From bc41b3895595da221a0b6b82292558f05e1686c9 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 15 Aug 2013 15:27:08 +0100
Subject: [PATCH] fix isExonOfNonCodingTranscript() searching for non-coding
GFF3 features
---
uk/ac/sanger/artemis/components/FeatureDisplay.java | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/FeatureDisplay.java b/uk/ac/sanger/artemis/components/FeatureDisplay.java
index 660625cac..611734d25 100644
--- a/uk/ac/sanger/artemis/components/FeatureDisplay.java
+++ b/uk/ac/sanger/artemis/components/FeatureDisplay.java
@@ -2645,7 +2645,7 @@ public class FeatureDisplay extends EntryGroupPanel
/**
* Check if this feature is an exon and is a child of a non-coding transcript
- * and is part of a GFF or database entry.
+ * and is a GFF3 feature.
* @param feature
* @param key
* @return
@@ -2653,7 +2653,7 @@ public class FeatureDisplay extends EntryGroupPanel
private boolean isExonOfNonCodingTranscript(final Feature feature, final String key)
{
if(key.equals(DatabaseDocument.EXONMODEL) &&
- GeneUtils.isGFFEntry(getEntryGroup()))
+ feature.getEmblFeature() instanceof GFFStreamFeature)
{
final String nonCodingTranscripts[] = GeneUtils.getNonCodingTranscripts();
try
@@ -2663,7 +2663,7 @@ public class FeatureDisplay extends EntryGroupPanel
{
final ChadoCanonicalGene chadoGene =
((GFFStreamFeature)feature.getEmblFeature()).getChadoGene();
- final String transcriptName = (String)qualifier.getValues().get(0);
+ final String transcriptName = qualifier.getValues().get(0);
final GFFStreamFeature transcript =
(GFFStreamFeature)chadoGene.getFeatureFromId(transcriptName);
final String transcriptKey = transcript.getKey().getKeyString();
--
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