*/
package jalview.ws;
-import jalview.ext.ensembl.EnsemblCdna;
-import jalview.ext.ensembl.EnsemblCds;
-import jalview.ext.ensembl.EnsemblGenome;
-import jalview.ext.ensembl.EnsemblProtein;
+import jalview.ext.ensembl.EnsemblGene;
+import jalview.ext.ensembl.EnsemblGenomes;
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.RfamFull;
import jalview.ws.dbsources.RfamSeed;
import jalview.ws.dbsources.Uniprot;
-import jalview.ws.dbsources.UniprotName;
import jalview.ws.dbsources.das.api.jalviewSourceI;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.List;
/**
- * This is the the concrete implementation of the sequence retrieval interface
- * and abstract class in jalview.ws.seqfetcher. This implements the run-time
- * discovery of sequence database clientss.
+ * This implements the run-time discovery of sequence database clients.
*
*/
public class SequenceFetcher extends ASequenceFetcher
public SequenceFetcher(boolean addDas)
{
- addDBRefSourceImpl(EnsemblProtein.class);
- // EnsemblTranscript would just replace EnsemblProtein as the proxy for
- // { DbSource="ENSEMBL", DbName="ENSEMBL (Protein)" }
- // addDBRefSourceImpl(EnsemblTranscript.class);
- addDBRefSourceImpl(EnsemblCds.class);
- addDBRefSourceImpl(EnsemblGenome.class);
- addDBRefSourceImpl(EnsemblCdna.class);
-
+ addDBRefSourceImpl(EnsemblGene.class);
+ addDBRefSourceImpl(EnsemblGenomes.class);
addDBRefSourceImpl(EmblSource.class);
addDBRefSourceImpl(EmblCdsSource.class);
addDBRefSourceImpl(Uniprot.class);
- addDBRefSourceImpl(UniprotName.class);
addDBRefSourceImpl(Pdb.class);
addDBRefSourceImpl(PfamFull.class);
addDBRefSourceImpl(PfamSeed.class);
- // ensures Seed alignment is 'default' for PFAM
- addDBRefSourceImpl(RfamFull.class);
addDBRefSourceImpl(RfamSeed.class);
+
if (addDas)
{
registerDasSequenceSources();