Bits *maskQuerySeq(struct dnaSeq *seq, boolean isProt,
boolean maskQuery, boolean lcMask)
/* Massage query sequence a bit, converting it to correct
* case (upper for protein/lower for DNA) and optionally
* returning upper/lower case info , and trimming poly A. */
{
Bits *qMaskBits = NULL;
verbose(2, "%s\n", seq->name);
if (isProt)
faToProtein(seq->dna, seq->size);
else
{
if (maskQuery)
{
if (lcMask)
toggleCase(seq->dna, seq->size);
qMaskBits = maskFromUpperCaseSeq(seq);
}
faToDna(seq->dna, seq->size);
}
if (seq->size > qWarnSize)
{
warn("Query sequence %s has size %d, it might take a while.",
seq->name, seq->size);
}
return qMaskBits;
}
boolean faSomeSpeedReadNext(struct lineFile *lf, DNA **retDna, int *retSize, char **retName, boolean isDna)
/* Read in DNA or Peptide FA record. */
{
char *poly;
int size;
if (!faMixedSpeedReadNext(lf, retDna, retSize, retName))
return FALSE;
size = *retSize;
poly = *retDna;
if (isDna)
faToDna(poly, size);
else
faToProtein(poly, size);
return TRUE;
}
