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_sort(PredictionTranscript *trans) {
PredictionExon *firstExon = PredictionTranscript_getExonAt(trans,0);
int strand;
int i;
for (i=0; i<PredictionTranscript_getExonCount(trans); i++) {
if (!PredictionTranscript_getExonAt(trans,i)) {
return;
}
}
strand = PredictionExon_getStrand(firstExon);
// Hack in using Exon function names
if (strand == 1) {
Vector_sort(PredictionTranscript_getExons(trans),Exon_forwardStrandCompFunc);
} else if (strand == -1) {
Vector_sort(PredictionTranscript_getExons(trans),Exon_reverseStrandCompFunc);
}
}
