static void test_sabotage_other_fail(CuTest *tc) {
unit *u, *u2;
region *r;
order *ord;
message *msg;
setup_sabotage();
r = test_create_region(0, 0, 0);
assert(r);
u = test_create_unit(test_create_faction(NULL), r);
u2 = test_create_unit(test_create_faction(NULL), r);
assert(u && u2);
u2->ship = test_create_ship(r, test_create_shiptype("boat"));
assert(u2->ship);
u->ship = u2->ship;
ship_update_owner(u->ship);
assert(ship_owner(u->ship) == u);
ord = create_order(K_SABOTAGE, u->faction->locale, "SCHIFF");
assert(ord);
CuAssertIntEquals(tc, 0, sabotage_cmd(u2, ord));
msg = test_get_last_message(u2->faction->msgs);
CuAssertStrEquals(tc, "destroy_ship_1", test_get_messagetype(msg));
msg = test_get_last_message(u->faction->msgs);
CuAssertStrEquals(tc, "destroy_ship_3", test_get_messagetype(msg));
CuAssertPtrNotNull(tc, r->ships);
free_order(ord);
test_cleanup();
}
static void test_getunit(CuTest *tc) {
unit *u, *u2;
order *ord;
attrib *a;
struct region *r;
struct locale *lang;
struct terrain_type *t_plain;
test_cleanup();
lang = get_or_create_locale("de");
test_translate_param(lang, P_TEMP, "TEMP");
/* note that the english order is FIGHT, not COMBAT, so this is a poor example */
t_plain = test_create_terrain("plain", LAND_REGION);
u = test_create_unit(test_create_faction(0), test_create_region(0, 0, t_plain));
a = a_add(&u->attribs, a_new(&at_alias));
a->data.i = atoi36("42"); /* this unit is also TEMP 42 */
r = test_create_region(1, 0, t_plain);
ord = create_order(K_GIVE, lang, itoa36(u->no));
init_order(ord);
CuAssertIntEquals(tc, GET_UNIT, getunit(u->region, u->faction, &u2));
CuAssertPtrEquals(tc, u, u2);
init_order(ord);
CuAssertIntEquals(tc, GET_NOTFOUND, getunit(r, u->faction, &u2));
CuAssertPtrEquals(tc, NULL, u2);
free_order(ord);
ord = create_order(K_GIVE, lang, itoa36(u->no + 1));
init_order(ord);
CuAssertIntEquals(tc, GET_NOTFOUND, getunit(u->region, u->faction, &u2));
CuAssertPtrEquals(tc, NULL, u2);
free_order(ord);
ord = create_order(K_GIVE, lang, "0");
init_order(ord);
CuAssertIntEquals(tc, GET_PEASANTS, getunit(u->region, u->faction, &u2));
CuAssertPtrEquals(tc, NULL, u2);
free_order(ord);
ord = create_order(K_GIVE, lang, "TEMP 42");
init_order(ord);
CuAssertIntEquals(tc, GET_UNIT, getunit(u->region, u->faction, &u2));
CuAssertPtrEquals(tc, u, u2);
free_order(ord);
test_cleanup();
}
static void test_tax_cmd(CuTest *tc) {
order *ord;
faction *f;
region *r;
unit *u;
item_type *sword, *silver;
request *taxorders = 0;
test_cleanup();
config_set("taxing.perlevel", "20");
test_create_world();
f = test_create_faction(NULL);
r = findregion(0, 0);
assert(r && f);
u = test_create_unit(f, r);
ord = create_order(K_TAX, f->locale, "");
assert(ord);
tax_cmd(u, ord, &taxorders);
CuAssertPtrNotNull(tc, test_find_messagetype(u->faction->msgs, "error48"));
test_clear_messages(u->faction);
silver = get_resourcetype(R_SILVER)->itype;
sword = it_get_or_create(rt_get_or_create("sword"));
new_weapontype(sword, 0, 0.0, NULL, 0, 0, 0, SK_MELEE, 1);
i_change(&u->items, sword, 1);
set_level(u, SK_MELEE, 1);
tax_cmd(u, ord, &taxorders);
CuAssertPtrNotNull(tc, test_find_messagetype(u->faction->msgs, "error_no_tax_skill"));
test_clear_messages(u->faction);
set_level(u, SK_TAXING, 1);
tax_cmd(u, ord, &taxorders);
CuAssertPtrEquals(tc, 0, test_find_messagetype(u->faction->msgs, "error_no_tax_skill"));
CuAssertPtrNotNull(tc, taxorders);
rsetmoney(r, 11);
expandtax(r, taxorders);
CuAssertPtrNotNull(tc, test_find_messagetype(u->faction->msgs, "income"));
/* taxing is in multiples of 10 */
CuAssertIntEquals(tc, 10, i_get(u->items, silver));
test_clear_messages(u->faction);
i_change(&u->items, silver, -i_get(u->items, silver));
rsetmoney(r, 1000);
taxorders = 0;
tax_cmd(u, ord, &taxorders);
expandtax(r, taxorders);
CuAssertIntEquals(tc, 20, i_get(u->items, silver));
test_clear_messages(u->faction);
free_order(ord);
test_cleanup();
}
static void test_read_unitid(CuTest *tc) {
unit *u;
order *ord;
attrib *a;
struct locale *lang;
struct terrain_type *t_plain;
test_cleanup();
lang = get_or_create_locale("de");
test_translate_param(lang, P_TEMP, "TEMP");
/* note that the english order is FIGHT, not COMBAT, so this is a poor example */
t_plain = test_create_terrain("plain", LAND_REGION);
u = test_create_unit(test_create_faction(0), test_create_region(0, 0, t_plain));
a = a_add(&u->attribs, a_new(&at_alias));
a->data.i = atoi36("42"); /* this unit is also TEMP 42 */
ord = create_order(K_GIVE, lang, "TEMP 42");
init_order(ord);
CuAssertIntEquals(tc, u->no, read_unitid(u->faction, u->region));
free_order(ord);
ord = create_order(K_GIVE, lang, "8");
init_order(ord);
CuAssertIntEquals(tc, 8, read_unitid(u->faction, u->region));
free_order(ord);
ord = create_order(K_GIVE, lang, "");
init_order(ord);
CuAssertIntEquals(tc, -1, read_unitid(u->faction, u->region));
free_order(ord);
ord = create_order(K_GIVE, lang, "TEMP");
init_order(ord);
CuAssertIntEquals(tc, -1, read_unitid(u->faction, u->region));
free_order(ord);
// bug https://bugs.eressea.de/view.php?id=1685
ord = create_order(K_GIVE, lang, "##");
init_order(ord);
CuAssertIntEquals(tc, -1, read_unitid(u->faction, u->region));
free_order(ord);
test_cleanup();
}
void
create_ship(region * r, unit * u, const struct ship_type *newtype, int want,
order * ord)
{
ship *sh;
int msize;
const construction *cons = newtype->construction;
order *new_order;
if (!eff_skill(u, SK_SHIPBUILDING, r)) {
cmistake(u, ord, 100, MSG_PRODUCE);
return;
}
if (besieged(u)) {
cmistake(u, ord, 60, MSG_PRODUCE);
return;
}
/* check if skill and material for 1 size is available */
if (eff_skill(u, cons->skill, r) < cons->minskill) {
ADDMSG(&u->faction->msgs, msg_feedback(u, u->thisorder,
"error_build_skill_low", "value", cons->minskill));
return;
}
msize = maxbuild(u, cons);
if (msize == 0) {
cmistake(u, ord, 88, MSG_PRODUCE);
return;
}
if (want > 0)
want = _min(want, msize);
else
want = msize;
sh = new_ship(newtype, r, u->faction->locale);
if (leave(u, false)) {
if (fval(u_race(u), RCF_CANSAIL)) {
u_set_ship(u, sh);
}
}
new_order =
create_order(K_MAKE, u->faction->locale, "%s %i", LOC(u->faction->locale,
parameters[P_SHIP]), sh->no);
replace_order(&u->orders, ord, new_order);
free_order(new_order);
build_ship(u, sh, want);
}
static void test_parse_maketemp(CuTest *tc) {
char cmd[32];
order *ord;
struct locale * lang = get_or_create_locale("en");
locale_setstring(lang, keyword(K_MAKE), "MAKE");
locale_setstring(lang, keyword(K_MAKETEMP), "MAKETEMP");
locale_setstring(lang, "TEMP", "TEMP");
init_locale(lang);
ord = parse_order("MAKET herp", lang);
CuAssertPtrNotNull(tc, ord);
CuAssertStrEquals(tc, "MAKETEMP herp", get_command(ord, cmd, sizeof(cmd)));
CuAssertIntEquals(tc, K_MAKETEMP, getkeyword(ord));
CuAssertIntEquals(tc, K_MAKETEMP, init_order(ord));
CuAssertStrEquals(tc, "herp", getstrtoken());
free_order(ord);
}
static void test_give_herbs(CuTest * tc) {
struct give env = { 0 };
struct order *ord;
test_setup_ex(tc);
env.f2 = env.f1 = test_create_faction(NULL);
setup_give(&env);
i_change(&env.src->items, env.itype, 10);
ord = create_order(K_GIVE, env.f1->locale, "%s %s", itoa36(env.dst->no), LOC(env.f1->locale, parameters[P_HERBS]));
assert(ord);
give_cmd(env.src, ord);
CuAssertIntEquals(tc, 0, i_get(env.src->items, env.itype));
CuAssertIntEquals(tc, 10, i_get(env.dst->items, env.itype));
free_order(ord);
test_teardown();
}
static void test_create_order(CuTest *tc) {
char cmd[32];
order *ord;
struct locale * lang;
test_cleanup();
lang = get_or_create_locale("en");
locale_setstring(lang, "keyword::move", "MOVE");
ord = create_order(K_MOVE, lang, "NORTH");
CuAssertPtrNotNull(tc, ord);
CuAssertIntEquals(tc, K_MOVE, getkeyword(ord));
CuAssertStrEquals(tc, "MOVE NORTH", get_command(ord, cmd, sizeof(cmd)));
CuAssertIntEquals(tc, K_MOVE, init_order(ord));
CuAssertStrEquals(tc, "NORTH", getstrtoken());
free_order(ord);
test_cleanup();
}
static void test_sabotage_self(CuTest *tc) {
unit *u;
region *r;
order *ord;
setup_sabotage();
r = test_create_region(0, 0, 0);
assert(r);
u = test_create_unit(test_create_faction(NULL), r);
assert(u && u->faction && u->region == r);
u->ship = test_create_ship(r, test_create_shiptype("boat"));
assert(u->ship);
ord = create_order(K_SABOTAGE, u->faction->locale, "SCHIFF");
assert(ord);
CuAssertIntEquals(tc, 0, sabotage_cmd(u, ord));
CuAssertPtrEquals(tc, 0, r->ships);
free_order(ord);
test_cleanup();
}
static void test_give_invalid_target(CuTest *tc) {
/* bug https://bugs.eressea.de/view.php?id=1685 */
struct give env = { 0 };
order *ord;
test_setup_ex(tc);
env.f1 = test_create_faction(NULL);
env.f2 = 0;
setup_give(&env);
i_change(&env.src->items, env.itype, 10);
ord = create_order(K_GIVE, env.f1->locale, "## KRAUT");
assert(ord);
give_cmd(env.src, ord);
CuAssertIntEquals(tc, 10, i_get(env.src->items, env.itype));
CuAssertPtrNotNull(tc, test_find_messagetype(env.f1->msgs, "feedback_unit_not_found"));
free_order(ord);
test_teardown();
}
static void test_setstealth_cmd(CuTest *tc) {
unit *u;
const struct locale *lang;
test_setup();
u = test_create_unit(test_create_faction(0), test_create_region(0,0,0));
lang = u->faction->locale;
u->flags = UFL_ANON_FACTION|UFL_SIEGE;
u->thisorder = create_order(K_SETSTEALTH, lang, "%s %s",
LOC(lang, parameters[P_FACTION]),
LOC(lang, parameters[P_NOT]));
setstealth_cmd(u, u->thisorder);
CuAssertIntEquals(tc, UFL_SIEGE, u->flags);
free_order(u->thisorder);
u->thisorder = create_order(K_SETSTEALTH, lang, "%s",
LOC(lang, parameters[P_FACTION]));
setstealth_cmd(u, u->thisorder);
CuAssertIntEquals(tc, UFL_SIEGE|UFL_ANON_FACTION, u->flags);
test_cleanup();
}
/** remove the unit from memory.
* this frees all memory that's only accessible through the unit,
* and you should already have called uunhash and removed the unit from the
* region.
*/
void free_unit(unit * u)
{
free(u->name);
free(u->display);
free_order(u->thisorder);
free_orders(&u->orders);
if (u->skills)
free(u->skills);
while (u->items) {
item *it = u->items->next;
u->items->next = NULL;
i_free(u->items);
u->items = it;
}
while (u->attribs)
a_remove(&u->attribs, u->attribs);
while (u->reservations) {
struct reservation *res = u->reservations;
u->reservations = res->next;
free(res);
}
}
static void test_give_men_requires_contact(CuTest * tc) {
struct give env = { 0 };
message * msg;
order *ord;
test_setup_ex(tc);
env.f1 = test_create_faction(NULL);
env.f2 = test_create_faction(NULL);
setup_give(&env);
msg = give_men(1, env.src, env.dst, NULL);
CuAssertStrEquals(tc, "feedback_no_contact", test_get_messagetype(msg));
CuAssertIntEquals(tc, 1, env.dst->number);
CuAssertIntEquals(tc, 1, env.src->number);
ord = create_order(K_GIVE, env.f1->locale, "%s ALLES PERSONEN", itoa36(env.dst->no));
test_clear_messages(env.f1);
give_cmd(env.src, ord);
CuAssertPtrEquals(tc, NULL, test_find_messagetype(env.f1->msgs, "give_person"));
CuAssertPtrNotNull(tc, test_find_messagetype(env.f1->msgs, "feedback_no_contact"));
msg_release(msg);
free_order(ord);
test_teardown();
}
static void test_sabotage_other_success(CuTest *tc) {
unit *u, *u2;
region *r;
order *ord;
setup_sabotage();
r = test_create_region(0, 0, 0);
assert(r);
u = test_create_unit(test_create_faction(NULL), r);
u2 = test_create_unit(test_create_faction(NULL), r);
assert(u && u2);
u2->ship = test_create_ship(r, test_create_shiptype("boat"));
assert(u2->ship);
u->ship = u2->ship;
ship_update_owner(u->ship);
assert(ship_owner(u->ship) == u);
ord = create_order(K_SABOTAGE, u->faction->locale, "SCHIFF");
assert(ord);
set_level(u2, SK_SPY, 1);
CuAssertIntEquals(tc, 0, sabotage_cmd(u2, ord));
CuAssertPtrEquals(tc, 0, r->ships);
free_order(ord);
test_cleanup();
}
int teach_cmd(unit * u, struct order *ord)
{
static const curse_type *gbdream_ct = NULL;
plane *pl;
region *r = u->region;
int teaching, i, j, count, academy = 0;
skill_t sk = NOSKILL;
if (gbdream_ct == 0)
gbdream_ct = ct_find("gbdream");
if (gbdream_ct) {
if (get_curse(u->region->attribs, gbdream_ct)) {
ADDMSG(&u->faction->msgs, msg_feedback(u, ord, "gbdream_noteach", ""));
return 0;
}
}
if ((u_race(u)->flags & RCF_NOTEACH) || fval(u, UFL_WERE)) {
cmistake(u, ord, 274, MSG_EVENT);
return 0;
}
pl = rplane(r);
if (pl && fval(pl, PFL_NOTEACH)) {
cmistake(u, ord, 273, MSG_EVENT);
return 0;
}
teaching = u->number * 30 * TEACHNUMBER;
if ((i = get_effect(u, oldpotiontype[P_FOOL])) > 0) { /* Trank "Dumpfbackenbrot" */
i = _min(i, u->number * TEACHNUMBER);
/* Trank wirkt pro Schueler, nicht pro Lehrer */
teaching -= i * 30;
change_effect(u, oldpotiontype[P_FOOL], -i);
j = teaching / 30;
ADDMSG(&u->faction->msgs, msg_message("teachdumb", "teacher amount", u, j));
}
if (teaching == 0)
return 0;
count = 0;
init_order(ord);
#if TEACH_ALL
if (getparam(u->faction->locale) == P_ANY) {
unit *student = r->units;
skill_t teachskill[MAXSKILLS];
int i = 0;
do {
sk = getskill(u->faction->locale);
teachskill[i++] = sk;
} while (sk != NOSKILL);
while (teaching && student) {
if (student->faction == u->faction) {
if (LongHunger(student))
continue;
if (getkeyword(student->thisorder) == K_STUDY) {
/* Input ist nun von student->thisorder !! */
init_order(student->thisorder);
sk = getskill(student->faction->locale);
if (sk != NOSKILL && teachskill[0] != NOSKILL) {
for (i = 0; teachskill[i] != NOSKILL; ++i)
if (sk == teachskill[i])
break;
sk = teachskill[i];
}
if (sk != NOSKILL
&& eff_skill_study(u, sk,
r) - TEACHDIFFERENCE > eff_skill_study(student, sk, r)) {
teaching -= teach_unit(u, student, teaching, sk, true, &academy);
}
}
}
student = student->next;
}
#ifdef TEACH_FRIENDS
while (teaching && student) {
if (student->faction != u->faction
&& alliedunit(u, student->faction, HELP_GUARD)) {
if (LongHunger(student))
continue;
if (getkeyword(student->thisorder) == K_STUDY) {
/* Input ist nun von student->thisorder !! */
init_order(student->thisorder);
sk = getskill(student->faction->locale);
if (sk != NOSKILL
&& eff_skill_study(u, sk, r) - TEACHDIFFERENCE >= eff_skill(student,
sk, r)) {
teaching -= teach_unit(u, student, teaching, sk, true, &academy);
}
}
}
student = student->next;
}
#endif
}
else
#endif
{
char zOrder[4096];
order *new_order;
zOrder[0] = '\0';
init_order(ord);
while (!parser_end()) {
unit *u2;
bool feedback;
getunit(r, u->faction, &u2);
++count;
/* Falls die Unit nicht gefunden wird, Fehler melden */
if (!u2) {
char tbuf[20];
const char *uid;
const char *token;
/* Finde den string, der den Fehler verursacht hat */
parser_pushstate();
init_order(ord);
for (j = 0; j != count - 1; ++j) {
/* skip over the first 'count' units */
getunit(r, u->faction, NULL);
}
token = getstrtoken();
/* Beginne die Fehlermeldung */
if (isparam(token, u->faction->locale, P_TEMP)) {
token = getstrtoken();
sprintf(tbuf, "%s %s", LOC(u->faction->locale,
parameters[P_TEMP]), token);
uid = tbuf;
}
else {
uid = token;
}
ADDMSG(&u->faction->msgs, msg_feedback(u, ord, "unitnotfound_id",
"id", uid));
parser_popstate();
continue;
}
feedback = u->faction == u2->faction
|| alliedunit(u2, u->faction, HELP_GUARD);
/* Neuen Befehl zusammenbauen. TEMP-Einheiten werden automatisch in
* ihre neuen Nummern uebersetzt. */
if (zOrder[0])
strcat(zOrder, " ");
strcat(zOrder, unitid(u2));
if (getkeyword(u2->thisorder) != K_STUDY) {
ADDMSG(&u->faction->msgs,
msg_feedback(u, ord, "teach_nolearn", "student", u2));
continue;
}
/* Input ist nun von u2->thisorder !! */
parser_pushstate();
init_order(u2->thisorder);
sk = getskill(u2->faction->locale);
parser_popstate();
if (sk == NOSKILL) {
ADDMSG(&u->faction->msgs,
msg_feedback(u, ord, "teach_nolearn", "student", u2));
continue;
}
/* u is teacher, u2 is student */
if (eff_skill_study(u2, sk, r) > eff_skill_study(u, sk,
r) - TEACHDIFFERENCE) {
if (feedback) {
ADDMSG(&u->faction->msgs, msg_feedback(u, ord, "teach_asgood",
"student", u2));
}
continue;
}
if (sk == SK_MAGIC) {
/* ist der Magier schon spezialisiert, so versteht er nur noch
* Lehrer seines Gebietes */
sc_mage *mage1 = get_mage(u);
sc_mage *mage2 = get_mage(u2);
if (!mage2 || !mage1 || (mage2->magietyp != M_GRAY
&& mage1->magietyp != mage2->magietyp)) {
if (feedback) {
ADDMSG(&u->faction->msgs, msg_feedback(u, ord,
"error_different_magic", "target", u2));
}
continue;
}
}
teaching -= teach_unit(u, u2, teaching, sk, false, &academy);
}
new_order = create_order(K_TEACH, u->faction->locale, "%s", zOrder);
replace_order(&u->orders, ord, new_order);
free_order(new_order); /* parse_order & set_order have each increased the refcount */
}
if (academy && sk != NOSKILL) {
academy = academy / 30; /* anzahl gelehrter wochen, max. 10 */
learn_skill(u, sk, academy / 30.0 / TEACHNUMBER);
}
return 0;
}
/*************************************************************************
* int main
*************************************************************************/
int main(int argc, char *argv[])
{
/* Data structures. */
int num_motifs; /* The number of motifs in the model. */
MOTIF_T motifs[2 * MAX_MOTIFS]; /* The motifs. */
STRING_LIST_T* motif_occurrences = NULL; /* Strings describing occurrences of
motifs */
BOOLEAN_T has_reverse_strand = FALSE; /* MEME file contained both strands */
ARRAY_T* background; /* Background probs for alphabet. */
ORDER_T* order_spacing; /* Linear HMM order and spacing. */
MATRIX_T* transp_freq = NULL; /* Matrix of inter-motif transitions freqs. */
MATRIX_T* spacer_ave = NULL; /* Matrix of average spacer lengths. */
MHMM_T * the_hmm = NULL; /* The HMM being constructed. */
/* Command line parameters. */
char * meme_filename; /* Input file containg motifs. */
char * hmm_type_str; /* HMM type. */
HMM_T hmm_type;
STRING_LIST_T* requested_motifs; /* Indices of requested motifs. */
int request_n; /* The user asked for the first n motifs. */
double e_threshold; /* E-value threshold for motif inclusion. */
double complexity_threshold; // For eliminating low-complexity motifs.
double p_threshold; /* p-value threshold for motif occurences. */
char* order_string; /* Motif order and spacing. */
int spacer_states; /* Number of states in each spacer. */
BOOLEAN_T fim; /* Represent spacers as free insertion
modules? */
BOOLEAN_T keep_unused; // Drop unused inter-motif transitions?
double trans_pseudo; /* Transition pseudocount. */
double spacer_pseudo; // Spacer (self-loop) pseudocount. */
char* description; // Descriptive text to be stored in model.
BOOLEAN_T print_header; /* Print file header? */
BOOLEAN_T print_params; /* Print parameter summary? */
BOOLEAN_T print_time; /* Print timing data (dummy: always false). */
/* Local variables. */
int i_motif;
/**********************************************
* COMMAND LINE PROCESSING
**********************************************/
// Define command line options.
cmdoption const options[] = {
{"type", OPTIONAL_VALUE},
{"description", REQUIRED_VALUE},
{"motif", REQUIRED_VALUE},
{"nmotifs", REQUIRED_VALUE},
{"ethresh", REQUIRED_VALUE},
{"lowcomp", REQUIRED_VALUE},
{"pthresh", REQUIRED_VALUE},
{"order", REQUIRED_VALUE},
{"nspacer", REQUIRED_VALUE},
{"fim", NO_VALUE},
{"keep-unused", NO_VALUE},
{"transpseudo", REQUIRED_VALUE},
{"spacerpseudo", REQUIRED_VALUE},
{"verbosity", REQUIRED_VALUE},
{"noheader", NO_VALUE},
{"noparams", NO_VALUE},
{"notime", NO_VALUE},
{"quiet", NO_VALUE},
};
int option_count = 18;
int option_index = 0;
// Define the usage message.
char usage[1000] = "";
strcat(usage, "USAGE: mhmm [options] <MEME file>\n");
strcat(usage, "\n");
strcat(usage, " Options:\n");
strcat(usage, " --type [linear|complete|star] (default=linear)\n");
strcat(usage, " --description <string> (may be repeated)\n");
strcat(usage, " --motif <motif #> (may be repeated)\n");
strcat(usage, " --nmotifs <#>\n");
strcat(usage, " --ethresh <E-value>\n");
strcat(usage, " --lowcomp <value>\n");
strcat(usage, " --pthresh <p-value>\n");
strcat(usage, " --order <string>\n");
strcat(usage, " --nspacer <spacer length> (default=1)\n");
strcat(usage, " --fim\n");
strcat(usage, " --keep-unused\n");
strcat(usage, " --transpseudo <pseudocount>\n");
strcat(usage, " --spacerpseudo <pseudocount>\n");
strcat(usage, " --verbosity 1|2|3|4|5 (default=2)\n");
strcat(usage, " --noheader\n");
strcat(usage, " --noparams\n");
strcat(usage, " --notime\n");
strcat(usage, " --quiet\n");
strcat(usage, "\n");
/* Make sure various options are set to NULL or defaults. */
meme_filename = NULL;
hmm_type_str = NULL;
hmm_type = INVALID_HMM;
requested_motifs = new_string_list();
request_n = 0;
e_threshold = 0.0;
complexity_threshold = 0.0;
p_threshold = 0.0;
order_string = NULL;
spacer_states = DEFAULT_SPACER_STATES,
fim = FALSE;
keep_unused = FALSE;
trans_pseudo = DEFAULT_TRANS_PSEUDO;
spacer_pseudo = DEFAULT_SPACER_PSEUDO;
description = NULL;
print_header = TRUE;
print_params = TRUE;
print_time = FALSE;
simple_setopt(argc, argv, option_count, options);
// Parse the command line.
while (1) {
int c = 0;
char* option_name = NULL;
char* option_value = NULL;
const char * message = NULL;
// Read the next option, and break if we're done.
c = simple_getopt(&option_name, &option_value, &option_index);
if (c == 0) {
break;
} else if (c < 0) {
simple_getopterror(&message);
die("Error processing command line options (%s)\n", message);
}
if (strcmp(option_name, "type") == 0) {
if (option_value != NULL) {
hmm_type_str = option_value;
}
} else if (strcmp(option_name, "description") == 0) {
description = option_value;
} else if (strcmp(option_name, "motif") == 0) {
add_string(option_value, requested_motifs);
} else if (strcmp(option_name, "nmotifs") == 0) {
request_n = atoi(option_value);
} else if (strcmp(option_name, "ethresh") == 0) {
e_threshold = atof(option_value);
} else if (strcmp(option_name, "lowcomp") == 0) {
complexity_threshold = atof(option_value);
} else if (strcmp(option_name, "pthresh") == 0) {
p_threshold = atof(option_value);
} else if (strcmp(option_name, "order") == 0) {
order_string = option_value;
} else if (strcmp(option_name, "nspacer") == 0) {
spacer_states = atoi(option_value);
} else if (strcmp(option_name, "fim") == 0) {
fim = TRUE;
} else if (strcmp(option_name, "keep-unused") == 0) {
keep_unused = TRUE;
} else if (strcmp(option_name, "transpseudo") == 0) {
trans_pseudo = atof(option_value);
} else if (strcmp(option_name, "spacerpseudo") == 0) {
spacer_pseudo = atof(option_value);
} else if (strcmp(option_name, "verbosity") == 0) {
verbosity = (VERBOSE_T)atoi(option_value);
} else if (strcmp(option_name, "noheader") == 0) {
print_header = FALSE;
} else if (strcmp(option_name, "noparams") == 0) {
print_params = FALSE;
} else if (strcmp(option_name, "notime") == 0) {
print_time = FALSE;
} else if (strcmp(option_name, "quiet") == 0) {
print_header = print_params = print_time = FALSE;
verbosity = QUIET_VERBOSE;
}
}
// Read the single required argument.
if (option_index + 1 != argc) {
fprintf(stderr, "%s", usage);
exit(1);
}
meme_filename = argv[option_index];
// Set up motif requests.
if (request_n != 0) {
if (get_num_strings(requested_motifs) != 0) {
die("Can't combine the -motif and -nmotifs options.\n");
} else {
for (i_motif = 0; i_motif < request_n; i_motif++) {
char motif_id[MAX_MOTIF_ID_LENGTH + 1];
sprintf(motif_id, "%d", i_motif + 1);
add_string(motif_id, requested_motifs);
}
}
}
/* Set the model type. */
hmm_type = convert_enum_type_str(hmm_type_str, LINEAR_HMM, HMM_STRS,
NUM_HMM_T);
/* Gotta have positive spacer length. */
if (spacer_states <= 0) {
die("Negative spacer length (%d).\n", spacer_states);
}
/* Make sure motifs weren't selected redundantly. */
// FIXME: Add tests for complexity threshold.
if ((get_num_strings(requested_motifs) != 0) && (e_threshold != 0.0)) {
die("Can't use -motif or -nmotifs with -ethresh.");
}
if ((get_num_strings(requested_motifs) != 0) && (order_string != NULL)) {
die("Can't use -motif or -nmotifs with -order.");
}
if ((order_string != NULL) && (e_threshold != 0.0)) {
die("Can't use -ethresh and -order.");
}
/* Prevent trying to build a complete or star model with ordering. */
if (order_string != NULL) {
if (hmm_type == COMPLETE_HMM)
die("Can't specify motif order with a completely connected model.");
else if (hmm_type == STAR_HMM)
die("Can't specify motif order with a star model.");
}
// Parse the order string.
order_spacing = create_order(order_string);
/**********************************************
* READING THE MOTIFS
**********************************************/
BOOLEAN_T read_file = FALSE;
double pseudocount = 0;
read_meme_file(
meme_filename,
"motif-file", // Take bg freq. from motif file.
pseudocount,
REQUIRE_PSPM,
&num_motifs,
motifs,
&motif_occurrences,
&has_reverse_strand,
&background
);
process_raw_motifs_for_model(
&num_motifs,
motifs,
motif_occurrences,
requested_motifs,
has_reverse_strand,
keep_unused,
p_threshold,
e_threshold,
complexity_threshold,
&order_spacing,
&transp_freq,
&spacer_ave,
trans_pseudo,
spacer_pseudo
);
/**********************************************
* BUILDING THE HMM
**********************************************/
/* Build the motif-based HMM. */
if (hmm_type == LINEAR_HMM) {
if (order_spacing != NULL) {
reorder_motifs(order_spacing, &num_motifs, motifs);
}
else {
die("No order specified for the motifs.\n"
"For the linear model the motif file must contain motif occurence\n"
"data or the motif order must be specified using "
"the --order option.");
}
build_linear_hmm(
background,
order_spacing,
spacer_states,
motifs,
num_motifs,
fim,
&the_hmm
);
} else if (hmm_type == COMPLETE_HMM) {
build_complete_hmm(
background,
spacer_states,
motifs,
num_motifs,
transp_freq,
spacer_ave,
fim,
&the_hmm
);
} else if (hmm_type == STAR_HMM) {
build_star_hmm(
background,
spacer_states,
motifs,
num_motifs,
fim,
&the_hmm
);
}
// Add some global information.
copy_string(&(the_hmm->motif_file), meme_filename);
/**********************************************
* WRITING THE HMM
**********************************************/
/* Print the header. */
if (print_header)
write_header(
program,
"",
description,
meme_filename,
NULL,
NULL,
stdout
);
/* Write the HMM. */
write_mhmm(verbosity, the_hmm, stdout);
/* Print the program parameters. */
if (print_params) {
printf("Program parameters for mhmm\n");
printf(" MEME file: %s\n", meme_filename);
printf(" Motifs:");
write_string_list(" ", requested_motifs, stdout);
printf("\n");
printf(" Model topology: %s\n",
convert_enum_type(hmm_type, HMM_STRS, NUM_HMM_T));
printf(" States per spacer: %d\n", spacer_states);
printf(" Spacers are free-insertion modules: %s\n",
boolean_to_string(fim));
printf("\n");
}
free_array(background);
free_string_list(requested_motifs);
free_order(order_spacing);
free_matrix(transp_freq);
free_matrix(spacer_ave);
for (i_motif = 0; i_motif < num_motifs; i_motif++)
free_motif(&(motifs[i_motif]));
free_mhmm(the_hmm);
return(0);
}
/***********************************************************************
* Parse the motif occurrences.
*
* Each motif occurence string contains the following items
* - sequence id,
* - sequence p-value,
* - number n of motif occurrences, and
* - length of sequence.
*
* This is followed by n triples containing
* - motif id,
* - occurrence position, and
* - occurrence p-value.
*
***********************************************************************/
static void parse_motif_occurrences(
STRING_LIST_T* motif_occurrences, // List of motif occurences OUT
BOOLEAN_T has_reverse_strand, // File included both strands? IN
double p_threshold, // P-value to include motif occurences. OUT
ORDER_T** order_spacing, // Motif order and spacing (linear HMM)
// IN OUT.
MATRIX_T** transp_freq, // Motif-to-motif transitions. OUT
MATRIX_T** spacer_ave, // Average inter-motif distances. OUT
int num_motifs, // Number of motifs retrieved. IN
MOTIF_T* motifs // The retrieved motifs. IN
) {
ORDER_T* new_order; // New order and spacing.
BOOLEAN_T find_order; // Should we look for the motif order?
// If we already have a motif order and spacing, don't find any more.
if (*order_spacing == NULL) {
find_order = TRUE;
} else {
find_order = FALSE;
}
new_order = NULL;
// Allocate the matrices.
*transp_freq = allocate_matrix(num_motifs + 2, num_motifs + 2);
*spacer_ave = allocate_matrix(num_motifs + 2, num_motifs + 2);
init_matrix(0.0, *transp_freq);
init_matrix(0.0, *spacer_ave);
int num_occurrence_strings = get_num_strings(motif_occurrences);
int i;
for (i = 0; i < num_occurrence_strings; i++) {
char* sequence_id; // ID of the current sequence.
float sequence_p; // pvalue of the entire sequence.
int num_occurs; // Number of motif occurences in this sequence.
int seq_length; // Length of the current sequence.
int i_occur; // Index of the current occurrence.
char prev_motif[MAX_MOTIF_ID_LENGTH + 1]; // Index of the previous motif.
int prev_position; // Location of the right edge of previous motif.
float motif_p; // P-value of the current occurrence.
char *c; // Dummy to hold return of strtok.
char* line = get_nth_string(i, motif_occurrences);
/* Read the sequence identifier, p-value, number of occurrences
and length. */
// tlb; sscanf crashes if strtok returns NULL so pass it "" then
sequence_id = strtok(line, " ");
if (sequence_id == NULL) {
die("Error reading motif occurrences.\n%s", line);
}
if (sscanf((c=strtok(NULL, " "))?c:"", "%f", &sequence_p) != 1) {
die("Can't read p-value of sequence %s.", sequence_id);
}
if (sscanf((c=strtok(NULL, " "))?c:"", "%d", &num_occurs) != 1) {
die("Can't read number of motif occurences in sequence %s.",
sequence_id);
}
if (sscanf((c=strtok(NULL, " "))?c:"", "%d", &seq_length) != 1) {
die("Can't read length of sequence %s.", sequence_id);
}
if (verbosity > NORMAL_VERBOSE) {
fprintf(stderr, "Reading motif occurrences for sequence %s.\n",
sequence_id);
}
// If requested, try to create an order string.
if (find_order) {
new_order = create_empty_order(num_occurs, sequence_p);
}
// Accumulate motif occurence data.
sprintf(prev_motif, "%d", 0);
prev_position = 0;
for (i_occur = 0; i_occur < num_occurs; i_occur++) {
char motif_id[MAX_MOTIF_ID_LENGTH + 1]; // ID of the current motif.
int motif_position; // Position of the current motif occurrence.
char *c; // Dummy to hold return of strtok.
// Read the three values.
if (sscanf((c=strtok(NULL, " "))?c:"", "%s", motif_id) != 1) {
die("Can't read index of occurrence %d in sequence %s.",
i_occur, sequence_id);
}
if (sscanf((c=strtok(NULL, " "))?c:"", "%d", &motif_position) != 1) {
die("Can't read position of occurrence %d in sequence %s.",
i_occur, sequence_id);
}
if (sscanf((c=strtok(NULL, " "))?c:"", "%f", &motif_p) != 1) {
die("Can't read p-value of occurrence %d in sequence %s.",
i_occur, sequence_id);
}
// Only include motifs that have been retained
if (have_motif(motif_id, num_motifs, motifs)) {
// Make sure we have strand information in the ID.
if (has_reverse_strand) {
add_strand(motif_id);
}
// Record this occurrence.
record_occurrence(sequence_id,
motif_id,
p_threshold,
motif_p,
prev_motif,
&prev_position,
motif_position,
*transp_freq,
*spacer_ave,
new_order,
num_motifs,
motifs);
/* Motifs are stored in order of their motif IDs, but they are
indexed from zero rather than one. */
prev_position = motif_position +
(motifs[find_matrix_location(motifs, motif_id, num_motifs) - 1]).length;
}
}
assert(seq_length >= prev_position);
// Record the transition to the end state.
record_occurrence(sequence_id,
END_TRANSITION,
p_threshold,
motif_p,
prev_motif,
&prev_position,
seq_length,
*transp_freq,
*spacer_ave,
new_order,
num_motifs,
motifs);
// Decide whether to keep the new order object.
if (find_order) {
if ((get_num_distinct(new_order) > get_num_distinct(*order_spacing)) ||
(((get_num_distinct(new_order) == get_num_distinct(*order_spacing))
&& (get_pvalue(new_order) < get_pvalue(*order_spacing))))) {
if (verbosity > NORMAL_VERBOSE) {
fprintf(stderr, "Storing order from sequence %s (%g < %g).\n",
sequence_id, get_pvalue(new_order),
get_pvalue(*order_spacing));
print_order_and_spacing(stderr, new_order);
}
free_order(*order_spacing);
*order_spacing = new_order;
} else {
free_order(new_order);
}
}
}
}
int teach_cmd(unit * teacher, struct order *ord)
{
plane *pl;
region *r = teacher->region;
skill_t sk_academy = NOSKILL;
int teaching, i, j, count, academy_students = 0;
if (r->attribs) {
if (get_curse(r->attribs, &ct_gbdream)) {
ADDMSG(&teacher->faction->msgs,
msg_feedback(teacher, ord, "gbdream_noteach", ""));
return 0;
}
}
if ((u_race(teacher)->flags & RCF_NOTEACH) || fval(teacher, UFL_WERE)) {
cmistake(teacher, ord, 274, MSG_EVENT);
return 0;
}
pl = rplane(r);
if (pl && fval(pl, PFL_NOTEACH)) {
cmistake(teacher, ord, 273, MSG_EVENT);
return 0;
}
teaching = teacher->number * TEACHNUMBER;
if ((i = get_effect(teacher, oldpotiontype[P_FOOL])) > 0) { /* Trank "Dumpfbackenbrot" */
if (i > teaching) i = teaching;
/* Trank wirkt pro Schueler, nicht pro Lehrer */
teaching -= i;
change_effect(teacher, oldpotiontype[P_FOOL], -i);
j = teaching;
ADDMSG(&teacher->faction->msgs, msg_message("teachdumb", "teacher amount", teacher, j));
}
if (teaching <= 0)
return 0;
count = 0;
init_order_depr(ord);
#if TEACH_ALL
if (getparam(teacher->faction->locale) == P_ANY) {
skill_t sk;
unit *scholar;
skill_t teachskill[MAXSKILLS];
int t = 0;
do {
sk = getskill(teacher->faction->locale);
teachskill[t] = getskill(teacher->faction->locale);
} while (sk != NOSKILL);
for (scholar = r->units; teaching > 0 && scholar; scholar = scholar->next) {
if (LongHunger(scholar)) {
continue;
}
else if (scholar->faction == teacher->faction) {
if (getkeyword(scholar->thisorder) == K_STUDY) {
/* Input ist nun von student->thisorder !! */
init_order(scholar->thisorder, scholar->faction->locale);
sk = getskill(scholar->faction->locale);
if (sk != NOSKILL && teachskill[0] != NOSKILL) {
for (t = 0; teachskill[t] != NOSKILL; ++t) {
if (sk == teachskill[t]) {
break;
}
}
sk = teachskill[t];
}
if (sk != NOSKILL
&& effskill_study(teacher, sk) - TEACHDIFFERENCE > effskill_study(scholar, sk)) {
teaching -= teach_unit(teacher, scholar, teaching, sk, true, &academy_students);
}
}
}
#ifdef TEACH_FRIENDS
else if (alliedunit(teacher, scholar->faction, HELP_GUARD)) {
if (getkeyword(scholar->thisorder) == K_STUDY) {
/* Input ist nun von student->thisorder !! */
init_order(scholar->thisorder, scholar->faction->locale);
sk = getskill(scholar->faction->locale);
if (sk != NOSKILL
&& effskill_study(teacher, sk) - TEACHDIFFERENCE >= effskill(scholar, sk, NULL)) {
teaching -= teach_unit(teacher, scholar, teaching, sk, true, &academy_students);
}
}
}
#endif
}
}
else
#endif
{
char zOrder[4096];
size_t sz = sizeof(zOrder);
order *new_order;
zOrder[0] = '\0';
init_order_depr(ord);
while (!parser_end()) {
skill_t sk;
unit *scholar;
bool feedback;
getunit(r, teacher->faction, &scholar);
++count;
/* Falls die Unit nicht gefunden wird, Fehler melden */
if (!scholar) {
char tbuf[20];
const char *uid;
const char *token;
/* Finde den string, der den Fehler verursacht hat */
parser_pushstate();
init_order_depr(ord);
for (j = 0; j != count - 1; ++j) {
/* skip over the first 'count' units */
getunit(r, teacher->faction, NULL);
}
token = getstrtoken();
/* Beginne die Fehlermeldung */
if (isparam(token, teacher->faction->locale, P_TEMP)) {
token = getstrtoken();
sprintf(tbuf, "%s %s", LOC(teacher->faction->locale,
parameters[P_TEMP]), token);
uid = tbuf;
}
else {
uid = token;
}
ADDMSG(&teacher->faction->msgs, msg_feedback(teacher, ord, "unitnotfound_id",
"id", uid));
parser_popstate();
continue;
}
feedback = teacher->faction == scholar->faction
|| alliedunit(scholar, teacher->faction, HELP_GUARD);
/* Neuen Befehl zusammenbauen. TEMP-Einheiten werden automatisch in
* ihre neuen Nummern uebersetzt. */
if (zOrder[0]) {
strncat(zOrder, " ", sz - 1);
--sz;
}
sz -= str_strlcpy(zOrder + 4096 - sz, itoa36(scholar->no), sz);
if (getkeyword(scholar->thisorder) != K_STUDY) {
ADDMSG(&teacher->faction->msgs,
msg_feedback(teacher, ord, "teach_nolearn", "student", scholar));
continue;
}
/* Input ist nun von student->thisorder !! */
parser_pushstate();
init_order(scholar->thisorder, scholar->faction->locale);
sk = getskill(scholar->faction->locale);
parser_popstate();
if (sk == NOSKILL) {
ADDMSG(&teacher->faction->msgs,
msg_feedback(teacher, ord, "teach_nolearn", "student", scholar));
continue;
}
if (effskill_study(scholar, sk) > effskill_study(teacher, sk)
- TEACHDIFFERENCE) {
if (feedback) {
ADDMSG(&teacher->faction->msgs, msg_feedback(teacher, ord, "teach_asgood",
"student", scholar));
}
continue;
}
if (sk == SK_MAGIC) {
/* ist der Magier schon spezialisiert, so versteht er nur noch
* Lehrer seines Gebietes */
magic_t mage2 = unit_get_magic(scholar);
if (mage2 != M_GRAY) {
magic_t mage1 = unit_get_magic(teacher);
if (mage1 != mage2) {
if (feedback) {
ADDMSG(&teacher->faction->msgs, msg_feedback(teacher, ord,
"error_different_magic", "target", scholar));
}
continue;
}
}
}
sk_academy = sk;
teaching -= teach_unit(teacher, scholar, teaching, sk, false, &academy_students);
}
new_order = create_order(K_TEACH, teacher->faction->locale, "%s", zOrder);
replace_order(&teacher->orders, ord, new_order);
free_order(new_order); /* parse_order & set_order have each increased the refcount */
}
if (academy_students > 0 && sk_academy!=NOSKILL) {
academy_teaching_bonus(teacher, sk_academy, academy_students);
}
init_order_depr(NULL);
return 0;
}
int
build_building(unit * u, const building_type * btype, int id, int want, order * ord)
{
region *r = u->region;
int n = want, built = 0;
building *b = NULL;
/* einmalige Korrektur */
const char *btname;
order *new_order = NULL;
const struct locale *lang = u->faction->locale;
static int rule_other = -1;
assert(u->number);
assert(btype->construction);
if (eff_skill(u, SK_BUILDING, r) == 0) {
cmistake(u, ord, 101, MSG_PRODUCE);
return 0;
}
/* Falls eine Nummer angegeben worden ist, und ein Gebaeude mit der
* betreffenden Nummer existiert, ist b nun gueltig. Wenn keine Burg
* gefunden wurde, dann wird nicht einfach eine neue erbaut. Ansonsten
* baut man an der eigenen burg weiter. */
/* Wenn die angegebene Nummer falsch ist, KEINE Burg bauen! */
if (id > 0) { /* eine Nummer angegeben, keine neue Burg bauen */
b = findbuilding(id);
if (!b || b->region != u->region) { /* eine Burg mit dieser Nummer gibt es hier nicht */
/* vieleicht Tippfehler und die eigene Burg ist gemeint? */
if (u->building && u->building->type == btype) {
b = u->building;
}
else {
/* keine neue Burg anfangen wenn eine Nummer angegeben war */
cmistake(u, ord, 6, MSG_PRODUCE);
return 0;
}
}
}
else if (u->building && u->building->type == btype) {
b = u->building;
}
if (b)
btype = b->type;
if (fval(btype, BTF_UNIQUE) && buildingtype_exists(r, btype, false)) {
/* only one of these per region */
cmistake(u, ord, 93, MSG_PRODUCE);
return 0;
}
if (besieged(u)) {
/* units under siege can not build */
cmistake(u, ord, 60, MSG_PRODUCE);
return 0;
}
if (btype->flags & BTF_NOBUILD) {
/* special building, cannot be built */
cmistake(u, ord, 221, MSG_PRODUCE);
return 0;
}
if ((r->terrain->flags & LAND_REGION) == 0) {
/* special terrain, cannot build */
cmistake(u, ord, 221, MSG_PRODUCE);
return 0;
}
if (btype->flags & BTF_ONEPERTURN) {
if (b && fval(b, BLD_EXPANDED)) {
cmistake(u, ord, 318, MSG_PRODUCE);
return 0;
}
n = 1;
}
if (b) {
if (rule_other < 0) {
rule_other =
get_param_int(global.parameters, "rules.build.other_buildings", 1);
}
if (!rule_other) {
unit *owner = building_owner(b);
if (!owner || owner->faction != u->faction) {
cmistake(u, ord, 1222, MSG_PRODUCE);
return 0;
}
}
}
if (b)
built = b->size;
if (n <= 0 || n == INT_MAX) {
if (b == NULL) {
if (btype->maxsize > 0) {
n = btype->maxsize - built;
}
else {
n = INT_MAX;
}
}
else {
if (b->type->maxsize > 0) {
n = b->type->maxsize - built;
}
else {
n = INT_MAX;
}
}
}
built = build(u, btype->construction, built, n);
switch (built) {
case ECOMPLETE:
/* the building is already complete */
cmistake(u, ord, 4, MSG_PRODUCE);
break;
case ENOMATERIALS:
ADDMSG(&u->faction->msgs, msg_materials_required(u, ord,
btype->construction, want));
break;
case ELOWSKILL:
case ENEEDSKILL:
/* no skill, or not enough skill points to build */
cmistake(u, ord, 50, MSG_PRODUCE);
break;
}
if (built <= 0) {
return built;
}
/* at this point, the building size is increased. */
if (b == NULL) {
/* build a new building */
b = new_building(btype, r, lang);
b->type = btype;
fset(b, BLD_MAINTAINED | BLD_WORKING);
/* Die Einheit befindet sich automatisch im Inneren der neuen Burg. */
if (u->number && leave(u, false)) {
u_set_building(u, b);
}
}
btname = LOC(lang, btype->_name);
if (want - built <= 0) {
/* gebäude fertig */
new_order = default_order(lang);
}
else if (want != INT_MAX) {
/* reduzierte restgröße */
const char *hasspace = strchr(btname, ' ');
if (hasspace) {
new_order =
create_order(K_MAKE, lang, "%d \"%s\" %i", n - built, btname, b->no);
}
else {
new_order =
create_order(K_MAKE, lang, "%d %s %i", n - built, btname, b->no);
}
}
else if (btname) {
/* Neues Haus, Befehl mit Gebäudename */
const char *hasspace = strchr(btname, ' ');
if (hasspace) {
new_order = create_order(K_MAKE, lang, "\"%s\" %i", btname, b->no);
}
else {
new_order = create_order(K_MAKE, lang, "%s %i", btname, b->no);
}
}
if (new_order) {
replace_order(&u->orders, ord, new_order);
free_order(new_order);
}
b->size += built;
fset(b, BLD_EXPANDED);
update_lighthouse(b);
ADDMSG(&u->faction->msgs, msg_message("buildbuilding",
"building unit size", b, u, built));
return built;
}
void main_loop(int argc, char *argv[], int max_hosts)
{
int i;
int host;
int *targeted_host;
FileData local_file_data;
FileData remote_file_data;
Order *order;
Direction direction;
bool use_cache;
char *top_dir;
FtpInit();
targeted_host = get_targeted_host(argc, argv, max_hosts);
for (i = 0;; i++) {
host = targeted_host[i];
if (host == -1) {
break;
}
message(PROCESS, cfgSectionNumberToName(host), 0, host);
direction = get_direction(host);
get_local_file_data(&local_file_data, host);
if (command_line_option.rebuild_cache) { /* -r | --rebuild-cache */
rebuild_cache(host);
free_file_data(&local_file_data);
continue;
}
if (command_line_option.catch_up) { /* -R | --catch-up */
catch_up(&local_file_data, host);
free_file_data(&local_file_data);
continue;
}
if (direction == DOWNLOAD || !does_cache_exist(host)) {
if (direction == DOWNLOAD) {
printf(_("Rebuilding cache for downloading...\n"));
} else {
printf(_("Cache file is not found.\nCreating a new one...\n"));
}
if (connect_to_remote_host(host) != 0) {
free_file_data(&local_file_data);
continue;
}
get_remote_file_data(&remote_file_data, host);
use_cache = FALSE;
} else {
load_cache(&remote_file_data, host);
use_cache = TRUE;
}
order = compare_both_hosts_and_generate_order(&local_file_data, &remote_file_data, config.local_top_dir[host], config.remote_top_dir[host], direction, host);
if (!does_need_update(order)) {
disconnect_from_remote_host(host);
if (direction == UPLOAD) {
printf(_("The remote host doesn't need updating.\n"));
} else {
printf(_("The local host doesn't need updating.\n"));
}
if (!use_cache) {
save_cache(&remote_file_data, host);
}
free_file_data(&remote_file_data);
free_file_data(&local_file_data);
continue;
}
if(command_line_option.list) {
disconnect_from_remote_host(host);
put_listing_of_updated_file(order, direction);
free_file_data(&remote_file_data);
free_file_data(&local_file_data);
continue;
}
if(command_line_option.nlist) {
disconnect_from_remote_host(host);
put_the_number_of_updated_file(order, direction);
free_file_data(&remote_file_data);
free_file_data(&local_file_data);
continue;
}
if (!use_cache) {
printf("\n");
}
put_num_updated_file(order, direction);
if (connect_to_remote_host(host) != 0) {
free_file_data(&remote_file_data);
free_file_data(&local_file_data);
continue;
}
if (direction == UPLOAD) {
top_dir = str_concat(config.remote_top_dir[host], "/", NULL);
} else {
top_dir = str_concat(config.local_top_dir[host], "/", NULL);
}
message(ENTER, top_dir, 0, host);
execute_order(order, &remote_file_data, direction, host);
message(LEAVE, top_dir, 0, host);
free(top_dir);
free_order(order);
disconnect_from_remote_host(host);
save_cache(&remote_file_data, host);
free_file_data(&remote_file_data);
free_file_data(&local_file_data);
}
free(targeted_host);
}
