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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblSeqProxy.java
diff --git
a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index
56eda5e
..
7f2fa59
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/
src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@
-735,7
+735,7
@@
public abstract class EnsemblSeqProxy extends EnsemblRestClient
* for sequence_variant on reverse strand, have to convert the allele
* values to their complements
*/
* for sequence_variant on reverse strand, have to convert the allele
* values to their complements
*/
- if (!forwardStrand && SequenceOntologyFactory.getInstance()
+ if (!forwardStrand && SequenceOntologyFactory.getSequenceOntology()
.isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
{
reverseComplementAlleles(copy);
.isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
{
reverseComplementAlleles(copy);
@@
-969,7
+969,7
@@
public abstract class EnsemblSeqProxy extends EnsemblRestClient
public static boolean isTranscript(String featureType)
{
return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
public static boolean isTranscript(String featureType)
{
return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
- || SequenceOntologyFactory.getInstance().isA(featureType,
+ || SequenceOntologyFactory.getSequenceOntology().isA(featureType,
SequenceOntologyI.TRANSCRIPT);
}
}
SequenceOntologyI.TRANSCRIPT);
}
}