Enumcodeatposition *gt_Enumcodeatposition_new(const GtEncseq *encseq,
GtReadmode readmode,
unsigned int prefixlength,
unsigned int numofchars)
{
Enumcodeatposition *ecp;
ecp = gt_malloc(sizeof *ecp);
ecp->encseq = encseq;
ecp->readmode = readmode;
ecp->multimappower = gt_initmultimappower(numofchars,prefixlength);
ecp->filltable = gt_initfilltable(numofchars,prefixlength);
ecp->prefixlength = prefixlength;
ecp->moveforward = GT_ISDIRREVERSE(readmode) ? true : false;
ecp->totallength = gt_encseq_total_length(encseq);
if (ecp->moveforward)
{
ecp->previousrange.start = ecp->previousrange.end = 0;
} else
{
ecp->previousrange.start = ecp->previousrange.end = ecp->totallength;
}
ecp->exhausted = false;
if (gt_encseq_has_specialranges(encseq))
{
ecp->sri = gt_specialrangeiterator_new(encseq,ecp->moveforward);
} else
{
ecp->sri = NULL;
}
return ecp;
}
Substriter *gt_substriter_new(const GtAlphabet *alphabet,unsigned int qvalue)
{
Substriter *substriter;
ALLOCASSIGNSPACE(substriter,NULL,Substriter,1);
substriter->qvalue = qvalue;
substriter->numofchars = gt_alphabet_num_of_chars(alphabet);
substriter->multimappower = gt_initmultimappower(substriter->numofchars,
qvalue);
return substriter;
}
Substriter *gt_substriter_new(const GtAlphabet *alphabet,unsigned int qvalue)
{
Substriter *substriter;
substriter = gt_malloc(sizeof *substriter);
substriter->qvalue = qvalue;
substriter->numofchars = gt_alphabet_num_of_chars(alphabet);
substriter->multimappower = gt_initmultimappower(substriter->numofchars,
qvalue);
return substriter;
}
static GtKmerstream *kmerstream_new(unsigned int numofchars,
unsigned int kmersize)
{
GtKmerstream *spwp;
gt_assert(kmersize <= (unsigned int) MAXPREFIXLENGTH);
spwp = gt_malloc(sizeof (*spwp));
spwp->multimappower = gt_initmultimappower(numofchars,kmersize);
kmerstream_init(spwp, numofchars, kmersize);
special_queue_init(&spwp->specialqueue,kmersize);
spwp->filltable = gt_filllargestchartable(numofchars,kmersize);
return spwp;
}
static Kmerstream *kmerstream_new(unsigned int numofchars,unsigned int kmersize)
{
Kmerstream *spwp;
gt_assert(kmersize <= (unsigned int) MAXPREFIXLENGTH);
spwp = gt_malloc(sizeof (*spwp));
spwp->multimappower = gt_initmultimappower(numofchars,kmersize);
spwp->lengthwithoutspecial = 0;
spwp->codewithoutspecial = 0;
spwp->kmersize = kmersize;
spwp->numofchars = numofchars;
spwp->windowwidth = 0;
spwp->firstindex = 0;
specialemptyqueue(&spwp->spos,kmersize);
spwp->filltable = gt_filllargestchartable(numofchars,kmersize);
return spwp;
}
