std::string input_manager::get_keyname(long ch, input_event_t inp_type, bool portable) const
{
if(inp_type == CATA_INPUT_KEYBOARD) {
const t_key_to_name_map::const_iterator a = keycode_to_keyname.find(ch);
if (a != keycode_to_keyname.end()) {
return a->second;
}
} else if(inp_type == CATA_INPUT_MOUSE) {
if(ch == MOUSE_BUTTON_LEFT) {
return "MOUSE_LEFT";
} else if(ch == MOUSE_BUTTON_RIGHT) {
return "MOUSE_RIGHT";
} else if(ch == SCROLLWHEEL_UP) {
return "SCROLL_UP";
} else if(ch == SCROLLWHEEL_DOWN) {
return "SCROLL_DOWN";
} else if(ch == MOUSE_MOVE) {
return "MOUSE_MOVE";
}
} else if (inp_type == CATA_INPUT_GAMEPAD) {
const t_key_to_name_map::const_iterator a = gamepad_keycode_to_keyname.find(ch);
if (a != gamepad_keycode_to_keyname.end()) {
return a->second;
}
} else {
return "UNKNOWN";
}
if (portable) {
return std::string("UNKNOWN_") + long_to_str(ch);
}
return string_format(_("unknown key %ld"), ch);
}
void ctx_update(const char *job_name, size_t niter)
{
if(niter % CTX_UPDATE_REPORT_RATE == 0)
{
char num_str[100];
long_to_str(niter, num_str);
status("[%s] Read %s entries (reads / read pairs)", job_name, num_str);
}
}
bool test_nw_srt_from(long test_consec, long start_rnd, avg_stat& spd_avg,
bool DEBUG_SRT_FROM = false, bool SPEED_TEST = false)
{
std::ostream& os = std::cout;
os << "TEST " << test_consec << "(seed=" << start_rnd << ")";
os.flush();
sort_glb glb1;
//glb1.init_head_ss();
glb1.stab_mutual_init();
//os << "START_RND=" << start_rnd << std::endl;
tak_mak rnd_gen(start_rnd);
k_row<elem_sor> all_elem;
row<op_sor> all_ops;
if(SPEED_TEST){
all_ops.set_cap(10000);
}
long num_elem = rnd_gen.gen_rand_int32_ie(1, 1000);
all_elem.set_cap(num_elem);
for(long aa = 0; aa <= num_elem; aa++){
elem_sor& ele = all_elem.inc_sz();
ele.es_id = "e=";
}
row<elem_sor*> tmp_rr1;
row<elem_sor*> tmp_rr2;
bool stop_all = false;
std::stringstream ss_tmp;
long num_lvs = rnd_gen.gen_rand_int32_ie(1, 10);
for(long bb = 1; ((bb < num_lvs) && ! stop_all); bb++){
glb1.sg_curr_stab_consec++;
DBG_CK(glb1.sg_curr_stab_consec >= bb);
DBG_CK(glb1.sg_curr_stab_consec >= glb1.sg_dbg_last_id);
std::string bb_ss = long_to_str(bb);
long num_reps_lv = rnd_gen.gen_rand_int32_ie(1, 10);
for(long dd = 0; ((dd < num_reps_lv) && ! stop_all); dd++){
DBG_CK(glb1.sg_curr_stab_consec >= glb1.sg_dbg_last_id);
long num_elem_rep = rnd_gen.gen_rand_int32_ie(1, num_elem);
for(long cc = 0; ((cc < num_elem_rep) && ! stop_all); cc++){
DBG_CK(glb1.sg_curr_stab_consec >= glb1.sg_dbg_last_id);
bool all_csecs = false;
long elem_idx = rnd_gen.gen_rand_int32_ie(1, num_elem);
SORTER_CK(all_elem.is_valid_idx(elem_idx));
elem_sor& ele = all_elem[elem_idx];
if(DEBUG_SRT_FROM){
ss_tmp.clear();
ss_tmp.seekg(0, std::ios::beg);
ss_tmp.str("");
ss_tmp.flush();
glb1.sort_to_row_and_all_consec<elem_sor>(tmp_rr1, all_csecs);
tmp_rr1.print_row_data(ss_tmp, true, "\n");
if(! tmp_rr1.is_sorted(cmp_elem_sr)){
//tmp_rr1.print_row_data(os, true, "\n");
std::string out_ss = ss_tmp.str();
os << out_ss;
os << "FAILED starting" << std::endl << ele << std::endl;
os << "START_RND=" << start_rnd << std::endl;
stop_all = true;
break;
}
}
std::string dbg_id_start = ele.es_id;
if(SPEED_TEST){
op_sor& the_op = all_ops.inc_sz();
the_op.op_elem = &ele;
the_op.op_id = bb;
} else {
DBG_CK(glb1.sg_curr_stab_consec >= bb);
DBG_CK(glb1.sg_curr_stab_consec >= glb1.sg_dbg_last_id);
ele.es_srt_bdr.sort_from(glb1, bb);
DBG_CK(glb1.sg_curr_stab_consec >= glb1.sg_dbg_last_id);
}
ele.es_id += "b" + bb_ss;
ele.add(bb);
std::string dbg_id_end = ele.es_id;
if(DEBUG_SRT_FROM){
glb1.sort_to_row_and_all_consec<elem_sor>(tmp_rr2, all_csecs);
if(! tmp_rr2.is_sorted(cmp_elem_sr)){
os << "STARTING" << std::endl;
std::string out_ss = ss_tmp.str();
os << out_ss;
//tmp_rr1.print_row_data(os, true, "\n");
os << std::endl << std::endl << "ENDING" << std::endl;
tmp_rr2.print_row_data(os, true, "\n");
os << "FAILED ending" << std::endl << ele << std::endl;
os << "curr_id=" << bb << std::endl;
os << "dbg_id_start=" << dbg_id_start << std::endl;
os << "dbg_id_end=" << dbg_id_end << std::endl;
os << "START_RND=" << start_rnd << std::endl;
stop_all = true;
ck_sorted_elems(tmp_rr2, cmp_elem_sr);
break;
}
}
}
}
}
os << "::";
os.flush();
//DBG_CK(glb1.sg_curr_stab_consec >= glb1.sg_dbg_last_id);
long num_srt_from = 0;
double run_speed = 0;
if(SPEED_TEST){
double start_tm = cpu_time();
for(long aa = 0; aa < all_ops.size(); aa++){
op_sor& the_op = all_ops[aa];
SORTER_CK(the_op.op_elem != NULL_PT);
SORTER_CK(the_op.op_id > 0);
the_op.op_elem->es_srt_bdr.sort_from(glb1, the_op.op_id);
num_srt_from++;
}
double finish_tm = cpu_time();
run_speed = num_srt_from / (finish_tm - start_tm);
if(finite(run_speed)){
spd_avg.add_val(run_speed);
}
}
//DBG_CK(glb1.sg_curr_stab_consec >= glb1.sg_dbg_last_id);
if(! stop_all){
row<elem_sor*> s_rr;
bool all_in_consec = false;
glb1.sort_to_row_and_all_consec<elem_sor>(s_rr, all_in_consec);
os << " #elem=" << num_elem << " #ops=" << num_srt_from << " speed=" << run_speed
<< " finite=" << finite(run_speed);
//os << "SIZE=" << s_rr.size() << bj_eol;
//s_rr.print_row_data(os, true, "\n");
//os << "NUM_ELEM=" << num_elem << std::endl;
//os << "START_RND=" << start_rnd << std::endl;
//os << std::endl;
bool finish_ok = true;
if(! s_rr.is_sorted(cmp_elem_sr)){
s_rr.print_row_data(os, true, "\n");
os << " START_RND=" << start_rnd << std::endl;
SORTER_CK(ck_sorted_elems(s_rr, cmp_elem_sr));
finish_ok = false;
}
glb1.sort_to_tmp_srss();
if(! glb1.sg_tmp_srss.is_sorted(cmp_sorsets)){
s_rr.print_row_data(os, true, "\n");
os << " START_RND=" << start_rnd << std::endl;
ck_sorted_sorsets(glb1.sg_tmp_srss, cmp_sorsets);
SORTER_CK(false);
finish_ok = false;
}
//os << "FINISHED OK=" << start_rnd << std::endl;
if(finish_ok){
os << " finished ok";
} else {
os << " FAILED !!!!!!!!!!!!!!!!!!!!!!!!!!!!";
os.flush();
abort_func(0);
}
//os << std::endl;
//glb1.release_all();
//glb1.init_head_ss();
glb1.stab_mutual_init();
}
//os << "START_RND=" << start_rnd << std::endl;
return ! stop_all;
}
void assemble_contigs_stats_print(const AssembleContigStats *s)
{
ctx_assert(s->lengths.len == s->junctns.len);
ctx_assert(s->lengths.len == s->num_contigs);
size_t i, ncontigs = s->num_contigs;
if(ncontigs == 0) {
status("[asm] No contigs assembled");
return;
}
qsort(s->lengths.b, ncontigs, sizeof(s->lengths.b[0]), cmp_size);
qsort(s->junctns.b, ncontigs, sizeof(s->junctns.b[0]), cmp_size);
size_t len_n50, jnc_n50;
size_t len_median, jnc_median, len_mean, jnc_mean;
size_t len_min, len_max, jnc_min, jnc_max;
// Calculate N50s
len_n50 = calc_N50(s->lengths.b, ncontigs, s->total_len);
jnc_n50 = calc_N50(s->junctns.b, ncontigs, s->total_junc);
// Calculate medians, means
len_median = MEDIAN(s->lengths.b, ncontigs);
jnc_median = MEDIAN(s->junctns.b, ncontigs);
len_mean = (double)s->total_len / ncontigs;
jnc_mean = (double)s->total_junc / ncontigs;
// Calculate min, max
len_min = s->lengths.b[0];
jnc_min = s->junctns.b[0];
len_max = s->lengths.b[ncontigs-1];
jnc_max = s->junctns.b[ncontigs-1];
// Print number of contigs
char num_contigs_str[50], reseed_str[50], seed_not_fnd_str[50];
char seed_kmers_str[50], seed_paths_str[50];
long_to_str(ncontigs, num_contigs_str);
long_to_str(s->num_reseed_abort, reseed_str);
long_to_str(s->num_seeds_not_found, seed_not_fnd_str);
long_to_str(s->num_contigs_from_seed_kmers, seed_kmers_str);
long_to_str(s->num_contigs_from_seed_paths, seed_paths_str);
status(PREFIX"pulled out %s contigs, %s from seed kmers, %s from seed paths",
num_contigs_str, seed_kmers_str, seed_paths_str);
status(PREFIX"no-reseed aborted %s times", reseed_str);
status(PREFIX"seed kmer not found %s times", seed_not_fnd_str);
char len_min_str[50], len_max_str[50], len_total_str[50];
char len_mean_str[50], len_median_str[50], len_n50_str[50];
char jnc_min_str[50], jnc_max_str[50], jnc_total_str[50];
char jnc_mean_str[50], jnc_median_str[50], jnc_n50_str[50];
// Use ulong_to_str instead of num_to_str to get better accuracy
// e.g. 966 instead of 1K
ulong_to_str(len_mean, len_mean_str);
ulong_to_str(jnc_mean, jnc_mean_str);
ulong_to_str(len_median, len_median_str);
ulong_to_str(jnc_median, jnc_median_str);
ulong_to_str(len_n50, len_n50_str);
ulong_to_str(jnc_n50, jnc_n50_str);
ulong_to_str(len_min, len_min_str);
ulong_to_str(jnc_min, jnc_min_str);
ulong_to_str(len_max, len_max_str);
ulong_to_str(jnc_max, jnc_max_str);
ulong_to_str(s->total_len, len_total_str);
ulong_to_str(s->total_junc, jnc_total_str);
status(PREFIX"Lengths: mean: %s median: %s N50: %s min: %s max: %s total: %s [kmers]",
len_mean_str, len_median_str, len_n50_str, len_min_str, len_max_str, len_total_str);
status(PREFIX"Junctions: mean: %s median: %s N50: %s min: %s max: %s total: %s [out >1]",
jnc_mean_str, jnc_median_str, jnc_n50_str, jnc_min_str, jnc_max_str, jnc_total_str);
status(PREFIX"Max junction density: %.2f\n", s->max_junc_density);
timestamp();
message(PREFIX" Outdegree: ");
char nout_str[50];
for(i = 0; i <= 4; i++) {
message("\t%zu:%s [%zu%%]", i, ulong_to_str(s->contigs_outdegree[i], nout_str),
(size_t)((100.0*s->contigs_outdegree[i])/(2.0*ncontigs)+0.5));
}
message("\n");
_print_path_dist(s->paths_held, AC_MAX_PATHS, "Paths held", ncontigs);
_print_path_dist(s->paths_cntr, AC_MAX_PATHS, "Paths counter", ncontigs);
const uint64_t *states = s->grphwlk_steps;
size_t nsteps = s->total_len - s->num_contigs, ncontigends = 2*s->num_contigs;
status(PREFIX"Traversal succeeded because:");
_print_grphwlk_state("Pop straight ......... ", states[GRPHWLK_POPFWD], nsteps);
_print_grphwlk_state("Col straight ......... ", states[GRPHWLK_COLFWD], nsteps);
_print_grphwlk_state("PopFork use colour ... ", states[GRPHWLK_POPFRK_COLFWD],nsteps);
_print_grphwlk_state("Go paths ............. ", states[GRPHWLK_USEPATH], nsteps);
const uint64_t *stops = s->stop_causes;
status(PREFIX"Traversal halted because:");
_print_grphwlk_state("No coverage .......... ", stops[ASSEM_STOP_NOCOVG], ncontigends);
_print_grphwlk_state("No colour covg ....... ", stops[ASSEM_STOP_NOCOLCOVG], ncontigends);
_print_grphwlk_state("No paths ............. ", stops[ASSEM_STOP_NOPATHS], ncontigends);
_print_grphwlk_state("Paths split .......... ", stops[ASSEM_STOP_SPLIT_PATHS], ncontigends);
_print_grphwlk_state("Missing paths ........ ", stops[ASSEM_STOP_MISSING_PATHS], ncontigends);
_print_grphwlk_state("Graph cycles ......... ", stops[ASSEM_STOP_CYCLE], ncontigends);
_print_grphwlk_state("Low step confidence .. ", stops[ASSEM_STOP_LOW_STEP_CONF], ncontigends);
_print_grphwlk_state("Low cumul. confidence ", stops[ASSEM_STOP_LOW_CUMUL_CONF],ncontigends);
size_t njunc = states[GRPHWLK_USEPATH] +
stops[ASSEM_STOP_NOPATHS] +
stops[ASSEM_STOP_SPLIT_PATHS] +
stops[ASSEM_STOP_MISSING_PATHS];
ctx_assert2(s->total_junc == states[GRPHWLK_USEPATH], "%zu vs %zu",
(size_t)s->total_junc, (size_t)states[GRPHWLK_USEPATH]);
status(PREFIX"Junctions:");
_print_grphwlk_state("Paths resolved", states[GRPHWLK_USEPATH], njunc);
}
void load_subhalo_catalogue(int num, struct halo_catalogue *cat)
{
int i,iboyd, ngroups, nids, nFiles, nsubhalos, subcount, groupcount,offset;
MyIDType idcount;
char buf[1000];
FILE *fd;
unsigned int j, *tmp;
nFiles = 1;
subcount = 0;
idcount = 0;
groupcount = 0;
for(i = 0; i < nFiles; i++)
{
sprintf(buf, "%s/groups_%03d/subhalo_tab_%03d.%d", OutputDir, num, num, i);
printf( "%s/groups_%03d/subhalo_tab_%03d.%d\n", OutputDir, num, num, i);
if(!(fd = fopen(buf, "r")))
{
printf("can't open file `%s'\n", buf);
exit(1);
}
if(i == 0 || i == nFiles - 1)
printf("reading '%s'\n", buf);
if(i == 1)
printf("...to...\n");
my_fread(&ngroups, sizeof(int), 1, fd);
printf("ngroup = %d\n",ngroups);
my_fread(&cat->TotNgroups, sizeof(int), 1, fd);
printf("TotNgroup = %d\n",cat->TotNgroups);
my_fread(&nids, sizeof(int), 1, fd);
printf("nids = %d\n",nids);
my_fread(&cat->TotNids, sizeof(long long), 1, fd);
printf("TotNids = %d\n",cat->TotNids);
my_fread(&nFiles, sizeof(int), 1, fd);
my_fread(&nsubhalos, sizeof(int), 1, fd);
printf("nsubhalos = %d\n",nsubhalos);
my_fread(&cat->TotNsubhalos, sizeof(int), 1, fd);
printf("TotNsubhalos = %d\n",cat->TotNsubhalos);
if(i == 0)
{
cat->IdList = mymalloc(sizeof(MyIDType) * cat->TotNids);
cat->SubLen = mymalloc(sizeof(int) * cat->TotNsubhalos);
cat->SubOffset = mymalloc(sizeof(MyIDType) * cat->TotNsubhalos);
cat->SubParentHalo = mymalloc(sizeof(int) * cat->TotNsubhalos);
cat->SubhaloMass = mymalloc(sizeof(float) * cat->TotNsubhalos);
cat->SubhaloPos = mymalloc(3 * sizeof(float ) * cat->TotNsubhalos);
cat->SubhaloVel = mymalloc(3 * sizeof(float ) * cat->TotNsubhalos);
cat->SubhaloCM = mymalloc(3 * sizeof(float ) * cat->TotNsubhalos);
cat->SubhaloSpin = mymalloc(3 * sizeof(float ) * cat->TotNsubhalos);
cat->SubhaloVelDisp = mymalloc(sizeof(float) * cat->TotNsubhalos);
cat->SubhaloVmax = mymalloc(sizeof(float) * cat->TotNsubhalos);
cat->SubhaloVmaxRad = mymalloc(sizeof(float) * cat->TotNsubhalos);
cat->SubhaloHalfMass = mymalloc(sizeof(float) * cat->TotNsubhalos);
cat->SubhaloMostBoundID = mymalloc(sizeof(MyIDType) * cat->TotNsubhalos);
cat->SubhaloGrNr = mymalloc(sizeof(int) * cat->TotNsubhalos);
cat->GroupNsubs = mymalloc(sizeof(int) * cat->TotNgroups);
cat->GroupFirstSub = mymalloc(sizeof(int) * cat->TotNgroups);
cat->Descendant = mymalloc(sizeof(struct descendant_data) * cat->TotNsubhalos);
cat->CountProgenitors = mymalloc(sizeof(int) * cat->TotNsubhalos);
}
fseek(fd, sizeof(int) * ngroups, SEEK_CUR); /* skip GroupLen */
fseek(fd, sizeof(int) * ngroups, SEEK_CUR); /* skip GroupOffset */
fseek(fd, sizeof(float) * ngroups, SEEK_CUR); /* skip GroupMass */
fseek(fd, 3 * sizeof(float) * ngroups, SEEK_CUR); /* skip GroupPos */
fseek(fd, sizeof(float) * ngroups, SEEK_CUR); /* skip Group_M_Mean200 */
fseek(fd, sizeof(float) * ngroups, SEEK_CUR); /* skip Group_R_Mean200 */
fseek(fd, sizeof(float) * ngroups, SEEK_CUR); /* skip Group_M_Crit200 */
fseek(fd, sizeof(float) * ngroups, SEEK_CUR); /* skip Group_R_Crit200 */
fseek(fd, sizeof(float) * ngroups, SEEK_CUR); /* skip Group_M_TopHat200 */
fseek(fd, sizeof(float) * ngroups, SEEK_CUR); /* skip Group_R_TopHat200 */
#ifdef SO_VEL_DISPERSIONS
fseek(fd, sizeof(float) * ngroups, SEEK_CUR); /* skip Group_VelDisp_Mean200 */
fseek(fd, sizeof(float) * ngroups, SEEK_CUR); /* skip Group_VelDisp_Crit200 */
fseek(fd, sizeof(float) * ngroups, SEEK_CUR); /* skip Group_VelDisp_TopHat200 */
#endif
fseek(fd, sizeof(int) * ngroups, SEEK_CUR); /* skip GroupContaminationCount */
fseek(fd, sizeof(float) * ngroups, SEEK_CUR); /* skip GroupContaminationMass */
//fseek(fd, sizeof(int) * ngroups, SEEK_CUR); /* skip GroupNsubs */
my_fread(&cat->GroupNsubs[groupcount], sizeof(int), ngroups, fd);
//fseek(fd, sizeof(int) * ngroups, SEEK_CUR); /* skip GroupFirstsub */
my_fread(&cat->GroupFirstSub[groupcount], sizeof(int), ngroups, fd);
my_fread(&cat->SubLen[subcount], sizeof(int), nsubhalos, fd);
tmp = mymalloc(sizeof(int) * nsubhalos);
my_fread(tmp, sizeof(int), nsubhalos, fd);
for(j = 0; j < nsubhalos; j++)
cat->SubOffset[subcount + j] = tmp[j]; /* copy it to 64 bit if needed */
myfree(tmp);
//myfree(buf);
my_fread(&cat->SubParentHalo[subcount], sizeof(int), nsubhalos, fd);
my_fread(&cat->SubhaloMass[subcount], sizeof(float), nsubhalos, fd);
//fseek(fd, sizeof(float) * nsubhalos, SEEK_CUR); /* skip SubhaloMass */
my_fread(&cat->SubhaloPos[3 * subcount], 3 * sizeof(float), nsubhalos, fd);
my_fread(&cat->SubhaloVel[3 * subcount], 3 * sizeof(float), nsubhalos, fd);
//fseek(fd, 3 * sizeof(float) * nsubhalos, SEEK_CUR); /* skip SubhaloCM */
my_fread(&cat->SubhaloCM[3 * subcount], 3 * sizeof(float), nsubhalos, fd);
my_fread(&cat->SubhaloVelDisp[subcount], sizeof(float), nsubhalos, fd);
my_fread(&cat->SubhaloVmax[subcount], sizeof(float), nsubhalos, fd);
my_fread(&cat->SubhaloVmaxRad[subcount], sizeof(float), nsubhalos, fd);
//fseek(fd, sizeof(float) * nsubhalos, SEEK_CUR); /* skip SubhaloVmaxRad */
my_fread(&cat->SubhaloHalfMass[subcount], sizeof(float), nsubhalos, fd);
my_fread(&cat->SubhaloMostBoundID[subcount], sizeof(MyIDType), nsubhalos, fd);
//fseek(fd, sizeof(int) * nsubhalos, SEEK_CUR); /* skip GrNr */
my_fread(&cat->SubhaloGrNr[subcount], sizeof(int), nsubhalos, fd);
fclose(fd);
subcount += nsubhalos;
groupcount += ngroups;
}
/* now check whether we had a 32-bit overflow in subhalo offset, and fix it if needed */
if(sizeof(MyIDType) > 4)
{
MyIDType previous_offset = 0, add = 0;
for(i = 0; i < cat->TotNsubhalos; i++)
{
if(cat->SubOffset[i] < previous_offset)
{
printf("deteced 32-bit overflow, correcting it\n");
add += (((long long) 1) << 32);
}
previous_offset = cat->SubOffset[i];
cat->SubOffset[i] += add;
}
}
long_to_str(buf, cat->TotNids);
printf("cat->TotNsubhalos = %d\n", cat->TotNsubhalos);
printf("cat->TotNids = %s\n", buf);
for(i = 0; i < nFiles; i++)
{
sprintf(buf, "%s/groups_%03d/subhalo_ids_%03d.%d", OutputDir, num, num, i);
printf("%s/groups_%03d/subhalo_ids_%03d.%d\n", OutputDir, num, num, i);
if(!(fd = fopen(buf, "r")))
{
printf("can't open file `%s'\n", buf);
exit(1);
}
if(i == 0 || i == nFiles - 1)
printf("reading '%s'\n", buf);
if(i == 1)
printf("...to...\n");
my_fread(&ngroups, sizeof(int), 1, fd);
my_fread(&cat->TotNgroups, sizeof(int), 1, fd);
my_fread(&nids, sizeof(int), 1, fd);
my_fread(&cat->TotNids, sizeof(long long), 1, fd);
my_fread(&nFiles, sizeof(int), 1, fd);
my_fread(&offset, sizeof(int), 1, fd);
printf("read all\n");
my_fread(&cat->IdList[idcount], sizeof(MyIDType), nids, fd);
fclose(fd);
idcount += nids;
}
//reassign_ids(cat->TotNids, cat->IdList);
}
