static void gt_querysubstringmatch(bool selfmatch,
const GtEncseq *dbencseq,
const ESASuffixptr *suftabpart,
GtReadmode readmode,
GtUword numberofsuffixes,
uint64_t queryunitnum,
GtQueryrepresentation *queryrep,
GtUword minmatchlength,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtQuerymatch *querymatchspaceptr)
{
GtMMsearchiterator *mmsi;
GtUword totallength, localqueryoffset = 0;
uint64_t localqueryunitnum = queryunitnum;
GtQuerysubstring querysubstring;
gt_assert(numberofsuffixes > 0);
totallength = gt_encseq_total_length(dbencseq);
querysubstring.queryrep = queryrep;
for (querysubstring.currentoffset = 0;
querysubstring.currentoffset <= queryrep->seqlen - minmatchlength;
querysubstring.currentoffset++)
{
GtUword dbstart;
mmsi = gt_mmsearchiterator_new(dbencseq,
suftabpart,
0, /* leftbound */
numberofsuffixes - 1, /* rightbound */
0, /* offset */
readmode,
&querysubstring,
minmatchlength);
while (gt_mmsearchiterator_next(&dbstart,mmsi))
{
if (gt_mmsearch_isleftmaximal(dbencseq,
readmode,
dbstart,
&querysubstring))
{
GtUword dbseqnum, dbseqstartpos, dbseqlen, extend;
extend = gt_mmsearch_extendright(dbencseq,
mmsi->esr,
readmode,
totallength,
dbstart + minmatchlength,
&querysubstring,
minmatchlength);
if (gt_encseq_has_multiseq_support(dbencseq))
{
dbseqnum = gt_encseq_seqnum(dbencseq,dbstart);
dbseqstartpos = gt_encseq_seqstartpos(dbencseq,dbseqnum);
dbseqlen = gt_encseq_seqlength(dbencseq,dbseqnum);
} else
{
dbseqnum = dbseqstartpos = dbseqlen = 0;
}
gt_querymatch_init(querymatchspaceptr,
minmatchlength + extend,
dbstart,
dbseqnum,
dbstart - dbseqstartpos,
dbseqlen,
0, /* score */
0, /* edist */
selfmatch,
localqueryunitnum,
minmatchlength + extend,
localqueryoffset,
queryrep->seqlen);
processquerymatch(processquerymatchinfo,querymatchspaceptr);
}
}
gt_mmsearchiterator_delete(mmsi);
mmsi = NULL;
if (gt_mmsearch_accessquery(queryrep,querysubstring.currentoffset)
== (GtUchar) SEPARATOR)
{
localqueryunitnum++;
localqueryoffset = 0;
} else
{
localqueryoffset++;
}
}
}
int gt_querysubstringmatchiterator_next(GtQuerysubstringmatchiterator *qsmi,
GtError *err)
{
gt_assert(qsmi != NULL);
while (true)
{
if (qsmi->query_seqlen < qsmi->userdefinedleastlength)
{
if (qsmi->seqit != NULL)
{
int retval = gt_seq_iterator_next(qsmi->seqit,
&qsmi->query_for_seqit,
&qsmi->query_seqlen,
&qsmi->desc,
err);
if (retval < 0)
{
return -1; /* error */
}
if (retval == 0)
{
return 1; /* no more sequences */
}
gt_assert(qsmi->query_seqlen > 0 && qsmi->query_for_seqit != NULL);
qsmi->queryrep.sequence = qsmi->query_for_seqit;
} else
{
if (qsmi->queryunitnum == qsmi->query_encseq_numofsequences)
{
return 1;
}
qsmi->queryrep.startpos = gt_encseq_seqstartpos(qsmi->queryrep.encseq,
qsmi->queryunitnum);
qsmi->query_seqlen = gt_encseq_seqlength(qsmi->queryrep.encseq,
qsmi->queryunitnum);
}
gt_assert(qsmi->query_seqlen > 0);
qsmi->queryrep.seqlen = qsmi->query_seqlen;
qsmi->querysubstring.currentoffset = 0;
}
if (qsmi->query_seqlen >= qsmi->userdefinedleastlength)
{
if (!qsmi->mmsi_defined)
{
gt_mmsearchiterator_reinit(qsmi->mmsi,
qsmi->dbencseq,
qsmi->suftabpart,
0, /* l */
qsmi->numberofsuffixes - 1, /* r */
0, /* offset */
qsmi->db_readmode,
&qsmi->querysubstring,
qsmi->userdefinedleastlength);
qsmi->mmsi_defined = true;
} else
{
if (gt_mmsearchiterator_next(&qsmi->dbstart,qsmi->mmsi))
{
GtUword extend;
if (gt_mmsearch_isleftmaximal(qsmi->dbencseq,
qsmi->db_readmode,
qsmi->dbstart,
&qsmi->querysubstring))
{
extend = gt_mmsearch_extendright(qsmi->dbencseq,
qsmi->mmsi->esr,
qsmi->db_readmode,
qsmi->totallength,
qsmi->dbstart +
qsmi->userdefinedleastlength,
&qsmi->querysubstring,
qsmi->userdefinedleastlength);
qsmi->matchlength = qsmi->userdefinedleastlength + extend;
return 0;
}
} else
{
qsmi->mmsi_defined = false;
if (qsmi->querysubstring.currentoffset +
qsmi->userdefinedleastlength < qsmi->query_seqlen)
{
qsmi->querysubstring.currentoffset++;
} else
{
qsmi->query_seqlen = 0;
qsmi->queryunitnum++;
}
}
}
} else
{
qsmi->query_seqlen = 0;
qsmi->queryunitnum++;
}
}
}
static int gt_querysubstringmatch_generic(
bool selfmatch,
const GtEncseq *dbencseq,
const ESASuffixptr *suftabpart,
GtReadmode readmode,
unsigned long numberofsuffixes,
uint64_t queryunitnum,
const GtQueryrep *queryrep,
unsigned long minmatchlength,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtQuerymatch *querymatchspaceptr,
GtError *err)
{
GtMMsearchiterator *mmsi;
unsigned long totallength, localqueryoffset = 0;
uint64_t localqueryunitnum = queryunitnum;
GtQuerysubstring querysubstring;
bool haserr = false;
gt_assert(numberofsuffixes > 0);
totallength = gt_encseq_total_length(dbencseq);
querysubstring.queryrep = queryrep;
for (querysubstring.offset = 0;
querysubstring.offset <= queryrep->length - minmatchlength;
querysubstring.offset++)
{
unsigned long dbstart;
mmsi = gt_mmsearchiterator_new_generic(dbencseq,
suftabpart,
0, /* leftbound */
numberofsuffixes-1, /* rightbound */
0, /* offset */
readmode,
&querysubstring,
minmatchlength);
while (!haserr && gt_mmsearchiterator_next(&dbstart,mmsi))
{
if (gt_mmsearch_isleftmaximal(dbencseq,
readmode,
dbstart,
&querysubstring))
{
unsigned long extend = gt_mmsearch_extendright(dbencseq,
mmsi->esr,
readmode,
totallength,
dbstart + minmatchlength,
&querysubstring,
minmatchlength);
gt_querymatch_fill(querymatchspaceptr,
minmatchlength + extend,
dbstart,
queryrep->readmode,
queryrep->reversecopy,
0, /* score */
0, /* edist */
selfmatch,
localqueryunitnum,
minmatchlength + extend,
localqueryoffset);
if (processquerymatch(processquerymatchinfo,
dbencseq,
querymatchspaceptr,
queryrep->sequence,
queryrep->length,
err) != 0)
{
haserr = true;
}
}
}
gt_mmsearchiterator_delete(mmsi);
mmsi = NULL;
if (!haserr)
{
if (gt_mmsearch_accessquery(queryrep,querysubstring.offset)
== (GtUchar) SEPARATOR)
{
localqueryunitnum++;
localqueryoffset = 0;
} else
{
localqueryoffset++;
}
}
}
return haserr ? -1 : 0;
}
