/* Initially, align all string pairs greedily, i.e. e.g. <abcd, ax> => <abcd,ax00> */
void initial_align() {
struct stringpair *pair;
int inlen, outlen, i, j, k;
for (pair = g_stringpairs; pair != NULL; pair = pair->next) {
inlen = intseqlen(pair->in);
outlen = intseqlen(pair->out);
pair->inaligned = malloc(sizeof(int) * (inlen+outlen+1));
pair->outaligned = malloc(sizeof(int) * (inlen+outlen+1));
for (i = 0, j = 0, k = 0; pair->in[i] != -1 || pair->out[j] != -1; k++) {
if (pair->in[i] == -1) {
pair->inaligned[k] = 0;
pair->outaligned[k] = pair->out[j];
j++;
}
else if (pair->out[j] == -1) {
pair->inaligned[k] = pair->in[i];
pair->outaligned[k] = 0;
i++;
} else {
pair->inaligned[k] = pair->in[i];
pair->outaligned[k] = pair->out[j];
i++;
j++;
}
}
pair->inaligned[k] = -1;
pair->outaligned[k] = -1;
add_counts(pair->inaligned, pair->outaligned);
}
}
void crp_train(int iterations, int burnin, int lag) {
struct stringpair *sp;
int i, j;
for (i = 0; i < iterations; i++) {
fprintf(stderr,"Alignment iteration: %i\n", i);
print_counts();
for (sp = g_stringpairs; sp != NULL; sp = sp->next) {
remove_counts(sp->inaligned, sp->outaligned); /* Remove counts before aligning */
fill_trellis(sp->in, sp->out, &cost_crp, MATRIX_MODE_GS);
for (j = 0; g_in_result[j] != -1; j++) {
sp->inaligned[j] = g_in_result[j];
sp->outaligned[j] = g_out_result[j];
}
sp->inaligned[j] = -1;
sp->outaligned[j] = -1;
add_counts(sp->inaligned, sp->outaligned); /* Add counts back from new alignment */
}
if (i > burnin && i % lag == 0) {
add_global_counts();
}
}
}
/*----------------------------------------------------------------------*/
int main(int argc, char **argv)
{
/* MBIO status variables */
int status = MB_SUCCESS;
int error = MB_ERROR_NO_ERROR;
/* MBIO read control parameters */
int read_datalist = MB_NO;
void *datalist;
int look_processed = MB_DATALIST_LOOK_UNSET;
double file_weight;
mb_path ifile;
/* MBIO read values */
int read_data;
/* counting variables */
counts filerecs;
counts totrecs;
/* processing variables */
options opts;
mbdefaults mbdflts;
/* set default options */
default_options(&opts);
/* mb_mem_debug_on(opts.verbose, &error); */
/* get mbsystem default values */
status = mb_defaults(opts.verbose, &(mbdflts.format), &(mbdflts.pings_get),
&(mbdflts.lonflip), mbdflts.bounds, mbdflts.btime_i,
mbdflts.etime_i, &(mbdflts.speedmin),
&(mbdflts.timegap));
if (status == MB_SUCCESS)
{
parse_options(opts.verbose, argc, argv, &opts, &error);
}
if (opts.errflg)
{
fprintf(stderr, "usage: %s\n", usage_message);
fprintf(stderr, "\nProgram <%s> Terminated\n", program_name);
error = MB_ERROR_BAD_USAGE;
exit(error);
}
/* print starting debug statements */
if (opts.verbose >= 1)
{
print_mbdefaults(opts.verbose, &opts, &mbdflts, &error);
}
/* if help desired then print it and exit */
if (opts.help)
{
fprintf(stderr, "\nProgram %s\n", program_name);
fprintf(stderr, "Version %s\n", rcs_id);
fprintf(stderr, "MB-system Version %s\n", MB_VERSION);
fprintf(stderr, "\nusage: %s\n", usage_message);
fprintf(stderr, "\n%s\n", help_message);
exit(error);
}
/* get format if required */
if (opts.format == 0)
{
mb_get_format(opts.verbose, opts.read_file, NULL, &(opts.format),
&error);
}
/* determine whether to read one file or a list of files */
if (opts.format < 0)
{
read_datalist = MB_YES;
}
/* open file list */
if (read_datalist == MB_YES)
{
if ((status =
mb_datalist_open(opts.verbose, &datalist, opts.read_file,
look_processed, &error)) != MB_SUCCESS)
{
char message[MAX_ERROR_STRING];
sprintf(message, "Unable to open data list file: %s\n",
opts.read_file);
error_exit(opts.verbose, MB_ERROR_OPEN_FAIL, "mb_datalist_open",
message);
}
if ((status =
mb_datalist_read(opts.verbose, datalist, ifile, &(opts.format),
&file_weight, &error)) == MB_SUCCESS)
{
read_data = MB_YES;
}
else
{
read_data = MB_NO;
}
}
/* else copy single filename to be read */
else
{
strcpy(ifile, opts.read_file);
read_data = MB_YES;
}
/* reset total record counter */
zero_counts(opts.verbose, &totrecs, &error);
/* loop over files to be read */
while (read_data == MB_YES)
{
/* reset file record counter */
zero_counts(opts.verbose, &filerecs, &error);
/* process the output files */
if (status == MB_SUCCESS)
{
status = process_output(opts.verbose, &mbdflts, &opts, ifile,
&filerecs, &error);
}
/* output counts */
filerecs.files_read++;
if (opts.verbose >= 1)
{
fprintf(stdout, "\nData records read from: %s\n", ifile);
print_counts(opts.verbose, &filerecs, &error);
}
/* add this file's counts to total */
add_counts(opts.verbose, &totrecs, &filerecs, &error);
/* figure out whether and what to read next */
if (read_datalist == MB_YES)
{
if ((status =
mb_datalist_read(opts.verbose, datalist, ifile, &(opts.format),
&file_weight, &error)) == MB_SUCCESS)
{
read_data = MB_YES;
}
else
{
read_data = MB_NO;
}
}
else
{
read_data = MB_NO;
}
} /* end loop over files in list */
/* output counts */
if (opts.verbose >= 1)
{
fprintf(stdout, "\nTotal data records read:\n");
print_counts(opts.verbose, &totrecs, &error);
}
if (read_datalist == MB_YES)
{
mb_datalist_close(opts.verbose, &datalist, &error);
}
/* check memory */
status = mb_memory_list(opts.verbose, &error);
/* mb_mem_debug_off(opts.verbose, &error); */
return (status);
} /* main */
