int gt_paircmp(int argc, const char **argv, GtError *err)
{
int parsed_args;
Cmppairwiseopt cmppairwise;
GtOPrval oprval;
gt_error_check(err);
oprval = parse_options(&parsed_args,&cmppairwise,argc, argv, err);
if (oprval == GT_OPTION_PARSER_OK)
{
unsigned long testcases;
gt_assert(parsed_args == argc);
showsimpleoptions(&cmppairwise);
testcases = applycheckfunctiontosimpleoptions(gt_checkgreedyunitedist,
&cmppairwise);
printf("# number of testcases: %lu\n",testcases);
}
freesimpleoption(&cmppairwise);
if (oprval == GT_OPTION_PARSER_REQUESTS_EXIT)
{
return 0;
}
if (oprval == GT_OPTION_PARSER_ERROR)
{
return -1;
}
return 0;
}
int gt_paircmp(int argc, const char **argv, GtError *err)
{
int parsed_args;
Cmppairwiseopt cmppairwise;
GtOPrval oprval;
gt_error_check(err);
oprval = parse_options(&parsed_args, &cmppairwise, argc, argv, err);
if (oprval == GT_OPTION_PARSER_OK)
{
gt_assert(parsed_args == argc);
showsimpleoptions(&cmppairwise);
if (cmppairwise.showedist)
{
GtUword edist;
edist = gt_computegreedyunitedist(
(const GtUchar *) gt_str_array_get(cmppairwise.strings,0),
(GtUword) strlen(gt_str_array_get(cmppairwise.strings,0)),
(const GtUchar *) gt_str_array_get(cmppairwise.strings,1UL),
(GtUword) strlen(gt_str_array_get(cmppairwise.strings,1UL)));
printf(GT_WU "\n", edist);
}
else
{
GtUword testcases;
testcases = applycheckfunctiontosimpleoptions(gt_checkgreedyunitedist,
&cmppairwise);
printf("# number of testcases: " GT_WU "\n", testcases);
}
}
freesimpleoption(&cmppairwise);
if (oprval == GT_OPTION_PARSER_REQUESTS_EXIT)
{
return 0;
}
if (oprval == GT_OPTION_PARSER_ERROR)
{
return -1;
}
return 0;
}
int gt_paircmp(int argc, const char **argv, GtError *err)
{
int parsed_args;
Cmppairwiseopt cmppairwise;
GtOPrval oprval;
gt_error_check(err);
oprval = parse_options(&parsed_args, &cmppairwise, argc, argv, err);
if (oprval == GT_OPTION_PARSER_OK)
{
gt_assert(parsed_args == argc);
showsimpleoptions(&cmppairwise);
if (cmppairwise.showedist)
{
GtUword edist, len1, len2;
GtStr *s1, *s2;
gt_assert(gt_str_array_size(cmppairwise.strings) >= 2);
s1 = gt_str_array_get_str(cmppairwise.strings,0);
s2 = gt_str_array_get_str(cmppairwise.strings,1UL);
len1 = gt_str_length(s1);
len2 = gt_str_length(s2);
edist = gt_computegreedyunitedist((const GtUchar *) gt_str_get(s1),
len1,
(const GtUchar *) gt_str_get(s2),
len2);
printf(GT_WU " " GT_WU " " GT_WU " " GT_WU "%% errors\n",
edist, len1,len2,(200 * edist)/(len1+len2));
}
else if (cmppairwise.print)
{
gt_print_edist_alignment(
(const GtUchar *) gt_str_array_get(cmppairwise.strings,0),0,
(GtUword) strlen(gt_str_array_get(cmppairwise.strings,0)),
(const GtUchar *) gt_str_array_get(cmppairwise.strings,1UL),0,
(GtUword) strlen(gt_str_array_get(cmppairwise.strings,1UL)));
} else
{
size_t idx;
Checkfunctiontabentry checkfunction_tab[] = {
MAKECheckfunctiontabentry(gt_checkgreedyunitedist),
MAKECheckfunctiontabentry(gt_checklinearspace),
MAKECheckfunctiontabentry(gt_checklinearspace_local),
MAKECheckfunctiontabentry(gt_checkaffinelinearspace),
MAKECheckfunctiontabentry(gt_checkaffinelinearspace_local)
};
for (idx = 0; idx < sizeof checkfunction_tab/sizeof checkfunction_tab[0];
idx++)
{
GtUword testcases
= applycheckfunctiontosimpleoptions(checkfunction_tab[idx].function,
&cmppairwise);
printf("# number of testcases for %s: " GT_WU "\n",
checkfunction_tab[idx].name,testcases);
}
}
}
freesimpleoption(&cmppairwise);
if (oprval == GT_OPTION_PARSER_REQUESTS_EXIT)
{
return 0;
}
if (oprval == GT_OPTION_PARSER_ERROR)
{
return -1;
}
return 0;
}
int gt_paircmp(int argc, const char **argv, GtError *err)
{
int parsed_args;
Cmppairwiseopt cmppairwise;
GtOPrval oprval;
GtFastaReader *reader0 = NULL,
*reader1 = NULL;
gt_error_check(err);
oprval = parse_options(&parsed_args, &cmppairwise, argc, argv, err);
if (oprval == GT_OPTION_PARSER_OK)
{
gt_assert(parsed_args == argc);
showsimpleoptions(&cmppairwise);
if (cmppairwise.showedist)
{
GtUword edist, len1, len2;
GtStr *s1, *s2;
gt_assert(gt_str_array_size(cmppairwise.strings) >= 2);
s1 = gt_str_array_get_str(cmppairwise.strings,0);
s2 = gt_str_array_get_str(cmppairwise.strings,1UL);
len1 = gt_str_length(s1);
len2 = gt_str_length(s2);
edist = gt_computegreedyunitedist((const GtUchar *) gt_str_get(s1),
len1,
(const GtUchar *) gt_str_get(s2),
len2);
printf(GT_WU " " GT_WU " " GT_WU " " GT_WU "%% errors\n",
edist, len1,len2,(200 * edist)/(len1+len2));
}
else if (cmppairwise.print)
{
const GtStr *str0 = gt_str_array_get_str(cmppairwise.strings,0),
*str1 = gt_str_array_get_str(cmppairwise.strings,1);
gt_print_edist_alignment((const GtUchar *) gt_str_get(str0),0,
gt_str_length(str0),
(const GtUchar *) gt_str_get(str1),0,
gt_str_length(str1));
} else
{
size_t idx;
Checkfunctiontabentry checkfunction_tab[] = {
MAKECheckfunctiontabentry(gt_checkgreedyunitedist),
MAKECheckfunctiontabentry(gt_checklinearspace),
MAKECheckfunctiontabentry(gt_checklinearspace_local),
MAKECheckfunctiontabentry(gt_checkaffinelinearspace),
MAKECheckfunctiontabentry(gt_checkaffinelinearspace_local),
MAKECheckfunctiontabentry(gt_checkdiagonalbandalign),
MAKECheckfunctiontabentry(gt_checkdiagonalbandaffinealign)
};
if (cmppairwise.fasta)
{
gt_assert(gt_str_array_size(cmppairwise.files) == 3);
cmppairwise.fastasequences0 = gt_str_array_new();
cmppairwise.fastasequences1 = gt_str_array_new();
reader0 = gt_fasta_reader_rec_new(gt_str_array_get_str(
cmppairwise.files,1UL));
gt_fasta_reader_run(reader0, NULL, save_fastaentry,
NULL, cmppairwise.fastasequences0, err);
reader1 = gt_fasta_reader_rec_new (gt_str_array_get_str(
cmppairwise.files,2UL));
gt_fasta_reader_run(reader1, NULL, save_fastaentry,
NULL, cmppairwise.fastasequences1, err);
gt_error_check(err);
}
for (idx = 0; idx < sizeof checkfunction_tab/sizeof checkfunction_tab[0];
idx++)
{
GtUword testcases;
printf("run %s\n",checkfunction_tab[idx].name);
testcases
= applycheckfunctiontosimpleoptions(checkfunction_tab[idx].function,
&cmppairwise);
printf("# number of testcases for %s: " GT_WU "\n",
checkfunction_tab[idx].name,testcases);
}
gt_fasta_reader_delete(reader0);
gt_fasta_reader_delete(reader1);
}
}
freesimpleoption(&cmppairwise);
if (oprval == GT_OPTION_PARSER_REQUESTS_EXIT)
{
return 0;
}
if (oprval == GT_OPTION_PARSER_ERROR)
{
return -1;
}
return 0;
}