static int gt_repfind_runner(GT_UNUSED int argc,
GT_UNUSED const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments, GtError *err)
{
bool haserr = false;
Maxpairsoptions *arguments = tool_arguments;
GtLogger *logger = NULL;
GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
GtXdropmatchinfo xdropmatchinfo;
gt_error_check(err);
xdropmatchinfo.querymatchspaceptr = querymatchspaceptr;
xdropmatchinfo.useq = gt_seqabstract_new_empty();
xdropmatchinfo.vseq = gt_seqabstract_new_empty();
xdropmatchinfo.arbitscores.mat = 2;
xdropmatchinfo.arbitscores.mis = -2;
xdropmatchinfo.arbitscores.ins = -3;
xdropmatchinfo.arbitscores.del = -3;
xdropmatchinfo.frontresource = gt_frontresource_new(100UL);
xdropmatchinfo.res = gt_xdrop_resources_new(&xdropmatchinfo.arbitscores);
xdropmatchinfo.belowscore = 5L;
logger = gt_logger_new(arguments->beverbose, GT_LOGGER_DEFLT_PREFIX, stdout);
if (parsed_args < argc)
{
gt_error_set(err,"superfluous arguments: \"%s\"",argv[argc-1]);
haserr = true;
}
if (!haserr)
{
if (gt_str_array_size(arguments->queryfiles) == 0)
{
if (arguments->samples == 0)
{
if (arguments->forward)
{
GtProcessmaxpairs processmaxpairs;
void *processmaxpairsdata;
if (arguments->searchspm)
{
processmaxpairs = gt_simplesuffixprefixmatchoutput;
processmaxpairsdata = NULL;
} else
{
if (arguments->extendseed)
{
processmaxpairs = gt_simplexdropselfmatchoutput;
processmaxpairsdata = (void *) &xdropmatchinfo;
} else
{
processmaxpairs = gt_simpleexactselfmatchoutput;
processmaxpairsdata = (void *) querymatchspaceptr;
}
}
if (gt_callenummaxpairs(gt_str_get(arguments->indexname),
arguments->userdefinedleastlength,
arguments->scanfile,
processmaxpairs,
processmaxpairsdata,
logger,
err) != 0)
{
haserr = true;
}
}
if (!haserr && arguments->reverse)
{
if (gt_callenumselfmatches(gt_str_get(arguments->indexname),
GT_READMODE_REVERSE,
arguments->userdefinedleastlength,
/*arguments->extendseed
? gt_processxdropquerymatches
:*/ gt_querymatch_output,
/*arguments->extendseed
? (void *) &xdropmatchinfo
:*/ NULL,
logger,
err) != 0)
{
haserr = true;
}
}
} else
{
if (gt_testmaxpairs(gt_str_get(arguments->indexname),
arguments->samples,
arguments->userdefinedleastlength,
(GtUword)
(100 * arguments->userdefinedleastlength),
logger,
err) != 0)
{
haserr = true;
}
}
} else
{
if (gt_callenumquerymatches(gt_str_get(arguments->indexname),
arguments->queryfiles,
false,
true,
false,
arguments->userdefinedleastlength,
NULL,
arguments->extendseed
? gt_processxdropquerymatches
: gt_querymatch_output,
arguments->extendseed
? (void *) &xdropmatchinfo
: NULL,
logger,
err) != 0)
{
haserr = true;
}
}
}
gt_querymatch_delete(querymatchspaceptr);
gt_seqabstract_delete(xdropmatchinfo.useq);
gt_seqabstract_delete(xdropmatchinfo.vseq);
gt_xdrop_resources_delete(xdropmatchinfo.res);
gt_frontresource_delete(xdropmatchinfo.frontresource);
gt_logger_delete(logger);
return haserr ? -1 : 0;
}
int gt_xdrop_unit_test(GT_UNUSED GtError *err)
{
int had_err = 0, i, j, s;
const GtUchar *strings[GT_XDROP_NUM_OF_TESTS] =
{(const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCCAAAGGGTTTCCCTTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTTTTTGGGGCCCCAAAATTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTNNNNTTTTGGGGCCCCAAAATTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCGCAAAGGGTTTCCCTTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCAAAGGGTTTCCCCTTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCTCAAAGGGTTTCCTTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTAAACAGATCACCCGCTTTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTAAACGGGTTTCTCAAAGGGTTCCCTTTTTTTTTTTTTTT"};
GtUword lengths[GT_XDROP_NUM_OF_TESTS] =
{54UL, 46UL, 50UL, 54UL, 54UL, 54UL, 46UL, 54UL},
eval_scores[GT_XDROP_NUM_OF_TESTS *
GT_XDROP_NUM_OF_TESTS *
GT_XDROP_NUM_OF_TESTS] =
{0, 13UL, 0, 1UL, 4UL, 1UL, 0, 7UL,
13UL, 0, 0, 14UL, 15UL, 14UL, 0, 15UL,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 14UL, 0, 0, 1UL, 2UL, 0, 1UL,
4UL, 15UL, 0, 1UL, 0, 8UL, 0, 1UL,
1UL, 14UL, 0, 2UL, 8UL, 0, 0, 4UL,
0, 0, 0, 0, 0, 0, 0, 0,
7UL, 15UL, 0, 1UL, 1UL, 4UL, 0, 0,
0, 13UL, 0, 1UL, 4UL, 5UL, 14UL, 7UL,
13UL, 0, 0, 14UL, 15UL, 14UL, 12UL, 15UL,
0, 0, 0, 20UL, 0, 19UL, 17UL, 0,
1UL, 14UL, 20UL, 0, 5UL, 6UL, 15UL, 8UL,
4UL, 15UL, 0, 5UL, 0, 8UL, 15UL, 10UL,
5UL, 14UL, 19UL, 6UL, 8UL, 0, 14UL, 4UL,
14UL, 12UL, 17UL, 15UL, 15UL, 14UL, 0, 14UL,
7UL, 15UL, 0, 8UL, 10UL, 4UL, 14UL, 0,
0, 13UL, 19UL, 1UL, 2UL, 2UL, 13UL, 3UL,
13UL, 0, 9UL, 14UL, 14UL, 13UL, 12UL, 14UL,
17UL, 4UL, 0, 18UL, 19UL, 16UL, 16UL, 18UL,
1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL,
2UL, 14UL, 18UL, 2UL, 0, 4UL, 13UL, 4UL,
2UL, 13UL, 19UL, 3UL, 4UL, 0, 13UL, 3UL,
14UL, 12UL, 17UL, 13UL, 13UL, 14UL, 0, 14UL,
3UL, 14UL, 18UL, 3UL, 4UL, 3UL, 13UL, 0,
0, 13UL, 17UL, 1UL, 2UL, 2UL, 14UL, 3UL,
13UL, 0, 4UL, 14UL, 15UL, 13UL, 12UL, 14UL,
19UL, 9UL, 0, 18UL, 18UL, 19UL, 17UL, 18UL,
1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL,
2UL, 14UL, 19UL, 2UL, 0, 4UL, 13UL, 4UL,
2UL, 13UL, 16UL, 3UL, 4UL, 0, 14UL, 3UL,
13UL, 12UL, 16UL, 13UL, 13UL, 13UL, 0, 13UL,
3UL, 14UL, 18UL, 3UL, 4UL, 3UL, 14UL, 0,
0, 0, 0, 1UL, 1UL, 1UL, 0, 1UL,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 0, 0, 0, 1UL, 0, 0, 1UL,
1UL, 0, 0, 1UL, 0, 0, 0, 1UL,
1UL, 0, 0, 0, 0, 0, 0, 1UL,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 0, 0, 1UL, 1UL, 1UL, 0, 0,
0, 0, 0, 1UL, 1UL, 1UL, 0, 1UL,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 0, 0, 0, 1UL, 2UL, 0, 1UL,
1UL, 0, 0, 1UL, 0, 0, 0, 1UL,
1UL, 0, 0, 2UL, 0, 0, 0, 1UL,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 0, 0, 1UL, 1UL, 1UL, 0, 0,
0, 13UL, 17UL, 1UL, 2UL, 2UL, 13UL, 3UL,
13UL, 0, 4UL, 14UL, 14UL, 13UL, 12UL, 14UL,
17UL, 4UL, 0, 18UL, 19UL, 16UL, 16UL, 19UL,
1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL,
2UL, 14UL, 19UL, 2UL, 0, 4UL, 13UL, 4UL,
2UL, 13UL, 16UL, 3UL, 4UL, 0, 13UL, 3UL,
13UL, 12UL, 16UL, 13UL, 13UL, 13UL, 0, 13UL,
3UL, 14UL, 19UL, 3UL, 4UL, 3UL, 13UL, 0,
0, 13UL, 0, 1UL, 2UL, 2UL, 5UL, 3UL,
13UL, 0, 0, 14UL, 15UL, 13UL, 0, 14UL,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 14UL, 0, 0, 2UL, 3UL, 5UL, 3UL,
2UL, 15UL, 0, 2UL, 0, 4UL, 5UL, 4UL,
2UL, 13UL, 0, 3UL, 4UL, 0, 6UL, 3UL,
5UL, 0, 0, 5UL, 5UL, 6UL, 0, 5UL,
3UL, 14UL, 0, 3UL, 4UL, 3UL, 5UL, 0};
GtSeqabstract *useq, *vseq;
GtXdropArbitraryscores score[GT_XDROP_NUM_OF_TESTS] = {{2, -2, -2, -2},
{2, -1, -1, -1},
{2, -1, -5, -2},
{2, -1, -2, -5},
{3, -2, -3, -3},
{3, -1, -1, -1},
{4, -1, -3, -3},
{10, -3, -8, -8}};
GtXdropresources *resources;
GtXdropbest best;
GtXdropscore dropscore = (GtXdropscore) 12;
GtMultieoplist *edit_ops = NULL;
GtAlignment *alignment;
bool rightextension = true;
gt_error_check(err);
for (s = 0; s < GT_XDROP_NUM_OF_TESTS; ++s) {
resources = gt_xdrop_resources_new(&score[s]);
for (i = 0; i < GT_XDROP_NUM_OF_TESTS && !had_err; ++i) {
for (j = 0; j < GT_XDROP_NUM_OF_TESTS; ++j) {
useq = gt_seqabstract_new_gtuchar(rightextension,GT_READMODE_FORWARD,
strings[i], lengths[i], 0,lengths[i]);
vseq = gt_seqabstract_new_gtuchar(rightextension, GT_READMODE_FORWARD,
strings[j], lengths[j], 0,lengths[j]);
gt_evalxdroparbitscoresextend(true, &best, resources, useq, vseq,
dropscore);
edit_ops = gt_xdrop_backtrack(resources, &best);
gt_ensure(edit_ops != NULL);
alignment = gt_alignment_new_with_seqs(strings[i], best.ivalue,
strings[j], best.jvalue);
gt_alignment_set_multieop_list(alignment, edit_ops);
gt_ensure(eval_scores[s*64+i*8+j] == gt_alignment_eval(alignment));
gt_multieoplist_delete(edit_ops);
gt_alignment_delete(alignment);
if (i == j) {
gt_evalxdroparbitscoresextend(false, &best, resources, useq, vseq,
dropscore);
edit_ops = gt_xdrop_backtrack(resources, &best);
alignment = gt_alignment_new_with_seqs(strings[i], best.ivalue,
strings[j], best.jvalue);
gt_alignment_set_multieop_list(alignment, edit_ops);
gt_ensure(eval_scores[s*64+i*8+j] == gt_alignment_eval(alignment));
gt_multieoplist_delete(edit_ops);
gt_alignment_delete(alignment);
}
gt_seqabstract_delete(useq);
gt_seqabstract_delete(vseq);
}
}
gt_xdrop_resources_delete(resources);
}
return had_err;
}