*/
package jalview.ws;
-import jalview.ext.ensembl.EnsemblCdna;
-import jalview.ext.ensembl.EnsemblCds;
import jalview.ext.ensembl.EnsemblGene;
-import jalview.ext.ensembl.EnsemblGenome;
-import jalview.ext.ensembl.EnsemblProtein;
+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);
- addDBRefSourceImpl(EnsemblCds.class);
- addDBRefSourceImpl(EnsemblGenome.class);
addDBRefSourceImpl(EnsemblGene.class);
- addDBRefSourceImpl(EnsemblCdna.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();
public String[] getOrderedSupportedSources()
{
String[] srcs = this.getSupportedDb();
- ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
+ ArrayList<String> dassrc = new ArrayList<String>(),
+ nondas = new ArrayList<String>();
for (int i = 0; i < srcs.length; i++)
{
boolean das = false, skip = false;
else
{
nm = dbs.getDbName();
- if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+ if (getSourceProxy(
+ srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
{
if (nm.startsWith("das:"))
{
nondas.add(srcs[i]);
}
}
- String[] tosort = nondas.toArray(new String[0]), sorted = nondas
- .toArray(new String[0]);
+ String[] tosort = nondas.toArray(new String[0]),
+ sorted = nondas.toArray(new String[0]);
for (int j = 0, jSize = sorted.length; j < jSize; j++)
{
tosort[j] = tosort[j].toLowerCase();