char *PredictionExon_getSeqString(PredictionExon *exon) {
char *seq;
if (PredictionExon_getSeqCacheString(exon)) {
return PredictionExon_getSeqCacheString(exon);
}
if (!PredictionExon_getSlice(exon)) {
fprintf(stderr, "Warning: this exon %s doesn't have a contig you won't get a seq\n", PredictionExon_getDisplayLabel(exon));
return NULL;
} else {
seq = BaseContig_getSubSeq(PredictionExon_getSlice(exon),
PredictionExon_getStart(exon),
PredictionExon_getEnd(exon),
1);
if (PredictionExon_getStrand(exon) == -1){
SeqUtil_reverseComplement(seq,strlen(seq));
}
}
PredictionExon_setSeqCacheString(exon, seq);
return PredictionExon_getSeqCacheString(exon);
}
void PredictionExon_loadGenomicMapper(Exon *exon, Mapper *mapper, IDType id, int start) {
// NIY Make the Exon_getContig consistent
Mapper_addMapCoordinates( mapper, id, start, start+Exon_getLength(exon)-1,
Exon_getStrand(exon), Slice_getSeqRegionId(PredictionExon_getSlice(exon)),
Exon_getStart(exon), Exon_getEnd(exon) );
}
MapperRangeSet *PredictionTranscript_genomic2cDNA(PredictionTranscript *trans, int start, int end, int strand, BaseContig *contig) {
Mapper *mapper;
// "ids" in mapper are contigs of exons, so use the same contig that should
// be attached to all of the exons...
if (!contig) {
Vector *translateable = PredictionTranscript_getAllTranslateableExons(trans);
PredictionExon *firstExon;
if (!Vector_getNumElement(translateable)) {
return MapperRangeSet_new();
}
firstExon = Vector_getElementAt(translateable, 0);
contig = (BaseContig*)PredictionExon_getSlice(firstExon);
Vector_free(translateable);
}
mapper = PredictionTranscript_getcDNACoordMapper(trans);
return Mapper_mapCoordinates(mapper,(IDType)contig, start, end, strand, "genomic");
}
