return canonical; + return searchRefs(ref, entry, + matchDbAndIdAndEitherMapOrEquivalentMapList); } + /** - * find RefEntry corresponding to a particular pattern - * the equals method of each entry is used, from String attributes right down to Mapping attributes. - * @param ref Set of references to search - * @param entry pattern to collect - null any entry for wildcard match + * 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 DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry) + public static List searchRefs(DBRefEntry[] refs, String accId) { - return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList); + return searchRefs(refs, new DBRefEntry("", "", accId), matchId); } - public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry, DbRefComp comparator) + + /** + * 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) { - if (ref==null || entry==null) - return null; - Vector rfs = new Vector(); - for (int i=0; i rfs = new ArrayList<>(); + if (refs == null || entry == null) { - if (comparator.matches(entry, ref[i])) - { - rfs.addElement(ref[i]); - } + return rfs; } - // TODO Auto-generated method stub - if (rfs.size()>0) + for (int i = 0; i < refs.length; i++) { - DBRefEntry[] rf = new DBRefEntry[rfs.size()]; - rfs.copyInto(rf); - return rf; + if (comparator.matches(entry, refs[i])) + { + rfs.add(refs[i]); + } } - return null; + return rfs; } - public interface DbRefComp { + + 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) { - 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.getSource()==null || refb.getSource().equals(refa.getSource())) + if (refa.getMap() == null || (refb.getMap() != null + && refb.getMap().equals(refa.getMap()))) { - 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 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() + } + } + 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) { - 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()))) { - 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; + return true; } - }; - /** - * 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() + } + } + 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) { - 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 (refa.getSource()!=null && refb.getSource()!=null - && refb.getSource().equals(refa.getSource())) + 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()))) { - // 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; + return true; + } } - }; - /** - * 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() + } + } + 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) { - 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) { - 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; + 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; } - }; - /** - * 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() + } + } + 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) { - 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) { - 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; + return true; } - }; - /** - * 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() + 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) { - 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) { - 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; + chaincode = " "; + } + // String mapstart = r.stringMatched(3); + // String mapend = r.stringMatched(4); + if (chaincode.equals(" ")) + { + chaincode = "_"; } - }; - /** - * 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 - * @return parsed version of entry that was added to seq (if any) - */ - public static DBRefEntry parseToDbRef(SequenceI seq, String dbname, String version, - String acn) + // 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.trim()); + } + } + 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 ref = null; - if (dbname!=null) + DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(), + sequence.getDBRefs()); + if (selfArray == null || selfArray.length == 0) { - String locsrc = jalview.util.DBRefUtils - .getCanonicalName(dbname); - if (locsrc.equals(jalview.datamodel.DBRefSource.PDB)) + // 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())) { - // 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]+)"); - if (r.search(acn.trim())) + 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()) { - String pdbid = r.stringMatched(1); - String chaincode = r.stringMatched(2); - String mapstart = r.stringMatched(3); - String mapend = r.stringMatched(4); - if (chaincode.equals(" ")) + 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()) { - chaincode = "_"; + // can't promote refs with mappings from a region of this sequence + // - eg CDS + continue; } - // construct pdb ref. - ref = new DBRefEntry(locsrc, version, pdbid+chaincode); - PDBEntry pdbr = new PDBEntry(); - pdbr.setId(pdbid); - seq.addPDBId(pdbr); } - } else { - // default: - ref = new DBRefEntry(locsrc, version, acn); + // 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()); + } } } - if (ref!=null) - { - seq.addDBRef(ref); - } - return ref; } - - + } + }