From b3ad9eb10b8d77634a5dae103fa0d0834e6ffe6a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 2 Oct 2017 15:41:02 +0100
Subject: [PATCH] JAL-2525 lookup transcript features by Ontology

---
 src/jalview/ext/ensembl/EnsemblGene.java |   21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

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.
+   * <p>
+   * 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<SequenceFeature> transcriptFeatures = new ArrayList<SequenceFeature>();
 
     String parentIdentifier = GENE_PREFIX + accId;
-    // todo optimise here by transcript type!
+
     List<SequenceFeature> sfs = geneSequence.getFeatures()
-            .getPositionalFeatures();
+            .getFeaturesByOntology(SequenceOntologyI.TRANSCRIPT);
+    sfs.addAll(geneSequence.getFeatures().getPositionalFeatures(
+            SequenceOntologyI.NMD_TRANSCRIPT_VARIANT));
 
     for (SequenceFeature sf : sfs)
     {
-      if (isTranscript(sf.getType()))
+      String parent = (String) sf.getValue(PARENT);
+      if (parentIdentifier.equals(parent))
       {
-        String parent = (String) sf.getValue(PARENT);
-        if (parentIdentifier.equals(parent))
-        {
-          transcriptFeatures.add(sf);
-        }
+        transcriptFeatures.add(sf);
       }
     }
 
-- 
1.7.10.2