package jalview.ws;
import jalview.ext.ensembl.EnsemblGene;
-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.ArrayList;
-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()
{
- this(true);
- }
-
- 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();
- }
}
/**
- * return an ordered list of database sources where non-das database classes
- * appear before das database classes
+ * return an ordered list of database sources excluding alignment only databases
*/
public String[] getOrderedSupportedSources()
{
String[] srcs = this.getSupportedDb();
- ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
+ ArrayList<String> src = new ArrayList<>();
+
for (int i = 0; i < srcs.length; i++)
{
- boolean das = false, skip = false;
- String nm;
+ boolean skip = false;
for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
{
// Skip the alignment databases for the moment - they're not useful for
{
skip = true;
}
- else
- {
- nm = dbs.getDbName();
- if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
- {
- if (nm.startsWith("das:"))
- {
- nm = nm.substring(4);
- das = true;
- }
- break;
- }
- }
}
if (skip)
{
continue;
}
- if (das)
{
- dassrc.add(srcs[i]);
- }
- else
- {
- nondas.add(srcs[i]);
+ src.add(srcs[i]);
}
}
- String[] tosort = nondas.toArray(new String[0]), sorted = nondas
- .toArray(new String[0]);
+ String[] tosort = src.toArray(new String[0]),
+ sorted = src.toArray(new String[0]);
for (int j = 0, jSize = sorted.length; j < jSize; j++)
{
tosort[j] = tosort[j].toLowerCase();
}
jalview.util.QuickSort.sort(tosort, sorted);
// construct array with all sources listed
-
- srcs = new String[sorted.length + dassrc.size()];
int i = 0;
for (int j = sorted.length - 1; j >= 0; j--, i++)
{
srcs[i] = sorted[j];
- sorted[j] = null;
- }
-
- sorted = dassrc.toArray(new String[0]);
- tosort = dassrc.toArray(new String[0]);
- for (int j = 0, jSize = sorted.length; j < jSize; j++)
- {
- tosort[j] = tosort[j].toLowerCase();
- }
- jalview.util.QuickSort.sort(tosort, sorted);
- for (int j = sorted.length - 1; j >= 0; j--, i++)
- {
- srcs[i] = sorted[j];
}
return srcs;
}
-
- /**
- * query the currently defined DAS source registry for sequence sources and
- * add a DasSequenceSource instance for each source to the SequenceFetcher
- * source list.
- */
- public void registerDasSequenceSources()
- {
- // TODO: define a context as a registry provider (either desktop,
- // jalview.bin.cache, or something else).
- for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry()
- .getSources())
- {
- if (source.isSequenceSource())
- {
- List<DbSourceProxy> dassources = source.getSequenceSourceProxies();
- for (DbSourceProxy seqsrc : dassources)
- {
- addDbRefSourceImpl(seqsrc);
- }
- }
- }
- }
-
}