void setreadintkeys(GtArray *riktab,
const char *keystring,
void *valueptr,
size_t sizeval,
bool *readflag)
{
Readintkeys rikvalue;
rikvalue.keystring = keystring;
rikvalue.readflag = readflag;
gt_assert(sizeval == 0 || sizeval == (size_t) 4 || sizeval == (size_t) 8);
switch (sizeval)
{
case 0: rikvalue.smallvalueptr = NULL;
rikvalue.bigvalueptr = NULL;
rikvalue.ptrdefined = false;
break;
case 4: gt_assert(sizeof (uint32_t) == (size_t) 4);
rikvalue.smallvalueptr = valueptr;
rikvalue.bigvalueptr = NULL;
rikvalue.ptrdefined = true;
break;
case 8: gt_assert(sizeof (uint64_t) == (size_t) 8);
rikvalue.bigvalueptr = valueptr;
rikvalue.smallvalueptr = NULL;
rikvalue.ptrdefined = true;
break;
}
rikvalue.found = false;
gt_array_add_elem(riktab,&rikvalue,sizeof (Readintkeys));
}
int gth_match_processor(GthMatchProcessorInfo *info, GthSeqCon *gen_seq_con,
GthSeqCon *ref_seq_con, GthMatch *match)
{
if (info->matchnumcounter) {
info->matchnumcounter[match->Storeseqnumreference]++;
if (info->maxnumofmatches > 0 &&
info->matchnumcounter[match->Storeseqnumreference] >
info->maxnumofmatches) {
/* discard matchA */
return 0;
}
}
if (!(info->refseqisindex && !info->online) &&
match->Storeseqnumreference != info->lastrefseqnum &&
gt_array_size(info->matches)) {
gt_assert(info->chain_collection && info->chaining_info);
/* chain all current matches */
calc_chains_from_matches(info->chain_collection, info->matches,
info->chaining_info, gen_seq_con, ref_seq_con,
info->rare, info->fragweightfactor,
info->jump_table_new, info->jump_table_new_reverse,
info->jump_table_delete);
/* and remove them afterwards */
gt_array_reset(info->matches);
}
/*...only if it does not equal the last one */
if (gt_array_size(info->matches) &&
gth_matches_are_equal(gt_array_get_last(info->matches), match)) {
return 0;
}
gt_array_add_elem(info->matches, match, sizeof *match);
/* update last reference sequence number */
info->lastrefseqnum = match->Storeseqnumreference;
return 0;
}
