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;
}
GtUword gt_pck_get_nonspecial_count(const FMindex *index)
{
const BWTSeq *bwtseq = (const BWTSeq *) index;
return BWTSeqAggTransformedCount(bwtseq,
MRAEncGetRangeSize(BWTSeqGetAlphabet(bwtseq),
0));
}
GtUword gt_pck_special_occ_in_nonspecial_intervals(const FMindex *index)
{
const BWTSeq *bwtseq = (const BWTSeq *) index;
GtUword count = 0,
*rangeOccs, first_special_row;
unsigned short idx, rangesize;
rangesize = (unsigned short) MRAEncGetRangeSize(BWTSeqGetAlphabet(bwtseq), 1);
rangeOccs = gt_calloc(rangesize, sizeof (GtUword));
first_special_row = gt_pck_get_nonspecial_count(index);
BWTSeqRangeOcc(bwtseq, 1, first_special_row, rangeOccs);
for (idx = 0; idx < rangesize; idx++)
count += rangeOccs[idx];
gt_free(rangeOccs);
return count;
}
GtUword gt_bwtrangesplitallwithspecial(Mbtab *mbtab,
GtUword *rangeOccs,
const FMindex *voidBwtSeq,
GtUword lbound,
GtUword ubound)
{
GtUword char_idx, range_idx, rangebase;
const BWTSeq *bwtseq = (const BWTSeq *) voidBwtSeq;
const MRAEnc *alphabet = BWTSeqGetAlphabet(bwtseq);
AlphabetRangeID numofranges = MRAEncGetNumRanges(alphabet);
AlphabetRangeSize rangesize = 0, totalrange = 0;
for (range_idx = 0; range_idx < (GtUword) numofranges; range_idx++)
{
GtUword rangeOcc_idx = 0;
rangesize = MRAEncGetRangeSize(alphabet, range_idx);
totalrange += rangesize;
BWTSeqPosPairRangeOcc(bwtseq, range_idx, lbound, ubound,rangeOccs);
rangebase = (GtUword) MRAEncGetRangeBase(alphabet, range_idx);
for (char_idx = rangebase;
char_idx < rangebase + rangesize; char_idx++)
{
if (rangeOccs[rangeOcc_idx] < rangeOccs[rangesize+rangeOcc_idx])
{
mbtab[char_idx].lowerbound = bwtseq->count[char_idx] +
rangeOccs[rangeOcc_idx];
mbtab[char_idx].upperbound = bwtseq->count[char_idx] +
rangeOccs[rangesize+rangeOcc_idx];
} else
{
mbtab[char_idx].lowerbound = mbtab[char_idx].upperbound = 0;
}
rangeOcc_idx++;
}
}
return totalrange;
}
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];
}
}
}
