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JAL-1705 further unit tests
[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
8c1e972
..
b2804f2
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/
src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@
-46,12
+46,6
@@
public abstract class EnsemblSeqProxy extends EnsemblRestClient
protected static final String ID = "ID";
protected static final String ID = "ID";
- /*
- * this needs special handling, as it isA sequence_variant in the
- * Sequence Ontology, but behaves in Ensembl as if it isA transcript
- */
- protected static final String NMD_VARIANT = "NMD_transcript_variant";
-
protected static final String NAME = "Name";
public enum EnsemblSeqType
protected static final String NAME = "Name";
public enum EnsemblSeqType
@@
-1105,7
+1099,7
@@
public abstract class EnsemblSeqProxy extends EnsemblRestClient
*/
public static boolean isTranscript(String featureType)
{
*/
public static boolean isTranscript(String featureType)
{
- return NMD_VARIANT.equals(featureType)
+ return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
|| SequenceOntologyFactory.getInstance().isA(featureType,
SequenceOntologyI.TRANSCRIPT);
}
|| SequenceOntologyFactory.getInstance().isA(featureType,
SequenceOntologyI.TRANSCRIPT);
}