X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGenome.java;h=4f59bc59c0aa042d8ecf99e924c98923d24651b7;hb=fdde9a078d7bdb46ed9fb7fe115ea83c84a19c81;hp=bde3c0f8ad23dc2aa02b25c55554ed4bb292b7eb;hpb=321caefc5a40cd735c93e0bfa450e0e04abc485d;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGenome.java b/src/jalview/ext/ensembl/EnsemblGenome.java index bde3c0f..4f59bc5 100644 --- a/src/jalview/ext/ensembl/EnsemblGenome.java +++ b/src/jalview/ext/ensembl/EnsemblGenome.java @@ -21,6 +21,11 @@ package jalview.ext.ensembl; import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.io.gff.SequenceOntologyI; + +import java.util.ArrayList; +import java.util.List; /** * A client to fetch genomic sequence from Ensembl @@ -94,22 +99,31 @@ public class EnsemblGenome extends EnsemblSeqProxy } /** - * Answers true if the sequence feature type is 'transcript' (or a subtype of - * transcript in the Sequence Ontology), and the ID of the feature is the - * transcript we are retrieving + * Answers a list of sequence features (if any) whose type is 'transcript' (or + * a subtype of transcript in the Sequence Ontology), and whose ID is the + * accession we are retrieving. + *
+ * Note we also include features of type "NMD_transcript_variant", although
+ * not strictly 'transcript' in the SO, as they used in Ensembl as if they
+ * were.
*/
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List