const char *char_data::get_whoname( )
{
char buf[MSL] = {'\0'};
short s1, s2, s3, s4, s5;
const char *output;
if ( IS_NPC(this) )
return "";
if ( IS_IMMORTAL(this) )
{
if ( strcmp(pcdata->who_name,"off") )
return pcdata->who_name;
switch ( get_level() )
{
case MAX_LEVEL - 0: return "@@l~* CREATOR *~@@N ";
case MAX_LEVEL - 1: return "@@B-* SUPREME *-@@N ";
case MAX_LEVEL - 2: return "@@a-=MAJOR GOD=-@@N ";
case MAX_LEVEL - 3: return "@@a--MINOR GOD--@@N ";
case MAX_LEVEL - 4: return "@@c - IMMORTAL -@@N ";
}
}
if ( IS_ADEPT(this) )
{
if ( strcmp(pcdata->who_name,"off") )
return pcdata->who_name;
switch ( get_level("adept") )
{
case 1: return "@@W Mystic @@N";
case 2: return "@@a Templar @@N";
case 3: return "@@l Illusionist @@N";
case 4: return "@@e Crusader @@N";
case 5: return "@@d Warlock @@N";
case 6: return "@@a Paladin @@N";
case 7: return "@@r Ranger @@N";
case 8: return "@@c Gladiator @@N";
case 9: return "@@l Shogun @@N";
case 10: return "@@e Shamen @@N";
case 11: return "@@r Druid @@N";
case 12: return "@@b Conjurer @@N";
case 13: return "@@l Elementalist @@N";
case 14: return "@@m Runemaster @@N";
case 15: return "@@d Shadowmaster @@N";
case 16: return "@@b Beastmaster @@N";
case 17: return "@@R Warlord @@N";
case 18: return "@@e Dragonlord @@N";
case 19: return "@@d Demonlord @@N";
case 20: return "@@m Realm Lord @@N";
}
}
if ( IS_REMORT(this) )
{
s1 = get_level("sor"); s2 = get_level("mon"); s3 = get_level("ass"); s4 = get_level("kni"); s5 = get_level("nec");
snprintf( buf, MSL, "@@m%2d %2d %2d %2d %2d@@N", s1 <= 0 ? 0 : s1, s2 <= 0 ? 0 : s2, s3 <= 0 ? 0 : s3, s4 <= 0 ? 0 : s4, s5 <= 0 ? 0 : s5 );
output = str_dup( buf );
return output;
}
else
{
s1 = get_level("mag"); s2 = get_level("cle"); s3 = get_level("thi"); s4 = get_level("war"); s5 = get_level("psi");
snprintf( buf, MSL, "@@b%2d %2d %2d %2d %2d@@N", s1 <= 0 ? 0 : s1, s2 <= 0 ? 0 : s2, s3 <= 0 ? 0 : s3, s4 <= 0 ? 0 : s4, s5 <= 0 ? 0 : s5 );
output = str_dup( buf );
return output;
}
return "";
}
void do_note( CHAR_DATA *ch, char *argument )
{
char buf[MAX_STRING_LENGTH];
char arg[MAX_INPUT_LENGTH];
NOTE_DATA *pnote;
int vnum;
int anum;
if ( IS_NPC(ch) )
return;
argument = one_argument( argument, arg );
smash_tilde( argument );
if ( !str_cmp( arg, "list" ) )
{
vnum = 0;
for ( pnote = note_list; pnote != NULL; pnote = pnote->next )
{
if ( is_note_to( ch, pnote ) )
{
sprintf( buf, "[%3d] %s: %s\n\r",
vnum, pnote->sender, pnote->subject );
send_to_char( buf, ch );
vnum++;
}
}
return;
}
if ( !str_cmp( arg, "read" ) )
{
bool fAll;
if ( !str_cmp( argument, "all" ) )
{
fAll = TRUE;
anum = 0;
}
else if ( is_number( argument ) )
{
fAll = FALSE;
anum = atoi( argument );
}
else
{
send_to_char( "Note read which number?\n\r", ch );
return;
}
vnum = 0;
for ( pnote = note_list; pnote != NULL; pnote = pnote->next )
{
if ( is_note_to( ch, pnote ) && ( vnum++ == anum || fAll ) )
{
sprintf( buf, "[%3d] %s: %s\n\r%s\n\rTo: %s\n\r",
vnum - 1,
pnote->sender,
pnote->subject,
pnote->date,
pnote->to_list
);
send_to_char( buf, ch );
send_to_char( pnote->text, ch );
return;
}
}
send_to_char( "No such note.\n\r", ch );
return;
}
if ( !str_cmp( arg, "+" ) )
{
note_attach( ch );
strcpy( buf, ch->pnote->text );
if ( strlen(buf) + strlen(argument) >= MAX_STRING_LENGTH - 4 )
{
send_to_char( "Note too long.\n\r", ch );
return;
}
strcat( buf, argument );
strcat( buf, "\n\r" );
free_string( ch->pnote->text );
ch->pnote->text = str_dup( buf );
send_to_char( "Ok.\n\r", ch );
return;
}
if ( !str_cmp( arg, "subject" ) )
{
note_attach( ch );
free_string( ch->pnote->subject );
ch->pnote->subject = str_dup( argument );
send_to_char( "Ok.\n\r", ch );
return;
}
if ( !str_cmp( arg, "to" ) )
{
note_attach( ch );
free_string( ch->pnote->to_list );
ch->pnote->to_list = str_dup( argument );
send_to_char( "Ok.\n\r", ch );
return;
}
if ( !str_cmp( arg, "clear" ) )
{
if ( ch->pnote != NULL )
{
free_string( ch->pnote->text );
free_string( ch->pnote->subject );
free_string( ch->pnote->to_list );
free_string( ch->pnote->date );
free_string( ch->pnote->sender );
ch->pnote->next = note_free;
note_free = ch->pnote;
ch->pnote = NULL;
}
send_to_char( "Ok.\n\r", ch );
return;
}
if ( !str_cmp( arg, "show" ) )
{
if ( ch->pnote == NULL )
{
send_to_char( "You have no note in progress.\n\r", ch );
return;
}
sprintf( buf, "%s: %s\n\rTo: %s\n\r",
ch->pnote->sender,
ch->pnote->subject,
ch->pnote->to_list
);
send_to_char( buf, ch );
send_to_char( ch->pnote->text, ch );
return;
}
if ( !str_cmp( arg, "post" ) )
{
FILE *fp;
char *strtime;
if ( ch->pnote == NULL )
{
send_to_char( "You have no note in progress.\n\r", ch );
return;
}
ch->pnote->next = NULL;
strtime = ctime( ¤t_time );
strtime[strlen(strtime)-1] = '\0';
ch->pnote->date = str_dup( strtime );
if ( note_list == NULL )
{
note_list = ch->pnote;
}
else
{
for ( pnote = note_list; pnote->next != NULL; pnote = pnote->next )
;
pnote->next = ch->pnote;
}
pnote = ch->pnote;
ch->pnote = NULL;
fclose( fpReserve );
if ( ( fp = fopen( NOTE_FILE, "a" ) ) == NULL )
{
perror( NOTE_FILE );
}
else
{
fprintf( fp, "Sender %s~\nDate %s~\nTo %s~\nSubject %s~\nText\n%s~\n\n",
pnote->sender,
pnote->date,
pnote->to_list,
pnote->subject,
pnote->text
);
fclose( fp );
}
fpReserve = fopen( NULL_FILE, "r" );
send_to_char( "Ok.\n\r", ch );
return;
}
if ( !str_cmp( arg, "remove" ) )
{
if ( !is_number( argument ) )
{
send_to_char( "Note remove which number?\n\r", ch );
return;
}
anum = atoi( argument );
vnum = 0;
for ( pnote = note_list; pnote != NULL; pnote = pnote->next )
{
if ( is_note_to( ch, pnote ) && vnum++ == anum )
{
note_remove( ch, pnote );
send_to_char( "Ok.\n\r", ch );
return;
}
}
send_to_char( "No such note.\n\r", ch );
return;
}
send_to_char( "Huh? Type 'help note' for usage.\n\r", ch );
return;
}
/////////////// DO FUNCTIONS ///////////////////
void do_kingdom(CHAR_DATA * ch, char *argument)
{
KINGDOM_DATA *kingdom;
CHAR_DATA *vch = 0;
DESCRIPTOR_DATA *d = 0;
char buf[MAX_STRING_LENGTH];
char arg1[MAX_STRING_LENGTH];
char arg2[MAX_STRING_LENGTH];
char arg3[MAX_STRING_LENGTH];
long id = 0;
long i = 0;
if(IS_NPC(ch))
return;
smash_tilde(argument);
argument = one_argument_case(argument, arg1);
argument = one_argument_case(argument, arg2);
strcpy(arg3, argument);
if(IS_IMMORTAL(ch) && ch->level == MAX_LEVEL)
{
if(!str_cmp(arg1, "save"))
{
write_kingdoms();
sprintf(buf,"cp %s %s.bak",KINGDOM_FILE,KINGDOM_FILE);
system(buf);
send_to_char("Done, and made backup.\n\r", ch);
return;
}
if(arg1[0] == '\0')
{
send_to_char("Syntax: kingdom create\n\r", ch);
return;
}
if(!str_cmp(arg1, "create"))
{
create_kingdom();
write_kingdoms();
send_to_char("Done.\n\r", ch);
return;
}
if((!is_number(arg1) || !str_cmp(arg1, "help")))
{
send_to_char("Syntax: kingdom <id #> <attribute> <value>\n\r", ch);
send_to_char(" kingdom <id #> delete\n\r", ch);
send_to_char("\n\r", ch);
send_to_char("Attributes:\n\r", ch);
send_to_char(" leader name points pks pds realpoints\n\r", ch);
send_to_char(" noansiname\n\r", ch);
send_to_char("\n\r", ch);
}
else
{
id = atoi(arg1);
if((kingdom = get_kingdom(id)) == &kingdom_default)
{
send_to_char("There is no such kingdom with that ID.\n\r", ch);
return;
}
if(!str_cmp(arg2, "leader"))
{
if((vch = get_char_world(ch, arg3)) == 0)
{
send_to_char("The leader must be logged on.\n\r", ch);
return;
}
free_string(kingdom->leader);
kingdom->leader = str_dup(arg3);
vch->pcdata->kingdom = id;
send_to_char("Done.\n\r", ch);
return;
}
if(!str_cmp(arg2, "name"))
{
free_string(kingdom->name);
kingdom->name = str_dup(arg3);
send_to_char("Done.\n\r", ch);
return;
}
if(!str_cmp(arg2, "noansiname"))
{
free_string(kingdom->noansiname);
kingdom->noansiname = str_dup(arg3);
send_to_char("Done.\n\r", ch);
return;
}
if(!str_cmp(arg2, "delete") && !str_cmp(arg3, "yes"))
{
delete_kingdom(kingdom->id);
return;
}
i = atoi(arg3);
if(!str_cmp(arg2, "points"))
{
kingdom->points = i;
send_to_char("Done.\n\r", ch);
return;
}
if(!str_cmp(arg2, "realpoints"))
{
kingdom->realpoints = i;
send_to_char("Done.\n\r", ch);
return;
}
if(!str_cmp(arg2, "pds"))
{
kingdom->pds = i;
send_to_char("Done.\n\r", ch);
return;
}
if(!str_cmp(arg2, "pks"))
{
kingdom->pks = i;
send_to_char("Done.\n\r", ch);
return;
}
if(!str_cmp(arg2, "assists"))
{
kingdom->assists = i;
send_to_char("Done.\n\r", ch);
return;
}
}
}
if(ch->pcdata->kingdom == 0) // player not in a kingdom
{
if(!str_cmp(arg1, "create"))
{
if(ch->pcdata->quest < 1000)
{
send_to_char("You need 1000 quest points to create a new kingdom.\n\r", ch);
return;
}
if(!arg2 || arg2[0] == '\0' || !arg3 || arg3[0] == '\0')
{
send_to_char
("Syntax (DO NOT MESS THIS UP!): kingdom create \"name WITH ansi\" \"name WITHOUT ansi\"\n\r",
ch);
send_to_char("I suggest you SAY the name a few times to make SURE THE ANSI IS CORRECT.\n\r",
ch);
send_to_char("And if you dont put a final {{x your kingdom will be DELETED.\n\r", ch);
send_to_char("If your kingdom name has more than one word surround it in QUOTES!\n\r", ch);
return;
}
if(ansistrlen(arg2) > 20 || strlen(arg3) > 20)
{
send_to_char("String length is limited to 20 characters!\n\r", ch);
return;
}
kingdom = create_kingdom();
ch->pcdata->kingdom = kingdom->id;
ch->pcdata->quest -= 1000;
free_string(kingdom->leader);
kingdom->leader = str_dup(ch->name);
free_string(kingdom->name);
kingdom->name = str_dup(arg2);
free_string(kingdom->noansiname);
kingdom->noansiname = str_dup(arg3);
kingdom_message(0, "%s has {WCREATED{X The %s Kingdom!", ch->name, kingdom->name);
write_kingdoms();
return;
}
if(ch->pcdata->kingdom_invite == 0)
{
send_to_char("You don't belong to a kingdom.\n\r", ch);
return;
}
// make sure kingdom still exists
if(get_kingdom(ch->pcdata->kingdom_invite) == &kingdom_default)
{
send_to_char("That kingdom was destroyed.\n\r", ch);
return;
}
if(!str_cmp(arg1, "accept"))
{
add_member(ch->pcdata->kingdom_invite, ch);
return;
}
if(!str_cmp(arg1, "decline"))
{
send_to_char("You decline the kingdom's invitation.\n\r", ch);
if((vch = get_char_world(ch, get_kingdom(ch->pcdata->kingdom_invite)->leader)) != 0)
{
sprintf(buf, "%s has declined your invitation.\n\r", ch->name);
send_to_char(buf, vch);
}
ch->pcdata->kingdom_invite = 0;
return;
}
send_to_char("Type either kingdom accept or kingdom decline.\n\r", ch);
return;
}
kingdom = get_kingdom(ch->pcdata->kingdom);
if(!str_cmp(arg1, "leave") && !str_cmp(arg2, "for") && !str_cmp(arg3, "good"))
{
send_to_char("You leave the kingdom!\n\r", ch);
remove_member(kingdom->id, ch->name);
remove_trustee(kingdom->id, ch->name);
return;
}
if(!str_prefix(arg1, "report"))
{
long percent;
char *color;
buf[0] = '\0';
sprintf(buf, "%-4s %-12s{X %5s :: %s\n\r",
"CMBT", "Name", "Hits", "Room" );
for(d = descriptor_list; d; d = d->next)
{
if(d->connected != CON_PLAYING || !(vch = d->character) || vch->pcdata->kingdom != kingdom->id)
continue;
percent = (long) ((float) UMAX(1, vch->hit) / (float) UMAX(1, vch->max_hit) * 100);
if(percent < 10)
color = "{R";
else if(percent < 40)
color = "{B";
else if(percent < 70)
color = "{Y";
else
color = "{C";
sprintf(buf + strlen(buf), "%-4s %s%-12s{X %5li :: %s\n\r",
vch->fighting ? !IS_NPC(vch->fighting) ? "{R(PK){X" : "{r(F){X" : "",
color, vch->name, vch->hit, !vch->in_room ? "somewhere" : vch->in_room->name);
}
send_to_char(buf, ch);
return;
}
if(!is_trustee(ch, kingdom->id))
{
send_to_char("Only leaders and trustees have power to modify their kingdom.\n\r", ch);
return;
}
if(arg1[0] == '\0' || arg2[0] == '\0')
{
if(is_leader(ch, kingdom->id) || IS_IMMORTAL(ch))
{
send_to_char("Syntax:\n\r", ch);
send_to_char(" kingdom report\n\r", ch);
send_to_char(" kingdom invite <player>\n\r", ch);
send_to_char(" kingdom outcast <member>\n\r", ch);
send_to_char(" kingdom war <kingdom ID>\n\r", ch);
send_to_char(" kingdom treaty <kingdom ID>\n\r", ch);
send_to_char(" kingdom rank <member> <rank>\n\r", ch);
send_to_char(" kingdom trust <member>\n\r", ch);
send_to_char(" kingdom recall\n\r", ch);
send_to_char("\n\r", ch);
}
send_to_char("Syntax: kingdom scry <person>\n\r", ch);
return;
}
if(is_leader(ch, kingdom->id))
{
if(!str_cmp(arg1, "recall"))
{
if(kingdom->points < KINGDOM_RECALL_COST)
{
sprintf(buf, "It costs %d kingdom points to set a recall point.\n\r", KINGDOM_RECALL_COST);
send_to_char(buf, ch);
return;
}
if(ch->in_room == 0)
{
send_to_char("You are in a 0 room, eek.\n\r", ch);
return;
}
kingdom->points -= KINGDOM_RECALL_COST;
kingdom->recall = ch->in_room->vnum;
kingdom_message(kingdom->id, "{MThe Kingdom Recall has been set to -> [%s]", ch->in_room->name);
return;
}
if(!str_cmp(arg1, "trust"))
{
if((vch = get_char_world(ch, arg2)) == 0 || IS_NPC(vch))
{
send_to_char("They need to be logged on.\n\r", ch);
return;
}
if(vch->pcdata->kingdom != ch->pcdata->kingdom)
{
send_to_char("They aren't in your kingdom!\n\r", ch);
return;
}
arg2[0] = UPPER(arg2[0]);
if( strstr(kingdom->trustees, arg2) == 0 )
add_trustee(kingdom->id, vch);
else
remove_trustee(kingdom->id, arg2);
return;
}
if(!str_cmp(arg1, "invite"))
{
if((vch = get_char_world(ch, arg2)) == 0)
{
send_to_char("They aren't logged on.\n\r", ch);
return;
}
if(IS_NPC(vch))
{
send_to_char("That's an NPC.\n\r", ch);
return;
}
if(vch->pcdata->kingdom)
{
send_to_char("They are already a part of another kingdom!\n\r", ch);
return;
}
vch->pcdata->kingdom_invite = ch->pcdata->kingdom;
sprintf(buf, "You are invited to join the %s Kingdom by %s.\n\r"
"Type kingdom accept or kingdom decline.\n\r", kingdom->name, ch->name);
send_to_char(buf, vch);
sprintf(buf, "You invite %s to join your glorious kingdom.\n\r", vch->name);
send_to_char(buf, ch);
return;
}
if(!str_cmp(arg1, "outcast"))
{
arg2[0] = UPPER(arg2[0]);
if( strstr(kingdom->members, arg2) == 0 )
{
send_to_char("That person isn't a member!\n\r",ch);
return;
}
if(remove_member(ch->pcdata->kingdom, arg2))
kingdom_message(0, "%s has been outcasted from the %s Kingdom!", capitalize(arg2), kingdom->name);
remove_trustee(kingdom->id, arg2);
return;
}
if(!str_cmp(arg1, "treaty"))
{
if(kingdom->treaty_pending)
{
if(!get_kingdom(kingdom->treaty_pending))
{
kingdom->treaty_pending = 0;
return;
}
if(has_treaty(kingdom->id, kingdom->treaty_pending))
{
send_to_char("You already have a treaty with them.\n\r", ch);
return;
}
if(!str_cmp(arg2, "accept"))
{
add_treaty(kingdom->id, kingdom->treaty_pending);
kingdom->treaty_pending = 0;
return;
}
if(!str_cmp(arg2, "decline"))
{
kingdom_message(kingdom->id, "Your kingdom declines a treaty with the %s Kingdom.",
get_kingdom(kingdom->treaty_pending)->name);
kingdom_message(kingdom->treaty_pending, "%s Kingdom has declined your treaty offer.", kingdom->name);
kingdom->treaty_pending = 0;
return;
}
sprintf(buf, "You have a treaty offer pending with the %s Kingdom.\n\r"
"Please type kingdom treaty accept or kingdom treaty decline.\n\r",
get_kingdom(kingdom->treaty_pending)->name);
send_to_char(buf, ch);
return;
}
if(!is_number(arg2) || get_kingdom(atoi(arg2)) == &kingdom_default)
{
send_to_char("There is no such kingdom to make a treaty with.\n\r", ch);
return;
}
i = atoi(arg2);
if(kingdom->id == i)
{
send_to_char("You already have a treaty with yourself, smart one.\n\r", ch);
return;
}
if(is_at_war(kingdom->id, i))
{
send_to_char("You are at {RWAR{N with that kingdom!\n\r", ch);
return;
}
if(has_treaty(kingdom->id, i))
{
remove_treaty(kingdom->id, i);
return;
}
if(get_kingdom(i)->treaty_pending)
{
send_to_char("They are already pending a treaty confirmation.\n\r", ch);
return;
}
get_kingdom(i)->treaty_pending = kingdom->id;
kingdom_message(i, "The %s Kingdom is asking for a treaty with your kingdom.", kingdom->name);
kingdom_message(kingdom->id, "You ask the %s Kingdom for a treaty.", get_kingdom(i)->name);
return;
}
if(!str_cmp(arg1, "war"))
{
if(!is_number(arg2) || get_kingdom(atoi(arg2)) == &kingdom_default)
{
send_to_char("There is no such kingdom to make war with.\n\r", ch);
return;
}
i = atoi(arg2);
if(i == kingdom->id)
{
send_to_char("That wouldn't be a very smart political move.\n\r", ch);
return;
}
if(get_kingdom(i) == &kingdom_default)
{
send_to_char("That kingdom doesn't exist.\n\r", ch);
return;
}
if(has_treaty(kingdom->id, i))
{
send_to_char("But you have a treaty with them!\n\r", ch);
return;
}
if(is_at_war(kingdom->id, i))
{
remove_war(kingdom->id, i);
return;
}
add_war(kingdom->id, i);
return;
}
if(!str_cmp(arg1, "rank"))
{
if(!arg3 || arg3[0] == '\0')
{
send_to_char("Rank who as what?\n\r", ch);
return;
}
if((vch = get_char_world(ch, arg2)) == 0 || IS_NPC(vch))
{
send_to_char("They aren't on at the moment.\n\r", ch);
return;
}
if(vch->pcdata->kingdom != ch->pcdata->kingdom)
{
send_to_char("They aren't apart of your kingdom!\n\r", ch);
return;
}
if(ansistrlen(arg3) > 15)
{
send_to_char("String length is limited to 20 characters.\n\r", ch);
return;
}
free_string(vch->pcdata->krank);
if(!str_cmp(arg3, "clear"))
{
vch->pcdata->krank = str_dup("");
return;
}
arg3[0] = UPPER(arg3[0]);
vch->pcdata->krank = str_dup(arg3);
send_to_char("Done.\n\r", ch);
return;
}
}
if(!str_cmp(arg1, "scry"))
{
if(arg2[0] == '\0')
{
send_to_char("You must supply the name of the person.\n\r", ch);
return;
}
if((vch = get_char_world(ch, arg2)) == 0 || IS_NPC(vch))
{
send_to_char("They are not online.\n\r", ch);
return;
}
if(kingdom->points < KINGDOM_SCRY_COST)
{
sprintf(buf, "It costs %d Kingdom Points to do this.\n\r", KINGDOM_SCRY_COST);
send_to_char(buf, ch);
return;
}
kingdom_message(kingdom->id, "%s has {cscryed{N %s {C. o O{N ({C%s{N)",
ch->name, vch->name, vch->in_room == 0 ? "Nowhere" : vch->in_room->name);
kingdom->points -= KINGDOM_SCRY_COST;
return;
}
// default message
do_kingdom(ch, "blah");
}
//////// NON-KINGDOM SPECIFIC CODE ////////
char *str_sep(char *str, char *sep)
{
char buf[MAX_STRING_LENGTH];
long addlen = 0;
long lensep;
long lenstr;
long i;
long k;
long compare;
long beginning;
if(str == 0 || sep == 0)
return 0;
lensep = strlen(sep);
lenstr = strlen(str);
for(i = 0, compare = 0, beginning = 0; i < lenstr; i++)
{
if(LOWER(str[i]) == LOWER(sep[compare]))
{
if(compare == 0)
{
if( i == 0 )
{
beginning = i;
}
else
{
beginning = i-1; // get rid of space behind name
addlen = 1;
}
}
if(++compare == lensep)
break;
}
else
{
compare = 0;
beginning = 0;
}
}
lensep += addlen;
if(compare > 0 && compare == lensep)
{
for(i = 0, k = 0; i < lenstr; i++)
{
if(i < beginning || i > (beginning + lensep - 1))
buf[k++] = str[i];
}
buf[k] = '\0';
if(strlen(buf) <= 3)
{
log_string(buf);
return str_dup("");
}
return str_dup(buf);
}
return 0;
}
int main(int argc, char *argv[]) {
TreeNode *tree = NULL;
TreeModel *backgd_mod = NULL;
int i, j,
size = DEFAULT_SIZE, meme_mode = 0, profile_mode = 0,
nrestarts = 10, npseudocounts = 5, nsamples = -1,
nmostprevalent = -1, tuple_size = -1, nbest = -1, sample_parms = 0,
nmotifs = DEFAULT_NUMBER, nseqs = -1, do_html = 0, do_bed = 0,
suppress_stdout = 0;
List *msa_name_list = NULL, *pos_examples = NULL, *init_list = NULL, *tmpl;
List *msas, *motifs;
SeqSet *seqset = NULL;
PooledMSA *pmsa = NULL;
msa_format_type msa_format = UNKNOWN_FORMAT;
Vector *backgd_mnmod = NULL;
Hashtable *hash=NULL;
String *output_prefix = str_new_charstr("phastm.");
double *has_motif = NULL;
double prior = PRIOR;
char c;
GFF_Set *bedfeats = NULL;
while ((c = getopt(argc, argv, "t:i:b:sk:md:pn:I:R:P:w:c:SB:o:HDxh")) != -1) {
switch (c) {
case 't':
tree = tr_new_from_file(phast_fopen(optarg, "r"));
break;
case 'i':
msa_format = msa_str_to_format(optarg);
if (msa_format == UNKNOWN_FORMAT)
die("ERROR: bad input format.\n");
break;
case 'b':
backgd_mod = tm_new_from_file(phast_fopen(optarg, "r"), 1);
break;
case 's':
break;
case 'k':
size = get_arg_int(optarg);
break;
case 'm':
meme_mode = 1;
break;
case 'd':
pos_examples = get_arg_list(optarg);
break;
case 'p':
profile_mode = 1;
break;
case 'n':
nrestarts = get_arg_int(optarg);
break;
case 'I':
init_list = get_arg_list(optarg);
break;
case 'P':
tmpl = str_list_as_int(get_arg_list(optarg));
if (lst_size(tmpl) != 2) die("ERROR: bad argument to -P.\n");
nmostprevalent = lst_get_int(tmpl, 0);
tuple_size = lst_get_int(tmpl, 1);
if (!(nmostprevalent > 0 && tuple_size > 0))
die("ERROR: bad argument nmostprevalent=%i tuple_size=%i\n",
nmostprevalent, tuple_size);
lst_free(tmpl);
break;
case 'R':
tmpl = str_list_as_int(get_arg_list(optarg));
if (lst_size(tmpl) != 2) die("ERROR: bad argument to -R.\n");
nsamples = lst_get_int(tmpl, 0);
tuple_size = lst_get_int(tmpl, 1);
if (!(nsamples > 0 && tuple_size > 0))
die("ERROR nsamples=%i tuple_sizse=%i\n", nsamples, tuple_size);
lst_free(tmpl);
break;
case 'c':
npseudocounts = get_arg_int(optarg);
break;
case 'w':
nbest = get_arg_int(optarg);
break;
case 'S':
sample_parms = 1;
break;
case 'B':
nmotifs = get_arg_int(optarg);
break;
case 'o':
str_free(output_prefix);
output_prefix = str_new_charstr(optarg);
str_append_char(output_prefix, '.');
break;
case 'H':
do_html = 1;
break;
case 'D':
do_bed = 1;
break;
case 'x':
suppress_stdout = 1;
break;
case 'h':
usage(argv[0]);
case '?':
die("Bad argument. Try '%s -h'.\n", argv[0]);
}
}
if (optind != argc - 1)
die("ERROR: List of alignment files required. Try '%s -h'.\n", argv[0]);
if ((nsamples > 0 && nmostprevalent > 0) ||
(nsamples > 0 && init_list != NULL) ||
(nmostprevalent > 0 && init_list != NULL))
die("ERROR: -I, -P, and -R are mutually exclusive.");
set_seed(-1);
msa_name_list = get_arg_list(argv[optind]);
if (backgd_mod != NULL && tree == NULL) tree = backgd_mod->tree;
if (tree == NULL && !meme_mode && !profile_mode)
die("ERROR: Must specify -t, -m, or -p.\n");
if ((init_list != NULL || nsamples > 0 || nmostprevalent > 0) &&
!sample_parms)
nrestarts = 1;
if (pos_examples != NULL) {
hash = hsh_new(lst_size(pos_examples));
for (i = 0; i < lst_size(pos_examples); i++)
hsh_put_int(hash, ((String*)lst_get_ptr(pos_examples, i))->chars, 1);
has_motif = smalloc(lst_size(msa_name_list) * sizeof(double));
}
/* open all MSAs */
msas = lst_new_ptr(lst_size(msa_name_list));
fprintf(stderr, "Reading alignment(s) ...\n");
for (i = 0, j = 0; i < lst_size(msa_name_list); i++) {
String *name = lst_get_ptr(msa_name_list, i);
FILE *mfile = phast_fopen(name->chars, "r");
msa_format_type temp_format;
MSA *msa;
if (msa_format == UNKNOWN_FORMAT)
temp_format = msa_format_for_content(mfile, 1);
else temp_format = msa_format;
msa = msa_new_from_file_define_format(mfile, temp_format, NULL);
phast_fclose(mfile);
if (nseqs == -1) nseqs = msa->nseqs;
if (!meme_mode &&
(msa->length - msa_num_gapped_cols(msa, STRIP_ANY_GAPS, -1, -1) < 300 ||
msa->nseqs != nseqs)) {
fprintf(stderr, "WARNING: ignoring alignment '%s' -- too few informative sites.\n", name->chars);
msa_free(msa);
continue;
}
if (msa_alph_has_lowercase(msa)) msa_toupper(msa);
msa_remove_N_from_alph(msa); /* Ns can be a problem */
lst_push_ptr(msas, msa);
if (has_motif != NULL) {
int k, hm = (hsh_get_int(hash, name->chars) == 1);
if (meme_mode) { /* here need to record at individ seq level */
has_motif = srealloc(has_motif,
(j + msa->nseqs + 1) * sizeof(double)); /* FIXME */
for (k = 0; k < msa->nseqs; k++) has_motif[j++] = hm;
}
else has_motif[j++] = hm;
}
}
if (!meme_mode) {
fprintf(stderr, "Extracting and pooling sufficient statistics ...\n");
pmsa = ss_pooled_from_msas(msas, 1, size, NULL, 0);
msa_remove_N_from_alph(pmsa->pooled_msa);
}
/* obtain individual sequences, if necessary */
if (nmostprevalent > 0 || nsamples > 0 || meme_mode) {
if (meme_mode) fprintf(stderr, "Converting to individual sequences ...\n");
else fprintf(stderr, "Obtaining reference sequences for pre-processing ...\n");
seqset = mtf_get_seqset(msas, meme_mode ? -1 : 1, 10 * size);
/* for now, assume 1st seq is reference */
msa_remove_N_from_alph(seqset->set);
}
if (nmostprevalent > 0) {
fprintf(stderr, "Obtaining %d most prevalent %d-tuples ...\n",
nmostprevalent, tuple_size);
init_list = lst_new_ptr(nmostprevalent);
mtf_get_common_ntuples(seqset, init_list, tuple_size, nmostprevalent);
}
else if (nsamples > 0) {
fprintf(stderr, "Sampling %d %d-tuples ...\n", nsamples, tuple_size);
init_list = lst_new_ptr(nsamples);
mtf_sample_ntuples(seqset, init_list, tuple_size, nsamples);
}
/* in meme_mode, backgd model can be specified as eq freqs in a .mod file */
if (meme_mode && backgd_mod != NULL && has_motif == NULL)
backgd_mnmod = backgd_mod->backgd_freqs;
/* estimate background model, if necessary */
else if (backgd_mod == NULL && (!meme_mode || has_motif == NULL)) {
fprintf(stderr, "Fitting background model%s ...\n",
has_motif == NULL ? "" : " (for use in initialization)");
/* if discriminative, be clear
backgd isn't really part of the
estimation procedure */
if (meme_mode) {
backgd_mnmod = vec_new(strlen(seqset->set->alphabet));
mtf_estim_backgd_mn(seqset, backgd_mnmod);
}
else {
backgd_mod = tm_new(tr_create_copy(tree), NULL, NULL, F81,
pmsa->pooled_msa->alphabet, 1, 0, NULL, -1);
tm_fit(backgd_mod, pmsa->pooled_msa,
tm_params_init(backgd_mod, .1, 5, 0),
-1, OPT_MED_PREC, NULL, 0, NULL);
}
}
/* select subset of init strings, if necessary */
if (nbest > 0 && init_list != NULL) {
fprintf(stderr, "Winnowing candidate start strings ...\n");
tmpl = lst_new_ptr(nbest);
mtf_winnow_starts(meme_mode ? (void*)seqset : (void*)pmsa,
init_list, nbest, tmpl, !meme_mode, size, tree,
meme_mode ? (void*)backgd_mnmod : (void*)backgd_mod,
has_motif);
lst_free(init_list);
init_list = tmpl;
}
/* Now find motifs */
motifs = mtf_find(meme_mode ? (void*)seqset : (void*)pmsa,
!meme_mode, size, nmotifs, tree,
meme_mode ? (void*)backgd_mnmod : (void*)backgd_mod,
has_motif, prior, nrestarts, init_list, sample_parms,
npseudocounts);
fprintf(stderr, "\n\n");
if (do_bed)
bedfeats = gff_new_set_init("phast_motif", "0.1b");
/* generate output */
for (i = 0; i < lst_size(motifs); i++) {
Motif *m = lst_get_ptr(motifs, i);
if (!suppress_stdout) {
if (lst_size(motifs) > 1)
printf("\n**********\nMOTIF #%d\n**********\n\n", i+1);
mtf_print(stdout, m);
}
if (do_html) {
String *fname = str_dup(output_prefix);
str_append_int(fname, i+1);
str_append_charstr(fname, ".html");
mtf_print_html(phast_fopen(fname->chars, "w+"), m);
str_free(fname);
}
if (do_bed)
mtf_add_features(m, bedfeats);
}
if (do_html) {
String *fname = str_dup(output_prefix);
str_append_charstr(fname, "index.html");
mtf_print_summary_html(phast_fopen(fname->chars, "w+"),
motifs, output_prefix);
str_free(fname);
}
if (do_bed) {
String *fname = str_dup(output_prefix);
str_append_charstr(fname, "bed");
gff_print_bed(phast_fopen(fname->chars, "w+"),
bedfeats, FALSE);
str_free(fname);
}
return 0;
}
static int rfc1524_mailcap_parse (BODY * a,
char *filename,
char *type, rfc1524_entry * entry, int opt)
{
FILE *fp;
char *buf = NULL;
size_t buflen;
char *ch;
char *field;
int found = FALSE;
int copiousoutput;
int composecommand;
int editcommand;
int printcommand;
int btlen;
int line = 0;
/* rfc1524 mailcap file is of the format:
* base/type; command; extradefs
* type can be * for matching all
* base with no /type is an implicit wild
* command contains a %s for the filename to pass, default to pipe on stdin
* extradefs are of the form:
* def1="definition"; def2="define \;";
* line wraps with a \ at the end of the line
* # for comments
*/
/* find length of basetype */
if ((ch = strchr (type, '/')) == NULL)
return FALSE;
btlen = ch - type;
if ((fp = fopen (filename, "r")) != NULL) {
while (!found && (buf = mutt_read_line (buf, &buflen, fp, &line)) != NULL) {
/* ignore comments */
if (*buf == '#')
continue;
debug_print (2, ("mailcap entry: %s\n", buf));
/* check type */
ch = get_field (buf);
if (ascii_strcasecmp (buf, type) && (ascii_strncasecmp (buf, type, btlen) || (buf[btlen] != 0 && /* implicit wild */
str_cmp (buf + btlen, "/*")))) /* wildsubtype */
continue;
/* next field is the viewcommand */
field = ch;
ch = get_field (ch);
if (entry)
entry->command = str_dup (field);
/* parse the optional fields */
found = TRUE;
copiousoutput = FALSE;
composecommand = FALSE;
editcommand = FALSE;
printcommand = FALSE;
while (ch) {
field = ch;
ch = get_field (ch);
debug_print (2, ("field: %s\n", field));
if (!ascii_strcasecmp (field, "needsterminal")) {
if (entry)
entry->needsterminal = TRUE;
}
else if (!ascii_strcasecmp (field, "copiousoutput")) {
copiousoutput = TRUE;
if (entry)
entry->copiousoutput = TRUE;
}
else if (!ascii_strncasecmp (field, "composetyped", 12)) {
/* this compare most occur before compose to match correctly */
if (get_field_text
(field + 12, entry ? &entry->composetypecommand : NULL, type,
filename, line))
composecommand = TRUE;
}
else if (!ascii_strncasecmp (field, "compose", 7)) {
if (get_field_text
(field + 7, entry ? &entry->composecommand : NULL, type,
filename, line))
composecommand = TRUE;
}
else if (!ascii_strncasecmp (field, "print", 5)) {
if (get_field_text (field + 5, entry ? &entry->printcommand : NULL,
type, filename, line))
printcommand = TRUE;
}
else if (!ascii_strncasecmp (field, "edit", 4)) {
if (get_field_text (field + 4, entry ? &entry->editcommand : NULL,
type, filename, line))
editcommand = TRUE;
}
else if (!ascii_strncasecmp (field, "nametemplate", 12)) {
get_field_text (field + 12, entry ? &entry->nametemplate : NULL,
type, filename, line);
}
else if (!ascii_strncasecmp (field, "x-convert", 9)) {
get_field_text (field + 9, entry ? &entry->convert : NULL,
type, filename, line);
}
else if (!ascii_strncasecmp (field, "test", 4)) {
/*
* This routine executes the given test command to determine
* if this is the right entry.
*/
char *test_command = NULL;
size_t len;
if (get_field_text (field + 4, &test_command, type, filename, line)
&& test_command) {
len = str_len (test_command) + STRING;
mem_realloc (&test_command, len);
rfc1524_expand_command (a, a->filename, type, test_command, len);
if (mutt_system (test_command)) {
/* a non-zero exit code means test failed */
found = FALSE;
}
mem_free (&test_command);
}
}
} /* while (ch) */
if (opt == M_AUTOVIEW) {
if (!copiousoutput)
found = FALSE;
}
else if (opt == M_COMPOSE) {
if (!composecommand)
found = FALSE;
}
else if (opt == M_EDIT) {
if (!editcommand)
found = FALSE;
}
else if (opt == M_PRINT) {
if (!printcommand)
found = FALSE;
}
if (!found) {
/* reset */
if (entry) {
mem_free (&entry->command);
mem_free (&entry->composecommand);
mem_free (&entry->composetypecommand);
mem_free (&entry->editcommand);
mem_free (&entry->printcommand);
mem_free (&entry->nametemplate);
mem_free (&entry->convert);
entry->needsterminal = 0;
entry->copiousoutput = 0;
}
}
} /* while (!found && (buf = mutt_read_line ())) */
fclose (fp);
} /* if ((fp = fopen ())) */
mem_free (&buf);
return found;
}
char *autocomplete(char *p, char *req_msg, const int ext, int * const error) {
int max_len = 0, min_len = INT_MAX, prefix_len = strlen(p);
assert(p);
req_list_init(&rl, (cur_buffer->opt.case_search ? strcmp : strdictcmp), false, false, EXTERNAL_FLAG_CHAR);
count_scanned = 0;
search_buff(cur_buffer, p, cur_buffer->encoding, cur_buffer->opt.case_search, false);
if (stop) {
req_list_free(&rl);
free(p);
return NULL;
}
if (ext) {
buffer *b = (buffer *)buffers.head;
while (b->b_node.next) {
if (b != cur_buffer) {
search_buff(b, p, cur_buffer->encoding, cur_buffer->opt.case_search, true);
if (stop) {
req_list_free(&rl);
free(p);
return NULL;
}
}
b = (buffer *)b->b_node.next;
}
}
for(int i = 0; i < rl.cur_entries; i++) {
const int l = strlen(rl.entries[i]);
if (max_len < l) max_len = l;
if (min_len > l) min_len = l;
}
/* We compact the table into a vector of char pointers. */
req_list_finalize(&rl);
free(p);
p = NULL;
#ifdef NE_TEST
/* During tests, we always output the middle entry. */
if (rl.cur_entries) {
if (rl.entries[rl.cur_entries/2][strlen(rl.entries[rl.cur_entries/2]) - 1] == EXTERNAL_FLAG_CHAR) rl.entries[rl.cur_entries/2][strlen(rl.entries[rl.cur_entries/2]) - 1] = 0;
p = str_dup(rl.entries[rl.cur_entries/2]);
}
*error = AUTOCOMPLETE_COMPLETED;
req_list_free(&rl);
return p;
#endif
if (rl.cur_entries > 0) {
qsort(rl.entries, rl.cur_entries, sizeof(char *), strdictcmpp);
/* Find maximum common prefix. */
int m = strlen(rl.entries[0]);
if (rl.entries[0][m-1] == EXTERNAL_FLAG_CHAR) m--;
for(int i = 1; i < rl.cur_entries; i++) {
int j;
for(j = 0; j < m; j++)
if (rl.entries[i][j] != rl.entries[0][j]) break;
m = j;
}
/* If we can output more characters than the prefix len, we do so without
starting the requester. */
if (m > prefix_len) {
p = malloc(m + 1);
strncpy(p, rl.entries[0], m);
p[m] = 0;
*error = min_len == m ? AUTOCOMPLETE_COMPLETED : AUTOCOMPLETE_PARTIAL;
}
else {
if (req_msg) print_message(req_msg);
int result = request_strings(&rl, 0);
if (result != ERROR) {
result = result >= 0 ? result : -result - 2;
/* Delete EXTERNAL_FLAG_CHAR at the end of the strings if necessary. */
if (rl.entries[result][strlen(rl.entries[result]) - 1] == EXTERNAL_FLAG_CHAR) rl.entries[result][strlen(rl.entries[result]) - 1] = 0;
p = str_dup(rl.entries[result]);
*error = AUTOCOMPLETE_COMPLETED;
}
else *error = AUTOCOMPLETE_CANCELLED;
reset_window();
}
}
else *error = AUTOCOMPLETE_NO_MATCH;
req_list_free(&rl);
D(fprintf(stderr, "autocomp returning '%s', entries: %d\n", p, rl.cur_entries);)
return p;
