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((*strands)[pos_1]);

174 bool

minus_2 =

((*strands)[pos_2]);

175

direct = first_direct != minus_2;

186 if

(mixed || base_width_1 > 1) {

191 if

(base_width_1 > 1) {

192

from_1 *= base_width_1;

194 if

(base_width_2 > 1) {

195

from_2 *= base_width_2;

201 if

(from_1 >= 0 && from_2 >= 0) {

204

from_1, from_2,

, direct, first_direct));

205

last_to_1 = first_direct ? from_1 +

: from_1;

207 else if

(from_1 < 0 && from_2 >= 0) {

210 if

(!first_direct && ins_pos == 0) {

215 while

(seg + skip_seg < numseg) {

216 int

p = starts[pos_1 + skip_seg*dim];

218

ins_pos = p + lens[seg + skip_seg];

225

ins_pos, from_2,

, direct, first_direct));

227 else if

(from_1 >= 0) {

229

last_to_1 = first_direct ? from_1 +

: from_1;

260 for

(seg = 0, pos_1 = row_1, pos_2 = row_2;

262

++seg, pos_1 += dim, pos_2 += dim) {

263 TSeqPos

from_1 = starts[pos_1];

264 TSeqPos

from_2 = starts[pos_2];

265 bool

present_1 = presents[pos_1];

266 bool

present_2 = presents[pos_2];

271 bool

first_direct =

true

;

273

first_direct = !

((*strands)[pos_1]);

274 bool

minus_2 =

((*strands)[pos_2]);

275

direct = first_direct != minus_2;

286 if

(mixed || base_width_1 > 1) {

291 if

(base_width_1 > 1) {

292

from_1 *= base_width_1;

294 if

(base_width_2 > 1) {

295

from_2 *= base_width_2;

301 if

(present_1 && present_2) {

304

from_1, from_2,

, direct, first_direct));

305

last_to_1 = first_direct ? from_1 +

: from_1;

307 else if

(!present_1 && present_2) {

310

last_to_1, from_2,

, direct, first_direct));

312 else if

(present_1) {

314

last_to_1 = first_direct ? from_1 +

: from_1;

333 int

guessed_width_1 = 0;

334 int

guessed_width_2 = 0;

337 bool

global_first_direct =

true

;

340 if

( !loc[row_1]->GetTotalRange().

Empty

() ) {

341

global_first_direct = !loc[row_1]->IsReverseStrand();

357 bool

first_direct = !loc[row_1]->IsReverseStrand();

358 bool

direct = first_direct != loc[row_2]->IsReverseStrand();

360 if

(len_1 > 0 && len_2 > 0) {

362

last_to_1 = first_direct ? rng_1.

() + len_1 : rng_1.

();

374 bool

row_1_is_protein = prot_to_nuc_diff < nuc_to_nuc_diff;

375 bool

row_2_is_protein = nuc_to_prot_diff < nuc_to_nuc_diff;

377 if

(nuc_to_nuc_diff != 0) {

382

guessed_width_1 = row_1_is_protein ? 3 : 1;

383

guessed_width_2 = row_2_is_protein ? 3 : 1;

388 if

(!row_1_is_protein && !row_2_is_protein) {

391 if

(len_1 != len_2) {

395

pairwise_aln.

(aln_rng);

401

direct, first_direct));

404

pairwise_aln.

(aln_rng);

406

}

else if

(row_2_is_protein) {

409 if

(len_1 / 3 < len_2) {

413

pairwise_aln.

(aln_rng);

419

direct, first_direct));

422

pairwise_aln.

(aln_rng);

427 if

(len_2 / 3 < len_1) {

431

pairwise_aln.

(aln_rng);

437

direct, first_direct));

440

pairwise_aln.

(aln_rng);

445 else if

(len_2 > 0) {

453 if

(guessed_width_1 == 0) {

456 if

(guessed_width_2 == 0) {

459

from_1 *= guessed_width_1;

460

from_2 *= guessed_width_2;

461 len

*= guessed_width_2;

462 bool

gap_direct = global_first_direct != loc[row_2]->IsReverseStrand();

464

from_1, from_2,

, gap_direct, global_first_direct));

466 else if

(len_1 > 0) {

467

last_to_1 = first_direct ? rng_1.

() + len_1 : rng_1.

();

498 bool

first_direct =

true

;

502

direct = first_direct != minus_2;

513 if

(mixed || base_width_1 > 1) {

518 if

(base_width_1 > 1) {

519

from_1 *= base_width_1;

521 if

(base_width_2 > 1) {

522

from_2 *= base_width_2;

529

from_1, from_2,

, direct, first_direct));

553 bool

first_row =

true

;

555

TAlnRngColl curr_row;

562

starts_1[seg], starts_1[seg], lens[seg]);

564

pairwise_aln.

(aln_rng);

566

curr_row.insert(aln_rng);

574 ITERATE

(TAlnRngColl, aln_rng_it, diff) {

575

pairwise_aln.

(*aln_rng_it);

591 for

(seg = 0; seg < sa.

GetNumseg

(); seg++) {

593

starts_1[seg], starts_2[seg], lens[seg],

594

strands ? !

((*strands)[seg]) :

true

));

609 _ALNMGR_ASSERT

((row_1 == 0 || row_1 == 1) && (row_2 == 0 || row_2 == 1));

624 "Product strands are not consistent."

);

626 bool

product_plus =

true

;

637 "Genomic strands are not consistent."

);

639 bool

genomic_plus =

true

;

645 bool

direct = product_plus == genomic_plus;

646 bool

first_direct = row_1 == 0 ? product_plus : genomic_plus;

652 TSeqPos

product_pos = product_plus ? product_start : product_end;

656 TSeqPos

genomic_pos = (genomic_plus ?

661 TSeqPos

product_len = product_end - product_start + 1;

662 TSeqPos

genomic_len = genomic_end - genomic_start + 1;

667 TSeqPos

starts[] = { product_start, genomic_start };

668 if

(row_1 == row_2 ||

674

starts[row_1], starts[row_2], genomic_len,

675

row_1 == row_2 ?

true

: direct,

688 switch

(chunk.

Which

()) {

690

product_len = genomic_len = chunk.

GetMatch

();

693

product_len = genomic_len = chunk.

GetDiag

();

707 TSeqPos

ppos = product_plus ? product_pos : product_pos - product_len + 1;

708 TSeqPos

gpos = genomic_plus ? genomic_pos : genomic_pos - genomic_len + 1;

709 if

(row_1 == 0 && row_2 == 0) {

710 if

(product_len != 0) {

713

ppos, ppos, product_len,

true

, first_direct));

714

last_product_to = first_direct ? ppos + product_len : ppos;

716

}

else if

(row_1 == 1 && row_2 == 1) {

717 if

(genomic_len != 0) {

720

gpos, gpos, genomic_len,

true

, first_direct));

721

last_genomic_to = first_direct ? gpos + genomic_len : gpos;

724 if

(product_len != 0 && product_len == genomic_len &&

732

ppos, gpos, genomic_len, direct, first_direct));

733

last_product_to = first_direct ? ppos + product_len : ppos;

734

last_genomic_to = direct ? gpos + genomic_len : gpos;

737

gpos, ppos, genomic_len, direct, first_direct));

738

last_product_to = direct ? ppos + product_len : ppos;

739

last_genomic_to = first_direct ? gpos + genomic_len : gpos;

745 if

(product_len == 0 && genomic_len != 0) {

747

last_product_to, gpos, genomic_len,

748

direct, first_direct));

750 else if

(product_len != 0 && genomic_len == 0) {

752

last_product_to += product_len;

755

last_product_to -= product_len;

759 else if

(row_1 == 1) {

760 if

(genomic_len == 0 && product_len != 0) {

762

last_genomic_to, ppos, product_len,

763

direct, first_direct));

765 else if

(genomic_len != 0 && product_len == 0) {

767

last_genomic_to += genomic_len;

770

last_genomic_to -= genomic_len;

777

product_pos += product_len;

779

product_pos -= product_len;

782

genomic_pos += genomic_len;

784

genomic_pos -= genomic_len;

794 const

objects::CSeq_loc& loc_1,

795 const

objects::CSeq_loc& loc_2,

805

loc_1.IsReverseStrand() == loc_2.IsReverseStrand();

822 if

(wid1 == 3 || wid2 == 3) {

849

start1 += len1 -

;

853

start2 += len2 -