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<String, String> canonicalSourceNameLookup = new HashMap<String, String>();
private static Map<String, String> dasCoordinateSystemsLookup = new HashMap<String, String>();
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);
}
/**
- * 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<String, Integer> srcs = new HashMap<String, Integer>();
- ArrayList<DBRefEntry> res = new ArrayList<DBRefEntry>();
-
- for (int i = 0; i < sources.length; i++)
+ HashSet<String> srcs = new HashSet<String>();
+ 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<DBRefEntry> res = new ArrayList<DBRefEntry>();
+ 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);
}
}
DBRefEntry[] reply = new DBRefEntry[res.size()];
return res.toArray(reply);
}
- res = null;
- // there are probable memory leaks in the hashtable!
return null;
}
}
/**
+ * Returns an array of those references that match the given accession id
+ * <ul>
+ * <li>database sources are the same</li>
+ * <li>accession ids are the same</li>
+ * <li>both have no mapping, or the mappings are the same</li>
+ * </ul>
+ *
+ * @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.
*
/**
* 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
* 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;
}
* 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)
* 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()))
{
* 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
*/
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()))
{
};
/**
+ * 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.
* <p>
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 == null ? o2.equals(o1) : o1.equals(o2));
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff