X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;fp=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=ad013241c136a5478645c24b94fb18073b2aecd4;hb=b3ad9eb10b8d77634a5dae103fa0d0834e6ffe6a;hp=365c1c24fbc91e429fb08313a8e8487573de541c;hpb=0277877a451258202cfe36f00419a4364af15a8a;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index 365c1c2..ad01324 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -428,6 +428,12 @@ public class EnsemblGene extends EnsemblSeqProxy /** * Returns a list of the transcript features on the sequence whose Parent is * the gene for the accession id. + *
+ * 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
@@ -439,19 +445,18 @@ public class EnsemblGene extends EnsemblSeqProxy
List