string revcomp(const string &dna, bool do_revcomp) {
if (!do_revcomp)
return dna;
string rcomp(dna);
for (size_t i = 0; i < dna.length(); i++) {
rcomp[dna.length() - i - 1] = complement_nucleotide(dna[i]);
}
// cout << dna << " " << dna.length() << " " << rcomp << " " << rcomp.length() << endl ;
return rcomp;
}
void report_summary(summary * s, summary * o, bool full)
{
FILE *F = NULL;
int i, newplayers = 0;
faction *f;
char zText[MAX_PATH];
if (full) {
sprintf(zText, "%s/parteien.full", basepath());
} else {
sprintf(zText, "%s/parteien", basepath());
}
F = fopen(zText, "w");
if (!F) {
perror(zText);
return;
}
#ifdef SUMMARY_BOM
else {
const unsigned char utf8_bom[4] = { 0xef, 0xbb, 0xbf, 0 };
fwrite(utf8_bom, 1, 3, F);
}
#endif
log_info("writing summary to file: parteien.\n");
fprintf(F, "%s\n%s\n\n", game_name(), gamedate2(default_locale));
fprintf(F, "Auswertung Nr: %d\n\n", turn);
fprintf(F, "Parteien: %s\n", pcomp(s->factions, o->factions));
fprintf(F, "Einheiten: %s\n", pcomp(s->nunits, o->nunits));
fprintf(F, "Spielerpopulation: %s\n", pcomp(s->playerpop, o->playerpop));
fprintf(F, " davon bewaffnet: %s\n", pcomp(s->armed_men, o->armed_men));
fprintf(F, " Helden: %s\n", pcomp(s->heroes, o->heroes));
if (full) {
fprintf(F, "Regionen: %d\n", listlen(regions));
fprintf(F, "Bewohnte Regionen: %d\n", s->inhabitedregions);
fprintf(F, "Landregionen: %d\n", s->landregionen);
fprintf(F, "Spielerregionen: %d\n", s->regionen_mit_spielern);
fprintf(F, "Landspielerregionen: %d\n", s->landregionen_mit_spielern);
fprintf(F, "Orkifizierte Regionen: %d\n", s->orkifizierte_regionen);
fprintf(F, "Inaktive Vulkane: %d\n", s->inactive_volcanos);
fprintf(F, "Aktive Vulkane: %d\n\n", s->active_volcanos);
}
for (i = 0; i < MAXRACES; i++) {
if (i != RC_TEMPLATE && i != RC_CLONE && s->factionrace[i]) {
const race *rc = get_race(i);
if (rc && playerrace(rc)) {
fprintf(F, "%13s%s: %s\n", LOC(default_locale, rc_name(rc, NAME_CATEGORY)),
LOC(default_locale, "stat_tribe_p"), pcomp(s->factionrace[i],
o->factionrace[i]));
}
}
}
if (full) {
fprintf(F, "\n");
{
struct language *plang = s->languages;
while (plang != NULL) {
struct language *olang = o->languages;
int nold = 0;
while (olang && olang->locale != plang->locale)
olang = olang->next;
if (olang)
nold = olang->number;
fprintf(F, "Sprache %12s: %s\n", locale_name(plang->locale),
rcomp(plang->number, nold));
plang = plang->next;
}
}
}
fprintf(F, "\n");
if (full) {
for (i = 0; i < MAXRACES; i++) {
if (s->poprace[i]) {
const race *rc = get_race(i);
fprintf(F, "%20s: %s\n", LOC(default_locale, rc_name(rc, NAME_PLURAL)),
rcomp(s->poprace[i], o->poprace[i]));
}
}
} else {
for (i = 0; i < MAXRACES; i++) {
if (i != RC_TEMPLATE && i != RC_CLONE && s->poprace[i]) {
const race *rc = get_race(i);
if (playerrace(rc)) {
fprintf(F, "%20s: %s\n", LOC(default_locale, rc_name(rc, NAME_PLURAL)),
rcomp(s->poprace[i], o->poprace[i]));
}
}
}
}
if (full) {
fprintf(F, "\nWaffen: %s\n", pcomp(s->waffen, o->waffen));
fprintf(F, "Ruestungen: %s\n",
pcomp(s->ruestungen, o->ruestungen));
fprintf(F, "ungezaehmte Pferde: %s\n", pcomp(s->pferde, o->pferde));
fprintf(F, "gezaehmte Pferde: %s\n",
pcomp(s->spielerpferde, o->spielerpferde));
fprintf(F, "Schiffe: %s\n", pcomp(s->schiffe, o->schiffe));
fprintf(F, "Gebaeude: %s\n", pcomp(s->gebaeude, o->gebaeude));
fprintf(F, "\nBauernpopulation: %s\n", pcomp(s->peasants, o->peasants));
fprintf(F, "Population gesamt: %d\n\n", s->playerpop + s->peasants);
fprintf(F, "Reichtum Spieler: %s Silber\n",
pcomp(s->playermoney, o->playermoney));
fprintf(F, "Reichtum Bauern: %s Silber\n",
pcomp(s->peasantmoney, o->peasantmoney));
fprintf(F, "Reichtum gesamt: %s Silber\n\n",
pcomp(s->playermoney + s->peasantmoney,
o->playermoney + o->peasantmoney));
}
fprintf(F, "\n\n");
newplayers = update_nmrs();
for (i = 0; i <= NMRTimeout(); ++i) {
if (i == NMRTimeout()) {
fprintf(F, "+ NMR:\t\t %d\n", nmrs[i]);
} else {
fprintf(F, "%d NMR:\t\t %d\n", i, nmrs[i]);
}
}
if (age) {
if (age[2] != 0) {
fprintf(F, "Erstabgaben:\t %d%%\n", 100 - (dropouts[0] * 100 / age[2]));
}
if (age[3] != 0) {
fprintf(F, "Zweitabgaben:\t %d%%\n", 100 - (dropouts[1] * 100 / age[3]));
}
}
fprintf(F, "Neue Spieler:\t %d\n", newplayers);
if (full) {
if (factions)
fprintf(F, "\nParteien:\n\n");
for (f = factions; f; f = f->next) {
out_faction(F, f);
}
if (NMRTimeout() && full) {
fprintf(F, "\n\nFactions with NMRs:\n");
for (i = NMRTimeout(); i > 0; --i) {
for (f = factions; f; f = f->next) {
if (i == NMRTimeout()) {
if (turn - f->lastorders >= i) {
out_faction(F, f);
}
} else {
if (turn - f->lastorders == i) {
out_faction(F, f);
}
}
}
}
}
}
fclose(F);
if (full) {
log_info("writing date & turn\n");
writeturn();
}
free(nmrs);
nmrs = NULL;
}
int do_file(char *fname, struct trie *root, int which){
FILE *fasta;
char *genome;
int glen;
int i;
char *window;
char *rcwindow;
int willInsert;
char dummy[SEQ_LENGTH];
int win = 0;
willInsert = 1;
fprintf(stderr, "\n\nInserting sequence from file %s\n", fname);
fasta = myfopen(fname, "r");
fgets(dummy, SEQ_LENGTH, fasta);
genome = readFasta(fasta, &glen);
window = (char *) mymalloc(sizeof(char) * WINDOW_SIZE+1);
rcwindow = (char *) mymalloc(sizeof(char) * WINDOW_SIZE+1);
i = 0;
while (i < glen - WINDOW_SIZE){
if (getWindow(genome, glen, &window, i) == 0 ){
i+=SLIDE_SIZE;
continue;
}
//while (getIndexWindow(fasta, &window, &willInsert) > 0){
//fprintf(stderr, "\rGetting windows from %s\t: %d%%", fname, ((int)(100.0*(float)(i+strlen(window))/(float)strlen(genome))));
if (VERBOSE)
printf("%s\n", window);
/* insert the window to the trie here */
if (willInsert){
// start location is i+1
// because i starts from 0 here; but
// we want the sequence index starting from 1
// STARTING POSITION FOR FORWARD
rcomp(window, rcwindow);
if (NOREV){
if (strcmp(window, rcwindow) < 0 )
insert(root, window, (i+1), fname, which);
else if (strcmp(window, rcwindow) > 0 )
insert(root, rcwindow, (-1*(i+1)), fname, which);
}
else{
insert(root, window, (i+1), fname, which);
insert(root, rcwindow, (-1*(i+1)), fname, which);
}
/*
insert(root, window, (i+1), fname, which);
if (!NOREV){
// reverse complement of this window is indexed by its negative
// value ENDING POSITION FOR REVERSE COMPLEMENT
rcomp(window, rcwindow);
if (strcmp(window, rcwindow))
insert(root, rcwindow, (-1*(i+1)), fname, which);
}*/
}
i+=SLIDE_SIZE;
if (i % 10000 == 0)
fprintf(stderr,"\r [%i] of [%d]", i, glen);
}
fprintf(stderr, "\n");
//free(genome);
fclose(fasta);
free(window);
free(rcwindow);
return 1;
}
