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NCBI C++ ToolKit: src/algo/structure/threader/thrdatd.c Source File

38 #pragma warning(disable:4244) 39 #pragma warning(disable:4018) 70  double

ScalingFactor,

float

PSSM_Weight) {

149  for

(

i

=0;

i

<(cdf->

sll

.

n

-1);

i

++) {

151  if

((qsq->

sac

.

mn

[

i

] > 0) && (qsq->

sac

.

mn

[

i

+1] > 0)) {

155

dist = (

int

) ((

double

)dist * 1.5);

156  if

(dist > cdf->

lll

.

llmx

[

i

+1]) {

170  for

(

i

=0;

i

<(cdf->

sll

.

n

-2);

i

++) {

173  if

((qsq->

sac

.

mn

[

i

] > 0) && (qsq->

sac

.

mn

[

i

+1] <= 0) && (qsq->

sac

.

mn

[

i

+2] > 0)) {

179  if

((dist - dist2) > cdf->

lll

.

llmx

[

i

+1]) {

180

cdf->

lll

.

llmx

[

i

+1] = dist - dist2;

182  if

((dist - dist2) > cdf->

lll

.

llmx

[

i

+2]) {

183

cdf->

lll

.

llmx

[

i

+2] = dist - dist2;

201

printf(

"nsc %d\n"

,nsc);

202

printf(

"nmt %d\n"

,nmt);

203

printf(

"nlp %d\n"

,nlp);

206

printf(

"nrt %d\n"

,nrt);

207

printf(

"ndi %d\n"

,ndi);

232

printf(

"allocated threading data structures\n"

);

242

sli->

no

=(

int

*)

calloc

(nsc,

sizeof

(

int

));

243

sli->

co

=(

int

*)

calloc

(nsc,

sizeof

(

int

));

244

sli->

lp

=(

int

*)

calloc

(nsc+1,

sizeof

(

int

));

245

sli->

cr

=(

int

*)

calloc

(nmt,

sizeof

(

int

));

248

printf(

"sli->nsc:%d nlp:%d nmt%d\n"

,sli->

nsc

,sli->

nlp

,sli->

nmt

);

249 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sli->

no

[

i

]); printf(

"sli->no\n"

);

250 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sli->

co

[

i

]); printf(

"sli->co\n"

);

251 for

(

i

=0;

i

<nlp;

i

++) printf(

"%d "

,sli->

lp

[

i

]); printf(

"sli->lp\n"

);

252 for

(

i

=0;

i

<nmt;

i

++) printf(

"%d "

,sli->

cr

[

i

]); printf(

"sli->cr\n"

);

258

sai->

al

=(

int

*)

calloc

(nsc,

sizeof

(

int

));

259

sai->

sq

=(

int

*)

calloc

(nmt,

sizeof

(

int

));

260

sai->

cf

=(

int

*)

calloc

(nmt,

sizeof

(

int

));

263

printf(

"sai->nsc:%d nmt%d\n"

,sai->

nsc

,sai->

nmt

);

264 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sai->

al

[

i

]); printf(

"sai->al\n"

);

265 for

(

i

=0;

i

<nmt;

i

++) printf(

"%d "

,sai->

sq

[

i

]); printf(

"sai->sq\n"

);

271

spe->

gss

=

calloc

(nsc,

sizeof

(

int

*));

272  for

(

i

=0;

i

<nsc;

i

++) spe->

gss

[

i

]=

calloc

(nsc,

sizeof

(

int

));

273

spe->

gs

=

calloc

(nsc,

sizeof

(

int

));

274

spe->

ms

=

calloc

(nsc,

sizeof

(

int

));

275

spe->

cs

=

calloc

(nsc,

sizeof

(

int

));

276

spe->

ls

=

calloc

(nsc,

sizeof

(

int

));

277

spe->

s0

=

calloc

(nsc,

sizeof

(

int

));

280 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,spe->

gs

[

i

]); printf(

"spe->gs\n"

);

281 for

(j=0; j<nsc; j++) {

282  for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,spe->

gss

[j][

i

]);

283

printf(

"spe->gss[%d]\n"

,j); }

290

spn->

nrr

=

calloc

(ndi,

sizeof

(

int

**));

291  for

(

i

=0;

i

<ndi;

i

++) spn->

nrr

[

i

]=

calloc

(nsc,

sizeof

(

int

*));

292  for

(

i

=0;

i

<ndi;

i

++)

for

(j=0; j<nsc; j++)

293

spn->

nrr

[

i

][j]=

calloc

(nsc,

sizeof

(

int

));

294

spn->

srr

=

calloc

(ndi,

sizeof

(

int

));

295

spn->

nrp

=

calloc

(ndi,

sizeof

(

int

**));

296  for

(

i

=0;

i

<ndi;

i

++) spn->

nrp

[

i

]=

calloc

(nsc,

sizeof

(

int

*));

297  for

(

i

=0;

i

<ndi;

i

++)

for

(j=0; j<nsc; j++)

298

spn->

nrp

[

i

][j]=

calloc

(nsc,

sizeof

(

int

));

299

spn->

srp

=

calloc

(ndi,

sizeof

(

int

));

300

spn->

nrf

=

calloc

(ndi,

sizeof

(

int

**));

301  for

(

i

=0;

i

<ndi;

i

++) spn->

nrf

[

i

]=

calloc

(nsc,

sizeof

(

int

*));

302  for

(

i

=0;

i

<ndi;

i

++)

for

(j=0; j<nsc; j++)

303

spn->

nrf

[

i

][j]=

calloc

(nrt,

sizeof

(

int

));

304

spn->

frf

=

calloc

(ndi,

sizeof

(

int

*));

305 for

(

i

=0;

i

<ndi;

i

++) spn->

frf

[

i

]=

calloc

(nrt,

sizeof

(

int

));

306

spn->

srf

=

calloc

(ndi,

sizeof

(

int

));

309

printf(

"spn->ndi:%d nsc:%d nrt%d\n"

,spn->

ndi

,spn->

nsc

,spn->

nrt

);

310 for

(k=0; k<ndi; k++)

for

(j=0; j<nsc; j++) {

311  for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,spn->

nrr

[k][j][

i

]);

312

printf(

"spn->nrr[%d][%d]\n"

,k,j); }

313 for

(

i

=0;

i

<ndi;

i

++) printf(

"%d "

,spn->

srr

[

i

]); printf(

"spn->srr\n"

);

314 for

(k=0; k<ndi; k++)

for

(j=0; j<nsc; j++) {

315  for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,spn->

nrp

[k][j][

i

]);

316

printf(

"spn->nrp[%d][%d]\n"

,k,j); }

317 for

(

i

=0;

i

<ndi;

i

++) printf(

"%d "

,spn->

srp

[

i

]); printf(

"spn->srp\n"

);

318 for

(k=0; k<ndi; k++)

for

(j=0; j<nsc; j++) {

319  for

(

i

=0;

i

<nrt;

i

++) printf(

"%d "

,spn->

nrf

[k][j][

i

]);

320

printf(

"spn->nrf[%d][%d]\n"

,k,j); }

321 for

(j=0; j<ndi; j++) {

322  for

(

i

=0;

i

<nrt;

i

++) printf(

"%d "

,spn->

frf

[j][

i

]);

323

printf(

"spn->frf[%d]\n"

,j); }

324 for

(

i

=0;

i

<ndi;

i

++) printf(

"%d "

,spn->

srf

[

i

]); printf(

"spn->srf\n"

);

330

spc->

srt

=

calloc

(nsc,

sizeof

(

int

*));

331  for

(

i

=0;

i

<nsc;

i

++) spc->

srt

[

i

]=

calloc

(nrt,

sizeof

(

int

));

333

spc->

lrt

=

calloc

(nlp,

sizeof

(

int

*));

334  for

(

i

=0;

i

<nlp;

i

++) spc->

lrt

[

i

]=

calloc

(nrt,

sizeof

(

int

));

335

spc->

rt

=

calloc

(nrt,

sizeof

(

int

));

336

spc->

rto

=

calloc

(nrt,

sizeof

(

int

));

339

printf(

"spc->nsc:%d nrt:%d nlp:%d\n"

,spc->

nsc

,spc->

nrt

,spc->

nlp

);

340 for

(j=0; j<nsc; j++) {

341  for

(

i

=0;

i

<nrt;

i

++) printf(

"%d "

,spc->

srt

[j][

i

]);

342

printf(

"spc->srt[%d]\n"

,j); }

343 for

(j=0; j<nlp; j++) {

344  for

(

i

=0;

i

<nrt;

i

++) printf(

"%d "

,spc->

lrt

[j][

i

]);

345

printf(

"spc->lrt[%d]\n"

,j); }

346 for

(

i

=0;

i

<nrt;

i

++) printf(

"%d "

,spc->

rt

[

i

]); printf(

"spc->rt\n"

);

347 for

(

i

=0;

i

<nrt;

i

++) printf(

"%d "

,spc->

rto

[

i

]); printf(

"spc->rto\n"

);

353

cxe->

rp

=

calloc

(nrt,

sizeof

(

float

));

354

cxe->

rrp

=

calloc

(nrt,

sizeof

(

float

*));

355  for

(

i

=0;

i

<nrt;

i

++) cxe->

rrp

[

i

]=

calloc

(

i

+1,

sizeof

(

float

));

356

cxe->

rre

=

calloc

(ndi,

sizeof

(

float

));

357

cxe->

rpe

=

calloc

(ndi,

sizeof

(

float

));

358

cxe->

rfe

=

calloc

(ndi,

sizeof

(

float

));

361

printf(

"cxe->nrt:%d ndi:%d\n"

,cxe->

nrt

,cxe->

ndi

);

362 for

(

i

=0;

i

<nrt;

i

++) printf(

"%.4f "

,cxe->

rp

[

i

]); printf(

"cxe->rp\n"

);

363 for

(j=0; j<nrt; j++) {

364  for

(

i

=0;

i

<nrt;

i

++) printf(

"%.4f "

,cxe->

rrp

[j][

i

]);

365

printf(

"cxe->rrp[%d]\n"

,j); }

366 for

(

i

=0;

i

<ndi;

i

++) printf(

"%.4f "

,cxe->

rre

[

i

]); printf(

"cxe->rre\n"

);

367 for

(

i

=0;

i

<ndi;

i

++) printf(

"%.4f "

,cxe->

rpe

[

i

]); printf(

"cxe->rpe\n"

);

368 for

(

i

=0;

i

<ndi;

i

++) printf(

"%.4f "

,cxe->

rfe

[

i

]); printf(

"cxe->rfe\n"

);

373

sgo->

si

=(

int

*)

calloc

(nsc,

sizeof

(

int

));

374

sgo->

so

=(

int

*)

calloc

(nsc,

sizeof

(

int

));

375

sgo->

to

=(

int

*)

calloc

(nsc,

sizeof

(

int

));

378

printf(

"sgo->nsc:%d\n"

,sgo->

nsc

);

379 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sgo->

si

[

i

]); printf(

"sgo->si\n"

);

380 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sgo->

so

[

i

]); printf(

"sgo->so\n"

);

381 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sgo->

to

[

i

]); printf(

"sgo->to\n"

);

387

pvl->

p

=(

float

*)

calloc

(qsq->

n

,

sizeof

(

float

));

388

pvl->

e

=(

float

*)

calloc

(qsq->

n

,

sizeof

(

float

));

389

pvl->

sq

=(

int

*)

calloc

(qsq->

n

,

sizeof

(

int

));

390

pvl->

aqi

=(

int

*)

calloc

(qsq->

n

,

sizeof

(

int

));

391

pvl->

r

=(

int

*)

calloc

(qsq->

n

,

sizeof

(

int

));

392

pvl->

o

=(

int

*)

calloc

(qsq->

n

,

sizeof

(

int

));

393

pvl->

lsg

=(

int

*)

calloc

(nsc+1,

sizeof

(

int

));

398

tts->

bw

=(

float

*)

calloc

(tts->

nw

,

sizeof

(

float

));

399

tts->

nb

=0;

for

(

i

=0;

i

<gsp->

nts

;

i

++) {

400  if

(tts->

nb

<gsp->

nti

[

i

]) tts->

nb

=gsp->

nti

[

i

];

402

printf(

"nts=%d nti=%d tts->nb=%d\n"

,

i

,gsp->

nti

[

i

],tts->

nb

);

405

tts->

ib

=(

float

*)

calloc

(tts->

nb

,

sizeof

(

float

));

409 cprl

(mtf,cdf,pmf,cpr,0);

412  for

(

i

=0;

i

<nsc;

i

++) {

414

printf(

"rr:%d rp:%d rf:%d cpr[%d]\n"

,cr->

rr

.

n

,cr->

rp

.

n

,cr->

rf

.

n

,

i

); }

419 for

(

i

=0;

i

<nsc;

i

++) {

429

cr->

rf

.

d

=

calloc

(cr->

rf

.

n

,

sizeof

(

int

)); } }

432 cprl

(mtf,cdf,pmf,cpr,1);

435 for

(

i

=0;

i

<nsc;

i

++) {

437

printf(

"rr:%d rp:%d rf:%d cpr[%d]\n"

,cr->

rr

.

n

,cr->

rp

.

n

,cr->

rf

.

n

,

i

); }

441 for

(

i

=0;

i

<nsc;

i

++) {

442

cl=cpl[

i

]; cr=cpr[

i

];

458 for

(

i

=0;

i

<nsc;

i

++) {

460  n

=cpr[

i

]->

rr

.

n

;

465

ca->

r

.r=

calloc

(

n

,

sizeof

(

int

));

466

ca->

r

.e=

calloc

(

n

,

sizeof

(

int

*));

467  for

(j=0;j<

n

;j++) ca->

r

.e[j]=

calloc

(nrt,

sizeof

(

int

));}

483

printf(

"ttb->n: %d mx: %d mn: %d\n"

,ttb->

n

,ttb->

mx

,ttb->

mn

);

484 for

(

i

=0;

i

<ttb->

n

;

i

++) printf(

"i:%d tg:%.4f tf:%d pr:%d nx:%d\n"

,

485  i

,ttb->

tg

[

i

],ttb->

tf

[

i

],ttb->

pr

[

i

],ttb->

nx

[

i

]);

492 for

(nrs=0;nrs<gsp->

nrs

;nrs++) {

494

printf(

"nrs:%d\n"

,nrs);

500 for

(

i

=0;

i

<nsc;

i

++) { sli->

no

[

i

]=-1; sli->

co

[

i

]=-1; }

503 for

(

i

=0;

i

<nmt;

i

++) sli->

cr

[

i

]=-1;

506 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sli->

no

[

i

]); printf(

"sli->no\n"

);

507 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sli->

co

[

i

]); printf(

"sli->co\n"

);

508 for

(

i

=0;

i

<nlp;

i

++) printf(

"%d "

,sli->

lp

[

i

]); printf(

"sli->lp\n"

);

509 for

(

i

=0;

i

<nmt;

i

++) printf(

"%d "

,sli->

cr

[

i

]); printf(

"sli->cr\n"

);

517

printf(

"gsp->iso: %d gsp->ito: %d\n"

,gsp->

iso

,gsp->

ito

);

518 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sgo->

si

[

i

]); printf(

"sgo->si\n"

);

519 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sgo->

so

[

i

]); printf(

"sgo->so\n"

);

520 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sgo->

to

[

i

]); printf(

"sgo->to\n"

);

524 for

(

i

=0;

i

<nsc;

i

++) {

532  switch

(j) {

case

0: {

ct

=sgo->

to

[cs];

534  case

1: {

ct

=(sgo->

to

[cs]==0) ? 1:0;

540  if

(!

slo0

(mtf,cdf,qsq,sli,cs,

ct

,&mn,&mx)) {

541

printf(

"slo0 failed at nrs:%d cs:%d ct:%d\n"

,nrs,cs,

ct

);

555  switch

(gsp->

isl

) {

573  for

(k=0;k<pvl->

n

;k++)

574

pvl->

p

[k]=1./pvl->

n

;

575

sli->

no

[cs]=mn+

rsmp

(pvl);

579  for

(k=0;k<pvl->

n

;k++)

580

pvl->

p

[k]=1./pvl->

n

;

581

sli->

co

[cs]=mn+

rsmp

(pvl);

618 for

(

i

=0;

i

<nsc;

i

++) {

621  for

(j=mn; j<=mx; j++) sli->

cr

[j]=

i

;

627 for

(

i

=1;

i

<nsc;

i

++) {

630

sli->

lp

[

i

]=mtf->

mll

[mn][mx]; }

636 for

(

i

=0;

i

<nsc;

i

++) sai->

al

[

i

]=-1;

642 for

(

i

=0;

i

<nsc;

i

++) { cs=sgo->

si

[

i

];

648  if

(!

sal0

(cdf,qsq,sli,sai,cs,&mn,&mx)) {

649

printf(

"failed sal0 nrs:%d cs:%d\n"

,nrs,cs);

663  for

(j=0;j<pvl->

n

;j++) pvl->

p

[j]=1./pvl->

n

;

664

sai->

al

[cs]=mn+

rsmp

(pvl);

671 for

(

i

=0;

i

<nsc;

i

++) {

672

mn=sai->

al

[

i

]-sli->

no

[

i

];

673

mx=sai->

al

[

i

]+sli->

co

[

i

];

675  for

(k=mn; k<=mx; k++) {

676

sai->

sq

[j]=qsq->

sq

[k];

681 for

(

i

=0;

i

<nsc;

i

++)

spci

(cdf,qsq,sli,sai,

i

,spc);

696 for

(

i

=0;

i

<nsc;

i

++)

spni

(cpr,sli,

i

,spn);

718 cxei

(spn,spc,pmf,sli,psm,cdf,cxe);

731 cpll

(cdf,pmf,qsq,cpr,sai,cpl);

734 for

(

i

=0;

i

<nsc;

i

++)

spel

(cpl,sai,sli,

i

,spe,cdf,psm,spc);

742 dgri

(spe,spn,cxe,tdg,psm,spc);

746 ttbi

(sai,sli,tdg,ttb,nrs,gsp->

als

);

749 if

(gsp->

trg

!=0) { trg[ngs]=tdg->

dg

; ngs++; }

774 for

(nts=0;nts<gsp->

nts

;nts++) {

777  for

(nti=0;nti<gsp->

nti

[nts];nti++) {

782  if

(gsp->

nac

[nts]>0) {

785  cpal

(pmf,cpr,sli,cpa);

788  for

(

i

=0;

i

<nsc;

i

++)

spea

(cdf,cpa,sai,sli,

i

,1,spe,psm,spc);

795  for

(nac=0;nac<gsp->

nac

[nts];nac++) {

802  for

(

i

=0;

i

<nsc;

i

++) { cs=sgo->

si

[

i

];

805  if

(

salr

(cdf,qsq,sli,sai,cs,&mn,&mx)==0) {

806

printf(

"failed salr nrs:%d, nts:%d nti:%d cs:%d\n"

,

809 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sai->

al

[

i

]); printf(

"sai->al\n"

);

810 for

(

i

=0;

i

<sai->

nmt

;

i

++) printf(

"%d "

,sai->

sq

[

i

]); printf(

"sai->sq\n"

);

812 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sli->

no

[

i

]); printf(

"sli->no\n"

);

813 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sli->

co

[

i

]); printf(

"sli->co\n"

);

814 for

(

i

=0;

i

<sli->

nlp

;

i

++) printf(

"%d "

,sli->

lp

[

i

]); printf(

"sli->lp\n"

);

815 for

(

i

=0;

i

<sli->

nmt

;

i

++) printf(

"%d "

,sli->

cr

[

i

]); printf(

"sli->cr\n"

);

823  for

(j=0; j<=mx-mn; j++) { al=mn+j;

826  salu

(cdf,qsq,sli,cs,al,sai);

830  spea

(cdf,cpa,sai,sli,cs,1,spe,psm,spc);

834

spcd=

spci

(cdf,qsq,sli,sai,cs,spc);

838  if

(spcd!=0)

cxei

(spn,spc,pmf,sli,psm,cdf,cxe);

841

pvl->

e

[j]=

dgri

(spe,spn,cxe,tdg,psm,spc);

846

al=mn+

algs

(pvl,gsp->

tma

[nts]);

849  salu

(cdf,qsq,sli,cs,al,sai);

853  spea

(cdf,cpa,sai,sli,cs,1,spe,psm,spc);

856

spcd=

spci

(cdf,qsq,sli,sai,cs,spc);

859  if

(spcd)

cxei

(spn,spc,pmf,sli,psm,cdf,cxe);

862  dgri

(spe,spn,cxe,tdg,psm,spc);

867  ttbi

(sai,sli,tdg,ttb,nrs,gsp->

als

);

870  if

(tdg->

dg

>tts->

ib

[nti]) tts->

ib

[nti]=tdg->

dg

;

873  if

(gsp->

trg

!=0) { trg[ngs]=tts->

ib

[nti]; ngs++; }

929  if

(gsp->

nlc

[nts]>0) {

932  cpll

(cdf,pmf,qsq,cpr,sai,cpl);

935  for

(

i

=0;

i

<nsc;

i

++)

spel

(cpl,sai,sli,

i

,spe,cdf,psm,spc);

942  for

(nlc=0;nlc<gsp->

nlc

[nts];nlc++) {

948  for

(

i

=0;

i

<nsc;

i

++) { cs=sgo->

si

[

i

];

953  switch

(j) {

case

0: {

ct

=sgo->

to

[cs];

955  case

1: {

ct

=(sgo->

to

[cs]==0) ? 1:0;

960  if

(

slor

(mtf,cdf,qsq,sli,sai,cs,

ct

,&mn,&mx)==0) {

961

printf(

"failed slor nrs:%d nts:%d nti:%d cs:%d ct:%d\n"

,

962

nrs,nts,nti,cs,

ct

);

964 for

(k=0;k<nsc;k++) printf(

"%d "

,sai->

al

[k]); printf(

"sai->al\n"

);

965 for

(k=0;k<nmt;k++) printf(

"%d "

,sai->

sq

[k]); printf(

"sai->sq\n"

);

967 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sli->

no

[

i

]); printf(

"sli->no\n"

);

968 for

(

i

=0;

i

<nsc;

i

++) printf(

"%d "

,sli->

co

[

i

]); printf(

"sli->co\n"

);

969 for

(

i

=0;

i

<nlp;

i

++) printf(

"%d "

,sli->

lp

[

i

]); printf(

"sli->lp\n"

);

970 for

(

i

=0;

i

<nmt;

i

++) printf(

"%d "

,sli->

cr

[

i

]); printf(

"sli->cr\n"

);

978  for

(k=0; k<=mx-mn; k++) { of=mn+k;

981  slou

(mtf,cdf,cs,

ct

,of,sli,sai,qsq);

986  spel

(cpl,sai,sli,cs,spe,cdf,psm,spc);

989  spci

(cdf,qsq,sli,sai,cs,spc);

992  if

(PSSM_Weight < 0.9999999) {

993  spni

(cpl,sli,cs,spn);

997  cxei

(spn,spc,pmf,sli,psm,cdf,cxe);

1000

pvl->

e

[k]=

dgri

(spe,spn,cxe,tdg,psm,spc);

1004

of=mn+

algs

(pvl,gsp->

tml

[nts]);

1007  slou

(mtf,cdf,cs,

ct

,of,sli,sai,qsq);

1012  spel

(cpl,sai,sli,cs,spe,cdf,psm,spc);

1015  spci

(cdf,qsq,sli,sai,cs,spc);

1018  if

(PSSM_Weight < 0.9999999) {

1019  spni

(cpl,sli,cs,spn);

1023  cxei

(spn,spc,pmf,sli,psm,cdf,cxe);

1026  dgri

(spe,spn,cxe,tdg,psm,spc); } }

1029  ttbi

(sai,sli,tdg,ttb,nrs,gsp->

als

);

1032  if

(tdg->

dg

>tts->

ib

[nti]) {tts->

ib

[nti]=tdg->

dg

;

1041  if

(gsp->

trg

!=0) { trg[ngs]=tts->

ib

[nti]; ngs++; }

1100  if

(gsp->

lms

[nts]>0 && (nti+1)>=gsp->

lms

[nts]) {

1101

tts->

gb

=

BIGNEG

;

for

(

i

=nti-gsp->

lmw

[nts]+1;

i

<=nti;

i

++)

1102  if

(tts->

gb

<tts->

ib

[

i

]) tts->

gb

=tts->

ib

[

i

];

1103  if

(tts->

gb

<(((

float

)gsp->

lmf

[nts])/100.)*ttb->

tg

[ttb->

mx

]) {

1105

tts->

lm

=1;

break

; }}

1112  if

(tts->

lm

==1)

break

;

1121 if

(nrs>=gsp->

crs

) {

1125  if

(tts->

tf

>=gsp->

cfm

&& tts->

ts

>=gsp->

csm

)

break

; }

1141  zsc

(ttb,psm,qsq,cpr,cdf,pmf,spe,sai,pvl,ScalingFactor);

1146  for

(

i

=0;

i

<ttb->

n

;

i

++) {

1148  zsc

(ttb,psm,qsq,cpr,cdf,pmf,spe,sai,pvl,ScalingFactor);

1199 for

(

i

=0;

i

<ndi;

i

++)

1200  for

(j=0; j<nsc; j++)

free

(spn->

nrr

[

i

][j]);

1203 for

(

i

=0;

i

<ndi;

i

++)

1204  for

(j=0; j<nsc; j++)

free

(spn->

nrp

[

i

][j]);

1207 for

(

i

=0;

i

<ndi;

i

++)

1208  for

(j=0; j<nsc; j++)

free

(spn->

nrf

[

i

][j]);

1215 for

(

i

=0;

i

<nsc;

i

++) {

1226 for

(

i

=0;

i

<nsc;

i

++)

free

(cpr[

i

]);

1231 for

(

i

=0;

i

<nsc;

i

++) {

1245 for

(

i

=0;

i

<nsc;

i

++)

free

(cpl[

i

]);

1250 for

(

i

=0;

i

<nsc;

i

++) {

1257  for

(j=0;j<

n

;j++)

free

(ca->

r

.e[j]);

1259 for

(

i

=0;

i

<nsc;

i

++)

free

(cpa[

i

]);

1316

cdfp->

sll

.

rfpt

= (

int

*)

calloc

(1,

sizeof

(

int

) * NumBlocks);

1317

cdfp->

sll

.

nomn

= (

int

*)

calloc

(1,

sizeof

(

int

) * NumBlocks);

1318

cdfp->

sll

.

nomx

= (

int

*)

calloc

(1,

sizeof

(

int

) * NumBlocks);

1319

cdfp->

sll

.

comn

= (

int

*)

calloc

(1,

sizeof

(

int

) * NumBlocks);

1320

cdfp->

sll

.

comx

= (

int

*)

calloc

(1,

sizeof

(

int

) * NumBlocks);

1321

cdfp->

sll

.

n

= NumBlocks;

1322

cdfp->

lll

.

llmn

= (

int

*)

calloc

(1,

sizeof

(

int

) * (NumBlocks+1));

1323

cdfp->

lll

.

llmx

= (

int

*)

calloc

(1,

sizeof

(

int

) * (NumBlocks+1));

1324

cdfp->

lll

.

lrfs

= (

int

*)

calloc

(1,

sizeof

(

int

) * (NumBlocks+1));

1325

cdfp->

lll

.

n

= NumBlocks+1;

1354  if

(FirstPass ==

FALSE

)

return

;

1357

fprintf(pFile,

"Core Definition:\n"

);

1358

fprintf(pFile,

"number of core segments: %4d\n"

, cdf->

sll

.

n

);

1359

fprintf(pFile,

" nomx nomn rfpt comn comx\n"

);

1360  for

(

i

=0;

i

<cdf->

sll

.

n

;

i

++) {

1361

fprintf(pFile,

" %6d %6d %6d %6d %6d\n"

,

1364

fprintf(pFile,

"number of loops (one more than core segs): %4d\n"

, cdf->

lll

.

n

);

1365

fprintf(pFile,

" llmn llmx lrfs\n"

);

1366  for

(

i

=0;

i

<cdf->

lll

.

n

;

i

++) {

1369

fprintf(pFile,

"number of fixed segments: %4d\n"

, cdf->

fll

.

n

);

1370

fprintf(pFile,

" nt ct sq\n"

);

1371  for

(

i

=0;

i

<cdf->

fll

.

n

;

i

++) {

1372

fprintf(pFile,

" %6d %6d %6d\n"

, cdf->

fll

.

nt

[

i

], cdf->

fll

.

ct

[

i

], cdf->

fll

.

sq

[

i

]);

1374

fprintf(pFile,

"\n"

);

1386

pssm->

n

= NumResidues;

1388

pssm->

ww

= (

int

**)

calloc

(1,NumResidues *

sizeof

(

int

*));

1389

pssm->

freqs

= (

int

**)

calloc

(1,NumResidues *

sizeof

(

int

*));

1390  for

(

i

=0;

i

<NumResidues;

i

++) {

1391

pssm->

ww

[

i

] = (

int

*)

calloc

(1,AlphabetSize *

sizeof

(

int

));

1392

pssm->

freqs

[

i

] = (

int

*)

calloc

(1,AlphabetSize *

sizeof

(

int

));

1404  for

(

i

=0;

i

<pssm->

n

;

i

++) {

1419  char

OutputOrder[] =

"ARNDCQEGHILKMFPSTWYV"

;

1422

fprintf(pFile,

"PSSM:\n"

);

1423

fprintf(pFile,

"Number of residues: %4d\n"

, psm->

n

);

1424

fprintf(pFile,

"Weights:\n"

);

1425  for

(

i

=0;

i

<strlen(OutputOrder);

i

++) {

1426

fprintf(pFile,

"%8c "

, OutputOrder[

i

]);

1428

fprintf(pFile,

"\n"

);

1429  for

(

i

=0;

i

<psm->

n

;

i

++) {

1430  for

(j=0; j<strlen(OutputOrder); j++) {

1431

fprintf(pFile,

"%8d "

, psm->

ww

[

i

][j]);

1433

fprintf(pFile,

"\n"

);

1435

fprintf(pFile,

"Frequencies:\n"

);

1436  for

(

i

=0;

i

<strlen(OutputOrder);

i

++) {

1437

fprintf(pFile,

"%8c "

, OutputOrder[

i

]);

1439

fprintf(pFile,

"\n"

);

1440  for

(

i

=0;

i

<psm->

n

;

i

++) {

1441  for

(j=0; j<strlen(OutputOrder); j++) {

1442

fprintf(pFile,

"%8d "

, psm->

freqs

[

i

][j]);

1444

fprintf(pFile,

"\n"

);

1446

fprintf(pFile,

"\n"

);

1458

qsqp->

n

= NumResidues;

1459

qsqp->

sq

= (

int

*)

calloc

(1,

sizeof

(

int

) * NumResidues);

1460

qsqp->

sac

.

n

= NumBlocks;

1461

qsqp->

sac

.

mn

= (

int

*)

calloc

(1,

sizeof

(

int

) * NumBlocks);

1462

qsqp->

sac

.

mx

= (

int

*)

calloc

(1,

sizeof

(

int

) * NumBlocks);

1465  for

(

i

=0;

i

<NumBlocks;

i

++) {

1466

qsqp->

sac

.

mn

[

i

] = -1;

1467

qsqp->

sac

.

mx

[

i

] = -1;

1490  char

ResLetters[32];

1493

strcpy(ResLetters,

"ARNDCQEGHILKMFPSTWYV"

);

1495

fprintf(pFile,

"Query Sequence:\n"

);

1496

fprintf(pFile,

"number of residues: %4d\n"

, qsqp->

n

);

1498  for

(

i

=0;

i

<=qsqp->

n

/30;

i

++) {

1499  for

(j=0; j<30; j++) {

1500

fprintf(pFile,

"%c "

, ResLetters[qsqp->

sq

[

i

*30 + j]]);

1502  if

(Count == qsqp->

n

) {

1503

fprintf(pFile,

"\n"

);

1507

fprintf(pFile,

"\n"

);

1511

fprintf(pFile,

"number of constraints: %4d\n"

, qsqp->

sac

.

n

);

1512

fprintf(pFile,

" mn mx\n"

);

1513  for

(

i

=0;

i

<qsqp->

sac

.

n

;

i

++) {

1514

fprintf(pFile,

" %6d %6d\n"

, qsqp->

sac

.

mn

[

i

], qsqp->

sac

.

mx

[

i

]);

1516

fprintf(pFile,

"\n"

);

1528

pmf->

rre

= (

int

***)

calloc

(1,NumDistances *

sizeof

(

int

**));

1529

pmf->

rrt

= (

int

***)

calloc

(1,NumDistances *

sizeof

(

int

**));

1530

pmf->

re

= (

int

**)

calloc

(1,NumDistances *

sizeof

(

int

*));

1531  for

(

i

=0;

i

<NumDistances;

i

++) {

1532

pmf->

rre

[

i

] = (

int

**)

calloc

(1,NumResTypes *

sizeof

(

int

*));

1533

pmf->

rrt

[

i

] = (

int

**)

calloc

(1,NumResTypes *

sizeof

(

int

*));

1534  for

(j=0; j<NumResTypes; j++) {

1535

pmf->

rre

[

i

][j] = (

int

*)

calloc

(1,NumResTypes *

sizeof

(

int

));

1536

pmf->

rrt

[

i

][j] = (

int

*)

calloc

(1,NumResTypes *

sizeof

(

int

));

1538

pmf->

re

[

i

] = (

int

*)

calloc

(1,NumResTypes *

sizeof

(

int

));

1540

pmf->

nrt

= NumResTypes;

1541

pmf->

ndi

= NumDistances;

1542

pmf->

ppi

= PeptideIndex;

1553  for

(

i

=0;

i

<pmf->

ndi

;

i

++) {

1554  for

(j=0; j<pmf->

nrt

; j++) {

1577

gsp->

nts

= NumTempSteps;

1578

gsp->

nti

= (

int

*)

calloc

(1,NumTempSteps *

sizeof

(

int

));

1579

gsp->

nac

= (

int

*)

calloc

(1,NumTempSteps *

sizeof

(

int

));

1580

gsp->

nlc

= (

int

*)

calloc

(1,NumTempSteps *

sizeof

(

int

));

1581

gsp->

tma

= (

int

*)

calloc

(1,NumTempSteps *

sizeof

(

int

));

1582

gsp->

tml

= (

int

*)

calloc

(1,NumTempSteps *

sizeof

(

int

));

1583

gsp->

lms

= (

int

*)

calloc

(1,NumTempSteps *

sizeof

(

int

));

1584

gsp->

lmw

= (

int

*)

calloc

(1,NumTempSteps *

sizeof

(

int

));

1585

gsp->

lmf

= (

int

*)

calloc

(1,NumTempSteps *

sizeof

(

int

));

1615

mtf->

n

= NumResidues;

1616

mtf->

rrc

.

n

= NumResResContacts;

1617

mtf->

rrc

.

r1

= (

int

*)

calloc

(1,NumResResContacts *

sizeof

(

int

));

1618

mtf->

rrc

.

r2

= (

int

*)

calloc

(1,NumResResContacts *

sizeof

(

int

));

1619

mtf->

rrc

.

d

= (

int

*)

calloc

(1,NumResResContacts *

sizeof

(

int

));

1620

mtf->

rpc

.

n

= NumResPepContacts;

1621

mtf->

rpc

.

r1

= (

int

*)

calloc

(1,NumResPepContacts *

sizeof

(

int

));

1622

mtf->

rpc

.

p2

= (

int

*)

calloc

(1,NumResPepContacts *

sizeof

(

int

));

1623

mtf->

rpc

.

d

= (

int

*)

calloc

(1,NumResPepContacts *

sizeof

(

int

));

1624

mtf->

mll

= (

int

**)

calloc

(1,NumResidues *

sizeof

(

int

*));

1625  for

(

i

=0;

i

<NumResidues;

i

++) {

1626

mtf->

mll

[

i

] = (

int

*)

calloc

(1,NumResidues *

sizeof

(

int

));

1644  for

(

i

=0;

i

<mtf->

n

;

i

++) {

1659

fprintf(pFile,

"Contact Lists, Loop Lengths:\n"

);

1660

fprintf(pFile,

"Number of residues: %4d\n"

, mtf->

n

);

1661

fprintf(pFile,

"Number of residue-residue contacts: %6d\n"

, mtf->

rrc

.

n

);

1662

fprintf(pFile,

"res index 1, res index 2, Distance interval\n"

);

1663  for

(

i

=0;

i

<mtf->

rrc

.

n

;

i

++) {

1664

fprintf(pFile,

" %9d %12d %18d\n"

, mtf->

rrc

.

r1

[

i

], mtf->

rrc

.

r2

[

i

], mtf->

rrc

.

d

[

i

]);

1666

fprintf(pFile,

"Number of residue-peptide contacts: %6d\n"

, mtf->

rpc

.

n

);

1667

fprintf(pFile,

"res index, peptide index, Distance interval\n"

);

1668  for

(

i

=0;

i

<mtf->

rpc

.

n

;

i

++) {

1669

fprintf(pFile,

" %7d %14d %18d\n"

, mtf->

rpc

.

r1

[

i

], mtf->

rpc

.

p2

[

i

], mtf->

rpc

.

d

[

i

]);

1671

fprintf(pFile,

"Minimum loop lengths:\n"

);

1672  for

(

i

=0;

i

<mtf->

n

;

i

++) {

1673  for

(j=0; j<mtf->

n

; j++) {

1674

fprintf(pFile,

" %4d"

, mtf->

mll

[

i

][j]);

1676

fprintf(pFile,

"\n"

);

1678

fprintf(pFile,

"\n"

);

1690

ttb->

n

= NumResults;

1691

ttb->

nsc

= NumCoreElements;

1692

ttb->

tg

= (

float

*)

calloc

(1,NumResults *

sizeof

(

float

));

1693

ttb->

ps

= (

float

*)

calloc

(1,NumResults *

sizeof

(

float

));

1694

ttb->

ms

= (

float

*)

calloc

(1,NumResults *

sizeof

(

float

));

1695

ttb->

cs

= (

float

*)

calloc

(1,NumResults *

sizeof

(

float

));

1696

ttb->

lps

= (

float

*)

calloc

(1,NumResults *

sizeof

(

float

));

1697

ttb->

zsc

= (

float

*)

calloc

(1,NumResults *

sizeof

(

float

));

1698

ttb->

g0

= (

float

*)

calloc

(1,NumResults *

sizeof

(

float

));

1699

ttb->

m0

= (

float

*)

calloc

(1,NumResults *

sizeof

(

float

));

1700

ttb->

errm

= (

float

*)

calloc

(1,NumResults *

sizeof

(

float

));

1701

ttb->

errp

= (

float

*)

calloc

(1,NumResults *

sizeof

(

float

));

1702

ttb->

tf

= (

int

*)

calloc

(1,NumResults *

sizeof

(

int

));

1703

ttb->

ts

= (

int

*)

calloc

(1,NumResults *

sizeof

(

int

));

1704

ttb->

ls

= (

int

*)

calloc

(1,NumResults *

sizeof

(

int

));

1705

ttb->

pr

= (

int

*)

calloc

(1,NumResults *

sizeof

(

int

));

1706

ttb->

nx

= (

int

*)

calloc

(1,NumResults *

sizeof

(

int

));

1707

ttb->

al

= (

int

**)

calloc

(1,NumCoreElements *

sizeof

(

int

*));

1708

ttb->

no

= (

int

**)

calloc

(1,NumCoreElements *

sizeof

(

int

*));

1709

ttb->

co

= (

int

**)

calloc

(1,NumCoreElements *

sizeof

(

int

*));

1710  for

(

i

=0;

i

<NumCoreElements;

i

++) {

1711

ttb->

al

[

i

] = (

int

*)

calloc

(1,NumResults *

sizeof

(

int

));

1712

ttb->

no

[

i

] = (

int

*)

calloc

(1,NumResults *

sizeof

(

int

));

1713

ttb->

co

[

i

] = (

int

*)

calloc

(1,NumResults *

sizeof

(

int

));

1740  for

(

i

=0;

i

<ttb->

nsc

;

i

++) {

1759

fprintf(pFile,

"Threading Results:\n"

);

1760

fprintf(pFile,

"number of threads: %6d\n"

, ttb->

n

);

1761

fprintf(pFile,

"number of core segments: %6d\n"

, ttb->

nsc

);

1762

fprintf(pFile,

"index of lowest energy thread: %6d\n"

, ttb->

mn

);

1763

fprintf(pFile,

"index of highest energy thread: %6d\n"

, ttb->

mx

);

1764

fprintf(pFile,

"for each thread:\n"

);

1765

fprintf(pFile,

" tg ps ms cs lps zsc\n"

);

1766  for

(

i

=0;

i

<ttb->

n

;

i

++) {

1767

fprintf(pFile,

" %12.5e %12.5e %12.5e %12.5e %12.5e %12.5e\n"

,

1768

ttb->

tg

[

i

], ttb->

ps

[

i

], ttb->

ms

[

i

], ttb->

cs

[

i

], ttb->

lps

[

i

], ttb->

zsc

[

i

]);

1770

fprintf(pFile,

" g0 m0 errm errp\n"

);

1771  for

(

i

=0;

i

<ttb->

n

;

i

++) {

1772

fprintf(pFile,

" %12.5e %12.5e %12.5e %12.5e\n"

,

1775

fprintf(pFile,

" tf ts ls pr nx\n"

);

1776  for

(

i

=0;

i

<ttb->

n

;

i

++) {

1777

fprintf(pFile,

" %6d %6d %6d %6d %6d\n"

,

1778

ttb->

tf

[

i

], ttb->

ts

[

i

], ttb->

ls

[

i

], ttb->

pr

[

i

], ttb->

nx

[

i

]);

1780

fprintf(pFile,

"threading alignments: %6d\n"

,

i

+1);

1781

fprintf(pFile,

"Centers:\n"

);

1782  for

(

i

=0;

i

<ttb->

n

;

i

++) {

1783  for

(j=0; j<ttb->

nsc

; j++) {

1784

fprintf(pFile,

" %4d"

, ttb->

al

[j][

i

] + 1);

1786

fprintf(pFile,

"\n"

);

1788

fprintf(pFile,

"N offsets:\n"

);

1789  for

(

i

=0;

i

<ttb->

n

;

i

++) {

1790  for

(j=0; j<ttb->

nsc

; j++) {

1791

fprintf(pFile,

" %4d"

, ttb->

no

[j][

i

]);

1793

fprintf(pFile,

"\n"

);

1795

fprintf(pFile,

"C offsets:\n"

);

1796  for

(

i

=0;

i

<ttb->

n

;

i

++) {

1797  for

(j=0; j<ttb->

nsc

; j++) {

1798

fprintf(pFile,

" %4d"

, ttb->

co

[j][

i

]);

1800

fprintf(pFile,

"\n"

);

1802

fprintf(pFile,

"\n"

);

1812

pToResults->

tg

[to] = pFromResults->

tg

[from];

1813

pToResults->

ps

[to] = pFromResults->

ps

[from];

1814

pToResults->

ms

[to] = pFromResults->

ms

[from];

1815

pToResults->

cs

[to] = pFromResults->

cs

[from];

1816

pToResults->

lps

[to] = pFromResults->

lps

[from];

1817

pToResults->

zsc

[to] = pFromResults->

zsc

[from];

1818

pToResults->

g0

[to] = pFromResults->

g0

[from];

1819

pToResults->

m0

[to] = pFromResults->

m0

[from];

1820

pToResults->

errm

[to] = pFromResults->

errm

[from];

1821

pToResults->

errp

[to] = pFromResults->

errp

[from];

1822

pToResults->

tf

[to] = pFromResults->

tf

[from];

1823

pToResults->

ts

[to] = pFromResults->

ts

[from];

1824

pToResults->

ls

[to] = pFromResults->

ls

[from];

1825

pToResults->

pr

[to] = pFromResults->

pr

[from];

1826

pToResults->

nx

[to] = pFromResults->

nx

[from];

1827  for

(

i

=0;

i

<pFromResults->

nsc

;

i

++) {

1828

pToResults->

al

[

i

][to] = pFromResults->

al

[

i

][from];

1829

pToResults->

no

[

i

][to] = pFromResults->

no

[

i

][from];

1830

pToResults->

co

[

i

][to] = pFromResults->

co

[

i

][from];

1844  int i

, j, SaveIndex, Index;

1845  double

HighestScore;

1849

Order = (

int

*)

calloc

(1,

sizeof

(

int

) * pResults->

n

);

1854  for

(

i

=0;

i

<pResults->

n

;

i

++) {

1855

HighestScore = -9999999999.0;

1858  for

(j=0; j<pResults->

n

; j++) {

1859  if

(CheckList[j] ==

FALSE

) {

1860  if

(pResults->

tg

[j] > HighestScore) {

1861

HighestScore = pResults->

tg

[j];

1867

Order[

i

] = SaveIndex;

1868

CheckList[SaveIndex] =

TRUE

;

1872

pOrderedResults =

NewThdTbl

(pResults->

n

, pResults->

nsc

);

1873  for

(

i

=0;

i

<pResults->

n

;

i

++) {

1874  CopyResult

(pResults, pOrderedResults, Order[

i

],

i

);

1876

pOrderedResults->

mx

= 0;

1877

pOrderedResults->

mn

= pResults->

n

- 1;

1880  for

(

i

=0;

i

<pResults->

n

;

i

++) {

1885  for

(

i

=0;

i

<pResults->

n

;

i

++) {

1887

pResults->

nx

[

i

] =

i

+1 < pResults->

n

?

i

+1 : 0;

1889

Index = pResults->

n

-

i

- 1;

1890

pResults->

pr

[Index] = Index-1 < 0 ? 0 : Index-1;

1894

pResults->

mx

= pOrderedResults->

mx

;

1895

pResults->

mn

= pOrderedResults->

mn

;

1913

SF = (float) ScalingFactor;

1915  for

(

i

=0;

i

<ttb->

n

;

i

++) {

1916

ttb->

tg

[

i

] *= SF;

1917

ttb->

ps

[

i

] *= SF;

1918

ttb->

ms

[

i

] *= SF;

1919

ttb->

cs

[

i

] *= SF;

1920

ttb->

lps

[

i

] *= SF;

1921

ttb->

zsc

[

i

] *= SF;

1922

ttb->

g0

[

i

] *= SF;

1923

ttb->

m0

[

i

] *= SF;

1924

ttb->

errm

[

i

] *= SF;

1925

ttb->

errp

[

i

] *= SF;

1935  return

((

int

)(Num + 0.5));

1938  return

((

int

)(Num - 0.5));

unsigned int

A callback function used to compare two keys in a database.

Uint1 Boolean

bool replacment for C

Gib_Scd * NewGibScd(int NumTempSteps)

Fld_Mtf * FreeFldMtf(Fld_Mtf *mtf)

Thd_Tbl * NewThdTbl(int NumResults, int NumCoreElements)

Rcx_Ptl * NewRcxPtl(int NumResTypes, int NumDistances, int PeptideIndex)

Rcx_Ptl * FreeRcxPtl(Rcx_Ptl *pmf)

Cor_Def * FreeCorDef(Cor_Def *cdfp)

Seq_Mtf * FreeSeqMtf(Seq_Mtf *pssm)

Seq_Mtf * NewSeqMtf(int NumResidues, int AlphabetSize)

void PrintCorDef(Cor_Def *cdf, FILE *pFile)

int atd(Fld_Mtf *mtf, Cor_Def *cdf, Qry_Seq *qsq, Rcx_Ptl *pmf, Gib_Scd *gsp, Thd_Tbl *ttb, Seq_Mtf *psm, float *trg, int zscs, double ScalingFactor, float PSSM_Weight)

void PrintThdTbl(Thd_Tbl *ttb, FILE *pFile)

int ThrdRound(double Num)

void ScaleThdTbl(Thd_Tbl *ttb, double ScalingFactor)

Qry_Seq * FreeQrySeq(Qry_Seq *qsqp)

Fld_Mtf * NewFldMtf(int NumResidues, int NumResResContacts, int NumResPepContacts)

void PrintFldMtf(Fld_Mtf *mtf, FILE *pFile)

void OrderThdTbl(Thd_Tbl *pResults)

void PrintQrySeq(Qry_Seq *qsqp, FILE *pFile)

Gib_Scd * FreeGibScd(Gib_Scd *gsp)

Thd_Tbl * FreeThdTbl(Thd_Tbl *ttb)

void PrintSeqMtf(Seq_Mtf *psm, FILE *pFile)

int CopyResult(Thd_Tbl *pFromResults, Thd_Tbl *pToResults, int from, int to)

Cor_Def * NewCorDef(int NumBlocks)

Qry_Seq * NewQrySeq(int NumResidues, int NumBlocks)

int algs(Rnd_Smp *pvl, int tm)

int slor(Fld_Mtf *mtf, Cor_Def *cdf, Qry_Seq *qsq, Cur_Loc *sli, Cur_Aln *sai, int cs, int ct, int *mn, int *mx)

void salu(Cor_Def *cdf, Qry_Seq *qsq, Cur_Loc *sli, int cs, int al, Cur_Aln *sai)

float dgri(Seg_Gsm *spe, Seg_Nsm *spn, Thd_Cxe *cxe, Thd_Gsm *tdg, Seq_Mtf *psm, Seg_Cmp *spc)

void spel(Cxl_Los **cpl, Cur_Aln *sai, Cur_Loc *sli, int cs, Seg_Gsm *spe, Cor_Def *cdf, Seq_Mtf *psm, Seg_Cmp *spc)

void slou(Fld_Mtf *mtf, Cor_Def *cdf, int cs, int ct, int of, Cur_Loc *sli, Cur_Aln *sai, Qry_Seq *qsq)

void cprl(Fld_Mtf *mtf, Cor_Def *cdf, Rcx_Ptl *pmf, Cxl_Los **cpr, int ct)

int slo0(Fld_Mtf *mtf, Cor_Def *cdf, Qry_Seq *qsq, Cur_Loc *sli, int cs, int ct, int *mn, int *mx)

void cpll(Cor_Def *cdf, Rcx_Ptl *pmf, Qry_Seq *qsq, Cxl_Los **cpr, Cur_Aln *sai, Cxl_Los **cpl)

int salr(Cor_Def *cdf, Qry_Seq *qsq, Cur_Loc *sli, Cur_Aln *sai, int cs, int *mn, int *mx)

void cpal(Rcx_Ptl *pmf, Cxl_Los **cpr, Cur_Loc *sli, Cxl_Als **cpa)

void spni(Cxl_Los **cpl, Cur_Loc *sli, int n, Seg_Nsm *spn)

int ttbi(Cur_Aln *sai, Cur_Loc *sli, Thd_Gsm *tdg, Thd_Tbl *ttb, int nrs, int o)

void spea(Cor_Def *cdf, Cxl_Als **cpa, Cur_Aln *sai, Cur_Loc *sli, int n, int h, Seg_Gsm *spe, Seq_Mtf *psm, Seg_Cmp *spc)

void sgoi(int is, int it, Rnd_Smp *pvl, Seg_Ord *sgo)

void cxei(Seg_Nsm *spn, Seg_Cmp *spc, Rcx_Ptl *pmf, Cur_Loc *sli, Seq_Mtf *psm, Cor_Def *cdf, Thd_Cxe *cxe)

int spci(Cor_Def *cdf, Qry_Seq *qsq, Cur_Loc *sli, Cur_Aln *sai, int n, Seg_Cmp *spc)

int sal0(Cor_Def *cdf, Qry_Seq *qsq, Cur_Loc *sli, Cur_Aln *sai, int cs, int *mn, int *mx)

void bwfi(Thd_Tbl *ttb, Gib_Scd *gsp, Thd_Tst *tts)

void zsc(Thd_Tbl *ttb, Seq_Mtf *psm, Qry_Seq *qsq, Cxl_Los **cpr, Cor_Def *cdf, Rcx_Ptl *pmf, Seg_Gsm *spe, Cur_Aln *sai, Rnd_Smp *pvl, double ScalingFactor)

voidp calloc(uInt items, uInt size)

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