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(old_length + diff);

182

NRawToDeltaSeq::SGap gap;

184

gap.length = delta_len;

185

gap.is_known =

false

;

186

gap.is_replace =

true

;

187

gaps[bsh].push_back(gap);

190

bsh_to_inst[bsh].second =

true

;

220 if

(!bsh_to_inst[bsh].second && new_inst->

IsSetLength

())

222

diffs[bsh][start] = diff;

224

new_inst->

(old_length + diff);

226

NRawToDeltaSeq::SGap gap;

228

gap.length = delta_len;

229

gap.is_known =

false

;

230

gap.is_replace =

true

;

231

gaps[bsh].push_back(gap);

233

bsh_to_inst[bsh].second =

true

;

261 for

(

const auto

& it : bsh_to_inst)

265 bool

modified = it.second.second;

285

wxTextEntryDialog dlg(

NULL

(

"Convert gaps longer or equal to"

(

"Convert Known Length Gaps to Unknown"

(

"100"

));

286

dlg.SetTextValidator(wxFILTER_NUMERIC);

287 if

(dlg.ShowModal() == wxID_OK)

289

wxString

= dlg.GetValue();

291 if

(

.ToLong(&min_size))

293 CScope

&scope = seh.GetScope();

308 bool

has_loc(

false

);

311 if

( (*iter)->IsLoc() )

326 if

(delta_i->Empty())

330 if

(sv.

IsInGap

(pos) && (

long

)delta_len >= min_size &&

343

}

catch

(

CException

) {}

catch

(std::exception ) {}

359 bool

create_xref_map =

true

;

361

create_xref_map =

false

;

369

wxTextEntryDialog dlg(

NULL

(

"Change length to"

(

"Change length of selected gaps"

(

"100"

));

370

dlg.SetTextValidator(wxFILTER_NUMERIC);

371 if

(dlg.ShowModal() == wxID_OK)

373

wxString

= dlg.GetValue();

375 if

(

.ToLong(&new_size))

380 bool

create_general_only =

false

;

386 const CGapEdit

* gap_edit =

dynamic_cast<const CGapEdit

>

((*it).object.GetPointer());

391 const CSeq_feat

* feat =

dynamic_cast<const CSeq_feat

>

((*it).object.GetPointer());

395

bsh = scope->GetBioseqHandle(feat->

GetLocation

());

400 if

(bsh_to_inst.

find

(bsh) != bsh_to_inst.

end

())

414 bool

has_loc(

false

);

417 if

( (*iter)->IsLoc() )

428

bsh_to_inst[bsh] = make_pair(new_inst,

false

);

438 const CGapEdit

* gap_edit =

dynamic_cast<const CGapEdit

>

((*it).object.GetPointer());

444 const CSeq_feat

* feat =

dynamic_cast<const CSeq_feat

>

((*it).object.GetPointer());

454 for

(

const auto

& d : diffs[bsh])

464 if

(delta_i->Empty())

473 int

diff =

static_cast<int>

(new_size);

477

diffs[bsh][start] = diff;

479

new_inst->

(old_length + diff);

483

NRawToDeltaSeq::SGap gap;

485

gap.length =

static_cast<int>

(new_size - delta_len);

486

gap.is_known =

true

;

487

gap.is_replace =

false

;

488

gaps[bsh].push_back(gap);

491

bsh_to_inst[bsh].second =

true

;

510

diff =

static_cast<int>

(new_size);

516 if

(!bsh_to_inst[bsh].second && new_inst->

IsSetLength

())

518

diffs[bsh][start] = diff;

520

new_inst->

(old_length + diff);

522

NRawToDeltaSeq::SGap gap;

524

gap.length =

static_cast<int>

(new_size - delta_len);

525

gap.is_known =

true

;

526

gap.is_replace =

false

;

527

gaps[bsh].push_back(gap);

529

bsh_to_inst[bsh].second =

true

;

558 for

(

const auto

& it : bsh_to_inst)

562 bool

modified = it.second.second;

574 if

(!diffs.

empty

())

577 for

(objects::CAlign_CI align_ci(tse); align_ci; ++ align_ci)

579 const

objects::CSeq_align& align = *align_ci;

581 int

num_rows = align.CheckNumRows();

584 if

(!align.IsSetSegs() || !align.GetSegs().IsDenseg() ||

585

!align.GetSegs().GetDenseg().IsSetStarts() || !align.GetSegs().GetDenseg().IsSetLens())

588

vector< TSignedSeqPos > starts(align.GetSegs().GetDenseg().GetStarts());

589 size_t

num_segs = align.GetSegs().GetDenseg().GetLens().size();

590 for

(

size_t

s = 0; s < num_segs; s++)

591 for

(

auto row

= 0;

row

< num_rows;

row

++)

600 for

(

const auto

& d : diffs[bsh])

605

starts[num_rows * s +

row

] = from;

609

new_align->

Assign

(align);

610

new_align->

().SetDenseg().SetStarts() = starts;

611

new_align->

().SetDenseg().TrimEndGaps();

612

new_align->

().SetDenseg().RemovePureGapSegs();

613

new_align->

().SetDenseg().Compact();

626 bool

create_xref_map =

true

;

627 apply_impl

(seh, old_to_new, create_xref_map);

628

create_xref_map =

false

;

629 return apply_impl

(seh, old_to_new, create_xref_map);

635 bool

any_modified =

false

;

641 bool

bsh_modified =

false

;

652 bool

has_loc(

false

);

655 if

( (*iter)->IsLoc() )

668

vector<pair<int, bool> > gap_len;

673 if

(delta_i->Empty())

680

gap_len.push_back(pair<int, bool> (delta_len, unknown));

684

gap_len.push_back(pair<int, bool> (0,

false

));

691

CDelta_ext::Tdata::iterator delta_i = new_inst->

SetExt

().SetDelta().Set().begin();

692 while

(delta_i != new_inst->

SetExt

().SetDelta().Set().end())

694 if

(delta_i->Empty())

701 int

delta_len = gap_len[

].first;

704

delta_i = new_inst->

SetExt

().SetDelta().Set().erase(delta_i);

712 bool

unknown = gap_len[

].second;

713 bool

modified =

false

;

714 for

(

size_t

j =

+ 1; j < gap_len.size(); j++)

716 if

(gap_len[j].

first

<= 0)

718

delta_len += gap_len[j].first;

719

unknown |= gap_len[j].second;

720

gap_len[j].first = -1;

735

new_inst->