- protected SequenceFeature makeCdsFeature(int[] exons, int exonStartIndex,
- String proteinName, String proteinAccessionId,
- Map<String, String> vals, int codonStart)
- {
- int exonNumber = exonStartIndex / 2 + 1;
- SequenceFeature sf = new SequenceFeature();
- sf.setBegin(Math.min(exons[exonStartIndex], exons[exonStartIndex + 1]));
- sf.setEnd(Math.max(exons[exonStartIndex], exons[exonStartIndex + 1]));
- sf.setDescription(String.format("Exon %d for protein '%s' EMBLCDS:%s",
- exonNumber, proteinName, proteinAccessionId));
- sf.setPhase(String.valueOf(codonStart - 1));
- sf.setStrand(exons[exonStartIndex] <= exons[exonStartIndex + 1] ? "+"
- : "-");
- sf.setValue(FeatureProperties.EXONPOS, exonNumber);
- sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
+ protected SequenceFeature makeCdsFeature(String type, String desc,
+ int begin, int end, String group, Map<String, String> vals)
+ {
+ SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);