*/
package jalview.ws;
-import jalview.bin.Instance;
-import jalview.datamodel.DBRefSource;
import jalview.ext.ensembl.EnsemblGene;
+import jalview.ws.dbsources.EmblCdsSource;
+import jalview.ws.dbsources.EmblSource;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.dbsources.PfamFull;
+import jalview.ws.dbsources.PfamSeed;
+import jalview.ws.dbsources.RfamSeed;
import jalview.ws.dbsources.Uniprot;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.List;
/**
- * Thread safe construction of database proxies. This implements the run-time
- * discovery of sequence database clients.
+ * This implements the run-time discovery of sequence database clients.
*
- * TODO: extend to a configurable database plugin mechanism where classes are
- * instantiated by reflection and queried for their DbRefSource and version
- * association.
*/
public class SequenceFetcher extends ASequenceFetcher
{
-
- /**
- * Returns a new SequenceFetcher singleton, or a mock object if one has been
- * set.
- *
- * @return
- */
- public static SequenceFetcher getInstance()
- {
- Instance j = Instance.getInstance();
- return (j.sequenceFetcher == null
- ? j.sequenceFetcher = new SequenceFetcher()
- : j.sequenceFetcher);
- }
-
- /**
- * Set the instance object to use (intended for unit testing with mock
- * objects).
- *
- * Be sure to reset to null in the tearDown method of any tests!
- *
- * @param sf
- */
- public static void setSequenceFetcher(SequenceFetcher sf)
- {
- Instance.getInstance().sequenceFetcher = sf;
- }
-
/**
- *
- * This public constructor is only is for use by testng to anonymously
- * subclass SequenceFetcher.
- *
+ * Thread safe construction of database proxies TODO: extend to a configurable
+ * database plugin mechanism where classes are instantiated by reflection and
+ * queried for their DbRefSource and version association.
*
*/
public SequenceFetcher()
{
- addAllDatabases();
- }
-
- public void addAllDatabases()
- {
- addDBRefSourceImpl(EnsemblGene.class); // includes EnsemblGenomes.class
- addDBRefSourceImpl(Uniprot.class); // includes UniprotName.class
- // addDBRefSourceImpl(EmblSource.class);
- // addDBRefSourceImpl(EmblCdsSource.class);
- // addDBRefSourceImpl(Pdb.class);
- // addDBRefSourceImpl(PfamFull.class);
- // addDBRefSourceImpl(PfamSeed.class);
- // addDBRefSourceImpl(RfamSeed.class);
- addDBRefSourceImpl(DBRefSource.EMBL,
- "jalview.ws.dbsources.EmblSource");
- addDBRefSourceImpl(DBRefSource.EMBLCDS,
- "jalview.ws.dbsources.EmblCdsSource");
- addDBRefSourceImpl(DBRefSource.PDB, "jalview.ws.dbsources.Pdb");
- addDBRefSourceImpl(DBRefSource.PFAM_FULL,
- "jalview.ws.dbsources.PfamFull");
- addDBRefSourceImpl(DBRefSource.PFAM_SEED,
- "jalview.ws.dbsources.PfamSeed");
- addDBRefSourceImpl(DBRefSource.RFAM_SEED,
- "jalview.ws.dbsources.RfamSeed");
+ addDBRefSourceImpl(EnsemblGene.class);
+ // addDBRefSourceImpl(EnsemblGenomes.class);
+ addDBRefSourceImpl(EmblSource.class);
+ addDBRefSourceImpl(EmblCdsSource.class);
+ addDBRefSourceImpl(Uniprot.class);
+ addDBRefSourceImpl(Pdb.class);
+ addDBRefSourceImpl(PfamFull.class);
+ addDBRefSourceImpl(PfamSeed.class);
+ addDBRefSourceImpl(RfamSeed.class);
}
/**
- * return an ordered list of database sources excluding alignment only
- * databases
+ * return an ordered list of database sources excluding alignment only databases
*/
public String[] getNonAlignmentSources()
{
String[] srcs = this.getSupportedDb();
List<String> src = new ArrayList<>();
- outer: for (int i = 0; i < srcs.length; i++)
+
+ for (int i = 0; i < srcs.length; i++)
{
+ boolean accept = true;
for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
{
// Skip the alignment databases for the moment - they're not useful for
// verifying a single sequence against its reference source
if (dbs.isAlignmentSource())
{
- continue outer;
+ accept = false;
+ break;
}
}
- src.add(srcs[i]);
+ if (accept)
+ {
+ src.add(srcs[i]);
+ }
}
Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
return src.toArray(new String[src.size()]);