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 PredictionTranscript_addExon(PredictionTranscript *trans, PredictionExon *exon, int *positionP) {
if (positionP) {
Vector_setElementAt(trans->exons, *positionP, exon);
} else {
Vector_addElement(trans->exons, exon);
}
if (exon && (!PredictionTranscript_getStartIsSet(trans) ||
PredictionExon_getStart(exon) < PredictionTranscript_getStart(trans))) {
PredictionTranscript_setStart(trans, PredictionExon_getStart(exon));
}
if (exon && (!PredictionTranscript_getEndIsSet(trans) ||
PredictionExon_getEnd(exon) > PredictionTranscript_getEnd(trans))) {
PredictionTranscript_setEnd(trans, PredictionExon_getEnd(exon));
}
}