GtUword gt_bwtrangesplitallwithoutspecial(Mbtab *mbtab,
GtUword *rangeOccs,
const FMindex *fmindex,
GtUword lbound,
GtUword ubound)
{
const BWTSeq *bwtseq = (const BWTSeq *) fmindex;
AlphabetRangeSize idx, rangesize
= MRAEncGetRangeSize(EISGetAlphabet(bwtseq->seqIdx),0);
gt_assert(sizeof (AlphabetRangeSize) <= sizeof (GtUword));
BWTSeqPosPairRangeOcc(bwtseq, 0, lbound, ubound,rangeOccs);
for (idx = 0; idx < rangesize; idx++)
{
if (rangeOccs[idx] < rangeOccs[rangesize+idx])
{
mbtab[idx].lowerbound = bwtseq->count[idx] + rangeOccs[idx];
mbtab[idx].upperbound = bwtseq->count[idx] + rangeOccs[rangesize+idx];
} else
{
mbtab[idx].lowerbound = mbtab[idx].upperbound = 0;
}
}
return (GtUword) rangesize;
}
static MRAEnc *
BWTSASSNewMRAEnc(const SASeqSrc *src)
{
const BWTSASeqSrc *bwtSASeqSrc;
gt_assert(src);
bwtSASeqSrc = constSASS2BWTSASS(src);
return MRAEncCopy(EISGetAlphabet(BWTSeqGetEncIdxSeq(bwtSASeqSrc->bwtSeq)));
}
extern Seqpos
BWTSeqGetRankSort(const BWTSeq *bwtSeq, Seqpos pos, AlphabetRangeID range,
struct extBitsRetrieval *extBits)
{
BitOffset locVarBits;
AlphabetRangeSize rSize;
gt_assert(bwtSeq->rangeSort[range] == SORTMODE_RANK);
EISRetrieveExtraBits(bwtSeq->seqIdx, pos, EBRF_RETRIEVE_CWBITS
| EBRF_RETRIEVE_VARBITS, extBits, bwtSeq->hint);
locVarBits = locateVarBits(bwtSeq, extBits);
rSize = MRAEncGetRangeSize(EISGetAlphabet(bwtSeq->seqIdx), range);
{
Seqpos ranks[rSize * 2];
Seqpos BWTRankTotal = 0;
AlphabetRangeSize i;
EISPosPairRangeRank(bwtSeq->seqIdx, range, extBits->start, pos, ranks,
bwtSeq->hint);
for (i = 0; i < rSize; ++i)
BWTRankTotal += ranks[i + rSize] - ranks[i];
return gt_bsGetSeqpos(extBits->varPart, extBits->varOffset + locVarBits
+ bwtSeq->bitsPerOrigRank * BWTRankTotal,
bwtSeq->bitsPerOrigRank);
}
}
void gt_bwtrangesplitwithoutspecial(GtArrayBoundswithchar *bwci,
GtUword *rangeOccs,
const FMindex *fmindex,
GtUword lbound,
GtUword ubound)
{
const BWTSeq *bwtseq = (const BWTSeq *) fmindex;
AlphabetRangeSize idx, rangesize;
rangesize = MRAEncGetRangeSize(EISGetAlphabet(bwtseq->seqIdx),0);
bwci->nextfreeBoundswithchar = 0;
BWTSeqPosPairRangeOcc(bwtseq, 0, lbound, ubound,rangeOccs);
for (idx = 0; idx < rangesize; idx++)
{
if (rangeOccs[idx] < rangeOccs[rangesize+idx])
{
bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar].inchar = idx;
bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar].lbound
= bwtseq->count[idx] + rangeOccs[idx];
bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar++].rbound
= bwtseq->count[idx] + rangeOccs[rangesize+idx];
}
}
}
