Sequence* free_Alignment ( Alignment *LA)
{
/* Does not free the A->S field (sequences of A)*/
Sequence *S;
//aln_stack checks the alignment has not already been freed
if ( LA==NULL || !aln_stack(LA,FREE_ALN)){return NULL;}
S=LA->S;
free_char ( LA->file, -1);
free_char ( LA->seq_al, -1);
free_int ( LA->seq_cache, -1);
free_int ( LA->cdna_cache, -1);
free_char ( LA->name,-1);
free_char ( LA->tree_order,-1);
vfree ( LA->generic_comment);
free_char ( LA->seq_comment, -1);
free_char ( LA->aln_comment, -1);
free_int ( LA->order, -1);
vfree ( LA->score_seq);
vfree ( LA->len);
free_profile (LA->P);
if ( LA->A){free_Alignment (LA->A);LA->A=NULL;}
vfree ( LA);
return S;
}
static int unload_module(void) {
unsigned int i = 0;
LNOTICE("unloaded module %s", module_name);
for (i = 0; i < profile_size; i++) {
close_socket(i);
free_profile(i);
}
#if UV_VERSION_MAJOR == 0
uv_async_send(&async_handle);
uv_loop_delete(loop);
#else
if (uv_loop_alive(loop)) {
uv_async_send(&async_handle);
}
uv_stop(loop);
uv_loop_close(loop);
free(loop);
#endif
/* Close socket */
return 0;
}
static int unload_module(void) {
unsigned int i = 0;
LNOTICE("unloaded module %s", module_name);
for (i = 0; i < profile_size; i++) {
if(sniffer_proto[i]) {
pcap_breakloop(sniffer_proto[i]);
pthread_join(call_thread[i],NULL);
}
if (reasm[i] != NULL) {
reasm_ip_free(reasm[i]);
reasm[i] = NULL;
}
if (tcpreasm[i] != NULL) {
tcpreasm_ip_free(tcpreasm[i]);
tcpreasm[i] = NULL;
}
free_profile(i);
}
/* Close socket */
//pcap_close(sniffer_proto);
return 0;
}
int main(void)
{
/* here are some profile records */
profile_list[0] = create_profile("Mrs", "Kydd", "1428-330 Fake Street",
"Unit 1428", "Edmonton", "Alberta", "A1B2C3");
profile_list[1] = create_profile("Mr", "Kydd", "94 Fake Street",
"Unit 505", "Edmonton", "Alberta", "A1B2C3");
profile_list[2] = create_profile("Mr", "Kydd", "43 Fake Street",
"Unit 227", "Sherwood Park", "Alberta", "D4E5F6");
profile_list[3] = create_profile("Leeroy", "Jenkins",
"1943 Fake Avenue", "Apt 123", "Sherwood Park",
"Alberta", "D4E5F6");
/* sort the profiles */
(void)qsort(&profile_list, MAX_RECORDS, sizeof(struct profile *),
profilecmp);
/* print them out! */
int i = 0;
for(i = 0; i < MAX_RECORDS; i++) {
(void)print_profile(profile_list[i]);
}
/* free memory */
for(i = 0; i < MAX_RECORDS; i++) {
(void)free_profile(profile_list[i]);
}
return 0;
}
static void profile_rwunlock(dir_profile_t *profile)
{
switch_thread_rwlock_unlock(profile->rwlock);
if (switch_test_flag(profile, PFLAG_DESTROY)) {
if (switch_thread_rwlock_tryrdlock(profile->rwlock) == SWITCH_STATUS_SUCCESS) {
free_profile(profile);
}
}
}
static int unload_module(void)
{
unsigned int i = 0;
LNOTICE("unloaded module %s", module_name);
for (i = 0; i < profile_size; i++)
free_profile(i);
return 0;
}
static int unload_module(void)
{
unsigned int i = 0;
LNOTICE("unloaded module transport_json");
for (i = 0; i < profile_size; i++) {
free_profile(i);
}
return 0;
}
static int unload_module(void)
{
LNOTICE("Unloaded %s", module_name);
unsigned int i = 0;
for (i = 0; i < profile_size; i++) {
free_profile(i);
}
return 0;
}
static int unload_module(void)
{
LNOTICE("unloaded module protocol_sip");
unsigned int i = 0;
for (i = 0; i < profile_size; i++) {
free_profile(i);
}
/* Close socket */
//pcap_close(sniffer_proto);
return 0;
}
int main(int argc, char *argv[])
{
float *T[MAXSEQ];
int i,j, istty, n=0;
int type, length, taxa_list=0;
float dist;
FILE *somewhere=NULL;
char *structure;
char *line=NULL, fname[FILENAME_MAX_LENGTH], *list_title=NULL;
plist *pr_pl, *mfe_pl;
pr_pl = mfe_pl = NULL;
command_line(argc, argv);
if((outfile[0]=='\0')&&(task=='m')&&(edit_backtrack))
strcpy(outfile,"backtrack.file");
if (outfile[0]!='\0') somewhere = fopen(outfile,"w");
if (somewhere==NULL) somewhere = stdout;
istty = (isatty(fileno(stdout))&&isatty(fileno(stdin)));
while (1) {
if ((istty)&&(n==0)) {
printf("\nInput sequence; @ to quit\n");
printf("%s\n", ruler);
}
type = 0;
do { /* get sequence to fold */
if (line!=NULL) free(line);
*fname='\0';
if ((line=get_line(stdin))==NULL) {type = 999; break;}
if (line[0]=='@') type = 999;
if (line[0]=='*') {
if (taxa_list==0) {
if (task=='m') taxa_list=1;
printf("%s\n", line);
type = 0;
} else {
list_title = strdup(line);
type = 888;
}
}
if (line[0]=='>') {
if (sscanf(line,">%" XSTR(FILENAME_ID_LENGTH) "s", fname)!=0)
strcat(fname, "_dp.ps");
if (taxa_list)
printf("%d : %s\n", n+1, line+1);
else printf("%s\n",line);
type = 0;
}
if (isalpha(line[0])) {
char *cp;
cp =strchr(line,' ');
if (cp) *cp='\0';
type = 1;
}
} while(type==0);
if( (task == 'm')&&(type>800) ) {
if (taxa_list)
printf("* END of taxa list\n");
printf("> p %d (pdist)\n",n);
for (i=1; i<n; i++) {
for (j=0; j<i; j++) {
printf("%g ",profile_edit_distance(T[i], T[j]));
if(edit_backtrack) fprintf(somewhere,"> %d %d\n",i+1,j+1);
print_aligned_lines(somewhere);
}
printf("\n");
}
if (type==888) { /* do another distance matrix */
n = 0;
printf("%s\n", list_title);
free(list_title);
}
}
if(type>800) {
for (i=0; i<n; i++)
free_profile(T[i]);
if (type == 888) continue;
if (outfile[0]!='\0') (void) fclose(somewhere);
if (line!= NULL) free(line);
return 0; /* finito */
}
length = (int) strlen(line);
for (i=0; i<length; i++) {
line[i]=toupper(line[i]);
if (!noconv && line[i] == 'T') line[i] = 'U';
}
/* init_pf_fold(length); <- obsolete */
structure = (char *) space((length+1)*sizeof(char));
(void) pf_fold(line,structure);
if (*fname=='\0')
sprintf(fname, "%d_dp.ps", n+1);
/* PS_dot_plot(line, fname); <- NOT THREADSAFE and obsolete function! */
/* get pairlist of probability matrix */
assign_plist_from_pr(&pr_pl, pr, length, 1e-5);
/* no previous mfe call thus no mfe structure information known */
mfe_pl = (plist *)space(sizeof(plist));
mfe_pl[0].i = mfe_pl[0].j = 0;
/* call threadsafe dot plot printing function */
PS_dot_plot_list(line, fname, pr_pl, mfe_pl, "");
T[n] = Make_bp_profile_bppm(pr, length);
if((istty)&&(task=='m')) printf("%s\n",structure);
free(structure);
free(mfe_pl);
free(pr_pl);
free_pf_arrays();
n++;
switch (task) {
case 'p' :
if (n==2) {
dist = profile_edit_distance(T[0],T[1]);
printf("%g\n",dist);
print_aligned_lines(somewhere);
free_profile(T[0]);
free_profile(T[1]);
n=0;
}
break;
case 'f' :
if (n>1) {
dist = profile_edit_distance(T[1], T[0]);
printf("%g\n",dist);
print_aligned_lines(somewhere);
free_profile(T[1]);
n=1;
}
break;
case 'c' :
if (n>1) {
dist = profile_edit_distance(T[1], T[0]);
printf("%g\n",dist);
print_aligned_lines(somewhere);
free_profile(T[0]);
T[0] = T[1];
n=1;
}
break;
case 'm' :
break;
default :
nrerror("This can't happen.");
} /* END switch task */
(void) fflush(stdout);
} /* END while */
if (line !=NULL) free(line);
return 0;
}
void main()
{
char *seq1="CGCAGGGAUACCCGCG", *seq2="GCGCCCAUAGGGACGC",
*struct1,* struct2,* xstruc;
float e1, e2, tree_dist, string_dist, profile_dist, kT;
Tree *T1, *T2;
swString *S1, *S2;
float *pf1, *pf2;
FLT_OR_DBL *bppm;
/* fold at 30C instead of the default 37C */
temperature = 30.; /* must be set *before* initializing */
/* allocate memory for structure and fold */
struct1 = (char* ) space(sizeof(char)*(strlen(seq1)+1));
e1 = fold(seq1, struct1);
struct2 = (char* ) space(sizeof(char)*(strlen(seq2)+1));
e2 = fold(seq2, struct2);
free_arrays(); /* free arrays used in fold() */
/* produce tree and string representations for comparison */
xstruc = expand_Full(struct1);
T1 = make_tree(xstruc);
S1 = Make_swString(xstruc);
free(xstruc);
xstruc = expand_Full(struct2);
T2 = make_tree(xstruc);
S2 = Make_swString(xstruc);
free(xstruc);
/* calculate tree edit distance and aligned structures with gaps */
edit_backtrack = 1;
tree_dist = tree_edit_distance(T1, T2);
free_tree(T1); free_tree(T2);
unexpand_aligned_F(aligned_line);
printf("%s\n%s %3.2f\n", aligned_line[0], aligned_line[1], tree_dist);
/* same thing using string edit (alignment) distance */
string_dist = string_edit_distance(S1, S2);
free(S1); free(S2);
printf("%s mfe=%5.2f\n%s mfe=%5.2f dist=%3.2f\n",
aligned_line[0], e1, aligned_line[1], e2, string_dist);
/* for longer sequences one should also set a scaling factor for
partition function folding, e.g: */
kT = (temperature+273.15)*1.98717/1000.; /* kT in kcal/mol */
pf_scale = exp(-e1/kT/strlen(seq1));
/* calculate partition function and base pair probabilities */
e1 = pf_fold(seq1, struct1);
/* get the base pair probability matrix for the previous run of pf_fold() */
bppm = export_bppm();
pf1 = Make_bp_profile_bppm(bppm, strlen(seq1));
e2 = pf_fold(seq2, struct2);
/* get the base pair probability matrix for the previous run of pf_fold() */
bppm = export_bppm();
pf2 = Make_bp_profile_bppm(bppm, strlen(seq2));
free_pf_arrays(); /* free space allocated for pf_fold() */
profile_dist = profile_edit_distance(pf1, pf2);
printf("%s free energy=%5.2f\n%s free energy=%5.2f dist=%3.2f\n",
aligned_line[0], e1, aligned_line[1], e2, profile_dist);
free_profile(pf1); free_profile(pf2);
}
