X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=9765a1a56b0c9fa43a6583310a079fae3f0882f9;hb=3ef44bef1f825d26977dedd1608469712a87fe15;hp=8163f05ff2b7d98f89b2cc5252ffd6b9cd289222;hpb=b6acaa87c22c1d31deb3f9b87a143def43ae34b7;p=jalview.git diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java index 8163f05..9765a1a 100755 --- a/src/jalview/util/DBRefUtils.java +++ b/src/jalview/util/DBRefUtils.java @@ -20,18 +20,39 @@ */ package jalview.util; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; - import java.util.ArrayList; import java.util.HashMap; import java.util.Hashtable; +import java.util.List; import java.util.Map; -import java.util.Vector; + +import com.stevesoft.pat.Regex; + +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; public class DBRefUtils { + 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); + canonicalSourceNameLookup.put("pdb", DBRefSource.PDB); + + dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB); + dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT); + dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBL); + // dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBLCDS); + } + /** * Utilities for handling DBRef objects and their collections. */ @@ -89,37 +110,20 @@ public class DBRefUtils * @return boolean true if Source DBRefEntry is compatible with DAS * CoordinateSystem name */ - public static Hashtable DasCoordinateSystemsLookup = null; public static boolean isDasCoordinateSystem(String string, DBRefEntry dBRefEntry) { - if (DasCoordinateSystemsLookup == null) + if (string == null || dBRefEntry == 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); + return false; } - - String coordsys = (String) DasCoordinateSystemsLookup.get(string + String coordsys = dasCoordinateSystemsLookup.get(string .toLowerCase()); - if (coordsys != null) - { - return coordsys.equals(dBRefEntry.getSource()); - } - return false; + return coordsys == null ? false : coordsys.equals(dBRefEntry + .getSource()); } - 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 @@ -131,34 +135,28 @@ public class DBRefUtils */ public static String getCanonicalName(String source) { - if (CanonicalSourceNameLookup == null) + if (source == 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); + return null; } - String canonical = (String) CanonicalSourceNameLookup.get(source + String canonical = canonicalSourceNameLookup.get(source .toLowerCase()); - if (canonical == null) - { - return source; - } - return canonical; + return canonical == null ? source : canonical; } /** - * find RefEntry corresponding to a particular pattern the equals method of - * each entry is used, from String attributes right down to Mapping - * attributes. + * Returns an array of those references that match the given entry, or null if + * no matches. 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 collect - null any entry for wildcard match + * pattern to match * @return */ public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry) @@ -167,32 +165,36 @@ public class DBRefUtils matchDbAndIdAndEitherMapOrEquivalentMapList); } - public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry, + /** + * Returns an array of those references that match the given entry, according + * to the given comparator. Returns null if no matches. + * + * @param refs + * an array of database references to search + * @param entry + * an entry to compare against + * @param comparator + * @return + */ + static DBRefEntry[] searchRefs(DBRefEntry[] refs, DBRefEntry entry, DbRefComp comparator) { - if (ref == null || entry == null) + if (refs == null || entry == null) { return null; } - Vector rfs = new Vector(); - for (int i = 0; i < ref.length; i++) + List rfs = new ArrayList(); + for (int i = 0; i < refs.length; i++) { - if (comparator.matches(entry, ref[i])) + if (comparator.matches(entry, refs[i])) { - rfs.addElement(ref[i]); + rfs.add(refs[i]); } } - // TODO Auto-generated method stub - if (rfs.size() > 0) - { - DBRefEntry[] rf = new DBRefEntry[rfs.size()]; - rfs.copyInto(rf); - return rf; - } - return null; + return rfs.size() == 0 ? null : rfs.toArray(new DBRefEntry[rfs.size()]); } - public interface DbRefComp + interface DbRefComp { public boolean matches(DBRefEntry refa, DBRefEntry refb); } @@ -402,14 +404,17 @@ public class DBRefUtils }; /** - * used by file parsers to generate DBRefs from annotation within file (eg - * stockholm) + * 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 anotate with reference + * 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, @@ -418,12 +423,14 @@ public class DBRefUtils DBRefEntry ref = null; if (dbname != null) { - String locsrc = jalview.util.DBRefUtils.getCanonicalName(dbname); - if (locsrc.equals(jalview.datamodel.DBRefSource.PDB)) + String locsrc = DBRefUtils.getCanonicalName(dbname); + if (locsrc.equals(DBRefSource.PDB)) { - // check for chaincode and mapping - // PFAM style stockhom PDB citation - com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex( + /* + * 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())) { @@ -433,8 +440,8 @@ public class DBRefUtils { chaincode = " "; } - String mapstart = r.stringMatched(3); - String mapend = r.stringMatched(4); + // String mapstart = r.stringMatched(3); + // String mapend = r.stringMatched(4); if (chaincode.equals(" ")) { chaincode = "_";