X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=a1f06e5faf993764db1ae985606cfecf99cb1f8e;hb=3ed5c0f91614bb7a3620ec3a968a54bafdbd74ad;hp=518c31049cfe457d02c674d587eb275d2bfa8b59;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java index 518c310..a1f06e5 100755 --- a/src/jalview/util/DBRefUtils.java +++ b/src/jalview/util/DBRefUtils.java @@ -27,14 +27,22 @@ import jalview.datamodel.SequenceI; import java.util.ArrayList; import java.util.HashMap; +import java.util.HashSet; import java.util.Hashtable; 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(); @@ -45,7 +53,25 @@ public class DBRefUtils 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); @@ -54,39 +80,36 @@ public class DBRefUtils } /** - * Utilities for handling DBRef objects and their collections. - */ - /** + * 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 - * Vector of DBRef objects to search + * DBRefEntry objects to search * @param sources - * String[] array of source DBRef IDs to retrieve - * @return Vector + * array of sources to select + * @return */ public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs, String[] sources) { - if (dbrefs == null) - { - return null; - } - if (sources == null) + if (dbrefs == null || sources == null) { return dbrefs; } - Map srcs = new HashMap(); - ArrayList res = new ArrayList(); - - 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); } - 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)) { - res.add(dbrefs[i]); + res.add(dbr); } } @@ -95,8 +118,6 @@ public class DBRefUtils DBRefEntry[] reply = new DBRefEntry[res.size()]; return res.toArray(reply); } - res = null; - // there are probable memory leaks in the hashtable! return null; } @@ -143,8 +164,8 @@ public class DBRefUtils } /** - * Returns an array of those references that match the given entry, or null if - * no matches. Currently uses a comparator which matches if + * 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
    • @@ -157,15 +178,35 @@ public class DBRefUtils * pattern to match * @return */ - public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry) + public static List 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. + * 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 @@ -174,14 +215,14 @@ public class DBRefUtils * @param comparator * @return */ - static DBRefEntry[] searchRefs(DBRefEntry[] refs, DBRefEntry entry, + static List searchRefs(DBRefEntry[] refs, DBRefEntry entry, DbRefComp comparator) { + List rfs = new ArrayList(); if (refs == null || entry == null) { - return null; + return rfs; } - List rfs = new ArrayList(); for (int i = 0; i < refs.length; i++) { if (comparator.matches(entry, refs[i])) @@ -189,7 +230,7 @@ public class DBRefUtils rfs.add(refs[i]); } } - return rfs.size() == 0 ? null : rfs.toArray(new DBRefEntry[rfs.size()]); + return rfs; } interface DbRefComp @@ -200,8 +241,10 @@ public class DBRefUtils /** * 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 @@ -230,27 +273,18 @@ public class DBRefUtils * 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 ((refa.getSource() == null || refb.getSource() == null) - || refb.getSource().equals(refa.getSource())) + if (nullOrEqual(refa.getSource(), refb.getSource()) + && nullOrEqual(refa.getVersion(), refb.getVersion()) + && nullOrEqual(refa.getAccessionId(), refb.getAccessionId()) + && nullOrEqual(refa.getMap(), refb.getMap())) { - 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 true; } return false; } @@ -260,18 +294,18 @@ public class DBRefUtils * 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 && 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 + // FIXME should be && not || here? || refb.getAccessionId().equals(refa.getAccessionId())) { if ((refa.getMap() == null || refb.getMap() == null) @@ -291,17 +325,16 @@ public class DBRefUtils * 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 && 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())) { @@ -328,8 +361,10 @@ public class DBRefUtils * 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 @@ -362,25 +397,22 @@ public class DBRefUtils }; /** - * 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. + * 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) { - // 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.getAccessionId() == null + || refa.getAccessionId().equals(refb.getAccessionId())) { if (refa.getMap() == null || refb.getMap() == null) { @@ -392,7 +424,7 @@ public class DBRefUtils || (refb.getMap().getMap() != null && refa.getMap().getMap() != null && (refb .getMap().getMap().equals(refa.getMap().getMap())))) - { // getMap().getMap().containsEither(false,refa.getMap().getMap()) + { return true; } } @@ -402,6 +434,23 @@ public class DBRefUtils }; /** + * 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. *

    @@ -472,4 +521,65 @@ public class DBRefUtils 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); + } + + /** + * 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; + } + }