diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java index b9377ea4663f30c7f1fb563755f03ed1077447c1..4fbff3e5ff69d037912e722870fa93ea760bd74a 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++)