X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=7e6f6534f81b5cb91cc390dd58100167ed3baffa;hb=1903e771d3dae79e9a57fcc1147efd37e8a51421;hp=2d4d61abfa27a14aa4f5cb44946c3242b85e98dd;hpb=19fe93b91d4c50834b1a7101da2b1c240c55ae84;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index 2d4d61a..7e6f653 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -23,6 +23,8 @@ package jalview.ext.ensembl; import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsModelI; import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.GeneLociI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; @@ -98,6 +100,12 @@ 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 @@ -110,7 +118,8 @@ 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
@@ -419,22 +508,21 @@ public class EnsemblGene extends EnsemblSeqProxy
protected List