X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=c8b59dab07d84dc40da950420c496f4d914ca94e;hb=2779b461347e684414f9e98e607e138b1e43db84;hp=915fa0aa04e5067731f1ebd8dceae9dc7a79f9d0;hpb=f41d78dbf890fbb7597f75019d05841312fa4f52;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index 915fa0a..c8b59da 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -98,6 +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 @@ -110,7 +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
@@ -434,22 +401,21 @@ public class EnsemblGene extends EnsemblSeqProxy
protected List