static void gt_mmsearchiterator_reinit(GtMMsearchiterator *mmsi,
const GtEncseq *dbencseq,
const ESASuffixptr *suftab,
GtUword leftbound,
GtUword rightbound,
GtUword itvoffset,
GtReadmode readmode,
const GtQuerysubstring *querysubstring,
GtUword minmatchlength)
{
mmsi->suftab = suftab;
if (mmsi->esr == NULL)
{
mmsi->esr = gt_encseq_create_reader_with_readmode(dbencseq, readmode, 0);
} else
{
gt_encseq_reader_reinit_with_readmode(mmsi->esr,dbencseq,readmode,0);
}
mmsi->lcpitv.left = leftbound;
mmsi->lcpitv.right = rightbound;
mmsi->lcpitv.offset = itvoffset;
if (!gt_mmsearch(dbencseq,mmsi->esr,suftab,readmode,&mmsi->lcpitv,
querysubstring,minmatchlength))
{
mmsi->lcpitv.left = 1UL;
mmsi->lcpitv.right = 0;
}
mmsi->sufindex = mmsi->lcpitv.left;
}
static GtMMsearchiterator *gt_mmsearchiterator_new_generic(
const GtEncseq *dbencseq,
const ESASuffixptr *suftab,
unsigned long leftbound,
unsigned long rightbound,
unsigned long itvoffset,
GtReadmode readmode,
const GtQuerysubstring *querysubstring,
unsigned long minmatchlength)
{
GtMMsearchiterator *mmsi = gt_malloc(sizeof *mmsi);
mmsi->lcpitv.left = leftbound;
mmsi->lcpitv.right = rightbound;
mmsi->lcpitv.offset = itvoffset;
mmsi->suftab = suftab;
mmsi->esr = gt_encseq_create_reader_with_readmode(dbencseq, readmode, 0);
if (!gt_mmsearch(dbencseq,mmsi->esr,suftab,readmode,&mmsi->lcpitv,
querysubstring,minmatchlength))
{
mmsi->lcpitv.left = 1UL;
mmsi->lcpitv.right = 0;
}
mmsi->sufindex = mmsi->lcpitv.left;
return mmsi;
}
