*/
SequenceI mapFromSequence = seq;
SequenceI mapToSequence = mappedSequence;
- if ((type == MappingType.NucleotideToPeptide && featureIsOnTarget)
- || (type == MappingType.PeptideToNucleotide && !featureIsOnTarget))
+ if ((MappingType.isDnaToPeptide(type) && featureIsOnTarget)
+ || (MappingType.isPeptideToDna(type) && !featureIsOnTarget))
{
mapFromSequence = mappedSequence;
mapToSequence = seq;
{
fromStart = alignToStart;
toStart = alignFromStart;
- toEnd = forwardStrand ? toStart + alignCount - 1 : toStart
- - (alignCount - 1);
+ toEnd = forwardStrand ? toStart + alignCount - 1
+ : toStart - (alignCount - 1);
int toLength = Math.abs(toEnd - toStart) + 1;
int fromLength = toLength * type.getFromRatio() / type.getToRatio();
fromEnd = fromStart + fromLength - 1;
}
/**
- * Returns a MappingType depending on the exonerate 'model' value.
+ * Returns a MappingType depending on the exonerate 'model' value
*
* @param model
* @return
{
MappingType result = null;
- if (model.contains(PROTEIN2DNA) || model.contains(PROTEIN2GENOME))
+ if (model.contains(PROTEIN2GENOME))
{
- result = MappingType.PeptideToNucleotide;
+ result = MappingType.PeptideToGenome;
}
- else if (model.contains(CODING2CODING) || model.contains(CODING2GENOME)
- || model.contains(CDNA2GENOME) || model.contains(GENOME2GENOME))
+ else if (model.contains(PROTEIN2DNA))
{
- result = MappingType.NucleotideToNucleotide;
+ result = MappingType.PeptideToCds;
+ }
+ else if (model.contains(CODING2GENOME))
+ {
+ result = MappingType.CdsToGenome;
+ }
+ else if (model.contains(CDNA2GENOME))
+ {
+ result = MappingType.CdnaToGenome;
+ }
+ else if (model.contains(CODING2CODING) || model.contains(GENOME2GENOME))
+ {
+ result = MappingType.GenomeToCdna;
}
return result;
}
return false;
}
+ /**
+ * An override to set feature group to "exonerate" instead of the default GFF
+ * source value (column 2)
+ */
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
Map<String, List<String>> set)
{
- SequenceFeature sf = super.buildSequenceFeature(gff, set);
- sf.setFeatureGroup("exonerate");
+ SequenceFeature sf = super.buildSequenceFeature(gff, TYPE_COL,
+ "exonerate", set);
return sf;
}