int32
abAbacus::addContig() {
if (tigStore)
uma = tigStore->loadMultiAlign(iid, type == AS_UNITIG);
if (uma == NULL)
fprintf(stderr,"Lookup failure in CNS: MultiAlign for unitig %d could not be found.\n",iid);
assert(uma != NULL);
// Contigs used to be added gapped, unitigs as ungapped.
// This caused no end of trouble in MergeMultiAligns and
// ReplaceEndUnitigInContig.
ResetVA_char(ungappedSequence);
ResetVA_char(ungappedQuality);
GetMultiAlignUngappedConsensus(uma, ungappedSequence, ungappedQuality);
sequence = Getchar(ungappedSequence,0);
quality = Getchar(ungappedQuality,0);
fragment.length = GetMultiAlignUngappedLength(uma);
fragment.utype = (type == AS_UNITIG) ? utype : AS_OTHER_UNITIG;
fragment.n_components = GetNumIntMultiPoss(uma->f_list) + GetNumIntUnitigPoss(uma->u_list);
fragment.components = SetUngappedFragmentPositions(type, fragment.n_components, uma);
//fprintf(stderr, "AppendFragToLocalStore()-- TIG %d len=%d\n", iid, fragment.length);
}
unsigned char Get_character()
{
unsigned char ret;
Printf("Enter a character: ");
ret = Getchar();
ret = Getchar();
return ret;
}
static void
getword(int first, int (*tst)(int))
{ int i=0, c;
yytext[i++]= (char) first;
while (tst(c = Getchar()))
{ yytext[i++] = (char) c;
if (c == '\\')
{ c = Getchar();
yytext[i++] = (char) c; /* no tst */
} }
yytext[i] = '\0';
Ungetch(c);
}
static int
getinline(void)
{ int c;
if (ReDiRect)
{ c = *ReDiRect++;
if (c == '\0')
{ ReDiRect = (char *) 0;
c = *Inliner[Inlining]++;
}
} else
{
c = *Inliner[Inlining]++;
}
if (c == '\0')
{
lineno = Inline_stub[Inlining]->cln;
Fname = Inline_stub[Inlining]->cfn;
Inlining--;
#if 0
if (verbose&32)
printf("spin: %s:%d, done inlining %s\n",
Fname, lineno, Inline_stub[Inlining+1]->nm->name);
#endif
return Getchar();
}
return c;
}
int
ncss_Getchar(void)
{
int c;
static int blankline = 1;
if ((c = Getchar()) != EOF)
{
if (blankline)
{
if (!ISSPACE(c))
{
blankline = 0;
}
}
else
{
if (c == '\n')
{
c = T_NCNULINE;
blankline = 1;
}
}
}
else
{
blankline = 1;
}
if (c == T_NCNULINE)
ncss_Line++;
return c;
}
static void
ncss(FILE *in, int *linesp, int *nclinesp)
{
int c;
int lines = 0;
int nclines = 0;
int boline = 1;
while ((c = Getchar()) != EOF)
{
if (c == '\n')
{
lines++;
boline = 1;
}
else if (boline && !ISSPACE(c))
{
boline = 0;
nclines++;
}
}
*linesp = lines;
*nclinesp = nclines;
}
bool buildUTGMessage(int32 ID, SnapUnitigMesg *utg) {
MultiAlignT *ma = ScaffoldGraph->tigStore->loadMultiAlign(ID, TRUE);
if (ma == NULL)
return(false);
utg->eaccession = AS_UID_fromInteger(getUID(uidServer));
utg->iaccession = ID;
utg->coverage_stat = ScaffoldGraph->tigStore->getUnitigCoverageStat(ID);
utg->microhet_prob = ScaffoldGraph->tigStore->getUnitigMicroHetProb(ID);
utg->status = ScaffoldGraph->tigStore->getUnitigStatus(ID);
utg->status = (utg->status == AS_UNASSIGNED ? AS_UNIQUE : utg->status);
utg->length = GetMultiAlignLength(ma);
utg->consensus = Getchar(ma->consensus, 0);
utg->quality = Getchar(ma->quality, 0);
utg->forced = 0;
utg->num_frags = GetNumIntMultiPoss(ma->f_list);
utg->num_vars = 0;
utg->f_list = (SnapMultiPos*)safe_malloc(utg->num_frags * sizeof(SnapMultiPos));
utg->v_list = NULL;
if (utg->consensus == NULL)
fprintf(stderr, "buildUTGMessage()-- unitig %d missing consensus sequence\n",
utg->iaccession);
assert(utg->consensus != NULL);
if (utg->length != strlen(utg->consensus))
fprintf(stderr, "buildUTGMessage()-- unitig %d length %d != consensus string length "F_SIZE_T"\n",
utg->iaccession, utg->length, strlen(utg->consensus));
assert(utg->length == strlen(utg->consensus));
for (int32 i=0; i<utg->num_frags; i++) {
IntMultiPos *imp = GetIntMultiPos(ma->f_list, i);
utg->f_list[i].type = imp->type;
utg->f_list[i].eident = FRGmap.lookup(imp->ident);
utg->f_list[i].position = imp->position;
utg->f_list[i].delta_length = imp->delta_length;
utg->f_list[i].delta = imp->delta;
}
return(true);
}
static int
follow(int tok, int ifyes, int ifno)
{ int c;
if ((c = Getchar()) == tok)
{ return ifyes;
}
Ungetch(c);
return ifno;
}
char GetName()
{
char c = Look;
if (!isalpha(Look))
{
sprintf(tmp, "Name");
Expected(tmp);
}
Getchar();
return toupper(c);
}
void Match(char x)
{
if (Look == x)
{
Getchar();
}
else
{
sprintf(tmp, "'%c'", x);
Expected(tmp);
}
}
static int
pre_proc(void)
{ char b[512];
int c, i = 0;
b[i++] = '#';
while ((c = Getchar()) != '\n' && c != EOF)
{ b[i++] = (char) c;
}
b[i] = '\0';
yylval = nn(ZN, 0, ZN, ZN);
yylval->sym = lookup(b);
return PREPROC;
}
static void
decomment_file(char *fname, FILE *f)
{
int c;
extern int Cppflag;
Input = f;
Cppflag = 1;
while ((c = Getchar()) != EOF)
{
putc(c, stdout);
}
}
static void
do_directive(int first)
{ int c = first; /* handles lines starting with pound */
getword(c, isalpha_);
if (strcmp(yytext, "#ident") == 0)
goto done;
if ((c = Getchar()) != ' ')
fatal("malformed preprocessor directive - # .", 0);
if (!isdigit_(c = Getchar()))
fatal("malformed preprocessor directive - # .lineno", 0);
getword(c, isdigit_);
lineno = atoi(yytext); /* pickup the line number */
if ((c = Getchar()) == '\n')
return; /* no filename */
if (c != ' ')
fatal("malformed preprocessor directive - .fname", 0);
if ((c = Getchar()) != '\"')
{ printf("got %c, expected \" -- lineno %d\n", c, lineno);
fatal("malformed preprocessor directive - .fname (%s)", yytext);
}
getword(Getchar(), notquote); /* was getword(c, notquote); */
if (Getchar() != '\"')
fatal("malformed preprocessor directive - fname.", 0);
/* strcat(yytext, "\""); */
Fname = lookup(yytext);
done:
while (Getchar() != '\n')
;
}
void
precondition(char *q)
{ int c, nest = 1;
for (;;)
{ c = Getchar();
*q++ = c;
switch (c) {
case '\n':
lineno++;
break;
case '[':
nest++;
break;
case ']':
if (--nest <= 0)
{ *--q = '\0';
return;
}
break;
}
}
fatal("cannot happen", (char *) 0); /* unreachable */
}
void
moveloop()
{
#if defined(MICRO) || defined(WIN32)
char ch;
int abort_lev;
#endif
int moveamt = 0, wtcap = 0, change = 0;
boolean didmove = FALSE, monscanmove = FALSE;
flags.moonphase = phase_of_the_moon();
if(flags.moonphase == FULL_MOON) {
You("are lucky! Full moon tonight.");
change_luck(1);
} else if(flags.moonphase == NEW_MOON) {
pline("Be careful! New moon tonight.");
}
flags.friday13 = friday_13th();
if (flags.friday13) {
pline("Watch out! Bad things can happen on Friday the 13th.");
change_luck(-1);
}
initrack();
/* Note: these initializers don't do anything except guarantee that
we're linked properly.
*/
decl_init();
monst_init();
monstr_init(); /* monster strengths */
objects_init();
commands_init();
(void) encumber_msg(); /* in case they auto-picked up something */
u.uz0.dlevel = u.uz.dlevel;
youmonst.movement = NORMAL_SPEED; /* give the hero some movement points */
for(;;) {
get_nh_event();
#ifdef POSITIONBAR
do_positionbar();
#endif
didmove = flags.move;
if(didmove) {
/* actual time passed */
youmonst.movement -= NORMAL_SPEED;
do { /* hero can't move this turn loop */
wtcap = encumber_msg();
flags.mon_moving = TRUE;
do {
monscanmove = movemon();
if (youmonst.movement >= NORMAL_SPEED)
{
curmonst = &youmonst;
break; /* it's now your turn */
}
} while (monscanmove);
flags.mon_moving = FALSE;
if (!monscanmove && youmonst.movement < NORMAL_SPEED) {
/* both you and the monsters are out of steam this round */
/* set up for a new turn */
struct monst *mtmp;
mcalcdistress(); /* adjust monsters' trap, blind, etc */
/* reallocate movement rations to monsters */
for (mtmp = fmon; mtmp; mtmp = mtmp->nmon)
mtmp->movement += mcalcmove(mtmp);
if(!rn2(u.uevent.udemigod ? 25 :
(depth(&u.uz) > depth(&stronghold_level)) ? 50 : 70))
(void) makemon((struct permonst *)0, 0, 0, NO_MM_FLAGS);
/* calculate how much time passed. */
#ifdef STEED
if (u.usteed && u.umoved) {
/* your speed doesn't augment steed's speed */
moveamt = mcalcmove(u.usteed);
} else
#endif
{
moveamt = youmonst.data->mmove;
if (Very_fast) { /* speed boots or potion */
/* average movement is 1.67 times normal */
moveamt += NORMAL_SPEED / 2;
if (rn2(3) == 0) moveamt += NORMAL_SPEED / 2;
} else if (Fast) {
/* average movement is 1.33 times normal */
if (rn2(3) != 0) moveamt += NORMAL_SPEED / 2;
}
}
switch (wtcap) {
case UNENCUMBERED: break;
case SLT_ENCUMBER: moveamt -= (moveamt / 4); break;
case MOD_ENCUMBER: moveamt -= (moveamt / 2); break;
case HVY_ENCUMBER: moveamt -= ((moveamt * 3) / 4); break;
case EXT_ENCUMBER: moveamt -= ((moveamt * 7) / 8); break;
default: break;
}
youmonst.movement += moveamt;
if (youmonst.movement < 0) youmonst.movement = 0;
settrack();
monstermoves++;
moves++;
/********************************/
/* once-per-turn things go here */
/********************************/
if (flags.bypasses) clear_bypasses();
if(Glib) glibr();
nh_timeout();
run_regions();
if (u.ublesscnt) u.ublesscnt--;
if(flags.time && !flags.run)
flags.botl = 1;
/* One possible result of prayer is healing. Whether or
* not you get healed depends on your current hit points.
* If you are allowed to regenerate during the prayer, the
* end-of-prayer calculation messes up on this.
* Another possible result is rehumanization, which requires
* that encumbrance and movement rate be recalculated.
*/
if (u.uinvulnerable) {
/* for the moment at least, you're in tiptop shape */
wtcap = UNENCUMBERED;
} else if (Upolyd && youmonst.data->mlet == S_EEL &&
!is_pool(u.ux,u.uy) && !Is_waterlevel(&u.uz) &&
!(u.uswallow &&
u.ustuck->data == &mons[PM_WATER_ELEMENTAL])) {
if (u.mh > 1) {
u.mh--;
flags.botl = 1;
} else if (u.mh < 1)
killer_format = KILLED_BY_AN,
rehumanize("inability to breathe air");
} else if (Upolyd && u.mh < u.mhmax) {
if (u.mh < 1)
rehumanize(0);
else if (Regeneration ||
(wtcap < MOD_ENCUMBER && !(moves%20))) {
flags.botl = 1;
u.mh++;
}
} else if (u.uhp < u.uhpmax &&
(wtcap < MOD_ENCUMBER || !u.umoved || Regeneration)) {
if (u.ulevel > 9 && !(moves % 3)) {
int heal, Con = (int) ACURR(A_CON);
if (Con <= 12) {
heal = 1;
} else {
heal = rnd(Con);
if (heal > u.ulevel-9) heal = u.ulevel-9;
}
flags.botl = 1;
u.uhp += heal;
if(u.uhp > u.uhpmax)
u.uhp = u.uhpmax;
} else if (Regeneration ||
(u.ulevel <= 9 &&
!(moves % ((MAXULEV+12) / (u.ulevel+2) + 1)))) {
flags.botl = 1;
u.uhp++;
}
}
/* moving around while encumbered is hard work */
if (wtcap > MOD_ENCUMBER && u.umoved) {
if(!(wtcap < EXT_ENCUMBER ? moves%30 : moves%10)) {
if (Upolyd && u.mh > 1) {
u.mh--;
} else if (!Upolyd && u.uhp > 1) {
u.uhp--;
} else {
You("pass out from exertion!");
exercise(A_CON, FALSE);
fall_asleep(-10, FALSE);
}
}
}
if ((u.uen < u.uenmax) &&
((wtcap < MOD_ENCUMBER &&
(!(moves%((MAXULEV + 8 - u.ulevel) *
(Role_if(PM_WIZARD) ? 3 : 4) / 6))))
|| Energy_regeneration)) {
u.uen += rn1((int)(ACURR(A_WIS) + ACURR(A_INT)) / 15 + 1,1);
if (u.uen > u.uenmax) u.uen = u.uenmax;
flags.botl = 1;
}
if(!u.uinvulnerable) {
if(Teleportation && !rn2(85)) {
xchar old_ux = u.ux, old_uy = u.uy;
tele();
if (u.ux != old_ux || u.uy != old_uy) {
if (!next_to_u()) {
check_leash(old_ux, old_uy);
}
#ifdef REDO
/* clear doagain keystrokes */
pushch(0);
savech(0);
#endif
}
}
/* delayed change may not be valid anymore */
if ((change == 1 && !Polymorph) ||
(change == 2 && u.ulycn == NON_PM))
change = 0;
if(Polymorph && !rn2(100))
change = 1;
else if (u.ulycn >= LOW_PM && !Upolyd &&
!rn2(80 - (20 * night())))
change = 2;
if (change && !Unchanging) {
if (multi >= 0) {
if (occupation)
stop_occupation();
else
nomul(0);
if (change == 1) polyself(FALSE);
else you_were();
change = 0;
}
}
if(u.utrap && u.utraptype == TT_LAVA) {
if(!is_lava(u.ux,u.uy))
u.utrap = 0;
else if (!u.uinvulnerable) {
u.utrap -= 1<<8;
if(u.utrap < 1<<8) {
killer_format = KILLED_BY;
killer = "molten lava";
You("sink below the surface and die.");
done(DISSOLVED);
} else if(didmove && !u.umoved) {
Norep("You sink deeper into the lava.");
u.utrap += rnd(4);
}
}
}
}
if(Searching && multi >= 0) (void) dosearch0(1);
dosounds();
/* hack - make sure damage from storms is not blamed
on the player */
flags.mon_moving = TRUE;
do_storms();
flags.mon_moving = FALSE;
gethungry();
age_spells();
exerchk();
invault();
if (u.uhave.amulet) amulet();
if (!rn2(40+(int)(ACURR(A_DEX)*3)))
u_wipe_engr(rnd(3));
if (u.uevent.udemigod && !u.uinvulnerable) {
if (u.udg_cnt) u.udg_cnt--;
if (!u.udg_cnt) {
intervene();
u.udg_cnt = rn1(200, 50);
}
}
restore_attrib();
/* underwater and waterlevel vision are done here */
if (Is_waterlevel(&u.uz))
movebubbles();
else if (Underwater)
under_water(0);
/* vision while buried done here */
else if (u.uburied) under_ground(0);
/* when immobile, count is in turns */
if(multi < 0) {
if (++multi == 0) { /* finished yet? */
unmul((char *)0);
/* if unmul caused a level change, take it now */
if (u.utotype) deferred_goto();
}
}
}
} while (youmonst.movement<NORMAL_SPEED); /* hero can't move loop */
/******************************************/
/* once-per-hero-took-time things go here */
/******************************************/
curmonst = &youmonst;
} /* actual time passed */
/****************************************/
/* once-per-player-input things go here */
/****************************************/
find_ac();
if(!flags.mv || Blind) {
/* redo monsters if hallu or wearing a helm of telepathy */
if (HHallucination &&
!Halluc_resistance) { /* update screen randomly */
/*
see_monsters();
see_objects();
see_traps();
if (u.uswallow) swallowed(0);
*/
if (u.uswallow) {
swallowed(1);
} else if (Underwater && !Is_waterlevel(&u.uz)) {
under_water(1);
} else if (u.uburied) {
under_ground(1);
} else {
register int x, y;
register struct rm *lev;
vision_recalc(2);
/*clear_nhwindow(WIN_MAP);*/
clear_glyph_buffer();
for (x = 1; x < COLNO; x++) {
lev = &levl[x][0];
for (y = 0; y < ROWNO; y++, lev++)
if (lev->glyph != cmap_to_glyph(S_stone))
show_glyph(x,y,lev->glyph);
}
vision_recalc(0);
see_monsters();
}
} else if (Unblind_telepat) {
see_monsters();
} else if (Warning || Warn_of_mon)
see_monsters();
if (vision_full_recalc) vision_recalc(0); /* vision! */
}
#ifdef REALTIME_ON_BOTL
if(iflags.showrealtime) {
/* Update the bottom line if the number of minutes has
* changed */
if(get_realtime() / 60 != realtime_data.last_displayed_time / 60)
flags.botl = 1;
}
#endif
if(flags.botl || flags.botlx) bot();
flags.move = 1;
if(multi >= 0 && occupation) {
#if defined(MICRO) || defined(WIN32)
abort_lev = 0;
if (kbhit()) {
if ((ch = Getchar()) == ABORT)
abort_lev++;
# ifdef REDO
else
pushch(ch);
# endif /* REDO */
}
if (!abort_lev && (*occupation)() == 0)
#else
if ((*occupation)() == 0)
#endif
occupation = 0;
if(
#if defined(MICRO) || defined(WIN32)
abort_lev ||
#endif
monster_nearby()) {
stop_occupation();
reset_eat();
}
#if defined(MICRO) || defined(WIN32)
if (!(++occtime % 7))
display_nhwindow(WIN_MAP, FALSE);
#endif
continue;
}
if ((u.uhave.amulet || Clairvoyant) &&
!In_endgame(&u.uz) && !BClairvoyant &&
!(moves % 15) && !rn2(2))
do_vicinity_map();
#ifdef WIZARD
if (iflags.sanity_check)
sanity_check();
#endif
#ifdef CLIPPING
/* just before rhack */
cliparound(u.ux, u.uy);
#endif
u.umoved = FALSE;
if (multi > 0) {
lookaround();
if (!multi) {
/* lookaround may clear multi */
flags.move = 0;
if (flags.time) flags.botl = 1;
continue;
}
if (flags.mv) {
if(multi < COLNO && !--multi)
flags.travel = iflags.travel1 = flags.mv = flags.run = 0;
domove();
} else {
--multi;
rhack(save_cm);
}
} else if (multi == 0) {
#ifdef MAIL
ckmailstatus();
#endif
rhack((char *)0);
}
if (u.utotype) /* change dungeon level */
deferred_goto(); /* after rhack() */
/* !flags.move here: multiple movement command stopped */
else if (flags.time && (!flags.move || !flags.mv))
flags.botl = 1;
if (vision_full_recalc) vision_recalc(0); /* vision! */
/* when running in non-tport mode, this gets done through domove() */
if ((!flags.run || iflags.runmode == RUN_TPORT) &&
(multi && (!flags.travel ? !(multi % 7) : !(moves % 7L)))) {
if (flags.time && flags.run) flags.botl = 1;
display_nhwindow(WIN_MAP, FALSE);
}
}
}
static
int
abAbacus::SetUngappedFragmentPositions(FragType type,int32 n_frags, MultiAlignT *uma) {
int32 num_frags = GetNumIntMultiPoss(uma->f_list);
int32 num_unitigs = GetNumIntUnitigPoss(uma->u_list);
HashTable_AS *unitigFrags = CreateScalarHashTable_AS();
int32 num_columns = GetMultiAlignLength(uma);
int32 ungapped_pos = 0;
int32 *gapped_positions = new int32 [num_columns + 1];
char *consensus = Getchar(uma->consensus,0);
for (int32 i=0; i<num_columns+1; i++) {
gapped_positions[i] = ungapped_pos;
if (consensus[i] != '-')
ungapped_pos++;
}
// Remember the first fragment we add.
int32 first_frag = GetNumCNS_AlignedContigElements(fragment_positions);
for (int32 ifrag=0; ifrag<num_frags; ifrag++) {
CNS_AlignedContigElement epos;
IntMultiPos *frag = GetIntMultiPos(uma->f_list, ifrag);
if (ExistsInHashTable_AS(unitigFrags, frag->ident, 0)) {
fprintf(stderr,"SetUngappedFragmentPositions()-- ident %d already in hashtable\n", frag->ident);
assert(0);
}
if (HASH_SUCCESS != InsertInHashTable_AS(unitigFrags, frag->ident, 0, 1, 0)) {
fprintf(stderr,"SetUngappedFragmentPositions()-- Failure to insert ident %d in hashtable\n", frag->ident);
assert(0);
}
assert(frag->position.bgn >= 0);
assert(frag->position.bgn < num_columns + 1);
assert(frag->position.end >= 0);
assert(frag->position.end < num_columns + 1);
epos.frg_or_utg = CNS_ELEMENT_IS_FRAGMENT;
epos.idx.fragment.frgIdent = frag->ident;
epos.idx.fragment.frgType = frag->type;
epos.idx.fragment.frgContained = frag->contained;
epos.idx.fragment.frgInUnitig = (type == AS_CONTIG) ? -1 : uma->maID;
epos.position.bgn = gapped_positions[frag->position.bgn];
epos.position.end = gapped_positions[frag->position.end];
//fprintf(stderr, "SetUngappedFragmentPositions()-- FRG id=%d type=%c pos=%d,%d (orig pos=%d,%d)\n",
// frag->ident, frag->type, epos.position.bgn, epos.position.end, frag->position.bgn, frag->position.end);
// Adjust the ungapped position if we fall within a gap
//
if (epos.position.bgn == epos.position.end) {
fprintf(stderr,"SetUngappedFragmentPositions()-- Encountered bgn==end=="F_S32" in ungapped coords within SetUngappedFragmentPositions for "F_CID "(gapped coords "F_S32","F_S32")\n",
epos.position.bgn,frag->ident,frag->position.bgn,frag->position.end);
assert(frag->position.bgn != frag->position.end);
if (frag->position.bgn < frag->position.end) {
if (epos.position.bgn > 0)
epos.position.bgn--;
else
epos.position.end++;
} else {
if (epos.position.end > 0)
epos.position.end--;
else
epos.position.bgn++;
}
fprintf(stderr,"SetUngappedFragmentPositions()-- Reset to "F_S32","F_S32"\n",
epos.position.bgn,
epos.position.end);
}
AppendVA_CNS_AlignedContigElement(fragment_positions, &epos);
}
for (int32 ifrag=0; ifrag < num_unitigs; ifrag++){
CNS_AlignedContigElement epos;
IntUnitigPos *unitig = GetIntUnitigPos(uma->u_list, ifrag);
epos.frg_or_utg = CNS_ELEMENT_IS_UNITIG;
epos.idx.unitig.utgIdent = unitig->ident;
epos.idx.unitig.utgType = unitig->type;
epos.position.bgn = gapped_positions[unitig->position.bgn];
epos.position.end = gapped_positions[unitig->position.end];
//fprintf(stderr, "SetUngappedFragmentPositions()-- UTG id=%d type=%c pos=%d,%d (orig pos=%d,%d)\n",
// unitig->ident, unitig->type, epos.position.bgn, epos.position.end, unitig->position.bgn, unitig->position.end);
AppendVA_CNS_AlignedContigElement(fragment_positions,&epos);
}
// This is used only by ReplaceEndUnitigInContig(). Mark fragments in the "anchoring" contig
// that belong to this unitig.
//
if (type != AS_CONTIG) {
Fragment *anchor = GetFragment(fragmentStore,0);
if ((anchor != NULL) &&
(anchor->type == AS_CONTIG)) {
CNS_AlignedContigElement *af = GetCNS_AlignedContigElement(fragment_positions, anchor->components);
for (int32 ifrag=0; ifrag < anchor->n_components; ifrag++, af++) {
if ((af->frg_or_utg == CNS_ELEMENT_IS_FRAGMENT) &&
(ExistsInHashTable_AS(unitigFrags, af->idx.fragment.frgIdent, 0)))
af->idx.fragment.frgInUnitig = uma->maID;
}
}
}
DeleteHashTable_AS(unitigFrags);
delete [] gapped_positions;
return first_frag;
}
void Init()
{
Getchar();
}
int32
main(int32 argc, char **argv) {
int32 arg = 1;
int32 err = 0;
int32 hlp = 0;
char * gkpStoreName = NULL;
int32 gkpStorePart = 0;
char * msgFile = NULL;
char * outputFileName= NULL;
char * seqAn = NULL;
char * wrkDir = NULL;
char * seqStoreName = NULL;
int32 seqStoreVer = 0;
int32 seqStorePart = 0;
argc = AS_configure(argc, argv);
while (arg < argc) {
if (strcmp(argv[arg], "-c") == 0) {
msgFile = argv[++arg];
} else if (strcmp(argv[arg], "-G") == 0) {
gkpStoreName = argv[++arg];
} else if (strcmp(argv[arg], "-S") == 0) {
gkpStorePart = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-o") == 0) {
outputFileName = argv[++arg];
} else if (strcmp(argv[arg], "-s") == 0) {
seqAn = argv[++arg];
} else if (strcmp(argv[arg], "-w") == 0) {
wrkDir = argv[++arg];
} else if (strcmp(argv[arg], "-u") == 0) {
seqStoreName = argv[++arg];
} else if (strcmp(argv[arg], "-V") == 0) {
seqStoreVer = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-p") == 0) {
seqStorePart = atoi(argv[++arg]);
} else {
err++;
}
arg++;
}
if ((err) || (gkpStoreName == NULL) || (msgFile == NULL) || (outputFileName == NULL) || seqAn == NULL) {
fprintf(stderr, "USAGE: SeqAn_CNS -G <gkpStore> -c <input.cgb> -o <output.cgi> -s <seqan_executable> [-u seqstore, required for contig consensus] [-w working directory]\n");
exit(1);
}
gkStore *gkpStore = new gkStore(gkpStoreName, FALSE, FALSE);
gkpStore->gkStore_loadPartition(gkpStorePart);
gkFragment fr;
GenericMesg *pmesg;
tSequenceDB *sequenceDB = NULL;
FILE *infp = fopen(msgFile,"r");
FILE *tempReads;
FILE *outfp = fopen(outputFileName, "w");
char fileName[AS_SEQAN_MAX_BUFFER_LENGTH];
char *prefix = outputFileName;
getFileName(prefix, wrkDir, AS_SEQAN_INPUT_NAME, fileName);
int32 i = 0;
while ((EOF != ReadProtoMesg_AS(infp, &pmesg))) {
int32 freeMem = 0;
if (pmesg->t == MESG_IUM) {
IntUnitigMesg *ium_mesg = (IntUnitigMesg *)pmesg->m;
if (strlen(ium_mesg->consensus) == 0) {
tempReads = fopen(fileName,"w");
for (i =0; i < ium_mesg->num_frags; i++) {
// get the fragment sequence
gkpStore->gkStore_getFragment(ium_mesg->f_list[i].ident, &fr, GKFRAGMENT_QLT);
uint32 clrBeg = fr.gkFragment_getClearRegionBegin();
uint32 clrEnd = fr.gkFragment_getClearRegionEnd ();
char *seqStart = fr.gkFragment_getSequence();
char *seq = seqStart+clrBeg;
seq[clrEnd] = 0;
AS_UTL_writeFastA(tempReads,
seq, clrEnd-clrBeg,
">"F_IID","F_IID"\n", ium_mesg->f_list[i].position.bgn, ium_mesg->f_list[i].position.end);
}
fclose(tempReads);
updateRecord(ium_mesg, fileName, seqAn, prefix, wrkDir);
freeMem = 1;
}
WriteProtoMesg_AS(outfp, pmesg);
if (freeMem) {
safe_free(ium_mesg->consensus);
safe_free(ium_mesg->quality);
}
}
else if (pmesg->t == MESG_ICM) {
IntConConMesg *icm_mesg = (IntConConMesg *)pmesg->m;
if (seqStoreName == NULL) {
fprintf(stderr, "USAGE: The -u option is required for contig consensus\n");
exit(1);
}
if (sequenceDB == NULL) {
sequenceDB = openSequenceDB(seqStoreName, FALSE, seqStoreVer);
openSequenceDBPartition(sequenceDB, seqStorePart);
}
if (strlen(icm_mesg->consensus) == 0) {
tempReads = fopen(fileName,"w");
for (i =0; i < icm_mesg->num_pieces; i++) {
// get the fragment sequence
gkpStore->gkStore_getFragment(icm_mesg->pieces[i].ident, &fr, GKFRAGMENT_QLT);
uint32 clrBeg = fr.gkFragment_getClearRegionBegin();
uint32 clrEnd = fr.gkFragment_getClearRegionEnd ();
char *seqStart = fr.gkFragment_getSequence();
char *seq = seqStart+clrBeg;
seq[clrEnd] = 0;
AS_UTL_writeFastA(tempReads,
seq, clrEnd-clrBeg,
">"F_IID","F_IID"\n", icm_mesg->pieces[i].position.bgn, icm_mesg->pieces[i].position.end);
}
// now handle the unitig messages
for (i =0; i < icm_mesg->num_unitigs; i++) {
VA_TYPE(char) *ungappedSequence = CreateVA_char(0);
VA_TYPE(char) *ungappedQuality = CreateVA_char(0);
MultiAlignT *uma = loadMultiAlignTFromSequenceDB(sequenceDB, icm_mesg->unitigs[i].ident, 1);
assert(uma != NULL);
GetMultiAlignUngappedConsensus(uma, ungappedSequence, ungappedQuality);
char * seq = Getchar(ungappedSequence,0);
AS_UTL_writeFastA(tempReads,
seq, strlen(seq),
">"F_IID","F_IID"\n", icm_mesg->unitigs[i].position.bgn, icm_mesg->unitigs[i].position.end);
}
fclose(tempReads);
updateICMRecord(icm_mesg, fileName, seqAn, prefix, wrkDir);
freeMem = 1;
}
WriteProtoMesg_AS(outfp, pmesg);
if (freeMem) {
safe_free(icm_mesg->consensus);
safe_free(icm_mesg->quality);
}
}
}
fclose(infp);
fclose(outfp);
return 0;
}
void
writeCCO(FILE *asmFile, bool doWrite) {
SnapConConMesg cco;
GenericMesg pmesg = { &cco, MESG_CCO };
GraphNodeIterator contigs;
ContigT *contig;
fprintf(stderr, "writeCCO()--\n");
InitGraphNodeIterator(&contigs, ScaffoldGraph->ContigGraph, GRAPH_NODE_DEFAULT);
while ((contig = NextGraphNodeIterator(&contigs)) != NULL) {
assert(contig->id >= 0);
assert(contig->id < GetNumGraphNodes(ScaffoldGraph->ContigGraph));
if (contig->flags.bits.isChaff)
continue;
NodeCGW_T *unitig = GetGraphNode(ScaffoldGraph->CIGraph, contig->info.Contig.AEndCI);
if ((ScaffoldGraph->tigStore->getNumUnitigs(contig->id, FALSE) == 1) &&
(contig->scaffoldID == NULLINDEX) &&
(unitig->info.CI.numInstances > 0))
// Contig is a surrogate instance
continue;
MultiAlignT *ma = ScaffoldGraph->tigStore->loadMultiAlign(contig->id, FALSE);
cco.eaccession = AS_UID_fromInteger(getUID(uidServer));
cco.iaccession = contig->id;
cco.placed = ScaffoldGraph->tigStore->getContigStatus(contig->id);
cco.length = GetMultiAlignLength(ma);
cco.consensus = Getchar(ma->consensus, 0);
cco.quality = Getchar(ma->quality, 0);
cco.forced = 0;
cco.num_pieces = GetNumIntMultiPoss(ma->f_list);
cco.num_unitigs = GetNumIntMultiPoss(ma->u_list);
cco.num_vars = GetNumIntMultiPoss(ma->v_list);
cco.pieces = NULL;
cco.unitigs = NULL;
cco.vars = NULL;
if (cco.consensus == NULL)
fprintf(stderr, "buildCCOMessage()-- contig %d missing consensus sequence\n",
cco.iaccession);
assert(cco.consensus != NULL);
if (cco.length != strlen(cco.consensus))
fprintf(stderr, "buildCCOMessage()-- contig %d length %d != consensus string length "F_SIZE_T"\n",
cco.iaccession, cco.length, strlen(cco.consensus));
assert(cco.length == strlen(cco.consensus));
if (cco.num_pieces > 0) {
cco.pieces = (SnapMultiPos *)safe_malloc(cco.num_pieces * sizeof(SnapMultiPos));
for(int32 i=0; i<cco.num_pieces; i++) {
IntMultiPos *imp = GetIntMultiPos(ma->f_list, i);
cco.pieces[i].type = imp->type;
cco.pieces[i].eident = FRGmap.lookup(imp->ident);
cco.pieces[i].delta_length = imp->delta_length;
cco.pieces[i].position = imp->position;
cco.pieces[i].delta = imp->delta;
}
}
if (cco.num_unitigs > 0) {
cco.unitigs = (UnitigPos *)safe_malloc(cco.num_unitigs * sizeof(UnitigPos));
for(int32 i=0; i<cco.num_unitigs; i++) {
IntUnitigPos *imp = GetIntUnitigPos(ma->u_list, i);
cco.unitigs[i].type = imp->type;
cco.unitigs[i].eident = UTGmap.lookup(imp->ident);
cco.unitigs[i].position = imp->position;
cco.unitigs[i].delta = imp->delta;
cco.unitigs[i].delta_length = imp->delta_length;
}
}
if (cco.num_vars > 0) {
cco.vars = (IntMultiVar *)safe_malloc(cco.num_vars * sizeof(IntMultiVar));
for(int32 i=0; i<cco.num_vars; i++) {
IntMultiVar *imv = GetIntMultiVar(ma->v_list, i);
cco.vars[i].var_id = imv->var_id;
cco.vars[i].phased_id = imv->phased_id;
cco.vars[i].position = imv->position;
cco.vars[i].num_reads = imv->num_reads;
cco.vars[i].num_alleles = imv->num_alleles;
cco.vars[i].num_alleles_confirmed = imv->num_alleles_confirmed;
cco.vars[i].min_anchor_size = imv->min_anchor_size;
cco.vars[i].var_length = imv->var_length;
cco.vars[i].alleles = imv->alleles;
cco.vars[i].var_seq_memory = imv->var_seq_memory;
cco.vars[i].read_id_memory = imv->read_id_memory;
cco.vars[i].enc_num_reads = NULL;
cco.vars[i].enc_weights = NULL;
cco.vars[i].enc_var_seq = NULL;
cco.vars[i].enc_read_ids = NULL;
}
}
if (doWrite)
WriteProtoMesg_AS(asmFile, &pmesg);
safe_free(cco.pieces);
safe_free(cco.unitigs);
safe_free(cco.vars);
CCOmap.add(cco.iaccession, cco.eaccession);
}
}
void
dumpContigInfo(ChunkInstanceT *contig) {
int contigOrientation;
MultiAlignT *ma;
char *seq1;
int len1;
VA_TYPE(char) *consensus = CreateVA_char(2048);
VA_TYPE(char) *quality = CreateVA_char(2048);
fprintf( stderr, "*********************** contig analysis **************************\n");
fprintf( stderr, "analyzing contig: %d\n", contig->id);
if (contig->offsetAEnd.mean < contig->offsetBEnd.mean)
contigOrientation = 0;
else
contigOrientation = 1;
fprintf(stderr, "contig orientation: %d\t length: %d contig offsetAEnd: %d\t offsetBEnd: %d\n",
contigOrientation,
(int)contig->bpLength.mean,
(int)contig->offsetAEnd.mean,
(int)contig->offsetBEnd.mean);
ma = ScaffoldGraph->tigStore->loadMultiAlign(contig->id, ScaffoldGraph->ContigGraph->type == CI_GRAPH);
// Get the consensus sequences for the contig from the Store
GetConsensus(ScaffoldGraph->ContigGraph, contig->id, consensus, quality);
seq1 = Getchar(consensus, 0);
len1 = strlen(seq1);
if (contigOrientation == 1)
reverseComplementSequence(seq1, len1);
if (len1 < 5000) {
fprintf( stderr, ">contig%d consensus seq (flipped to reflect scaff orientation)\n", contig->id);
fprintf( stderr, "%s\n", seq1);
} else {
char tmpchar = seq1[2500];
seq1[2500] = '\0';
fprintf( stderr, ">contig%d left end\n", contig->id);
fprintf( stderr, "%s\n", seq1);
seq1[2500] = tmpchar;
fprintf( stderr, ">contig%d right end\n", contig->id);
fprintf( stderr, "%s\n", seq1 + len1 - 2501);
}
#if 1
int numUnitigs = GetNumIntUnitigPoss(ma->u_list);
fprintf( stderr, "number unitigs: %d\n", numUnitigs);
int i;
for (i = 0; i < numUnitigs; i++) {
IntUnitigPos *upos = GetIntUnitigPos( ma->u_list, i);
ChunkInstanceT *unitig = GetGraphNode( ScaffoldGraph->CIGraph, upos->ident);
MultiAlignT *uma = ScaffoldGraph->tigStore->loadMultiAlign(unitig->id, ScaffoldGraph->CIGraph->type == CI_GRAPH);
IntMultiPos *ump;
int icntfrag;
fprintf( stderr, " unitig: %d\t num frags: %ld surrogate: %d\n", unitig->id, GetNumIntMultiPoss(uma->f_list),
(unitig->flags.bits.isStoneSurrogate || unitig->flags.bits.isWalkSurrogate));
if (unitig->flags.bits.isStoneSurrogate ||
unitig->flags.bits.isWalkSurrogate) {
fprintf (stderr, " surrogate unitig offsetAEnd: %f, offsetBEnd: %f\n", unitig->offsetAEnd.mean, unitig->offsetBEnd.mean);
unitig = GetGraphNode( ScaffoldGraph->CIGraph, unitig->info.CI.baseID);
fprintf ( stderr, " using original unitig: %d\n", unitig->id);
uma = ScaffoldGraph->tigStore->loadMultiAlign(unitig->id,
ScaffoldGraph->CIGraph->type == CI_GRAPH);
}
// now print out info on the frags in the unitig
for (icntfrag = 0; icntfrag < GetNumIntMultiPoss(uma->f_list); icntfrag++) {
IntMultiPos *imp = GetIntMultiPos(uma->f_list, icntfrag);
CIFragT *frag = GetCIFragT(ScaffoldGraph->CIFrags, imp->ident);
fprintf(stderr, " frag: %6d\t contig pos (5p, 3p): %6d, %6d\n",
imp->ident, (int) frag->contigOffset5p.mean, (int) frag->contigOffset3p.mean);
}
}
#endif
#if 1
CIEdgeT * e;
GraphEdgeIterator edges(ScaffoldGraph->ContigGraph, contig->id, ALL_END, ALL_EDGES);
// FALSE == ITERATOR_VERBOSE
while((e = edges.nextRaw()) != NULL)
PrintGraphEdge( stderr, ScaffoldGraph->ContigGraph, "Analyzing edge", e, 0);
#endif
DeleteVA_char(consensus);
DeleteVA_char(quality);
}
int
lex(void)
{ int c;
again:
c = Getchar();
yytext[0] = (char) c;
yytext[1] = '\0';
switch (c) {
case EOF:
return c;
case '\n': /* newline */
lineno++;
/* make most semi-colons optional */
if (implied_semis
&& context
&& in_seq
&& par_cnt == 0
&& follows_token(last_token))
{ if (0)
{ printf("insert ; line %d, last_token %d in_seq %d\n",
lineno-1, last_token, in_seq);
}
ValToken(1, SEMI);
}
/* else fall thru */
case '\r': /* carriage return */
goto again;
case ' ': case '\t': case '\f': /* white space */
goto again;
case '#': /* preprocessor directive */
if (in_comment) goto again;
if (pp_mode)
{ last_token = PREPROC;
return pre_proc();
}
do_directive(c);
goto again;
case '\"':
getword(c, notquote);
if (Getchar() != '\"')
fatal("string not terminated", yytext);
strcat(yytext, "\"");
SymToken(lookup(yytext), STRING)
case '$':
getword('\"', notdollar);
if (Getchar() != '$')
fatal("ltl definition not terminated", yytext);
strcat(yytext, "\"");
SymToken(lookup(yytext), STRING)
case '\'': /* new 3.0.9 */
c = Getchar();
if (c == '\\')
{ c = Getchar();
if (c == 'n') c = '\n';
else if (c == 'r') c = '\r';
else if (c == 't') c = '\t';
else if (c == 'f') c = '\f';
}
if (Getchar() != '\'' && !in_comment)
fatal("character quote missing: %s", yytext);
ValToken(c, CONST)
default:
break;
}
if (isdigit_(c))
{ long int nr;
getword(c, isdigit_);
errno = 0;
nr = strtol(yytext, NULL, 10);
if (errno != 0)
{ fprintf(stderr, "spin: value out of range: '%s' read as '%d'\n",
yytext, (int) nr);
}
ValToken((int)nr, CONST)
}
if (isalpha_(c) || c == '_')
{ getword(c, isalnum_);
if (!in_comment)
{ c = check_name(yytext);
if (c)
{ last_token = c;
return c;
}
/* else fall through */
}
goto again;
}
if (ltl_mode)
{ switch (c) {
case '-': c = follow('>', IMPLIES, '-'); break;
case '[': c = follow(']', ALWAYS, '['); break;
case '<': c = follow('>', EVENTUALLY, '<');
if (c == '<')
{ c = Getchar();
if (c == '-')
{ c = follow('>', EQUIV, '-');
if (c == '-')
{ Ungetch(c);
c = '<';
}
} else
{ Ungetch(c);
c = '<';
} }
default: break;
} }
switch (c) {
case '/': c = follow('*', 0, '/');
if (!c) { in_comment = 1; goto again; }
break;
case '*': c = follow('/', 0, '*');
if (!c) { in_comment = 0; goto again; }
break;
case ':': c = follow(':', SEP, ':'); break;
case '-': c = follow('>', ARROW, follow('-', DECR, '-')); break;
case '+': c = follow('+', INCR, '+'); break;
case '<': c = follow('<', LSHIFT, follow('=', LE, LT)); break;
case '>': c = follow('>', RSHIFT, follow('=', GE, GT)); break;
case '=': c = follow('=', EQ, ASGN); break;
case '!': c = follow('=', NE, follow('!', O_SND, SND)); break;
case '?': c = follow('?', R_RCV, RCV); break;
case '&': c = follow('&', AND, '&'); break;
case '|': c = follow('|', OR, '|'); break;
case ';': c = SEMI; break;
case '.': c = follow('.', DOTDOT, '.'); break;
case '{': scope_seq[scope_level++]++; set_cur_scope(); break;
case '}': scope_level--; set_cur_scope(); break;
default : break;
}
ValToken(0, c)
}
void
moveloop()
{
#ifdef MICRO
char ch;
int abort_lev;
#endif
int moverate = 0;
boolean didmove = 0;
/* Note: these initializers don't do anything except guarantee that
we're linked properly.
*/
decl_init();
monst_init();
monstr_init(); /* monster strengths */
objects_init();
(void) encumber_msg(); /* in case they auto-picked up something */
for(;;) {
#ifdef CLIPPING
cliparound(u.ux, u.uy);
#endif
#if defined(MAC_MPW32) && !defined(MODEL_FAR)
UnloadAllSegments(); /* Marks non-resident segments as purgeable */
#endif
get_nh_event();
didmove = flags.move;
if(flags.move) { /* actual time passed */
#ifdef POLYSELF
int oldmtimedone;
#endif
int wtcap;
if (u.utotype) deferred_goto();
wtcap = encumber_msg();
#ifdef POLYSELF
oldmtimedone = u.mtimedone;
#endif
#ifdef SOUNDS
dosounds();
#endif
if(moverate <= 0) {
/* calculate how much time passed. */
int moveamt = 0;
if(Fast & ~INTRINSIC) moveamt = 6;
else if(Fast) moveamt = 8;
else moveamt = 12;
switch(wtcap) {
case UNENCUMBERED: break;
case SLT_ENCUMBER: moveamt = (moveamt * 4) / 3; break;
case MOD_ENCUMBER: moveamt *= 2; break;
case HVY_ENCUMBER: moveamt *= 4; break;
default: moveamt *= 12; break;
}
moverate += moveamt;
settrack();
}
if(moverate > 0) {
movemon();
/* a monster may have levteleported player -dlc */
if (u.utotype) deferred_goto();
if(!rn2(u.uevent.udemigod ? 25 :
(depth(&u.uz) >
depth(&stronghold_level))
? 50 : 70))
(void) makemon((struct permonst *)0, 0, 0);
++monstermoves;
remove_cadavers(&fobj);
remove_cadavers(&invent);
moverate -= 12;
}
if(Glib) glibr();
nh_timeout();
++moves;
if (u.ublesscnt) u.ublesscnt--;
if(flags.time) flags.botl = 1;
/* One possible result of prayer is healing. Whether or
* not you get healed depends on your current hit points.
* If you are allowed to regenerate during the prayer, the
* end-of-prayer calculation messes up on this.
*/
if (u.uinvulnerable)
;
else
#ifdef POLYSELF
if (u.mtimedone && u.mh < u.mhmax) {
if (u.mh < 1) {
rehumanize();
moverate = 0;
} else if (Regeneration ||
(wtcap < MOD_ENCUMBER && !(moves%20))) {
flags.botl = 1;
u.mh++;
}
} else
#endif
if(u.uhp < u.uhpmax) {
if(u.ulevel > 9) {
int heal;
if(HRegeneration ||
(!(moves%3) &&
(wtcap < MOD_ENCUMBER || !flags.mv))) {
flags.botl = 1;
if (ACURR(A_CON) <= 12) heal = 1;
else heal = rnd((int) ACURR(A_CON)-12);
if (heal > u.ulevel-9) heal = u.ulevel-9;
u.uhp += heal;
if(u.uhp > u.uhpmax)
u.uhp = u.uhpmax;
}
} else if(HRegeneration ||
((wtcap < MOD_ENCUMBER || !flags.mv) &&
(!(moves%((MAXULEV+12)/(u.ulevel+2)+1))))) {
flags.botl = 1;
u.uhp++;
}
}
if (wtcap > MOD_ENCUMBER && flags.mv) {
if(!(wtcap < EXT_ENCUMBER ? moves%30 : moves%10)) {
if(u.uhp > 1) {
u.uhp--;
} else {
pline("You pass out from exertion!");
exercise(A_CON, FALSE);
nomul(-10);
u.usleep = 1;
}
}
}
if ((u.uen < u.uenmax) &&
((wtcap < MOD_ENCUMBER &&
(!(moves%((MAXULEV + 1 - u.ulevel) *
(pl_character[0] == 'W' ? 3 : 4) / 2))))
|| Energy_regeneration)) {
u.uen +=
rn1((int)(ACURR(A_WIS) + ACURR(A_INT)) / 10 + 1,1);
if (u.uen > u.uenmax) u.uen = u.uenmax;
flags.botl = 1;
}
if(!u.uinvulnerable) {
if(Teleportation && !rn2(85)) {
#ifdef REDO /* clear doagain keystrokes */
pushch(0);
savech(0);
#endif
tele();
}
#ifdef POLYSELF
if(Polymorph && !rn2(100)) {
if (multi >= 0) {
if (occupation)
stop_occupation();
else
nomul(0);
}
polyself();
moverate = 0;
} else if (u.ulycn >= 0 && !rn2(80 - (20 * night()))) {
if (multi >= 0) {
if (occupation)
stop_occupation();
else
nomul(0);
}
you_were();
moverate = 0;
}
#endif
}
if(Searching && multi >= 0) (void) dosearch0(1);
do_storms();
hatch_eggs();
burn_lamps();
gethungry();
exerchk();
invault();
amulet();
if (!rn2(40+(int)(ACURR(A_DEX)*3)))
u_wipe_engr(rnd(3));
if (u.uevent.udemigod && !u.uinvulnerable) {
if (u.udg_cnt) u.udg_cnt--;
if (!u.udg_cnt) {
intervene();
u.udg_cnt = rn1(200, 50);
}
}
restore_attrib();
/* underwater and waterlevel vision are done here */
if (Is_waterlevel(&u.uz))
movebubbles();
else if (Underwater)
under_water(0);
#ifdef POLYSELF
if ((oldmtimedone && !u.mtimedone) ||
(!oldmtimedone && u.mtimedone)) moverate = 0;
#endif
}
if(multi < 0) {
if(!++multi){
pline("%s",nomovemsg ? nomovemsg :
(const char *)"You can move again.");
nomovemsg = 0;
u.usleep = 0;
if(afternmv) (*afternmv)();
afternmv = 0;
}
}
find_ac();
if(!flags.mv || Blind) {
/* redo monsters if hallu or wearing a helm of telepathy */
if (Hallucination ||
(HTelepat & (WORN_HELMET|WORN_AMUL|W_ART)))
see_monsters();
/* redo objects if hallucinating */
if (Hallucination) see_objects();
/* update swallowed display */
if (Hallucination && u.uswallow) swallowed(0);
if (vision_full_recalc) vision_recalc(0); /* vision! */
}
if(flags.botl || flags.botlx) bot();
flags.move = 1;
if(multi >= 0 && occupation) {
#ifdef MICRO
abort_lev = 0;
if (kbhit()) {
if ((ch = Getchar()) == ABORT)
abort_lev++;
# ifdef REDO
else
pushch(ch);
# endif /* REDO */
}
if (!abort_lev && (*occupation)() == 0)
#else
if ((*occupation)() == 0)
#endif
occupation = 0;
if(
#ifdef MICRO
abort_lev ||
#endif
monster_nearby()) {
stop_occupation();
reset_eat();
}
#ifdef MICRO
if (!(++occtime % 7))
display_nhwindow(WIN_MAP, FALSE);
#endif
continue;
}
if((u.uhave.amulet || Clairvoyant) && !In_endgame(&u.uz) &&
!(moves%15) && !rn2(2))
do_vicinity_map();
if(u.utrap && u.utraptype == TT_LAVA) {
if(!is_lava(u.ux,u.uy))
u.utrap = 0;
else {
u.utrap -= 1<<8;
if(u.utrap < 1<<8) {
killer_format = KILLED_BY;
killer = "molten lava";
You("sink below the surface and suffocate.");
done(DROWNING); /*whatever*/
} else if(didmove && !u.umoved) {
Norep("You sink deeper into the lava.");
u.utrap += rnd(4);
}
}
}
u.umoved = FALSE;
if(!didmove || moverate <= 0) {
if(multi > 0) {
lookaround();
if(!multi) { /* lookaround may clear multi */
flags.move = 0;
continue;
}
if(flags.mv) {
if(multi < COLNO && !--multi)
flags.mv = flags.run = 0;
domove();
} else {
--multi;
rhack(save_cm);
}
} else if(multi == 0) {
#ifdef MAIL
ckmailstatus();
#endif
rhack(NULL);
}
}
if (vision_full_recalc) vision_recalc(0); /* vision! */
if(multi && multi%7 == 0)
display_nhwindow(WIN_MAP, FALSE);
}
}
void
PrintMultiAlignT(FILE *out,
MultiAlignT *ma,
gkStore *frag_store,
int32 show_qv,
int32 dots,
uint32 clrrng_flag) {
int32 depth;
int32 i;
int32 window;
char **multia=NULL;
int32 **idarray;
int32 **oriarray;
char *consensus = Getchar(ma->consensus,0);
char *quality = Getchar(ma->quality,0);
gkFragment rsp;
dots = 0;
if ((consensus == NULL) || (consensus[0] == 0)) {
fprintf(out, "No MultiAlignment to print for tig %d -- no consensus sequence present.\n", ma->maID);
return;
}
int32 length = strlen(consensus);
IMP2Array(GetIntMultiPos(ma->f_list,0),
GetNumIntMultiPoss(ma->f_list),
GetNumchars(ma->consensus),
frag_store,
&depth,
&multia,
&idarray,
&oriarray,
clrrng_flag);
fprintf(out,"<<< begin Contig %d >>>",ma->maID);;
char gruler[MULTIALIGN_PRINT_WIDTH + 200];
char uruler[MULTIALIGN_PRINT_WIDTH + 200];
int32 ungapped = 1;
int32 tick = 1;
for (window=0;window<length;) {
int32 row_id = 0;
int32 orient = 0;
int32 rowlen = (window + MULTIALIGN_PRINT_WIDTH < length) ? MULTIALIGN_PRINT_WIDTH : length - window;
fprintf(out, "\n");
fprintf(out, "\n");
fprintf(out, "<<< Contig %d, gapped length: %d >>>\n",ma->maID, length);
{
memset(gruler, 0, MULTIALIGN_PRINT_WIDTH + 200);
memset(uruler, 0, MULTIALIGN_PRINT_WIDTH + 200);
for (int32 rowind=0; rowind<rowlen; rowind++) {
if (((window + 1 + rowind) % 25) == 0)
sprintf(gruler + rowind, "| GAP=%d", window + 1 + rowind);
if ((ungapped % 25) == 0)
sprintf(uruler + rowind, "| UNG=%d", ungapped);
if (consensus[window + rowind] != '-')
ungapped++;
}
for (int32 i=0; i<MULTIALIGN_PRINT_WIDTH; i++) {
if (gruler[i] == 0)
gruler[i] = ' ';
if (uruler[i] == 0)
uruler[i] = ' ';
}
for (int32 i=MULTIALIGN_PRINT_WIDTH-1; (i >= 0) && (gruler[i] == ' '); i--)
gruler[i] = 0;
for (int32 i=MULTIALIGN_PRINT_WIDTH-1; (i >= 0) && (uruler[i] == ' '); i--)
uruler[i] = 0;
fprintf(out, "%s\n", gruler);
fprintf(out, "%s\n", uruler);
}
{
char save = consensus[window + rowlen];
consensus[window+rowlen] = 0;
fprintf(out,"%s cns (uid,iid) type\n", consensus+window);
consensus[window+rowlen] = save;
}
{
char save = quality[window + rowlen];
quality[window+rowlen] = 0;
fprintf(out,"%s qlt\n", quality+window);
quality[window+rowlen] = save;
}
for (i=0;i<depth;i++) {
assert(multia[2*i] != NULL);
// Change matching bases to '.' or lowercase.
// Count the number of non-blank letters.
int32 nonBlank = 0;
for (int32 j=0; j<MULTIALIGN_PRINT_WIDTH; j++) {
if (window + j > length)
break;
if (multia[2*i][window+j] == consensus[window+j]) {
if (dots) {
multia[2*i] [window+j] = '.';
multia[2*i+1][window+j] = ' ';
} else {
multia[2*i][window+j] = tolower(multia[2*i][window+j]);
}
}
if (multia[2*i][window+j] != ' ')
nonBlank++;
if (idarray[i][window + j] > 0) {
row_id = idarray[i][window + j];
orient = oriarray[i][window + j];
}
}
if (nonBlank == 0)
continue;
// Figure out the ID and orientation for this block
frag_store->gkStore_getFragment(row_id, &rsp, GKFRAGMENT_INF);
{
char save = multia[2*i][window + MULTIALIGN_PRINT_WIDTH];
multia[2*i][window + MULTIALIGN_PRINT_WIDTH] = 0;
fprintf(out, "%s %c (%s,%d)\n",
multia[2*i]+window,
(orient>0)?'>':'<',
AS_UID_toString(rsp.gkFragment_getReadUID()),
row_id);
multia[2*i][window + MULTIALIGN_PRINT_WIDTH] = save;
}
if (show_qv) {
char save = multia[2*i+1][window + MULTIALIGN_PRINT_WIDTH];
multia[2*i+1][window + MULTIALIGN_PRINT_WIDTH] = 0;
fprintf(out, "%s\n", multia[2*i+1]+window);
multia[2*i+1][window + MULTIALIGN_PRINT_WIDTH] = save;
}
}
window += MULTIALIGN_PRINT_WIDTH;
}
fprintf(out,"\n<<< end Contig %d >>>\n", ma->maID);
for (i=0;i<2*depth;i++)
safe_free(multia[i]);
safe_free(multia);
for (i=0;i<depth;i++) {
safe_free(idarray[i]);
safe_free(oriarray[i]);
}
safe_free(idarray);
safe_free(oriarray);
}
Symbol *
prep_inline(Symbol *s, Lextok *nms)
{ int c, nest = 1, dln, firstchar, cnr;
char *p;
Lextok *t;
static char Buf1[SOMETHINGBIG], Buf2[RATHERSMALL];
static int c_code = 1;
for (t = nms; t; t = t->rgt)
if (t->lft)
{ if (t->lft->ntyp != NAME)
fatal("bad param to inline %s", s?s->name:"--");
t->lft->sym->hidden |= 32;
}
if (!s) /* C_Code fragment */
{ s = (Symbol *) emalloc(sizeof(Symbol));
s->name = (char *) emalloc(strlen("c_code")+26);
sprintf(s->name, "c_code%d", c_code++);
s->context = context;
s->type = CODE_FRAG;
} else
s->type = PREDEF;
p = &Buf1[0];
Buf2[0] = '\0';
for (;;)
{ c = Getchar();
switch (c) {
case '[':
if (s->type != CODE_FRAG)
goto bad;
precondition(&Buf2[0]); /* e.g., c_code [p] { r = p-r; } */
continue;
case '{':
break;
case '\n':
lineno++;
/* fall through */
case ' ': case '\t': case '\f': case '\r':
continue;
default :
printf("spin: saw char '%c'\n", c);
bad: fatal("bad inline: %s", s->name);
}
break;
}
dln = lineno;
if (s->type == CODE_FRAG)
{ if (verbose&32)
sprintf(Buf1, "\t/* line %d %s */\n\t\t",
lineno, Fname->name);
else
strcpy(Buf1, "");
} else
sprintf(Buf1, "\n#line %d \"%s\"\n{", lineno, Fname->name);
p += strlen(Buf1);
firstchar = 1;
cnr = 1; /* not zero */
more:
c = Getchar();
*p++ = (char) c;
if (p - Buf1 >= SOMETHINGBIG)
fatal("inline text too long", 0);
switch (c) {
case '\n':
lineno++;
cnr = 0;
#if 0
if (nest <= 0)
{ *--p = '\0';
}
#endif
break;
case '{':
cnr++;
nest++;
break;
case '}':
cnr++;
if (--nest <= 0)
{ *p = '\0';
if (s->type == CODE_FRAG)
*--p = '\0'; /* remove trailing '}' */
def_inline(s, dln, &Buf1[0], &Buf2[0], nms);
if (firstchar)
printf("%3d: %s, warning: empty inline definition (%s)\n",
dln, Fname->name, s->name);
return s; /* normal return */
}
break;
case '#':
if (cnr == 0)
{ p--;
do_directive(c); /* reads to newline */
} else
{ firstchar = 0;
cnr++;
}
break;
case '\t':
case ' ':
case '\f':
cnr++;
break;
default:
firstchar = 0;
cnr++;
break;
}
goto more;
}
void
moveloop()
{
#if defined(MICRO) || defined(WIN32)
char ch;
int abort_lev;
#endif
int moveamt = 0, wtcap = 0, change = 0;
boolean didmove = FALSE, monscanmove = FALSE;
flags.moonphase = phase_of_the_moon();
if(flags.moonphase == FULL_MOON) {
You("are lucky! Full moon tonight.");
change_luck(1);
} else if(flags.moonphase == NEW_MOON) {
pline("Be careful! New moon tonight.");
}
flags.friday13 = friday_13th();
if (flags.friday13) {
pline("Watch out! Bad things can happen on Friday the 13th.");
change_luck(-1);
}
/* KMH -- February 2 */
flags.groundhogday = groundhog_day();
if (flags.groundhogday)
pline("Happy Groundhog Day!");
initrack();
/* Note: these initializers don't do anything except guarantee that
we're linked properly.
*/
decl_init();
monst_init();
monstr_init(); /* monster strengths */
objects_init();
#ifdef WIZARD
if (wizard) add_debug_extended_commands();
#endif
(void) encumber_msg(); /* in case they auto-picked up something */
if (defer_see_monsters) {
defer_see_monsters = FALSE;
see_monsters();
}
u.uz0.dlevel = u.uz.dlevel;
youmonst.movement = NORMAL_SPEED; /* give the hero some movement points */
for(;;) {
get_nh_event();
#ifdef POSITIONBAR
do_positionbar();
#endif
didmove = flags.move;
if(didmove) {
/* actual time passed */
youmonst.movement -= NORMAL_SPEED;
do { /* hero can't move this turn loop */
wtcap = encumber_msg();
flags.mon_moving = TRUE;
do {
monscanmove = movemon();
if (youmonst.movement > NORMAL_SPEED)
break; /* it's now your turn */
} while (monscanmove);
flags.mon_moving = FALSE;
if (!monscanmove && youmonst.movement < NORMAL_SPEED) {
/* both you and the monsters are out of steam this round */
/* set up for a new turn */
struct monst *mtmp;
mcalcdistress(); /* adjust monsters' trap, blind, etc */
/* reallocate movement rations to monsters */
for (mtmp = fmon; mtmp; mtmp = mtmp->nmon)
mtmp->movement += mcalcmove(mtmp);
if(!rn2(u.uevent.udemigod ? 25 :
(depth(&u.uz) > depth(&stronghold_level)) ? 50 : 70))
(void) makemon((struct permonst *)0, 0, 0, NO_MM_FLAGS);
/* calculate how much time passed. */
#ifdef STEED
if (u.usteed && u.umoved) {
/* your speed doesn't augment steed's speed */
moveamt = mcalcmove(u.usteed);
} else
#endif
{
moveamt = youmonst.data->mmove;
if (Very_fast) { /* speed boots or potion */
/* average movement is 1.67 times normal */
moveamt += NORMAL_SPEED / 2;
if (rn2(3) == 0) moveamt += NORMAL_SPEED / 2;
} else if (Fast) {
/* average movement is 1.33 times normal */
if (rn2(3) != 0) moveamt += NORMAL_SPEED / 2;
}
if (tech_inuse(T_BLINK)) { /* TECH: Blinking! */
/* Case Average Variance
* -------------------------
* Normal 12 0
* Fast 16 12
* V fast 20 12
* Blinking 24 12
* F & B 28 18
* V F & B 30 18
*/
moveamt += NORMAL_SPEED * 2 / 3;
if (rn2(3) == 0) moveamt += NORMAL_SPEED / 2;
}
}
switch (wtcap) {
case UNENCUMBERED: break;
case SLT_ENCUMBER: moveamt -= (moveamt / 4); break;
case MOD_ENCUMBER: moveamt -= (moveamt / 2); break;
case HVY_ENCUMBER: moveamt -= ((moveamt * 3) / 4); break;
case EXT_ENCUMBER: moveamt -= ((moveamt * 7) / 8); break;
default: break;
}
youmonst.movement += moveamt;
if (youmonst.movement < 0) youmonst.movement = 0;
settrack();
monstermoves++;
moves++;
/********************************/
/* once-per-turn things go here */
/********************************/
if (flags.bypasses) clear_bypasses();
if(Glib) glibr();
nh_timeout();
run_regions();
#ifdef DUNGEON_GROWTH
dgn_growths(TRUE, TRUE);
#endif
if (u.ublesscnt) u.ublesscnt--;
if(flags.time && !flags.run)
flags.botl = 1;
/* One possible result of prayer is healing. Whether or
* not you get healed depends on your current hit points.
* If you are allowed to regenerate during the prayer, the
* end-of-prayer calculation messes up on this.
* Another possible result is rehumanization, which requires
* that encumbrance and movement rate be recalculated.
*/
if (u.uinvulnerable) {
/* for the moment at least, you're in tiptop shape */
wtcap = UNENCUMBERED;
} else if (Upolyd && youmonst.data->mlet == S_EEL && !is_pool(u.ux,u.uy) && !Is_waterlevel(&u.uz)) {
if (u.mh > 1) {
u.mh--;
flags.botl = 1;
} else if (u.mh < 1)
rehumanize();
} else if (Upolyd && u.mh < u.mhmax) {
if (u.mh < 1)
rehumanize();
else if (Regeneration ||
(wtcap < MOD_ENCUMBER && !(moves%20))) {
flags.botl = 1;
u.mh++;
}
} else if (u.uhp < u.uhpmax &&
(wtcap < MOD_ENCUMBER || !u.umoved || Regeneration)) {
/*
* KMH, balance patch -- New regeneration code
* Healthstones have been added, which alter your effective
* experience level and constitution (-2 cursed, +1 uncursed,
* +2 blessed) for the basis of regeneration calculations.
*/
int efflev = u.ulevel + u.uhealbonus;
int effcon = ACURR(A_CON) + u.uhealbonus;
int heal = 1;
if (efflev > 9 && !(moves % 3)) {
if (effcon <= 12) {
heal = 1;
} else {
heal = rnd(effcon);
if (heal > efflev-9) heal = efflev-9;
}
flags.botl = 1;
u.uhp += heal;
if(u.uhp > u.uhpmax)
u.uhp = u.uhpmax;
} else if (Regeneration ||
(efflev <= 9 &&
!(moves % ((MAXULEV+12) / (u.ulevel+2) + 1)))) {
flags.botl = 1;
u.uhp++;
}
}
if (!u.uinvulnerable && u.uen > 0 && u.uhp < u.uhpmax &&
tech_inuse(T_CHI_HEALING)) {
u.uen--;
u.uhp++;
flags.botl = 1;
}
/* moving around while encumbered is hard work */
if (wtcap > MOD_ENCUMBER && u.umoved) {
if(!(wtcap < EXT_ENCUMBER ? moves%30 : moves%10)) {
if (Upolyd && u.mh > 1) {
u.mh--;
} else if (!Upolyd && u.uhp > 1) {
u.uhp--;
} else {
You("pass out from exertion!");
exercise(A_CON, FALSE);
fall_asleep(-10, FALSE);
}
}
}
/* KMH -- OK to regenerate if you don't move */
if ((u.uen < u.uenmax) && (Energy_regeneration ||
((wtcap < MOD_ENCUMBER || !flags.mv) &&
(!(moves%((MAXULEV + 15 - u.ulevel) *
(Role_if(PM_WIZARD) ? 3 : 4) / 6)))))) {
u.uen += rn1((int)(ACURR(A_WIS) + ACURR(A_INT)) / 15 + 1,1);
#ifdef WIZ_PATCH_DEBUG
pline("mana was = %d now = %d",temp,u.uen);
#endif
if (u.uen > u.uenmax) u.uen = u.uenmax;
flags.botl = 1;
}
if(!u.uinvulnerable) {
if(Teleportation && !rn2(85)) {
xchar old_ux = u.ux, old_uy = u.uy;
tele();
if (u.ux != old_ux || u.uy != old_uy) {
if (!next_to_u()) {
check_leash(&youmonst, old_ux, old_uy, TRUE);
}
#ifdef REDO
/* clear doagain keystrokes */
pushch(0);
savech(0);
#endif
}
}
long ch = (80 - (40 * night())) / 2 *
(Race_if(PM_HUMAN_WEREWOLF) ?
u.ulevel * u.ulevel :
2);
ch = (ch > LARGEST_INT) ? LARGEST_INT : ch;
/* delayed change may not be valid anymore */
if ((change == 1 && !Polymorph) ||
(change == 2 && u.ulycn == NON_PM))
change = 0;
if(Polymorph && !rn2(100))
change = 1;
else if (u.ulycn >= LOW_PM && !Upolyd &&
!rn2((int)ch))
change = 2;
if (change && !Unchanging) {
if (multi >= 0) {
if (occupation)
stop_occupation();
else
nomul(0);
if (change == 1) polyself(FALSE);
else you_were();
change = 0;
}
}
} /* !u.uinvulnerable */
if(Searching && multi >= 0) (void) dosearch0(1);
dosounds();
do_storms();
gethungry();
age_spells();
exerchk();
invault();
if (u.uhave.amulet) amulet();
if (!rn2(40+(int)(ACURR(A_DEX)*3))) u_wipe_engr(rnd(3));
if (u.uevent.udemigod && !u.uinvulnerable) {
if (u.udg_cnt) u.udg_cnt--;
if (!u.udg_cnt) {
intervene();
u.udg_cnt = rn1(200, 50);
}
}
restore_attrib();
/* underwater and waterlevel vision are done here */
if (Is_waterlevel(&u.uz))
movebubbles();
else if (Underwater)
under_water(0);
/* vision while buried done here */
else if (u.uburied) under_ground(0);
/* when immobile, count is in turns */
if(multi < 0) {
if (++multi == 0) { /* finished yet? */
unmul((char *)0);
/* if unmul caused a level change, take it now */
if (u.utotype) deferred_goto();
}
}
}
} while (youmonst.movement<NORMAL_SPEED); /* hero can't move loop */
/******************************************/
/* once-per-hero-took-time things go here */
/******************************************/
} /* actual time passed */
/****************************************/
/* once-per-player-input things go here */
/****************************************/
find_ac();
if(!flags.mv || Blind) {
/* redo monsters if hallu or wearing a helm of telepathy */
if (Hallucination) { /* update screen randomly */
see_monsters();
see_objects();
see_traps();
if (u.uswallow) swallowed(0);
} else if (Unblind_telepat) {
see_monsters();
} else if (Warning || Warn_of_mon)
see_monsters();
if (vision_full_recalc) vision_recalc(0); /* vision! */
}
if(flags.botl || flags.botlx) bot();
flags.move = 1;
if(multi >= 0 && occupation) {
#if defined(MICRO) || defined(WIN32)
abort_lev = 0;
if (kbhit()) {
if ((ch = Getchar()) == ABORT)
abort_lev++;
# ifdef REDO
else
pushch(ch);
# endif /* REDO */
}
if (!abort_lev && (*occupation)() == 0)
#else
if ((*occupation)() == 0)
#endif
occupation = 0;
if(
#if defined(MICRO) || defined(WIN32)
abort_lev ||
#endif
monster_nearby()) {
stop_occupation();
reset_eat();
}
#if defined(MICRO) || defined(WIN32)
if (!(++occtime % 7))
display_nhwindow(WIN_MAP, FALSE);
#endif
continue;
}
if ((u.uhave.amulet || Clairvoyant) &&
!In_endgame(&u.uz) && !BClairvoyant &&
!(moves % 15) && !rn2(2))
do_vicinity_map();
if(u.utrap && u.utraptype == TT_LAVA) {
if(!is_lava(u.ux,u.uy))
u.utrap = 0;
else if (!u.uinvulnerable) {
u.utrap -= 1<<8;
if(u.utrap < 1<<8) {
killer_format = KILLED_BY;
killer = "molten lava";
You("sink below the surface and die.");
done(DISSOLVED);
} else if(didmove && !u.umoved) {
Norep("You sink deeper into the lava.");
u.utrap += rnd(4);
}
}
}
#ifdef WIZARD
if (iflags.sanity_check)
sanity_check();
#endif
#ifdef CLIPPING
/* just before rhack */
cliparound(u.ux, u.uy);
#endif
u.umoved = FALSE;
if (multi > 0) {
lookaround();
if (!multi) {
/* lookaround may clear multi */
flags.move = 0;
if (flags.time) flags.botl = 1;
continue;
}
if (flags.mv) {
if(multi < COLNO && !--multi)
flags.travel = iflags.travel1 = flags.mv = flags.run = 0;
domove();
} else {
--multi;
rhack(save_cm);
}
} else if (multi == 0) {
#ifdef MAIL
ckmailstatus();
#endif
rhack((char *)0);
}
if (u.utotype) /* change dungeon level */
deferred_goto(); /* after rhack() */
/* !flags.move here: multiple movement command stopped */
else if (flags.time && (!flags.move || !flags.mv))
flags.botl = 1;
if (vision_full_recalc) vision_recalc(0); /* vision! */
/* when running in non-tport mode, this gets done through domove() */
if ((!flags.run || iflags.runmode == RUN_TPORT) &&
(multi && (!flags.travel ? !(multi % 7) : !(moves % 7L)))) {
if (flags.time && flags.run) flags.botl = 1;
display_nhwindow(WIN_MAP, FALSE);
}
}
}
