From fe35e26cd1892a69fa8d10e0e825d680a6e8b811 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 22 Oct 2012 10:13:34 +0100
Subject: [PATCH] fix for updating polypeptide residues in pseudogene
---
.../artemis/components/genebuilder/GeneUtils.java | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
index 92c614335..e68e62c40 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
@@ -1509,15 +1509,14 @@ public class GeneUtils
{
String transcriptName =
chadoGene.getTranscriptFromName(GeneUtils.getUniqueName(gffFeature));
-
- List splicedFeatures =
- chadoGene.getSplicedFeaturesOfTranscript(transcriptName);
- for (int i = 0; i < splicedFeatures.size(); i++)
+ List<Feature> splicedFeatures =
+ chadoGene.getSplicedFeaturesOfTranscript(transcriptName);
+ for (Feature emblFeature: splicedFeatures)
{
- Feature emblFeature = (Feature) splicedFeatures.get(i);
if (emblFeature.getKey().getKeyString().equals(
- DatabaseDocument.EXONMODEL))
+ DatabaseDocument.EXONMODEL) ||
+ emblFeature.getKey().getKeyString().equals("pseudogenic_exon"))
{
uk.ac.sanger.artemis.Feature f =
(uk.ac.sanger.artemis.Feature) emblFeature.getUserData();
--
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