From 5af0581e8da43356c6b7991168be9c777e602411 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 18 Jan 2008 14:28:18 +0000
Subject: [PATCH] fix for duplicateGeneModel
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6955 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../components/genebuilder/GeneUtils.java | 18 +++++++++++++++---
1 file changed, 15 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
index b9377ea46..4fbff3e5f 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
@@ -366,15 +366,27 @@ public class GeneUtils
newFeatures= duplicateFeatures(chadoGene.get3UtrOfTranscript(transcriptName), newchadoGene);
for(int k=0; k<newFeatures.size(); k++)
- newchadoGene.add3PrimeUtr(newTranscriptName, (Feature)newFeatures.get(k));
+ {
+ uk.ac.sanger.artemis.Feature utrFeature =
+ (uk.ac.sanger.artemis.Feature)newFeatures.get(k);
+ newchadoGene.add3PrimeUtr(newTranscriptName, utrFeature.getEmblFeature());
+ }
newFeatures = duplicateFeatures(chadoGene.get5UtrOfTranscript(transcriptName), newchadoGene);
for(int k=0; k<newFeatures.size(); k++)
- newchadoGene.add5PrimeUtr(newTranscriptName, (Feature)newFeatures.get(k));
+ {
+ uk.ac.sanger.artemis.Feature utrFeature =
+ (uk.ac.sanger.artemis.Feature)newFeatures.get(k);
+ newchadoGene.add5PrimeUtr(newTranscriptName, utrFeature.getEmblFeature());
+ }
newFeatures = duplicateFeatures(chadoGene.getOtherFeaturesOfTranscript(transcriptName), newchadoGene);
for(int k=0; k<newFeatures.size(); k++)
- newchadoGene.addOtherFeatures(newTranscriptName, (Feature)newFeatures.get(k));
+ {
+ uk.ac.sanger.artemis.Feature otherFeature =
+ (uk.ac.sanger.artemis.Feature)newFeatures.get(k);
+ newchadoGene.addOtherFeatures(newTranscriptName, otherFeature.getEmblFeature());
+ }
newFeatures = duplicateFeatures(chadoGene.getSplicedFeaturesOfTranscript(transcriptName), newchadoGene);
for(int k=0; k<newFeatures.size(); k++)
--
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