int mb_cu_init(char *addr, unsigned int port, unsigned int local_port)
{
printf("\n\n"
"= = = = = = = = = = = = = = = = = = =\n"
"\n"
"module\t:%s\n"
"version\t:%s\n"
"date\t:"__DATE__" "__TIME__"\n"
"\n"
"= = = = = = = = = = = = = = = = = = =\n"
"\n\n"
, MB_NAME
, MB_VERSION);
g_mb_req_list = list_new();
//printf("init g_mb_req_list:%p\n", g_mb_req_list);
g_seq = seq_new();
g_mb_hdl = mb_hdl_new(addr
, port
, g_seq
, g_mb_req_list);
if(g_mb_hdl == NULL)
{
printf("mb cu init error!\n");
return -1;
}
else
{
printf("mb cu init success!\n");
}
return 0;
}
create_monster() {
if (IS_CLONE) {
set_name("bert");
set_living_name("bert");
default_config_npc(100);
config_default_trade();
set_money_give_reduce( ({ 0, 2, 3, 3 }) );
seq_new("foo");
seq_addfirst("foo", ({ "@@do_give" }) );
static int64_t * seq_create (seqhash_t *s, const char *name)
{
int rc;
int64_t *v;
if (zhash_lookup (s->vhash, name)) {
errno = EEXIST;
return (NULL);
}
v = seq_new ();
rc = zhash_insert (s->vhash, xstrdup (name), v);
assert (rc >= 0);
zhash_freefn (s->vhash, name, free);
return (v);
}
void run_scan( int argc, char *argv[] )
{
/* Martin A. Hansen, September 2008 */
/* For each file in argv scan the file for */
/* bipartite motifs and output the motifs */
/* and their count. */
char *file = NULL;
int i = 0;
seq_entry *entry = NULL;
uint *count_array = NULL;
// size_t new_nmemb = 0;
count_array = count_array_new( COUNT_ARRAY_NMEMB );
entry = seq_new( MAX_SEQ_NAME, MAX_SEQ );
for ( i = 1; i < argc; i++ )
{
file = argv[ i ];
fprintf( stderr, "Scanning file: %s\n", file );
scan_file( file, entry, count_array );
fprintf( stderr, "done.\n" );
}
// fprintf( stderr, "Printing motifs: ... " );
// count_array_print( count_array, COUNT_ARRAY_NMEMB, CUTOFF );
// fprintf( stderr, "done.\n" );
file = argv[ 1 ];
fprintf( stderr, "Rescanning file: %s\n", file );
rescan_file( file, entry, count_array, CUTOFF );
fprintf( stderr, "done.\n" );
seq_destroy( entry );
mem_free( &count_array );
}
int main(int argc, char **argv) {
Seq *seq;
char *seq_str;
gzFile f;
if(argc != 2) {
fprintf(stderr, "usage: %s <nuc_str>\n", argv[0]);
exit(2);
}
seq = seq_new();
seq_read_str(seq, argv[1]);
fprintf(stderr, "seq->len=%ld\n", seq->len);
seq_str = seq_get_seqstr(seq);
fprintf(stderr, "%s\n", seq_str);
my_free(seq_str);
fprintf(stderr, "reading from fasta\n");
f = gzopen("test.fa.gz", "wb");
seq_write_fasta_record(seq, f);
gzclose(f);
fprintf(stderr, "writing to fasta\n");
f = gzopen("test.fa.gz", "rb");
seq_read_fasta_record(seq, f);
gzclose(f);
fprintf(stderr, "seq->len=%ld\n", seq->len);
seq_str = seq_get_seqstr(seq);
fprintf(stderr, "%s\n", seq_str);
my_free(seq_str);
seq_free(seq);
return 0;
}
create_monster()
{
/* We ignore the master object
*/
if (!IS_CLONE)
return;
set_name("ugluk");
set_race_name("troll");
set_adj("nasty");
set_long("It is a very ugly and nasty lookin' troll.\n");
/* Average stat: 5
*/
default_config_npc(5);
/* But we want it to have more hitpoints
*/
set_base_stat(SS_CON, 20);
set_hp(1000);
seq_new("do_things");
seq_addfirst("do_things",({"@@arm_me","say Ok, come on you bastards!"}));
int main(int argc, char **argv) {
char **fasta_files;
int seed_len, i, n_fasta_files;
ChrTable *chr_tab;
SeedTable *seed_tab;
Seq *seq;
gzFile gzf, out_gzf;
char *out_filename;
if(argc < 4) {
fprintf(stderr, "usage: %s <seed_len> <chromInfo.txt> "
"<output_seed_index.gz> [chr1.fa.gz [chr2.fa.gz [...]]]\n",
argv[0]);
exit(2);
}
seed_len = util_parse_long(argv[1]);
fasta_files = &argv[4];
n_fasta_files = argc - 4;
out_filename = argv[3];
/* read chromosomes and make table containing offsets for both
* forward and reverse strands (so we can represent genomic
* coordinates with a single long integer).
*/
chr_tab = chr_table_read(argv[2]);
fprintf(stderr, "there are %d chromosomes, total length: %u\n",
chr_tab->n_chr, chr_tab->total_chr_len);
/* create a table to hold seed matches */
fprintf(stderr, "initializing seed table\n");
seed_tab = seed_table_new(seed_len);
/* open an output file to write seed table to */
if(util_file_exists(out_filename)) {
my_err("output file %s already exists\n", out_filename);
exit(2);
}
out_gzf = util_must_gzopen(out_filename, "wb");
/*
* first pass: count number of matches to each seed
*/
seq = seq_new();
for(i = 0; i < n_fasta_files; i++) {
fprintf(stderr, "reading sequence from file %s\n", fasta_files[i]);
gzf = util_must_gzopen(fasta_files[i], "rb");
while(seq_read_fasta_record(seq, gzf)) {
fprintf(stderr, "%s %ld\n", seq->name, seq->len);
fprintf(stderr, "counting seed matches\n");
count_matches(chr_tab, seed_tab, seq);
}
gzclose(gzf);
}
/*
* second pass: store location of each match
*/
for(i = 0; i < n_fasta_files; i++) {
fprintf(stderr, "reading sequence from file %s\n", fasta_files[i]);
gzf = util_must_gzopen(fasta_files[i], "rb");
while(seq_read_fasta_record(seq, gzf)) {
fprintf(stderr, "%s %ld\n", seq->name, seq->len);
fprintf(stderr, "recording seed match positions\n");
add_matches(chr_tab, seed_tab, seq);
}
gzclose(gzf);
}
seq_free(seq);
/* write table to file in binary format */
fprintf(stderr, "writing seed table to file %s\n", out_filename);
seed_table_write(seed_tab, out_gzf);
gzclose(out_gzf);
chr_table_free(chr_tab);
seed_table_free(seed_tab);
return 0;
}
