static void
dump_info(GstVaapiDisplay *display)
{
GArray *profiles, *formats;
profiles = gst_vaapi_display_get_decode_profiles(display);
if (!profiles)
g_error("could not get VA decode profiles");
print_profiles(profiles, "decoders");
g_array_unref(profiles);
profiles = gst_vaapi_display_get_encode_profiles(display);
if (!profiles)
g_error("could not get VA encode profiles");
print_profiles(profiles, "encoders");
g_array_unref(profiles);
formats = gst_vaapi_display_get_image_formats(display);
if (!formats)
g_error("could not get VA image formats");
print_formats(formats, "image");
g_array_unref(formats);
formats = gst_vaapi_display_get_subpicture_formats(display);
if (!formats)
g_error("could not get VA subpicture formats");
print_formats(formats, "subpicture");
g_array_unref(formats);
dump_properties(display);
}
/**
* @brief Output the result of profile check.
*/
static void
BULKLOAD_PROFILE_PRINT()
{
int i;
double seconds[10];
const char *GLOBALs[] = { "INIT", "READER", "WRITER", "RESET", "FLUSH", "MERGE", "INDEX", "REINDEX", "FINI" };
const char *READERs[] = { "SOURCE", "PARSER" };
const char *WRITERs[] = { "TOAST", "TABLE", "INDEX" };
const char *MERGEs[] = { "UNIQUE", "INSERT", "TERM" };
/* GLOBAL */
i = 0;
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_init);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_reader);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_writer);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_reset);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_flush);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_merge);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_index);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_reindex);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_fini);
print_profiles("GLOBAL", i, GLOBALs, seconds);
/* READER */
i = 0;
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_reader_source);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_reader_parser);
print_profiles("READER", i, READERs, seconds);
/* WRITER */
i = 0;
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_writer_toast);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_writer_table);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_writer_index);
print_profiles("WRITER", i, WRITERs, seconds);
/* MERGE */
i = 0;
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_merge_unique);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_merge_insert);
seconds[i++] = INSTR_TIME_GET_DOUBLE(prof_merge_term);
print_profiles("MERGE", i, MERGEs, seconds);
}
//input first the fasta file, then the sample_1000.out file run on the fasta, then options
int main(int argc, char *argv[]) {
int i,total,notcommon,most;
char **mostfreq;
FILE *fp;
OUTPUT = DEF_OUTPUT;
INPUT = NULL;
NATIVE = NULL;
FILTER = 0;
NOISE = DEF_NOISE;
MIN_HEL_LEN = DEF_MIN_HEL_LEN;
// THRESH_FREQ = DEF_THRESH_FREQ;
THRESH_FREQ = 0;
THRESH_COMMON = DEF_THRESH_COMMON;
VERBOSE = 0;
NUMFREQ = 0;
NUMPROF = 0;
PROF_FREQ = 0;
// PROF_FREQ = DEF_PROF_FREQ;
NUMSTRUCTS = 0;
THRESH_STRUCT = DEF_THRESH_STRUCT;
LENGTH = 0;
STATS = 0;
GRAPH = 1;
REP_STRUCT = 0;
if (argc < 3) {
fprintf(stderr,"Not enough arguments\n");
exit(EXIT_FAILURE);
}
//OUTPUT = malloc(strlen(argv[1])+5);
//sprintf(OUTPUT,"%s.dot",argv[1]);
for (i = 3; i < argc; i++) {
//printf("argv[%d] is %s\n",i,argv[i]);
if (!strcmp(argv[i],"-f")) {
FILTER = 1;
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&NUMFREQ)) {
// sscanf(argv[i+1],"%s",val);
//printf("val is %s and argv %s\n",val,argv[i+1]);
NUMFREQ = atoi(argv[i+1]);
i++;
}
else
NUMFREQ = DEF_NUMFREQ;
}
else if (!strcmp(argv[i],"-z")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&NOISE)) {
NOISE = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-h")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&THRESH_FREQ)) {
THRESH_FREQ = atof(argv[i+1]);
if (THRESH_FREQ < 0 || THRESH_FREQ > 100) {
fprintf(stderr,"Error: invalid input %f for frequency threshold\n",THRESH_FREQ);
THRESH_FREQ = DEF_THRESH_FREQ;
}
i++;
}
}
else if (!strcmp(argv[i],"-c")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&THRESH_COMMON)) {
THRESH_COMMON = atof(argv[i+1]);
if (THRESH_COMMON < 0.0 || THRESH_COMMON > 100.0) {
fprintf(stderr,"Error: invalid input %f for common threshold\n",THRESH_COMMON);
THRESH_COMMON = DEF_THRESH_COMMON;
}
i++;
}
}
else if (!strcmp(argv[i],"-q")) {
//PRUNE = 1;
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&NUMPROF)) {
NUMPROF = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-p")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&PROF_FREQ)) {
PROF_FREQ = atof(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-l")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&MIN_HEL_LEN)) {
MIN_HEL_LEN = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-s")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&NUMSTRUCTS)) {
NUMSTRUCTS = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-t")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&THRESH_STRUCT)) {
THRESH_STRUCT = atof(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-o")) {
if (i + 1 <= argc - 1) {
OUTPUT = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-i")) {
if (i + 1 <= argc - 1) {
INPUT = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-n")) {
if (i + 1 <= argc - 1) {
NATIVE = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-v"))
VERBOSE = 1;
else if (!strcmp(argv[i],"-a"))
STATS = 1;
else if (!strcmp(argv[i],"-g"))
GRAPH = 0;
else if (!strcmp(argv[i],"-r"))
REP_STRUCT = 1;
}
if (!(bp = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for bp failed");
exit(EXIT_FAILURE);
}
if (!(marginals = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for marginals failed");
exit(EXIT_FAILURE);
}
if (!(idhash = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for idhash failed");
exit(EXIT_FAILURE);
}
if (!(binary = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for binary failed");
exit(EXIT_FAILURE);
}
total = process_structs(argv[1],argv[2]);
if (THRESH_FREQ==0)
THRESH_FREQ = set_h_dropoff(marginals, H_START);
if (VERBOSE) {
printf("Threshold to find frequent helices: %.1f\%\n",THRESH_FREQ);
printf("Maximum number of frequent helices: ");
if (NUMFREQ == 0)
puts("no limit");
else
printf("%d\n",NUMFREQ);
/*
printf("Threshold to select frequent profiles: %.1f\%\n",PROF_FREQ);
printf("Maximum number of profiles: ");
if (NUMPROF == 0)
puts("no limit");
else
printf("%d\n",NUMPROF);
*/
printf("Number of structures processed: %d\n",NUMSTRUCTS);
}
printf("Total number of equivalence helix classes: %d\n",total-1);
if (VERBOSE)
print_all_helices(total);
// make_graph(marginals,max,id,total,argv[1],fp);
mostfreq = find_freq(total);
printf("Total number of selected helices: %d\n",hashtbl_numkeys(freq));
notcommon = make_profiles(argv[2]);
printf("Total number of profiles: %d\n",hashtbl_numkeys(cluster));
print_profiles();
if (PROF_FREQ == 0) {
PROF_FREQ = set_h_dropoff(cluster,P_START);
if (VERBOSE)
printf("setting p to %.1f\n",PROF_FREQ);
}
most = select_profiles(mostfreq,notcommon)-1;
printf("Total number of selected profiles: %d\n",hashtbl_numkeys(cluster));
if (hashtbl_numkeys(cluster) == 0)
GRAPH = 0;
if (hashtbl_numkeys(cluster) > 23 && GRAPH) {
GRAPH = 0;
printf("Total number of profiles above threshold %.1f is %d: disabling graph\n",PROF_FREQ,hashtbl_numkeys(cluster));
}
if (REP_STRUCT) {
//fp = fopen("structures.out","w");
//fprintf(fp,"Processing %s\n",argv[2]);
find_consensus();
print_consensus(argv[1]);
//print_cluster(argv[1]);
//fclose(fp);
}
if (GRAPH) {
fp = fopen(OUTPUT,"w");
insert_graph(fp,argv[1],most);
fputs("}",fp);
fclose(fp);
}
hashtbl_destroy(bp);
hashtbl_destroy(marginals);
hashtbl_destroy(idhash);
hashtbl_destroy(binary);
hashtbl_destroy(freq);
hashtbl_destroy(cluster);
hashtbl_destroy(bracket);
hashtbl_destroy(infreq);
return 0;
}
//input first the fasta file, then the sample_1000.out file run on the fasta, then options
int main(int argc, char *argv[]) {
int i, h, minh,p;
HASHTBL *deleteHash;
FILE *fp;
Set *set;
Options *opt;
if (argc < 3) {
fprintf(stderr,"Not enough arguments\n");
exit(EXIT_FAILURE);
}
set = make_Set(argv[2]);
opt = set->opt;
for (i = 3; i < argc; i++) {
//printf("argv[%d] is %s\n",i,argv[i]);
if (!strcmp(argv[i],"-h")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&(opt->HC_FREQ))) {
opt->HC_FREQ = atof(argv[i+1]);
if (opt->HC_FREQ < 0 || opt->HC_FREQ > 100) {
fprintf(stderr,"Error: invalid input %f for frequency threshold\n",opt->HC_FREQ);
opt->HC_FREQ = 0;
}
i++;
}
}
else if (!strcmp(argv[i],"-p")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&(opt->PROF_FREQ))) {
opt->PROF_FREQ = atof(argv[i+1]);
if (opt->PROF_FREQ < 0 || opt->PROF_FREQ > 100) {
fprintf(stderr,"Error: invalid input %f for frequency threshold\n",opt->PROF_FREQ);
opt->PROF_FREQ = 0;
}
i++;
}
}
else if (!strcmp(argv[i],"-c")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&(opt->COVERAGE))) {
opt->COVERAGE = atof(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-f")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&(opt->NUM_FHC))) {
opt->NUM_FHC = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-s")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&(opt->NUM_SPROF))) {
opt->NUM_SPROF = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-l")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&(opt->MIN_HEL_LEN))) {
opt->MIN_HEL_LEN = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-u")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&(opt->NUMSTRUCTS))) {
opt->NUMSTRUCTS = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-m")) {
if (i + 1 <= argc - 1) {
opt->PNOISE = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-o")) {
if (i + 1 <= argc - 1) {
opt->OUTPUT = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-i")) {
if (i + 1 <= argc - 1) {
opt->INPUT = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-n")) {
if (i + 1 <= argc - 1) {
opt->NATIVE = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-k")) {
if (i + 1 <= argc - 1) {
opt->CYCLES = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-v"))
opt->VERBOSE = 1;
else if (!strcmp(argv[i],"-g"))
opt->GRAPH = 0;
else if (!strcmp(argv[i],"-r"))
opt->REP_STRUCT = 1;
else if (!strcmp(argv[i],"-t"))
opt->TOPDOWN = 1;
else if (!strcmp(argv[i],"-a"))
opt->ALTTHRESH = 0;
}
input_seq(set,argv[1]);
process_structs(set);
reorder_helices(set);
minh = print_all_helices(set);
printf("Total number of helix classes: %d\n",set->hc_num);
if (set->opt->TOPDOWN) {
printf("Total number of extended profiles: %d\n",set->prof_num);
h = top_down_h(set,minh);
//if (set->opt->VERBOSE)
printf("Number of featured helix classes: %d\n",h+1);
find_freq(set);
p = top_down_p(set,h);
//if (set->opt->VERBOSE)
printf("Number of selected profiles: %d\n",p+1);
print_topdown_prof(set,h,p);
} else {
if (set->opt->NUM_FHC)
set->opt->HC_FREQ = set_num_fhc(set);
else if (set->opt->HC_FREQ==0)
set->opt->HC_FREQ = set_threshold(set,H_START);
if (set->opt->VERBOSE) {
printf("Threshold to find frequent helices: %.1f\%\n",set->opt->HC_FREQ);
printf("Number of structures processed: %d\n",set->opt->NUMSTRUCTS);
}
find_freq(set);
printf("Total number of featured helix classes: %d\n",set->num_fhc);
make_profiles(set);
printf("Total number of profiles: %d\n",set->prof_num);
print_profiles(set);
if (set->opt->NUM_SPROF)
set->opt->PROF_FREQ = set_num_sprof(set);
else if (set->opt->PROF_FREQ == 0) {
set->opt->PROF_FREQ = set_p_threshold(set,P_START);
}
if (set->opt->VERBOSE)
printf("setting p to %.1f\n",set->opt->PROF_FREQ);
select_profiles(set);
printf("Total number of selected profiles: %d\n",set->num_sprof);
}
