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JAL-1926 JAL-2106 fix name for flag controlling addition of secondary structure annot...
[jalview.git]
/
src
/
jalview
/
ws
/
SequenceFetcher.java
diff --git
a/src/jalview/ws/SequenceFetcher.java
b/src/jalview/ws/SequenceFetcher.java
index
16bbfe6
..
65179a2
100644
(file)
--- a/
src/jalview/ws/SequenceFetcher.java
+++ b/
src/jalview/ws/SequenceFetcher.java
@@
-21,7
+21,7
@@
package jalview.ws;
import jalview.ext.ensembl.EnsemblGene;
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.EmblCdsSource;
import jalview.ws.dbsources.EmblSource;
import jalview.ws.dbsources.Pdb;
@@
-39,9
+39,7
@@
import java.util.ArrayList;
import java.util.List;
/**
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 class SequenceFetcher extends ASequenceFetcher
@@
-59,11
+57,8
@@
public class SequenceFetcher extends ASequenceFetcher
public SequenceFetcher(boolean addDas)
{
public SequenceFetcher(boolean addDas)
{
- addDBRefSourceImpl(EnsemblProtein.class);
- // addDBRefSourceImpl(EnsemblCds.class);
- // addDBRefSourceImpl(EnsemblGenome.class);
addDBRefSourceImpl(EnsemblGene.class);
addDBRefSourceImpl(EnsemblGene.class);
- // addDBRefSourceImpl(EnsemblCdna.class);
+ addDBRefSourceImpl(EnsemblGenomes.class);
addDBRefSourceImpl(EmblSource.class);
addDBRefSourceImpl(EmblCdsSource.class);
addDBRefSourceImpl(Uniprot.class);
addDBRefSourceImpl(EmblSource.class);
addDBRefSourceImpl(EmblCdsSource.class);
addDBRefSourceImpl(Uniprot.class);
@@
-71,8
+66,6
@@
public class SequenceFetcher extends ASequenceFetcher
addDBRefSourceImpl(Pdb.class);
addDBRefSourceImpl(PfamFull.class);
addDBRefSourceImpl(PfamSeed.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)
{
addDBRefSourceImpl(RfamSeed.class);
if (addDas)
{