X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=50dfa908778093da87dbca01b020cbd3b9a67d43;hb=f3d0dc3395aff566e8005e6a6a9a13bf795c14a4;hp=f46cb1be90e234133ffe68bc3d76aaec3b758fd3;hpb=f23f5cefe9c66bfa8b877c707d25862cabba3ddf;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index f46cb1b..50dfa90 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -381,6 +381,12 @@ 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
@@ -392,19 +398,18 @@ public class EnsemblGene extends EnsemblSeqProxy
List