Constraint_list *prepare_cl_for_moca ( Constraint_list *CL)
{
int a, b, c;
int tot_l, l;
char **name, **seq;
Sequence *NS=NULL;
/*Prepare the constraint list*/
CL->do_self=1;
CL->get_dp_cost=moca_slow_get_dp_cost;
CL->evaluate_residue_pair=moca_residue_pair_extended_list;
/*Prepare the moca parameters*/
(CL->moca)->evaluate_domain=evaluate_moca_domain;
(CL->moca)->cache_cl_with_domain=cache_cl_with_moca_domain;
(CL->moca)->make_nol_aln=make_moca_nol_aln;
/*Prepare the packing of the sequences*/
for ( a=0, b=1; a< (CL->S)->nseq; a++)b+=strlen ( (CL->S)->seq[a])+1;
seq =declare_char ( 1,b+1);
name=declare_char( 1,30);
CL->packed_seq_lu =declare_int ( b, 2);
for (tot_l=1,a=0; a< (CL->S)->nseq; a++)
{
strcat (seq[0], (CL->S)->seq[a]);
strcat (seq[0], "X");
l=strlen((CL->S)->seq[a]);
for ( c=1; c<= l; c++, tot_l++)
{
CL->packed_seq_lu[tot_l][0]=a;
CL->packed_seq_lu[tot_l][1]=c;
}
CL->packed_seq_lu[tot_l++][0]=UNDEFINED;
}
sprintf ( name[0], "catseq");
NS=fill_sequence_struc(1, seq, name, NULL);
CL->S=add_sequence (NS, CL->S, 0);
free_char( seq, -1);
free_char(name, -1);
free_sequence (NS, NS->nseq);
return CL;
}
Alignment *free_data_in_aln (Alignment *A)
{
//Frees only the sequence data (keeps profile information)
A->seq_al=free_char (A->seq_al, -1);
A->seq_comment=free_char (A->seq_comment, -1);
A->aln_comment=free_char (A->aln_comment, -1);
A->name=free_char (A->name, -1);
A->expanded_order=free_char (A->expanded_order, -1);
A->order=free_int (A->order, -1);
A->seq_cache=free_int (A->seq_cache, -1);
A->cdna_cache=free_int (A->cdna_cache, -1);
A->score_res=free_int (A->score_res, -1);
free_sequence (A->S, -1);
A->S=NULL;
return A;
}
int *code_seq (char *seq, char *type)
{
static int *code;
static int *aa, ng;
int a, b, l;
if (!aa)
{
char **gl;
if ( strm (type, "DNA") || strm (type, "RNA"))
{
gl=declare_char (4,5);
sprintf ( gl[ng++], "Aa");
sprintf ( gl[ng++], "Gg");
sprintf ( gl[ng++], "TtUu");
sprintf ( gl[ng++], "Cc");
}
else
{
gl=make_group_aa ( &ng, "mafft");
}
aa=(int*)vcalloc ( 256, sizeof (int));
for ( a=0; a<ng; a++)
{
for ( b=0; b< strlen (gl[a]); b++)
{
aa[(int)gl[a][b]]=a;
}
}
free_char (gl, -1);
}
l=strlen (seq);
if ( code) code--;
if ( !code || read_array_size (code, sizeof (int))<(l+2))
{
vfree (code);
code=(int*)vcalloc (l+2, sizeof (int));
}
code[0]=ng;
code++;
for (a=0; a<l; a++)
{
code[a]=aa[(int)seq[a]];
}
code[a]=END_ARRAY;
return code;
}
Sequence* free_Alignment ( Alignment *LA)
{
/* Does not free the A->S field (sequences of A)*/
Sequence *S;
//aln_stack checks the alignment has not already been freed
if ( LA==NULL || !aln_stack(LA,FREE_ALN)){return NULL;}
S=LA->S;
free_char ( LA->file, -1);
free_char ( LA->seq_al, -1);
free_int ( LA->seq_cache, -1);
free_int ( LA->cdna_cache, -1);
free_char ( LA->name,-1);
free_char ( LA->tree_order,-1);
vfree ( LA->generic_comment);
free_char ( LA->seq_comment, -1);
free_char ( LA->aln_comment, -1);
free_int ( LA->order, -1);
vfree ( LA->score_seq);
vfree ( LA->len);
free_profile (LA->P);
if ( LA->A){free_Alignment (LA->A);LA->A=NULL;}
vfree ( LA);
return S;
}
void free_sequence ( Sequence *LS, int nseq)
{
if ( !LS) return;
free_char ( LS->file, -1);
free_char ( LS->seq_comment, -1);
free_char ( LS->aln_comment, -1);
free_char ( LS->seq, -1);
free_char ( LS->name,-1);
free_int (LS->dc, -1);
free_arrayN((void*)LS->T, 2);
vfree (LS->type);
vfree (LS->len);
free_weights (LS->W);
//Don't free LS->blastdb;
vfree (LS);
}
/* usun arty ktorym uplynela zywotnosc z postaci o imieniu name */
void remove_artefact_art_destroy( char *name )
{
CHAR_DATA * ch;
ch = load_char_remote( name );
/* je¿eli 'ch' nie istnieje */
if ( !ch )
{
char buf[MSL];
sprintf(buf, "%s: brak pliku postaci %s", __func__, name );
log_string( buf );
return;
}
save_char_obj( ch, FALSE, TRUE );
free_char( ch );
}
Weights* free_weights ( Weights* W)
{
if ( !W)return NULL;
vfree(W->comments);
vfree(W->mode);
free_char(W->seq_name, -1);
free_float(W->PW_SD,-1);
free_float(W->PW_ID, -1);
vfree(W->SEQ_W);
vfree(W);
return NULL;
}
int open_window( GlobalFunc *global )
{
int i;
natorder = native_order();
msgf = global( LWMESSAGEFUNCS_GLOBAL, GFUSE_TRANSIENT );
filereq = global( LWFILEREQFUNC_GLOBAL, GFUSE_TRANSIENT );
rasf = global( LWRASTERFUNCS_GLOBAL, GFUSE_TRANSIENT );
panf = global( LWPANELFUNCS_GLOBAL, GFUSE_TRANSIENT );
if ( !msgf || !filereq || !rasf || !panf )
return AFUNC_BADGLOBAL;
panf->globalFun = global;
if( !( panel = PAN_CREATE( panf, PANEL_TITLE ))) {
msgf->error( PLUGIN_NAME " couldn't create its panel,", "not sure why." );
return AFUNC_OK;
}
panf->set( panel, PAN_USERKEYS, handle_key );
panf->set( panel, PAN_USEROPEN, handle_panopen );
cras[ 0 ] = create_char( COLOR_WHITE, SYSTEM_Ic( 30 ), rasf );
cras[ 1 ] = create_char( COLOR_BLACK, SYSTEM_Ic( 2 ), rasf );
cras[ 2 ] = create_char( COLOR_BLACK, SYSTEM_Ic( 15 ), rasf );
create_controls();
panf->open( panel, PANF_BLOCKING );
PAN_KILL( panf, panel );
for ( i = 0; i < 3; i++ )
free_char( cras[ i ], rasf );
free_icon( rasf );
return AFUNC_OK;
}
/* Extract a ch completely from the world, and leave his stuff behind */
void extract_char(struct char_data *ch, bool pull)
{
struct obj_data *obj;
struct char_data *k, *next_char;
struct descriptor_data *t_desc;
int l, was_in;
extern struct char_data *combat_list;
void die_follower(struct char_data *ch);
if ( !IS_NPC(ch) && !ch->desc )
{
for ( t_desc = descriptor_list; t_desc; t_desc = t_desc->next )
{
if ( t_desc->original == ch )
do_return( t_desc->character, "", 0 );
}
}
if ( ch->in_room == NOWHERE )
{
log( "Extract_char: NOWHERE" );
exit( 1 );
}
if ( ch->followers || ch->master )
die_follower(ch);
while ( ( obj = ch->carrying ) != NULL )
{
obj_from_char( obj );
obj_to_room( obj, ch->in_room );
}
if ( ch->specials.fighting )
stop_fighting( ch );
for ( k = combat_list; k ; k = next_char )
{
next_char = k->next_fighting;
if ( k->specials.fighting == ch )
stop_fighting( k );
}
/* Must remove from room before removing the equipment! */
was_in = ch->in_room;
char_from_room( ch );
if ( !pull )
char_to_room(ch, real_room(3001));
/* clear equipment_list */
for ( l = 0; l < MAX_WEAR; l++ )
{
if ( ch->equipment[l] )
obj_to_room(unequip_char(ch,l), was_in);
}
GET_AC(ch) = 100;
if ( ch->desc && ch->desc->original )
do_return( ch, "", 0 );
if ( IS_NPC(ch) && ch->nr > -1 )
mob_index[ch->nr].number--;
if ( pull )
{
if ( ch == character_list )
character_list = ch->next;
else
{
for ( k = character_list; k && k->next != ch; k = k->next )
;
if ( k )
k->next = ch->next;
else
{
log( "Extract_char: bad char list" );
abort();
}
}
free_char( ch );
}
}
void do_finger( CHAR_DATA *ch, char *argument )
{
char arg[MAX_INPUT_LENGTH];
char buf[MAX_STRING_LENGTH];
CHAR_DATA *victim;
FILE *fp;
bool fOld;
one_argument( argument, arg );
if ( arg[0] == '\0' )
{
send_to_char( "Finger whom?\n\r", ch );
return;
}
if ( ( victim = get_char_world( ch, arg ) ) != NULL)
{
if (!IS_NPC(victim))
{
act( "$N is on right now!", ch, NULL, victim, TO_CHAR );
return;
}
}
victim = new_char();
victim->pcdata = new_pcdata();
fOld = FALSE;
sprintf( buf, "%s%s", PLAYER_DIR, capitalize( arg ) );
if ( ( fp = fopen( buf, "r" ) ) != NULL )
{
int iNest;
for ( iNest = 0; iNest < MAX_NEST; iNest++ )
rgObjNest[iNest] = NULL;
fOld = TRUE;
for ( ; ; )
{
char letter;
char *word;
letter = fread_letter( fp );
if ( letter == '*' )
{
fread_to_eol( fp );
continue;
}
if ( letter != '#' )
{
bug( "Load_char_obj: # not found.", 0 );
break;
}
word = fread_word( fp );
if ( !str_cmp( word, "PLAYER" ) ) fread_char( victim, fp );
else if ( !str_cmp( word, "OBJECT" ) ) break;
else if ( !str_cmp( word, "O" ) ) break;
else if ( !str_cmp( word, "PET" ) ) break;
else if ( !str_cmp( word, "END" ) ) break;
else
{
bug( "Load_char_obj: bad section.", 0 );
break;
}
}
fclose( fp );
}
if ( !fOld )
{
send_to_char("No player by that name exists.\n\r",ch);
free_pcdata(victim->pcdata);
free_char(victim);
return;
}
if ( (victim->level > LEVEL_HERO) && (victim->level > ch->level) )
{
send_to_char("The gods wouldn't like that.\n\r",ch);
free_pcdata(victim->pcdata);
free_char(victim);
return;
}
sprintf(buf,"%s last logged off on %s",
victim->name, (char *) ctime(&victim->llogoff));
send_to_char(buf,ch);
free_pcdata(victim->pcdata);
free_char(victim);
return;
}
/* Extract a ch completely from the world, and leave his stuff behind */
void extract_char_smarter(struct char_data *ch, int save_room)
{
struct obj_data *i;
struct char_data *k, *next_char;
struct descriptor_data *t_desc;
int l, was_in, j;
extern long mob_count;
extern struct char_data *combat_list;
void do_save(struct char_data *ch, char *argument, int cmd);
void do_return(struct char_data *ch, char *argument, int cmd);
void die_follower(struct char_data *ch);
if(IS_SET(ch->specials.act, ACT_FIGURINE) && ch->link)
extract_obj(ch->link);
if(!IS_NPC(ch) && !ch->desc) {
for(t_desc = descriptor_list; t_desc; t_desc = t_desc->next)
if(t_desc->original==ch)
do_return(t_desc->character, "", 0);
}
if (ch->in_room == NOWHERE) {
logE("NOWHERE extracting char. (handler.c, extract_char)");
/*
** problem from linkdeath
*/
char_to_room(ch, 4); /* 4 == all purpose store */
}
if (ch->followers || ch->master)
die_follower(ch);
if(ch->desc) {
/* Forget snooping */
if ((ch->desc->snoop.snooping) && (ch->desc->snoop.snooping->desc))
ch->desc->snoop.snooping->desc->snoop.snoop_by = 0;
if (ch->desc->snoop.snoop_by) {
send_to_char("Your victim is no longer among us.\n\r",
ch->desc->snoop.snoop_by);
if (ch->desc->snoop.snoop_by->desc)
ch->desc->snoop.snoop_by->desc->snoop.snooping = 0;
}
ch->desc->snoop.snooping = ch->desc->snoop.snoop_by = 0;
}
if (ch->carrying) {
/* transfer ch's objects to room */
if (!IS_IMMORTAL(ch)) {
while(ch->carrying) {
i=ch->carrying;
obj_from_char(i);
obj_to_room(i, ch->in_room);
check_falling_obj(i, ch->in_room);
}
} else {
send_to_char("Here, you dropped some stuff, let me help you get rid of that.\n\r",ch);
/*
equipment too
*/
for (j=0; j<MAX_WEAR; j++) {
if (ch->equipment[j])
obj_to_char(unequip_char(ch, j), ch);
}
while (ch->carrying) {
i = ch->carrying;
obj_from_char(i);
extract_obj(i);
}
}
}
if (ch->specials.fighting)
stop_fighting(ch);
for (k = combat_list; k ; k = next_char) {
next_char = k->next_fighting;
if (k->specials.fighting == ch)
stop_fighting(k);
}
if (MOUNTED(ch)) {
Dismount(ch, MOUNTED(ch), POSITION_STANDING);
}
if (RIDDEN(ch)) {
Dismount(RIDDEN(ch), ch, POSITION_STANDING);
}
/* Must remove from room before removing the equipment! */
was_in = ch->in_room;
char_from_room(ch);
/* clear equipment_list */
for (l = 0; l < MAX_WEAR; l++)
if (ch->equipment[l])
obj_to_room(unequip_char(ch,l), was_in);
if (IS_NPC(ch)) {
for (k=character_list; k; k=k->next) {
if (k->specials.hunting)
if (k->specials.hunting == ch) {
k->specials.hunting = 0;
}
if (Hates(k, ch)) {
RemHated(k, ch);
}
if (Fears(k, ch)) {
RemFeared(k, ch);
}
if (k->orig == ch) {
k->orig = 0;
}
}
} else {
for (k=character_list; k; k=k->next) {
if (k->specials.hunting)
if (k->specials.hunting == ch) {
k->specials.hunting = 0;
}
if (Hates(k, ch)) {
ZeroHatred(k, ch);
}
if (Fears(k, ch)) {
ZeroFeared(k, ch);
}
if (k->orig == ch) {
k->orig = 0;
}
}
}
/* pull the char from the list */
if (ch == character_list)
character_list = ch->next;
else {
for(k = character_list; (k) && (k->next != ch); k = k->next);
if(k)
k->next = ch->next;
else {
logE("Trying to remove ?? from character_list.(handler.c,extract_char)");
exit(0);
}
}
if (ch->specials.gname)
free(ch->specials.gname);
GET_AC(ch) = 100;
if (ch->desc) {
if (ch->desc->original)
do_return(ch, "", 0);
if (!strcmp(GET_NAME(ch), "Odin's heroic minion")) {
free(GET_NAME(ch));
GET_NAME(ch) = strdup("111111");
}
save_char(ch, save_room);
}
t_desc = ch->desc;
if(ch->term) {
ScreenOff(ch);
ch->term = 0;
}
if (IS_NPC(ch)) {
if (ch->nr > -1) /* if mobile */
mob_index[ch->nr].number--;
FreeHates(ch);
FreeFears(ch);
mob_count--;
free_char(ch);
}
if (t_desc) {
t_desc->connected = CON_SLCT;
SEND_TO_Q(MENU, t_desc);
}
}
/* Extract a ch completely from the world, and leave his stuff behind */
void extract_char(struct char_data * ch)
{
struct char_data *k, *temp;
struct descriptor_data *t_desc;
struct obj_data *obj;
int i, freed = 0;
//int j;
extern struct char_data *combat_list;
ACMD(do_return);
void die_follower(struct char_data * ch);
if (!IS_NPC(ch) && !ch->desc) {
for (t_desc = descriptor_list; t_desc; t_desc = t_desc->next) {
if (t_desc->original == ch) {
do_return(t_desc->character, "", 0, 0);
}
}
}
if (ch->in_room == NOWHERE) {
log("SYSERR: NOWHERE extracting char. (handler.c, extract_char)");
exit(1);
}
if (ch->followers || ch->master) {
die_follower(ch);
}
if (RIDING(ch) || RIDDEN_BY(ch))
dismount_char(ch);
REMOVE_BIT(PLR_FLAGS(ch), PLR_FISHING);
REMOVE_BIT(PLR_FLAGS(ch), PLR_FISH_ON);
REMOVE_BIT(PLR_FLAGS(ch), PLR_DIGGING);
REMOVE_BIT(PLR_FLAGS(ch), PLR_DIG_ON);
REMOVE_BIT(PLR_FLAGS(ch), PLR_FIRE_ON);
REMOVE_BIT(PRF_FLAGS(ch), PRF_NOTSELF);
//REMOVE_BIT(PRF_FLAGS(ch), PRF_DISGUISE);
//REMOVE_BIT(PLR_FLAGS(ch), PLR_MAGE);
//REMOVE_BIT(PLR_FLAGS(ch), PLR_MONK);
//REMOVE_BIT(PLR_FLAGS(ch), PLR_KNIGHT);
//REMOVE_BIT(PLR_FLAGS(ch), PLR_CLERIC);
//REMOVE_BIT(PLR_FLAGS(ch), PLR_BARD);
//REMOVE_BIT(PLR_FLAGS(ch), PLR_BEGGAR);
REMOVE_BIT(PLR_FLAGS(ch), PLR_COURIER);
REMOVE_BIT(PLR_FLAGS(ch), PLR_BEAR);
REMOVE_BIT(PLR_FLAGS(ch), PLR_BIRD);
REMOVE_BIT(PLR_FLAGS(ch), PLR_WOLF);
REMOVE_BIT(PLR_FLAGS(ch), PLR_RABBIT);
REMOVE_BIT(PLR_FLAGS(ch), PLR_CAT);
/* Forget snooping, if applicable */
if (ch->desc) {
if (ch->desc->snooping) {
ch->desc->snooping->snoop_by = NULL;
ch->desc->snooping = NULL;
}
if (ch->desc->snoop_by) {
SEND_TO_Q("Your victim is no longer among us.\r\n",
ch->desc->snoop_by);
ch->desc->snoop_by->snooping = NULL;
ch->desc->snoop_by = NULL;
}
}
/* transfer objects to room, if any */
while (ch->carrying) {
obj = ch->carrying;
obj_from_char(obj);
obj_to_room(obj, ch->in_room);
}
/* transfer equipment to room, if any */
for (i = 0; i < NUM_WEARS; i++) {
if (GET_EQ(ch, i)) {
obj_to_room(unequip_char(ch, i), ch->in_room);
}
}
if (FIGHTING(ch)) {
stop_fighting(ch);
}
for (k = combat_list; k; k = temp) {
temp = k->next_fighting;
if (FIGHTING(k) == ch) {
stop_fighting(k);
}
}
char_from_room(ch);
/* pull the char from the list */
REMOVE_FROM_LIST(ch, character_list, next);
if (ch->desc && ch->desc->original) {
do_return(ch, NULL, 0, 0);
}
if (!IS_NPC(ch)) {
save_char(ch, NOWHERE);
Crash_delete_crashfile(ch);
} else {
if (GET_MOB_RNUM(ch) > -1) { /* if mobile */
mob_index[GET_MOB_RNUM(ch)].number--;
}
clearMemory(ch); /* Only NPC's can have memory */
if (SCRIPT(ch)) {
extract_script(SCRIPT(ch));
}
free_char(ch);
freed = 1;
}
if (!freed && ch->desc != NULL) {
STATE(ch->desc) = CON_MENU;
SEND_TO_Q(MENU, ch->desc);
} else { /* if a player gets purged from within the game */
if (ch->master || ch->followers)
die_follower(ch);
if (!freed) {
free_char(ch);
}
}
}
int main(int argc, char **args)
{
char *str = (char *) malloc(200);
do
{
printf("Please enter the expression(Enter \"exit\" to quit): ");
scanf("%s", str);
if (strcmp(str, "exit") == 0)
{
break;
}
//构建栈
s_stack s;
stack_init(&s, free_char);
char *p = str;
bool isValid = true;
//遍历表达式
while (*p != '\0')
{
//如果是左括号，入栈
if (*p == '(' || *p == '[' || *p == '{')
{
char *ch = (char *) malloc(1);
*ch = *p;
stack_push(&s, ch);
}
//如果是右括号，出栈
else if (*p == ')' || *p == ']' || *p == '}')
{
char *ch;
if (s.ele_count == 0)
{
isValid = false;
break;
}
stack_pop(&s, &ch);
//左右括号匹配合法
if ((*ch == '(' && *p == ')') || (*ch == '[' && *p == ']') || (*ch == '{' && *p == '}'))
{
free_char(ch);
}
//左右括号匹配非法
else
{
free_char(ch);
isValid = false;
break;
}
}
p++;
if (*p == '\0' && s.ele_count > 0)
{
isValid = false;
break;
}
}
//销毁栈
stack_destroy(&s);
if (isValid)
{
printf("%s OK.\n", str);
}
else
{
printf("\"%s\" expression is invalid.\n", str);
}
}
while (1);
free(str);
return 0;
}
/* Extract a ch completely from the world, and leave his stuff behind */
void extract_char_final(struct char_data *ch)
{
struct char_data *k, *temp;
struct descriptor_data *d;
struct obj_data *obj;
int i;
if (IN_ROOM(ch) == NOWHERE) {
log("SYSERR: NOWHERE extracting char %s. (%s, extract_char_final)",
GET_NAME(ch), __FILE__);
exit(1);
}
/* We're booting the character of someone who has switched so first we need
* to stuff them back into their own body. This will set ch->desc we're
* checking below this loop to the proper value. */
if (!IS_NPC(ch) && !ch->desc) {
for (d = descriptor_list; d; d = d->next)
if (d->original == ch) {
do_return(d->character, NULL, 0, 0);
break;
}
}
if (ch->desc) {
/* This time we're extracting the body someone has switched into (not the
* body of someone switching as above) so we need to put the switcher back
* to their own body. If this body is not possessed, the owner won't have a
* body after the removal so dump them to the main menu. */
if (ch->desc->original)
do_return(ch, NULL, 0, 0);
else {
/* Now we boot anybody trying to log in with the same character, to help
* guard against duping. CON_DISCONNECT is used to close a descriptor
* without extracting the d->character associated with it, for being
* link-dead, so we want CON_CLOSE to clean everything up. If we're
* here, we know it's a player so no IS_NPC check required. */
for (d = descriptor_list; d; d = d->next) {
if (d == ch->desc)
continue;
if (d->character && GET_IDNUM(ch) == GET_IDNUM(d->character))
STATE(d) = CON_CLOSE;
}
STATE(ch->desc) = CON_MENU;
write_to_output(ch->desc, "%s", CONFIG_MENU);
}
}
/* On with the character's assets... */
if (ch->followers || ch->master)
die_follower(ch);
/* Check to see if we are grouped! */
if (GROUP(ch))
leave_group(ch);
/* transfer objects to room, if any */
while (ch->carrying) {
obj = ch->carrying;
obj_from_char(obj);
obj_to_room(obj, IN_ROOM(ch));
}
/* transfer equipment to room, if any */
for (i = 0; i < NUM_WEARS; i++)
if (GET_EQ(ch, i))
obj_to_room(unequip_char(ch, i), IN_ROOM(ch));
if (FIGHTING(ch))
stop_fighting(ch);
for (k = combat_list; k; k = temp) {
temp = k->next_fighting;
if (FIGHTING(k) == ch)
stop_fighting(k);
}
/* Whipe character from the memory of hunters and other intelligent NPCs... */
for (temp = character_list; temp; temp = temp->next) {
/* PCs can't use MEMORY, and don't use HUNTING() */
if (!IS_NPC(temp))
continue;
/* If "temp" is hunting our extracted char, stop the hunt. */
if (HUNTING(temp) == ch)
HUNTING(temp) = NULL;
/* If "temp" has allocated memory data and our ch is a PC, forget the
* extracted character (if he/she is remembered) */
if (!IS_NPC(ch) && GET_POS(ch) == POS_DEAD && MEMORY(temp))
forget(temp, ch); /* forget() is safe to use without a check. */
}
char_from_room(ch);
if (IS_NPC(ch)) {
if (GET_MOB_RNUM(ch) != NOTHING) /* prototyped */
mob_index[GET_MOB_RNUM(ch)].number--;
clearMemory(ch);
if (SCRIPT(ch))
extract_script(ch, MOB_TRIGGER);
if (SCRIPT_MEM(ch))
extract_script_mem(SCRIPT_MEM(ch));
} else {
save_char(ch);
Crash_delete_crashfile(ch);
}
/* If there's a descriptor, they're in the menu now. */
if (IS_NPC(ch) || !ch->desc)
free_char(ch);
}
int make_fasta_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL, int *diag)
{
/*TREATMENT OF THE TERMINAL GAP PENALTIES*/
/*TG_MODE=0---> gop and gep*/
/*TG_MODE=1---> --- gep*/
/*TG_MODE=2---> --- ---*/
int TG_MODE, gop, l_gop, gep,l_gep, maximise;
/*VARIABLES FOR THE MULTIPLE SEQUENCE ALIGNMENT*/
int a, b,c,k, t;
int l1, l2,eg, ch, sub,score=0, last_i=0, last_j=0, i, delta_i, j, pos_j, ala, alb, LEN, n_diag, match1, match2;
int su, in, de, tr;
int **C, **D, **I, **trace, **pos0, **LD;
int lenal[2], len;
char *buffer, *char_buf;
char **aln, **al;
/********Prepare Penalties******/
gop=CL->gop*SCORE_K;
gep=CL->gep*SCORE_K;
TG_MODE=CL->TG_MODE;
maximise=CL->maximise;
/********************************/
n_diag=diag[0];
l1=lenal[0]=strlen (A->seq_al[l_s[0][0]]);
l2=lenal[1]=strlen (A->seq_al[l_s[1][0]]);
if ( getenv ("DEBUG_TCOFFEE"))fprintf ( stderr, "\n\tNdiag=%d%% ", (diag[0]*100)/(l1+l2));
/*diag:
diag[1..n_diag]--> flaged diagonal in order;
diag[0]=0--> first diagonal;
diag[n_diag+1]=l1+l2-1;
*/
/*numeration of the diagonals strats from the bottom right [1...l1+l2-1]*/
/*sequence s1 is vertical and seq s2 is horizontal*/
/*D contains the best Deletion in S2==>comes from diagonal N+1*/
/*I contains the best insertion in S2=> comes from diagonal N-1*/
C=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
D=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
LD=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
I=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
trace=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
al=declare_char (2,lenal[0]+lenal[1]+lenal[1]+1);
len= MAX(lenal[0],lenal[1])+1;
buffer=(char*)vcalloc ( 2*len, sizeof (char));
char_buf=(char*) vcalloc (2*len, sizeof (char));
pos0=aln2pos_simple ( A,-1, ns, l_s);
C[0][0]=0;
t=(TG_MODE==0)?gop:0;
for ( j=1; j<= n_diag; j++)
{
l_gop=(TG_MODE==0)?gop:0;
l_gep=(TG_MODE==2)?0:gep;
if ( (diag[j]-lenal[0])<0 )
{
trace[0][j]=UNDEFINED;
continue;
}
C[0][j]=(diag[j]-lenal[0])*l_gep +l_gop;
D[0][j]=(diag[j]-lenal[0])*l_gep +l_gop+gop;
}
D[0][j]=D[0][j-1]+gep;
t=(TG_MODE==0)?gop:0;
for ( i=1; i<=lenal[0]; i++)
{
l_gop=(TG_MODE==0)?gop:0;
l_gep=(TG_MODE==2)?0:gep;
C[i][0]=C[i][n_diag+1]=t=t+l_gep;
I[i][0]=D[i][n_diag+1]=t+ gop;
for ( j=1; j<=n_diag; j++)
{
C[i][j]=C[i][0];
D[i][j]=I[i][j]=I[i][0];
}
for (eg=0, j=1; j<=n_diag; j++)
{
pos_j=diag[j]-lenal[0]+i;
if (pos_j<=0 || pos_j>l2 )
{
trace[i][j]=UNDEFINED;
continue;
}
sub=(CL->get_dp_cost) ( A, pos0, ns[0], l_s[0], i-1, pos0, ns[1], l_s[1],pos_j-1, CL );
/*1 identify the best insertion in S2:*/
l_gop=(i==lenal[0])?((TG_MODE==0)?gop:0):gop;
l_gep=(i==lenal[0])?((TG_MODE==2)?0:gep):gep;
len=(j==1)?0:(diag[j]-diag[j-1]);
if ( a_better_than_b(I[i][j-1], C[i][j-1]+l_gop, maximise))eg++;
else eg=1;
I[i][j]=best_of_a_b (I[i][j-1], C[i][j-1]+l_gop, maximise)+len*l_gep;
/*2 Identify the best deletion in S2*/
l_gop=(pos_j==lenal[1])?((TG_MODE==0)?gop:0):gop;
l_gep=(pos_j==lenal[1])?((TG_MODE==2)?0:gep):gep;
len=(j==n_diag)?0:(diag[j+1]-diag[j]);
delta_i=((i-len)>0)?(i-len):0;
if ( a_better_than_b(D[delta_i][j+1],C[delta_i][j+1]+l_gop, maximise)){LD[i][j]=LD[delta_i][j+1]+1;}
else {LD[i][j]=1;}
D[i][j]=best_of_a_b (D[delta_i][j+1],C[delta_i][j+1]+l_gop, maximise)+len*l_gep;
/*Identify the best way*/
/*
score=C[i][j]=best_int ( 3, maximise, &fop, I[i][j], C[i-1][j]+sub, D[i][j]);
fop-=1;
if ( fop<0)trace[i][j]=fop*eg;
else if ( fop>0 ) {trace[i][j]=fop*LD[i][j];}
else if ( fop==0) trace[i][j]=0;
*/
su=C[i-1][j]+sub;
in=I[i][j];
de=D[i][j];
/*HERE ("%d %d %d", su, in, de);*/
if (su>=in && su>=de)
{
score=su;
tr=0;
}
else if (in>=de)
{
score=in;
tr=-eg;
}
else
{
score=de;
tr=LD[i][j];
}
trace[i][j]=tr;
C[i][j]=score;
last_i=i;
last_j=j;
}
}
/*
[0][Positive]
^ ^
| /
| /
| /
| /
|/
[Neg]<-------[*]
*/
i=last_i;
j=last_j;
ala=alb=0;
match1=match2=0;
while (!(match1==l1 && match2==l2))
{
if ( match1==l1)
{
len=l2-match2;
for ( a=0; a< len; a++)
{
al[0][ala++]=0;
al[1][alb++]=1;
match2++;
}
k=0;
break;
/*k=-(j-1);*/
}
else if ( match2==l2)
{
len=l1-match1;
for ( a=0; a< len; a++)
{
al[0][ala++]=1;
al[1][alb++]=0;
match1++;
}
k=0;
break;
/*k= n_diag-j;*/
}
else
{
k=trace[i][j];
}
if ( k==0)
{
if ( match2==l2 || match1==l1);
else
{
al[0][ala++]=1;
al[1][alb++]=1;
i--;
match1++;
match2++;
}
}
else if ( k>0)
{
len=diag[j+k]-diag[j];
for ( a=0; a<len; a++)
{
if ( match1==l1)break;
al[0][ala++]=1;
al[1][alb++]=0;
match1++;
}
i-=len;
j+=k;
}
else if ( k<0)
{
k*=-1;
len=diag[j]-diag[j-k];
for ( a=0; a<len; a++)
{
if ( match2==l2)break;
al[0][ala++]=0;
al[1][alb++]=1;
match2++;
}
j-=k;
}
}
LEN=ala;
c=LEN-1;
invert_list_char ( al[0], LEN);
invert_list_char ( al[1], LEN);
if ( A->declared_len<=LEN)A=realloc_aln2 ( A,A->max_n_seq, 2*LEN);
aln=A->seq_al;
for ( c=0; c< 2; c++)
{
for ( a=0; a< ns[c]; a++)
{
ch=0;
for ( b=0; b< LEN; b++)
{
if (al[c][b]==1)
char_buf[b]=aln[l_s[c][a]][ch++];
else
char_buf[b]='-';
}
char_buf[b]='\0';
aln[l_s[c][a]]=csprintf (aln[l_s[c][a]],"%s", char_buf);
}
}
A->len_aln=LEN;
A->nseq=ns[0]+ns[1];
free_int (pos0, -1);
free_int (C, -1);
free_int (D, -1);
free_int (I, -1);
free_int (trace, -1);
free_int (LD, -1);
free_char ( al, -1);
vfree(buffer);
vfree(char_buf);
return score;
}
int myers_miller_pair_wise (Alignment *A,int *ns, int **ls,Constraint_list *CL )
{
int **pos;
int a,b, i, j, l,l1, l2, len;
int *S;
char ** char_buf;
int score;
/********Prepare Penalties******/
//ns2master_ns (ns,ls, &sns,&sls);
sns=ns;
sls=ls;
/********************************/
pos=aln2pos_simple ( A,-1, ns, ls);
l1=strlen (A->seq_al[ls[0][0]]);
l2=strlen (A->seq_al[ls[1][0]]);
S=(int*)vcalloc (l1+l2+1, sizeof (int));
last=0;
sapp=S;
score=diff (A,ns, ls, 0, l1, 0, l2, 0, 0, CL, pos);
diff (NULL,ns, ls, 0, l1, 0, l2, 0, 0, CL, pos);
i=0;
j=0;
sapp=S;
len=0;
while (!(i==l1 && j==l2))
{
if (*sapp==0) {
i++;
j++;
len++;
}
else if ( *sapp<0) {
i-=*sapp;
len-=*sapp;
}
else if ( *sapp>0) {
j+=*sapp;
len+=*sapp;
}
sapp++;
}
A=realloc_aln2 ( A,A->max_n_seq,len+1);
char_buf=declare_char (A->max_n_seq,len+1);
i=0;
j=0;
sapp=S;
len=0;
while (!(i==l1 && j==l2))
{
if (*sapp==0)
{
for (b=0; b< ns[0]; b++)
char_buf[ls[0][b]][len]=A->seq_al[ls[0][b]][i];
for (b=0; b< ns[1]; b++)
char_buf[ls[1][b]][len]=A->seq_al[ls[1][b]][j];
i++;
j++;
len++;
}
else if ( *sapp>0)
{
l=*sapp;
for ( a=0; a<l; a++, j++, len++)
{
for (b=0; b< ns[0]; b++)
char_buf[ls[0][b]][len]='-';
for (b=0; b< ns[1]; b++)
char_buf[ls[1][b]][len]=A->seq_al[ls[1][b]][j];
}
}
else if ( *sapp<0)
{
l=-*sapp;
for ( a=0; a<l; a++, i++, len++)
{
for (b=0; b< ns[0]; b++)
char_buf[ls[0][b]][len]=A->seq_al[ls[0][b]][i];;
for (b=0; b< ns[1]; b++)
char_buf[ls[1][b]][len]='-';
}
}
sapp++;
}
A->len_aln=len;
A->nseq=ns[0]+ns[1];
for ( a=0; a< ns[0]; a++) {
char_buf[ls[0][a]][len]='\0';
sprintf ( A->seq_al[ls[0][a]], "%s", char_buf[ls[0][a]]);
}
for ( a=0; a< ns[1]; a++) {
char_buf[ls[1][a]][len]='\0';
sprintf ( A->seq_al[ls[1][a]], "%s", char_buf[ls[1][a]]);
}
vfree (S);
free_char ( char_buf, -1);
l1=strlen (A->seq_al[ls[0][0]]);
l2=strlen (A->seq_al[ls[1][0]]);
if ( l1!=l2) exit(1);
free_int (pos, -1);
return score;
}
//leci po liscie artow i sprawdza wszystkie pliki graczy z llisty
void scan_players_for_artefacts()
{
struct dirent * pDirent = NULL;
DIR *pDir = NULL;
ARTEFACT_DATA *atmp = NULL;
ARTEFACT_OWNER *otmp = NULL;
ARTEFACT_STORER *storer = NULL, *temp_storer = NULL, *first_storer = NULL;
int czas;
pDir = opendir( "../player/" );
if ( !pDir )
{
bugf( "Cannot open players directory. Skipping check." );
return; // can't continue.
}
//jedziemy po plikach
while ( TRUE )
{
pDirent = readdir( pDir );
if ( !pDirent )
{
break;
}
for ( atmp = artefact_system; atmp; atmp = atmp->next )
{
for ( otmp = atmp->first_owner;otmp;otmp = otmp->next )
{
{
CHAR_DATA * ch;
ch = load_char_remote( otmp->owner );
if ( !ch )
{
remove_name_from_artefact_list( otmp->owner );
continue;
}
otmp->last_logoff = ch->pcdata->last_logoff;
free_char( ch );
}
remove_artefact_art_destroy( otmp->owner );
//i tu tera sprawdzanie przetrzymywania
czas = ( current_time - ( otmp->last_logoff ) ) / ( 24 * 60 * 60 );
if ( atmp->max_day < czas ) //przetrzymane, zabieramy kolesiowi
{
storer = new_storer_data();
storer->name = otmp->owner;
storer->vnum = atmp->avnum;
storer->next = NULL;
if ( first_storer == NULL )
{
first_storer = storer;
}
else
{
temp_storer->next = storer;
}
temp_storer = storer;
}
} /*alast=atmp;*/
} //fory
break;
}
closedir( pDir );
//dobra to teraz wywalanie,modlmy sie zeby dzialalo
for ( temp_storer = first_storer;temp_storer;temp_storer = temp_storer->next )
{
remove_artefact_remote( temp_storer->name, temp_storer->vnum );
}
return ;
}
int make_fasta_cdna_pair_wise (Alignment *B,Alignment *A,int*in_ns, int **l_s,Constraint_list *CL, int *diag)
{
int a,c,p,k;
Dp_Result *DPR;
static Dp_Model *M;
int l0, l1;
int len_i, len_j;
int f0=0, f1=0;
int deltaf0, deltaf1, delta;
int nr1, nr2;
int ala, alb, aa0, aa1;
int type;
char **al;
int **tl_s;
int *tns;
/*DEBUG*/
int debug_cdna_fasta=0;
Alignment *DA;
int score;
int state,prev_state;
int t, e;
int a1, a2;
l0=strlen ( B->seq_al[l_s[0][0]]);
l1=strlen ( B->seq_al[l_s[1][0]]);
al=declare_char (2, l0+l1+1);
B=realloc_aln2 (B,B->nseq,l0+l1+1);
free_int (B->cdna_cache, -1);
B->cdna_cache=declare_int(1, l0+l1+1);
if ( !M)M=initialize_dna_dp_model (CL);
M->diag=diag;
tl_s=declare_int (2, 2);tns=vcalloc(2, sizeof(int));tl_s[0][0]=0;tl_s[1][0]=3;tns[0]=tns[1]=1;
DPR=make_fast_dp_pair_wise (A,tns, tl_s,CL,M);
vfree(tns);free_int(tl_s, -1);
/*new_trace_back*/
a=p=0;
aa0=aa1=ala=alb=0;
while ( (k=DPR->traceback[a++])!=M->START);
while ( (k=DPR->traceback[a++])!=M->END)
{
f0=M->model_properties[k][M->F0];
f1=M->model_properties[k][M->F1];
len_i=M->model_properties[k][M->LEN_I];
len_j=M->model_properties[k][M->LEN_J];
type=M->model_properties[k][M->TYPE];
if (type==M->CODING0)
{
deltaf0=(aa0*3+f0)-ala;
deltaf1=(aa1*3+f1)-alb;
delta=MAX(deltaf0, deltaf1);
for (nr1=0, nr2=0,c=0; c<delta; c++, nr1++, nr2++,p++)
{
if (nr1<deltaf0 && ala<l0)al[0][p]=B->seq_al[l_s[0][0]][ala++];
else al[0][p]='-';
if (nr2<deltaf1 && alb<l1)al[1][p]=B->seq_al[l_s[1][0]][alb++];
else al[1][p]='-';
B->cdna_cache[0][p]=M->NON_CODING;
if ( is_gap(al[1][p]) && is_gap(al[0][p]))p--;
else if ( debug_cdna_fasta)fprintf (stderr, "\nUM: %c %c", al[0][p], al[1][p]);
}
for ( c=0; c< 3; c++, p++)
{
if ( c==0)B->cdna_cache[0][p]=M->CODING0;
else if ( c==1)B->cdna_cache[0][p]=M->CODING1;
else if ( c==2)B->cdna_cache[0][p]=M->CODING2;
if (ala<l0)al[0][p]=B->seq_al[l_s[0][0]][ala++];
else al[0][p]='-';
if (alb<l1)al[1][p]=B->seq_al[l_s[1][0]][alb++];
else al[1][p]='-';
if ( is_gap(al[1][p]) && is_gap(al[0][p]))p--;
else if ( debug_cdna_fasta)fprintf (stderr, "\n%d: %c %c",k, al[0][p], al[1][p]);
}
}
aa0+=len_i;
aa1+=len_j;
}
deltaf0=(aa0*3+f0)-ala;
deltaf1=(aa1*3+f1)-alb;
delta=MAX(deltaf0, deltaf1);
for (nr1=0, nr2=0,c=0; c<delta; c++, nr1++, nr2++,p++)
{
if (nr1<deltaf0 && ala<l0)al[0][p]=B->seq_al[l_s[0][0]][ala++];
else al[0][p]='-';
if (nr2<deltaf1 && alb<l1)al[1][p]=B->seq_al[l_s[1][0]][alb++];
else al[1][p]='-';
B->cdna_cache[0][p]=M->NON_CODING;
if ( is_gap(al[1][p]) && is_gap(al[0][p]))p--;
else if ( debug_cdna_fasta)fprintf (stderr, "\nUM: %c %c", al[0][p], al[1][p]);
}
/*End New traceback*/
al[0][p]='\0';
al[1][p]='\0';
sprintf( B->seq_al[l_s[0][0]], "%s", al[0]);
sprintf( B->seq_al[l_s[1][0]], "%s", al[1]);
B->len_aln=strlen (al[0]);
B->nseq=2;
if ( debug_cdna_fasta)
{
fprintf ( stderr, "\nA-A=%d, %d", CL->M['a'-'A']['a'-'A'], CL->M['a'-'A']['a'-'A'] *SCORE_K);
for ( a=1; a<diag[0]; a++)
{
fprintf ( stderr, "\nchosen diag: %d", diag[a]);
}
fprintf ( stderr, "\n GOP=%d GEP=%d TG_MODE=%d", M->gop, M->gep, M->TG_MODE);
fprintf ( stderr, "\nF_GOP=%d F_GEP=%d F_TG_MODE=%d", M->gop, M->gep, M->F_TG_MODE);
DA=copy_aln (B, NULL);
DA=realloc_aln2 (DA,6,(DA->len_aln+1));
for ( a=0; a<B->len_aln; a++)
{
fprintf ( stderr, "\n%d", DA->cdna_cache[0][a]);
if (DA->cdna_cache[0][a]>=M->CODING0)DA->seq_al[DA->nseq][a]=DA->cdna_cache[0][a]-M->nstate+'0';
else DA->seq_al[DA->nseq][a]=DA->cdna_cache[0][a]-M->nstate+'0';
if (DA->cdna_cache[0][a]==M->CODING0)
{
DA->seq_al[DA->nseq+1][a]=translate_dna_codon (DA->seq_al[0]+a,'*');
DA->seq_al[DA->nseq+2][a]=translate_dna_codon (DA->seq_al[1]+a,'*');
}
else
{
DA->seq_al[DA->nseq+1][a]='-';
DA->seq_al[DA->nseq+2][a]='-';
}
}
DA->nseq+=3;
print_aln (DA);
free_aln(DA);
score=0;
for (prev_state=M->START,a=0; a< DA->len_aln;)
{
state=DA->cdna_cache[0][a];
t=M->model[prev_state][state];
if ( DA->cdna_cache[0][a]==M->CODING0)
{
a1=translate_dna_codon (A->seq_al[0]+a,'x');
a2=translate_dna_codon (A->seq_al[1]+a,'x');
if ( a1!='x' && a2!='x')
{
e=CL->M[a1-'A'][a2-'A']*SCORE_K;
}
}
else if ( DA->cdna_cache[0][a]>M->CODING0);
else
{
e=M->model_properties[B->cdna_cache[0][a]][M->EMISSION];
}
if ( e==UNDEFINED || t==UNDEFINED) fprintf ( stderr, "\nPROBLEM %d\n", a);
fprintf ( stderr, "\n[%c..%c: %d(e)+%d(t)=%d]", A->seq_al[0][a], A->seq_al[1][a], e,t,e+t);
score+=e+t;
prev_state=state;
if (B->cdna_cache[0][a]==M->NON_CODING)a++;
else a+=3;
}
}
for ( a=0; a<B->len_aln; a++)
{
if ( B->cdna_cache[0][a]<M->CODING0)B->cdna_cache[0][a]=0;
else B->cdna_cache[0][a]=1;
}
free_char ( al, -1);
return DPR->score;
}
Sequence *free_constraint_list (Constraint_list *CL)
{
Sequence *S;
int a, b;
Constraint_list *pCL;
/*Prepare the selective freeing of the CL data structure:
If the CL has been obtained from copy, every pointer that is identical to the parent CL (CL->pCL)
will not be saved.
*/
if ( !CL)return NULL;
else S=CL->S;
if ( CL->copy_mode==SOFT_COPY && !CL->pCL)
{vfree(CL); return S;}
else if ( CL->copy_mode==SOFT_COPY)
{
pCL=CL->pCL;
CL->residue_index=NULL;
if ( CL->M ==pCL->M )CL->M=NULL;
if (CL->start_index ==pCL->start_index )CL->start_index=NULL;
if (CL->end_index ==pCL->end_index )CL->end_index=NULL;
if ( CL->fp ==pCL->fp )CL->fp=NULL;
if ( CL->matrices_list ==pCL->matrices_list )CL->matrices_list=NULL;
if ( CL->STRUC_LIST ==pCL->STRUC_LIST )CL->STRUC_LIST=NULL;
if ( CL->W ==pCL->W )CL->W=NULL;
if ( CL->DM ==pCL->DM )CL->DM=NULL;
if ( CL->ktupDM ==pCL->ktupDM )CL->ktupDM=NULL;
if ( CL->translation ==pCL->translation )CL->translation=NULL;
if ( CL->moca ==pCL->moca )CL->moca=NULL;
if ( CL->Prot_Blast ==pCL->Prot_Blast )CL->Prot_Blast=NULL;
if ( CL->DNA_Blast ==pCL->DNA_Blast )CL->DNA_Blast=NULL;
if ( CL->Pdb_Blast ==pCL->Pdb_Blast )CL->Pdb_Blast=NULL;
if ( CL->seq_for_quadruplet ==pCL->seq_for_quadruplet )CL->seq_for_quadruplet=NULL;
if ( CL->TC ==pCL->TC )CL->TC=NULL;
}
/*End of selective freeing of the CL data structure*/
if ( CL->residue_index)free_arrayN(CL->residue_index, 3);
if ( CL->M)free_int (CL->M, -1);
if ( CL->fp)vfclose (CL->fp);
if ( CL->matrices_list)free_char(CL->matrices_list,-1);
if ( CL->start_index)free_int ( CL->start_index,-1);
if ( CL->end_index)free_int ( CL->end_index,-1);
if ( CL->STRUC_LIST)free_sequence ( CL->STRUC_LIST, (CL->STRUC_LIST)->nseq);
if ( CL->W)free_weights (CL->W);
CL->DM=free_distance_matrix (CL->DM);
CL->ktupDM=free_distance_matrix (CL->ktupDM);
if ( CL->translation)vfree(CL->translation);
if ( CL->moca)free_moca (CL->moca);
if ( CL->Prot_Blast)free_blast_param ( CL->Prot_Blast);
if ( CL->DNA_Blast) free_blast_param ( CL->DNA_Blast);
if ( CL->Pdb_Blast) free_blast_param ( CL->Pdb_Blast);
if ( CL->TC) free_TC_param ( CL->TC);
if (CL->seq_for_quadruplet)vfree (CL->seq_for_quadruplet);
vfree(CL);
return S;
}
Alignment* copy_aln ( Alignment *A, Alignment *B)
{
int a, b;
int nnseq;
int nlen;
/* c[100]=10;*/
if ( A==NULL){free_aln(B); return NULL;}
nnseq=MAX(A->nseq, A->max_n_seq);
nlen=A->len_aln+1;
if (B)
B=realloc_alignment2 (B, nnseq, nlen);
else
B=declare_aln2 (nnseq, nlen);
B->S=A->S;
/*SIZES*/
B->max_len=A->max_len;
B->min_len=A->min_len;
B->declared_len=nlen;
B->max_n_seq=nnseq;
B->nseq=A->nseq;
B->len_aln=A->len_aln;
/*sequence Information*/
if ( A->generic_comment)
{
vfree(B->generic_comment);
B->generic_comment=vcalloc (strlen(A->generic_comment)+1, sizeof (char));
sprintf ( B->generic_comment, "%s", A->generic_comment);
}
if ( (A->S)==NULL){vfree (B->len); B->len=vcalloc ( A->max_n_seq, sizeof (int));}
ga_memcpy_int ( A->len, B->len, B->nseq);
B->seq_comment=copy_char ( A->seq_comment, B->seq_comment, -1,-1);
B->aln_comment=copy_char ( A->aln_comment, B->aln_comment, -1,-1);
B->name=copy_char ( A->name, B->name, -1,-1);
B->file=copy_char ( A->file, B->file, -1,-1);
B->tree_order=copy_char ( A->tree_order, B->tree_order, -1,-1);
B->expanded_order=A->expanded_order;
free_char ( B->seq_al, -1);
B->seq_al=declare_char(B->max_n_seq, B->declared_len);
// HERE ("A: MAX_NSEQ=%d %d %d %d",B->nseq, B->max_n_seq, B->declared_len, B->len_aln);
// HERE ("B: MAX_NSEQ=%d %d %d %d",A->nseq, A->max_n_seq, A->declared_len, A->len_aln);
for ( a=0; a< nnseq; a++)
{
if (A->seq_al[a])
{
for ( b=0; b< A->len_aln; b++)
B->seq_al[a][b]=A->seq_al[a][b];
}
}
B->order=copy_int ( A->order, B->order, -1, -1);
B->S=A->S;
if (A->seq_cache)
{
B->seq_cache=copy_int ( A->seq_cache, B->seq_cache,-1,-1);
}
if (A->cdna_cache)
{
B->cdna_cache=copy_int ( A->cdna_cache, B->cdna_cache,-1,-1);
}
B->P=copy_profile (A->P);
B->Dp_result=A->Dp_result;
/*Score*/
if ( (A->S)==NULL){vfree (B->score_seq); B->score_seq=vcalloc ( A->max_n_seq, sizeof (int));}
ga_memcpy_int( A->score_seq,B->score_seq,B->nseq);
B->score_res=A->score_res;
B->score_aln=A->score_aln;
B->score=A->score;
B->ibit=A->ibit;
B->cpu=A->cpu;
B->finished=A->finished;
/*Output Options*/
B->output_res_num=A->output_res_num;
B->residue_case=A->residue_case;
B->expand=A->expand;
B->CL=A->CL;
B->random_tag=A->random_tag;
/*Make the function Recursive */
if ( A->A)
{
B->A=copy_aln (A->A, NULL);
}
else B->A=NULL;
return B;
}
void remove_artefact_remote( char *name, unsigned int vnum )
{
CHAR_DATA * ch;
OBJ_DATA *obj;
char buf[ MAX_STRING_LENGTH ];
char buf1[ MAX_STRING_LENGTH ];
sprintf( buf1, "imie: %s vnum: %d", name, vnum );
log_string( buf1 );
//sprawdzalismy juz czy istnieje plik wiec:
ch = load_char_remote( name );
if ( ch == NULL )
{
bugf( "load_char_remote: no match '%s'.", name );
remove_name_from_artefact_list( ch->name );
return;
}
if ( !ch->carrying )
{
free_char( ch );
return;
}
//dobra to szuka i od razu wywala z listy
if ( ch->carrying->pIndexData->vnum == vnum )
{
obj = ch->carrying;
ch->carrying = ch->carrying->next_content;
}
else if ( ( obj = przeszukanie( ch->carrying, vnum, NULL ) ) == NULL )
{
remove_name_from_artefact_list( ch->name );
restore_char_on_artefact_list( ch );
return ;
}
sprintf( buf, "ZABRANO PRZETRZYMYWANY ARTEFAKT: Posiadacz:%s Avnum:%s,%d", ch->name, obj->name, obj->pIndexData->vnum );
log_string( buf );
append_file_format_daily(NULL, ARTEFACT_LOG_FILE, "%s -> PRZETRZYMANY :%s vnum:%d (DEL)",ch->name, obj->short_descr, obj->pIndexData->vnum);
get_money_from_rent( ch, obj );
//sprawdzic czy kase zapisuje na nowo
//daty nie zmieniac przypadkiem !!!
//logowac to
//tu koncowe rzeczy
obj->carried_by = NULL;
obj->next_content = NULL;
//to sprawdzic czy w workach tez liczone
ch->carry_number -= get_obj_number( obj );
ch->carry_weight -= get_obj_weight( obj );
save_char_obj( ch, FALSE, TRUE ); //z TRUE nei zapisuje nowej daty
//to cos zle dziala, dodaje zamiast odejmowac ;)
remove_name_from_artefact_list( ch->name );
restore_char_on_artefact_list( ch );
free_char( ch );
return ;
}
