X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=0d5fc26facc10310199f1cf1a03d02443ec95cb2;hb=41bb6b94cc3cba97055e0ec02ac42c52f1483700;hp=24e3e955fe442972c96f99ae6257cfaa0fecfa14;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index 24e3e95..0d5fc26 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.SequenceFeatures; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; import jalview.schemes.FeatureColour; @@ -97,6 +98,12 @@ public class EnsemblGene extends EnsemblSeqProxy return EnsemblSeqType.GENOMIC; } + @Override + protected String getObjectType() + { + return OBJECT_TYPE_GENE; + } + /** * Returns an alignment containing the gene(s) for the given gene or * transcript identifier, or external identifier (e.g. Uniprot id). If given a @@ -109,7 +116,8 @@ public class EnsemblGene extends EnsemblSeqProxy *
+ * Transcript features are those of type "transcript", or any of its sub-types
+ * in the Sequence Ontology e.g. "mRNA", "processed_transcript". We also
+ * include "NMD_transcript_variant", because this type behaves like a
+ * transcript identifier in Ensembl, although strictly speaking it is not in
+ * the SO.
*
* @param accId
* @param geneSequence
@@ -419,23 +403,21 @@ public class EnsemblGene extends EnsemblSeqProxy
protected List