List<int[]> mapTo = new ArrayList<int[]>();
mapTo.add(new int[] { 1, transcriptLength });
MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
- new EnsemblCdna(getDomain()).transferFeatures(
- gene.getSequenceFeatures(), transcript.getDatasetSequence(),
- mapping, parentId);
+ EnsemblCdna cdna = new EnsemblCdna(getDomain());
+ cdna.transferFeatures(gene.getSequenceFeatures(),
+ transcript.getDatasetSequence(), mapping, parentId);
/*
* fetch and save cross-references
*/
- new EnsemblCdna(getDomain()).getCrossReferences(transcript);
+ cdna.getCrossReferences(transcript);
/*
* and finally fetch the protein product and save as a cross-reference
*/
- new EnsemblCdna(getDomain()).addProteinProduct(transcript);
+ cdna.addProteinProduct(transcript);
return transcript;
}