int
brot_main(const char *cmdline)
{
struct brot_args_info brot_args;
SeqMatrix* sm = NULL;
int retval = 0;
Scmf_Rna_Opt_data* sim_data = NULL;
GFile* entropy_file = NULL;
/* command line parsing */
brot_cmdline_parser_init (&brot_args);
retval = brot_cmdline_parser_string (cmdline, &brot_args, get_progname());
if (retval == 0)
{
retval = brot_cmdline_parser_required (&brot_args, get_progname());
}
/* postprocess arguments */
if (retval == 0)
{
retval = brot_cmdline_parser_postprocess (&brot_args);
}
/* init simulation data */
if (retval == 0)
{
sim_data = SCMF_RNA_OPT_DATA_NEW_INIT(brot_args.inputs[1],
strlen (brot_args.inputs[1]),
RNA_ALPHABET,
strlen(RNA_ALPHABET)/2,
((-1) * ((logf (1 / 0.000001f)) / (strlen (brot_args.inputs[1])))));
if (sim_data == NULL)
{
retval = 1;
}
}
/* init matrix */
if (retval == 0)
{
sm = SEQMATRIX_NEW;
if (sm != NULL)
{
retval = SEQMATRIX_INIT (
alphabet_size (scmf_rna_opt_data_get_alphabet (sim_data)),
strlen (brot_args.inputs[1]),
sm);
/*seqmatrix_print_2_stdout (6, sm);*/
}
else
{
retval = 1;
}
}
/* fix certain sites in the matrix */
if (retval == 0)
{
retval = adopt_site_presettings (&brot_args,
scmf_rna_opt_data_get_alphabet (sim_data),
sm);
}
/* open entropy file if name given */
if (brot_args.entropy_output_given)
{
entropy_file = GFILE_OPEN (brot_args.entropy_output_arg,
strlen (brot_args.entropy_output_arg),
GFILE_VOID, "a");
if (entropy_file == NULL)
{
retval = 1;
}
else
{
if (gfile_printf (entropy_file, "# bROT settings:\n") < 0)
{
retval = 1;
}
else if (gfile_printf (entropy_file, "# steps: %lu\n",
brot_args.steps_arg) < 0)
{
retval = 1;
}
else if (gfile_printf (entropy_file, "# temp: %f\n",
brot_args.temp_arg) < 0)
{
retval = 1;
}
else if (gfile_printf (entropy_file, "# beta-short: %f\n",
brot_args.beta_short_arg) < 0)
{
retval = 1;
}
else if (gfile_printf (entropy_file, "# beta-long: %f\n",
brot_args.beta_long_arg) < 0)
{
retval = 1;
}
else if (gfile_printf (entropy_file, "# speedup-threshold: %f\n",
brot_args.speedup_threshold_arg) < 0)
{
retval = 1;
}
else if (gfile_printf (entropy_file, "# min-cool: %f\n",
brot_args.min_cool_arg) < 0)
{
retval = 1;
}
else if (gfile_printf (entropy_file, "# scale-cool: %f\n",
brot_args.scale_cool_arg) < 0)
{
retval = 1;
}
else if (gfile_printf (entropy_file, "# lambda: %f\n",
brot_args.lambda_arg) < 0)
{
retval = 1;
}
else if (gfile_printf (entropy_file, "# sm-entropy: %f\n",
brot_args.sm_entropy_arg) < 0)
{
retval = 1;
}
}
}
if (retval == 0)
{
if (brot_args.scoring_arg == scoring_arg_simpleNN)
{
/* special to NN usage: structure has to be of size >= 2 */
if (strlen (brot_args.inputs[1]) > 1)
{
retval = simulate_using_simplenn_scoring (&brot_args,
sm,
sim_data,
entropy_file);
}
else
{
THROW_ERROR_MSG (NN_2_SMALL_WARNING,
brot_args.inputs[1],
(unsigned long) strlen (brot_args.inputs[1]));
retval = 1;
}
}
else if (brot_args.scoring_arg == scoring_arg_nussinov)
{
retval = simulate_using_nussinov_scoring (&brot_args,
sm,
sim_data,
entropy_file);
}
else if (brot_args.scoring_arg == scoring_arg_NN)
{
/* special to NN usage: structure has to be of size >= 2 */
if (strlen (brot_args.inputs[1]) > 1)
{
retval = simulate_using_nn_scoring (&brot_args,
sm,
sim_data,
entropy_file);
}
else
{
THROW_ERROR_MSG (NN_2_SMALL_WARNING,
brot_args.inputs[1],
(unsigned long) strlen (brot_args.inputs[1]));
retval = 1;
}
}
}
/* close entropy file */
if (retval == 0)
{
retval = gfile_close (entropy_file);
}
else
{
gfile_close (entropy_file);
}
if (retval == 0)
{
/* seqmatrix_print_2_stdout (2, sm); */
mprintf ("%s\n", scmf_rna_opt_data_get_seq(sim_data));
}
/* finalise */
brot_cmdline_parser_free (&brot_args);
seqmatrix_delete (sm);
scmf_rna_opt_data_delete (sim_data);
if (retval == 0)
{
return EXIT_SUCCESS;
}
else
{
return EXIT_FAILURE;
}
}
int
brot_main(const char *cmdline)
{
struct brot_args_info brot_args;
SeqMatrix* sm = NULL;
int retval = 0;
Scmf_Rna_Opt_data* sim_data = NULL;
GFile* entropy_file = NULL;
GFile* simulation_file = NULL;
/* command line parsing */
brot_cmdline_parser_init (&brot_args);
retval = brot_cmdline_parser_string (cmdline, &brot_args, get_progname());
if (retval == 0)
{
retval = brot_cmdline_parser_required (&brot_args, get_progname());
}
/* postprocess arguments */
if (retval == 0)
{
retval = brot_cmdline_parser_postprocess (&brot_args, cmdline);
}
/* init simulation data */
if (retval == 0)
{
sim_data = SCMF_RNA_OPT_DATA_NEW_INIT(brot_args.inputs[1],
strlen (brot_args.inputs[1]),
RNA_ALPHABET,
strlen(RNA_ALPHABET)/2,
((-1) * ((logf (1 / 0.000001f)) / (strlen (brot_args.inputs[1])))),
brot_args.file_given);
if (sim_data == NULL)
{
retval = 1;
}
}
/* init matrix */
if (retval == 0)
{
sm = SEQMATRIX_NEW;
if (sm != NULL)
{
retval = SEQMATRIX_INIT (
alphabet_size (scmf_rna_opt_data_get_alphabet (sim_data)),
scmf_rna_opt_data_get_rna_size(sim_data),
/* strlen (brot_args.inputs[1]), */
sm);
/*seqmatrix_print_2_stdout (6, sm);*/
}
else
{
retval = 1;
}
}
/* fix certain sites in the matrix */
if (retval == 0)
{
retval = adopt_site_presettings (&brot_args,
scmf_rna_opt_data_get_alphabet (sim_data),
sim_data,
sm);
}
/* open entropy file if name given */
if (retval == 0)
{
print_verbose ("# Entropy file (-p): ");
if (brot_args.entropy_output_given)
{
print_verbose ("%s", brot_args.entropy_output_arg);
entropy_file = GFILE_OPEN (brot_args.entropy_output_arg,
strlen (brot_args.entropy_output_arg),
GFILE_VOID, "a");
if (entropy_file == NULL)
{
retval = 1;
}
else
{
retval = brot_settings_2_file (entropy_file, cmdline);
}
}
/* open simulation/ matrix file if name given */
print_verbose ("\n# Simulation/ Matrix file (-m): ");
if (brot_args.simulation_output_given)
{
print_verbose ("%s", brot_args.simulation_output_arg);
simulation_file = GFILE_OPEN (brot_args.simulation_output_arg,
strlen (brot_args.simulation_output_arg),
GFILE_VOID, "a");
if (simulation_file == NULL)
{
retval = 1;
}
else
{
retval = brot_settings_2_file (simulation_file, cmdline);
if (retval == 0)
{
if (gfile_printf (simulation_file, "START\n") < 0)
{
retval = 1;
}
}
}
}
}
if (retval == 0)
{
print_verbose ("\n# Scoring scheme (-c): ");
if (brot_args.scoring_arg == scoring_arg_simpleNN)
{
print_verbose ("simpleNN\n");
/* special to NN usage: structure has to be of size >= 2 */
if (strlen (brot_args.inputs[1]) > 1)
{
retval = simulate_using_simplenn_scoring (&brot_args,
sm,
sim_data,
entropy_file,
simulation_file);
}
else
{
THROW_ERROR_MSG (NN_2_SMALL_WARNING,
brot_args.inputs[1],
(unsigned long) strlen (brot_args.inputs[1]));
retval = 1;
}
}
else if (brot_args.scoring_arg == scoring_arg_nussinov)
{
print_verbose ("nussinov\n");
retval = simulate_using_nussinov_scoring (&brot_args,
sm,
sim_data,
entropy_file,
simulation_file);
}
else if (brot_args.scoring_arg == scoring_arg_NN)
{
print_verbose ("NN\n");
/* special to NN usage: structure has to be of size >= 2 */
if (strlen (brot_args.inputs[1]) > 1)
{
retval = simulate_using_nn_scoring (&brot_args,
sm,
sim_data,
entropy_file,
simulation_file);
}
else
{
THROW_ERROR_MSG (NN_2_SMALL_WARNING,
brot_args.inputs[1],
(unsigned long) strlen (brot_args.inputs[1]));
retval = 1;
}
}
}
/* close files */
if (retval == 0)
{
retval = gfile_close (entropy_file);
}
else
{
gfile_close (entropy_file);
}
if (simulation_file != NULL)
{
if (gfile_printf (simulation_file, "END\n") < 0)
{
retval = 1;
}
}
if (retval == 0)
{
retval = gfile_close (simulation_file);
}
else
{
gfile_close (simulation_file);
}
if (retval == 0)
{
/*seqmatrix_print_2_stdout (2, sm);*/
mprintf ("%s\n", scmf_rna_opt_data_get_seq(sim_data));
}
/* finalise */
brot_cmdline_parser_free (&brot_args);
seqmatrix_delete (sm);
scmf_rna_opt_data_delete (sim_data);
if (retval == 0)
{
return EXIT_SUCCESS;
}
else
{
return EXIT_FAILURE;
}
}