int tr_trans_task(int argc, char *argv[])
{
FILE *fp;
MultiAlign *ma, *tma;
if (argc == 1) return tr_trans_usage();
fp = tr_get_fp(argv[1]);
tma = ma_read_alignment(fp, 1);
ma = ma_trans_align(tma, 1); /* translate to amino acids */
tr_align_output(stdout, ma);
ma_free(ma);
ma_free(tma);
if (fp != stdin) fclose(fp);
return 0;
}
int tr_filter_task(int argc, char *argv[])
{
int c, is_collapse = 0;
int is_nucl = 0;
int cut_off = 15;
FILE *fp;
int is_mask = 1;
int is_mask_segments = 1;
MultiAlign *ma;
while ((c = getopt(argc, argv, "F:ngMN")) >= 0) {
switch (c) {
case 'n': is_nucl = 1; break;
case 'g': is_collapse = 1; break;
case 'N': is_mask_segments = 0; break;
case 'M': is_mask = 0; break;
case 'F': cut_off = atoi(optarg); break;
}
}
if (optind == argc) return tr_filter_usage();
fp = tr_get_fp(argv[optind]);
ma = ma_read_alignment(fp, is_nucl);
if (is_mask) ma_apply_mask(ma);
ma_filter(ma, is_collapse, cut_off, is_mask_segments);
tr_align_output(stdout, ma);
ma_free(ma);
if (fp != stdin) fclose(fp);
return 0;
}
void tr_delete_task(Task *t)
{
if (t->aln) ma_free(t->aln);
if (t->spec_tree) {
tr_delete_tree_SDIptr(t->tree);
if (t->subtree) tr_delete_tree_SDIptr(t->subtree);
tr_delete_tree(t->spec_tree);
}
if (t->tree) tr_delete_tree_SDIptr(t->tree);
if (t->compared) tr_delete_tree(t->compared);
if (t->subtree && tr_search(t->tree, t->subtree) == 0) /* not a node in t->tree */
tr_delete_tree(t->subtree);
if (t->tree) tr_delete_tree(t->tree);
if (t->cut) free(t->cut);
if (t->ortho) tr_delete_ortho(t->ortho);
if (t->n_con) {
int i;
for (i = 0; i < t->n_con; ++i)
tr_delete_tree(t->constraint[i]);
free(t->constraint);
}
if (t->n_sub) {
int i;
for (i = 0; i < t->n_sub; ++i)
free(t->sub_name[i]);
free(t->sub_name);
}
free(t);
}
void lengthfixed_mtmp::free(void *p, size_t sz)
{
NUT_DEBUGGING_ASSERT_ALIVE;
assert(NULL != p && _granularity == std::max(sz, sizeof(void*)));
while(true)
{
if (_free_num >= (int) MAX_FREE_NUM) // NOTE _free_num 只起参考作用
{
ma_free(_alloc, p, _granularity);
return;
}
const TagedPtr<void> old_head(_head.cas);
*reinterpret_cast<void**>(p) = old_head.ptr;
const TagedPtr<void> new_head(p, old_head.tag + 1);
if (atomic_cas(&(_head.cas), old_head.cas, new_head.cas))
{
// NOTE _free_num 在多线程下并不可靠
if (NULL == old_head.ptr)
_free_num = 1;
else
++_free_num;
return;
}
}
}
void lengthfixed_mtmp::clear()
{
NUT_DEBUGGING_ASSERT_ALIVE;
void *p = _head.ptr;
while (NULL != p)
{
void *next = *reinterpret_cast<void**>(p);
ma_free(_alloc, p, _granularity);
p = next;
}
_head.ptr = NULL;
_free_num = 0;
}
void lengthfixed_stmp::free(void *p, size_t sz)
{
NUT_DEBUGGING_ASSERT_ALIVE;
assert(NULL != p && _granularity == std::max(sz, sizeof(void*)));
if (_free_num >= (int) MAX_FREE_NUM)
{
ma_free(_alloc, p, _granularity);
return;
}
*reinterpret_cast<void**>(p) = _head;
_head = p;
++_free_num;
}
int tr_mfa2aln_task(int argc, char *argv[])
{
MultiAlign *ma;
FILE *fp;
int c, is_nucl = 0;
while ((c = getopt(argc, argv, "n")) >= 0) {
switch (c) {
case 'n': is_nucl = 1; break;
}
}
if (optind == argc) return tr_mfa2aln_usage();
fp = tr_get_fp(argv[optind]);
ma = ma_read_alignment(fp, is_nucl);
tr_align_aln_output(stdout, ma);
ma_free(ma);
if (fp != stdin) fclose(fp);
return 0;
}
/*
Release SSL and free resources
Will be automatically executed by
mysql_server_end() function
SYNOPSIS
my_ssl_end()
void
RETURN VALUES
void
*/
void ma_tls_end()
{
if (ma_tls_initialized)
{
pthread_mutex_lock(&LOCK_openssl_config);
#if OPENSSL_VERSION_NUMBER < 0x10100000L
CRYPTO_set_locking_callback(NULL);
CRYPTO_set_id_callback(NULL);
{
int i;
for (i=0; i < CRYPTO_num_locks(); i++)
pthread_mutex_destroy(&LOCK_crypto[i]);
}
ma_free((gptr)LOCK_crypto);
LOCK_crypto= NULL;
#endif
if (SSL_context)
{
SSL_CTX_free(SSL_context);
SSL_context= NULL;
}
if (mariadb_deinitialize_ssl)
{
#if OPENSSL_VERSION_NUMBER < 0x10100000L
ERR_remove_state(0);
#endif
EVP_cleanup();
CRYPTO_cleanup_all_ex_data();
ERR_free_strings();
CONF_modules_free();
CONF_modules_unload(1);
}
ma_tls_initialized= FALSE;
pthread_mutex_unlock(&LOCK_openssl_config);
pthread_mutex_destroy(&LOCK_openssl_config);
}
return;
}
unsigned int ma_tls_get_finger_print(MARIADB_TLS *ctls, unsigned char *fp, unsigned int len)
{
EVP_MD *digest= (EVP_MD *)EVP_sha1();
X509 *cert;
MYSQL *mysql;
unsigned int fp_len;
if (!ctls || !ctls->ssl)
return 0;
mysql= SSL_get_app_data(ctls->ssl);
if (!(cert= SSL_get_peer_certificate(ctls->ssl)))
{
my_set_error(mysql, CR_SSL_CONNECTION_ERROR, SQLSTATE_UNKNOWN,
ER(CR_SSL_CONNECTION_ERROR),
"Unable to get server certificate");
return 0;
}
if (len < EVP_MAX_MD_SIZE)
{
my_set_error(mysql, CR_SSL_CONNECTION_ERROR, SQLSTATE_UNKNOWN,
ER(CR_SSL_CONNECTION_ERROR),
"Finger print buffer too small");
return 0;
}
fp_len= len;
if (!X509_digest(cert, digest, fp, &fp_len))
{
ma_free(fp);
my_set_error(mysql, CR_SSL_CONNECTION_ERROR, SQLSTATE_UNKNOWN,
ER(CR_SSL_CONNECTION_ERROR),
"invalid finger print of server certificate");
return 0;
}
return (fp_len);
}
/*
Release SSL and free resources
Will be automatically executed by
mysql_server_end() function
SYNOPSIS
my_ssl_end()
void
RETURN VALUES
void
*/
void ma_tls_end()
{
if (ma_tls_initialized)
{
int i;
pthread_mutex_lock(&LOCK_openssl_config);
CRYPTO_set_locking_callback(NULL);
CRYPTO_set_id_callback(NULL);
for (i=0; i < CRYPTO_num_locks(); i++)
pthread_mutex_destroy(&LOCK_crypto[i]);
ma_free((gptr)LOCK_crypto);
LOCK_crypto= NULL;
if (SSL_context)
{
SSL_CTX_free(SSL_context);
SSL_context= NULL;
}
if (mariadb_deinitialize_ssl)
{
ERR_remove_state(0);
EVP_cleanup();
CRYPTO_cleanup_all_ex_data();
ERR_free_strings();
CONF_modules_free();
CONF_modules_unload(1);
sk_SSL_COMP_free(SSL_COMP_get_compression_methods());
}
ma_tls_initialized= FALSE;
pthread_mutex_unlock(&LOCK_openssl_config);
pthread_mutex_destroy(&LOCK_openssl_config);
}
return;
}
/**
* Synchronize memory mapping with the file.
* Called from process context.
*/
static void
tempesta_unmap_file(struct file *file, unsigned long addr, unsigned long len,
int node)
{
mm_segment_t oldfs;
MArea *ma;
loff_t off = 0;
ssize_t r;
mutex_lock(&map_mtx);
ma = ma_lookup(addr, node);
if (!ma) {
TDB_WARN("Cannot sync memory area for %#lx address at node"
" %d\n", addr, node);
goto err;
}
oldfs = get_fs();
set_fs(get_ds());
r = kernel_write(file, (void *)ma->start, len, &off);
if (r != len) {
TDB_WARN("Cannot sync mapping %lx of size %lu pages\n",
ma->start, ma->pages);
goto err_fs;
}
err_fs:
set_fs(oldfs);
err:
fput(file);
ma_free(addr, node);
mutex_unlock(&map_mtx);
}
int tr_distmat_task(int argc, char *argv[])
{
extern Matrix *ma_init_matrix(const MultiAlign *ma);
extern void ma_init_nucl_data();
int type = -1;
int is_nucl = 0;
DistParam *dp;
MultiAlign *ma;
Matrix *mat;
FILE *fp;
if (argc < 3) return tr_distmat_usage();
if (strcmp(argv[1], "dn") == 0) { type = DIST_DN; is_nucl = 1; }
else if (strcmp(argv[1], "ds") == 0) { type = DIST_DS; is_nucl = 1; }
else if (strcmp(argv[1], "dm") == 0) { type = DIST_DM; is_nucl = 1; }
else if (strcmp(argv[1], "jtt") == 0) type = DIST_JTT;
else if (strcmp(argv[1], "kimura") == 0) type = DIST_KIMURA;
else if (strcmp(argv[1], "mm") == 0) type = DIST_MM;
else if (strcmp(argv[1], "dns") == 0) { type = -1; is_nucl = 1; }
else {
fprintf(stderr, "ERROR: unrecognized type %s\n", argv[1]);
return 1;
}
fp = tr_get_fp(argv[2]);
ma = ma_read_alignment(fp, is_nucl);
if (is_nucl) { /* special consideration for nucleotide alignment */
MultiAlign *ma_tmp;
ma_init_nucl_data();
ma_tmp = ma;
ma = ma_trans_align(ma_tmp, 0);
if (ma == 0) {
fprintf(stderr, "ERROR: it seems that your input contains errors!\n");
return 1;
}
ma_free(ma_tmp);
}
mat = ma_init_matrix(ma);
if (type >= 0) {
dp = ma_alloc_DistParam(type);
ma_cal_dist(mat, ma, 0, dp);
tr_matrix_output(stdout, mat);
ma_free_DistParam(dp);
} else {
Matrix *mat_ds;
int i, j;
float *p_dn, *p_ds;
/* calculate dn */
dp = ma_alloc_DistParam(DIST_DN);
ma_cal_dist(mat, ma, 0, dp);
ma_free_DistParam(dp);
/* calculate ds */
mat_ds = ma_init_matrix(ma);
dp = ma_alloc_DistParam(DIST_DS);
ma_cal_dist(mat_ds, ma, 0, dp);
ma_free_DistParam(dp);
for (i = 0; i < ma->n; ++i) {
p_dn = mat->dist + i * ma->n;
p_ds = mat_ds->dist + i * ma->n;
for (j = 0; j < i; ++j)
printf("%.6f\t%.6f\t%s\t%s\n", p_dn[j], p_ds[j], ma->name[i], ma->name[j]);
}
tr_delete_matrix(mat_ds);
}
ma_free(ma);
tr_delete_matrix(mat);
if (fp != stdin) fclose(fp);
return 0;
}
