X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=424d40bd45f4f83b975e0d0e2eead6682ee19109;hb=a4ace9297e743fb504dffd43ebb11074db263e10;hp=b8f1dd566d9f0f68df83bc0fc501490b06a8d971;hpb=9623cea766a766683243235557ad48e6f7659e6a;p=jalview.git diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java index b8f1dd5..424d40b 100755 --- a/src/jalview/util/DBRefUtils.java +++ b/src/jalview/util/DBRefUtils.java @@ -24,18 +24,24 @@ import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; -import jalview.ws.seqfetcher.DbSourceProxy; 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 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(); @@ -46,7 +52,13 @@ 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); dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB); dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT); @@ -55,39 +67,33 @@ public class DBRefUtils } /** - * Utilities for handling DBRef objects and their collections. - */ - /** * * @param dbrefs - * Vector of DBRef objects to search + * array of DBRef objects to search * @param sources * String[] array of source DBRef IDs to retrieve - * @return Vector + * @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); } } @@ -96,8 +102,6 @@ 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; } @@ -165,6 +169,25 @@ public class DBRefUtils } /** + * Returns an array 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 ref + * Set of references to search + * @param entry + * pattern to match + * @return + */ + public static DBRefEntry[] searchRefs(DBRefEntry[] ref, String accId) + { + return searchRefs(ref, new DBRefEntry("", "", accId), matchId); + } + + /** * Returns an array of those references that match the given entry, according * to the given comparator. Returns null if no matches. * @@ -201,8 +224,10 @@ 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 @@ -231,27 +256,18 @@ 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; } @@ -261,18 +277,18 @@ 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) @@ -292,17 +308,16 @@ 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())) { @@ -329,8 +344,10 @@ 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 @@ -369,17 +386,13 @@ public class DBRefUtils */ 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())) { @@ -403,6 +416,23 @@ 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. *

@@ -474,35 +504,19 @@ public class DBRefUtils } /** - * Extract valid accession strings from a query string. Used by the - * SequenceFetcher and DBRefFetcher to create valid accession strings from an - * ID string for database sources with a Regex validation field. + * Returns true if either object is null, or they are equal * - * @param proxy - * @param q - * @return q if proxy.getAccessionValidator()==null, otherwise the matched - * region or the first subgroup match from the matched region + * @param o1 + * @param o2 + * @return */ - public static String processQueryToAccessionFor(DbSourceProxy proxy, - String q) + public static boolean nullOrEqual(Object o1, Object o2) { - if (proxy.getAccessionValidator() != null) - { - Regex vgr = proxy.getAccessionValidator(); - vgr.search(q); - if (vgr.numSubs() > 0) - { - return (vgr.stringMatched(1)); - } - else - { - return (vgr.stringMatched()); - } - } - else + if (o1 == null || o2 == null) { - return (q); + return true; } + return (o1 == null ? o2.equals(o1) : o1.equals(o2)); } }