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JAL-1705 more lenient test for 'sequence retrieved'
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblCds.java
diff --git
a/src/jalview/ext/ensembl/EnsemblCds.java
b/src/jalview/ext/ensembl/EnsemblCds.java
index
22c0a06
..
ec5780f
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblCds.java
+++ b/
src/jalview/ext/ensembl/EnsemblCds.java
@@
-2,7
+2,8
@@
package jalview.ext.ensembl;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.io.gff.SequenceOntology;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
import java.util.List;
import java.util.List;
@@
-51,8
+52,8
@@
public class EnsemblCds extends EnsemblSeqProxy
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
- if (SequenceOntology.getInstance().isA(sf.getType(),
- SequenceOntology.CDS))
+ if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+ SequenceOntologyI.CDS))
{
return false;
}
{
return false;
}
@@
-67,8
+68,8
@@
public class EnsemblCds extends EnsemblSeqProxy
@Override
protected boolean identifiesSequence(SequenceFeature sf, String accId)
{
@Override
protected boolean identifiesSequence(SequenceFeature sf, String accId)
{
- if (SequenceOntology.getInstance().isA(sf.getType(),
- SequenceOntology.CDS))
+ if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+ SequenceOntologyI.CDS))
{
String parentFeature = (String) sf.getValue(PARENT);
if (("transcript:" + accId).equals(parentFeature))
{
String parentFeature = (String) sf.getValue(PARENT);
if (("transcript:" + accId).equals(parentFeature))