*/
package jalview.ws;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+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;
/**
- * This implements the run-time discovery of sequence database clients.
+ * Thread safe construction of database proxies. 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
+public class SequenceFetcher extends ASequenceFetcher implements ApplicationSingletonI
{
+ /*
+ * set a mock fetcher here for testing only - reset to null afterwards
+ */
+ private static SequenceFetcher mockFetcher;
+
+ /**
+ * Returns a new SequenceFetcher singleton, or a mock object if one has been
+ * set.
+ *
+ * @return
+ */
+ public static SequenceFetcher getInstance()
+ {
+ return mockFetcher != null ? mockFetcher
+ : (SequenceFetcher) ApplicationSingletonProvider
+ .getInstance(SequenceFetcher.class);
+ }
+
/**
- * 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.
+ * 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)
+ {
+ mockFetcher = sf;
+ }
+
+ /**
+ *
+ * This public constructor is only is for use by testng to anonymously
+ * subclass SequenceFetcher.
+ *
*
*/
public SequenceFetcher()
{
- 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);
+ 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");
}
/**
- * 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<>();
-
- for (int i = 0; i < srcs.length; i++)
+ outer: 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())
{
- accept = false;
- break;
+ continue outer;
}
}
- if (accept)
- {
- src.add(srcs[i]);
- }
+ src.add(srcs[i]);
}
Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
return src.toArray(new String[src.size()]);