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> (

int

)newLength - 1) {

142 offset

= aln_start_new - (aln_start - orig_start);

148

}

else if

(orig_start > aln_stop) {

150 offset

= aln_start_new - (orig_start - aln_stop);

157 offset

= aln_stop_new + (orig_start - aln_stop);

158 if

(

> (

int

)newLength - 1) {

166 if

(orig_stop < aln_start) {

168 offset

= aln_stop_new + (aln_start - orig_stop);

169 if

(

> (

int

)newLength - 1) {

175 offset

= aln_start_new - (aln_start - orig_stop);

181

}

else if

(orig_stop > aln_stop){

183 offset

= aln_start_new - (orig_stop - aln_stop);

190 offset

= aln_stop_new + (orig_stop - aln_stop);

191 if

(

> (

int

)newLength - 1) {

199 if

(is_circular && pTargetInt->

GetFrom

() > pTargetInt->

GetTo

()) {

203

pTargetInt->

SetTo

(start);

243 switch

(origLoc.

Which

()) {

247

shortInt->SetId().Assign(pnt.

GetId

());

248

shortInt->SetFrom(pnt.

GetPoint

());

256

shortInt->SetFuzz_from().

(fuzz);

259

shortInt->SetFuzz_to().Assign(fuzz);

263 CRef<CSeq_interval>

pTargetInt = s_MapInterval(*shortInt, newId, align, is_circular, scope, newLength);

265

mappedLoc->SetInt(*pTargetInt);

273

mappedLoc->SetInt(*pTargetInt);

280 bool

subloc_added =

false

;

282 CRef<CSeq_interval>

sub_interval = s_MapInterval(*cit, newId, align, is_circular, scope, newLength);

285

subloc_added =

true

;

288 if

(subloc_added)

return

mappedLoc;

293 bool

subloc_added =

false

;

294 for

(

auto

&& cit : origLoc.

GetMix

().

Get

()) {

295 CRef<CSeq_loc>

target_loc = s_MapLocation(*cit, newId, align, is_circular, scope, newLength);

298

subloc_added =

true

;

301 if

(subloc_added)

return

mappedLoc;

350 if

((processed1 && !processed2) || (!processed1 && processed2)) {

353 if

(processed1 && processed2

361 if

(!SameStrand(loc1, loc2)) {

367 while

(loc1_it && loc2_it) {

368 if

(loc1_it.GetRange() != loc2_it.GetRange()) {

374 if

(loc1_it || loc2_it) {

381 #define FUSE_STRINGFIELDS(Var1, Var2, Field) \ 383 string orig_value = (Var1).IsSet##Field() ? (Var1).Get##Field() : kEmptyStr; \ 384 string value = (Var2).IsSet##Field() ? (Var2).Get##Field() : kEmptyStr; \ 385 if (!NStr::EqualNocase(orig_value, value) && edit::AddValueToString(orig_value, value, edit::eExistingText_append_semi)) { \ 386 (Var1).Set##Field(orig_value); \ 390 #define FUSE_BOOLEANFIELDS(Var1, Var2, Field) \ 392 bool fused_value = (Var1).IsSet##Field() ? (Var1).Get##Field() : false; \ 393 bool value = (Var2).IsSet##Field() ? (Var2).Get##Field() : false; \ 394 if (fused_value || value) { \ 395 (Var1).Set##Field(true); \ 397 (Var1).Reset##Field(); \ 401 #define FUSE_LISTFIELDS(Var1, Var2, Type, Field) \ 402 if ((Var2).IsSet##Field() && !(Var2).Get##Field().empty()) { \ 403 C##Type::T##Field& cont = (Var1).Set##Field(); \ 404 copy((Var2).Get##Field().begin(), (Var2).Get##Field().end(), back_inserter(cont)); \ 407 #define FUSE_VECTORFIELDS(Var1, Var2, Type, Field) \ 409 if ((Var2).IsSet##Field() && !(Var2).Get##Field().empty()) { \ 410 size_t new_size = (Var2).Get##Field().size(); \ 411 new_size += (Var1).IsSet##Field() ? (Var1).Get##Field().size() : 0; \ 412 C##Type::T##Field& cont = (Var1).Set##Field(); \ 413 cont.reserve(new_size); \ 414 copy((Var2).Get##Field().begin(), (Var2).Get##Field().end(), back_inserter(cont)); \ 474 if

(ci->IsFtable()) {

489

: m_OldBsh(updseq_in.GetNCOldBioseq()),

490

m_UpdBsh(updseq_in.GetUpdateBioseq()),

491

m_Align(updseq_in.GetAlignment()),

499 "Sequence can not be updated: either the update sequence or the alignment is missing"

);

504 "Sequence can not be updated: update parameters are not valid"

);

509 "The old sequence can not be updated: unsupported seq-gap"

);

516 "The update sequence contains gaps features.\nPlease convert your file so that gaps are runs of N's before updating the sequence."

);

534 return

old_raw || old_delta;

572

descr.assign(

"No change"

);

576

descr.assign(

"Replace sequence"

);

579 Patch

(create_general_only);

580

descr.assign(

"Patch sequence"

);

584

descr.assign(

"Extend 5' end"

);

588

descr.assign(

"Extend 3' end"

);

628

newLength =

m_NewEntry

->GetSeq().GetInst().GetLength();

632 if

((*it)->IsSeq()) {

633

newLength = (*it)->GetSeq().GetLength();

728 TSeqPos

offset_old = 0, offset_import = 0;

730

offset_old =

m_UpdBsh

.GetBioseqLength();

733

offset_import =

m_OldBsh

.GetBioseqLength();

789 NCBI_THROW

(

CSeqUpdateException

, eInternal,

"Could not replace the old sequence: old sequence is neither raw nor it can be converted to raw."

);

805

new_inst->

SetSeq_data

().SetIupacna().Set(seqdata);

808 NCBI_THROW

(

CSeqUpdateException

, eInternal,

"Could not replace the old sequence: update sequence is neither raw nor it can be converted to raw."

);

822 _ASSERT

(oldseqRow != updseqRow);

840 if

(aln_start < aln_start_upd)

843

aln_start -= aln_start_upd;

846 TSeqPos

right_edge = upd_length - 1 - aln_stop_upd;

847

aln_stop += right_edge;

848 if

(aln_stop > old_length - 1)

849

aln_stop = old_length - 1;

858

old_seq.

(0, aln_start, old_5prime);

859

patched.append(old_5prime);

863 if

(aln_start_upd < aln_stop_upd) {

865

upd_seq.

(aln_start_upd, aln_stop_upd + 1, middle);

866

patched.append(middle);

870 if

(aln_stop + 1 < old_length) {

872

old_seq.

(aln_stop + 1, old_length, old_3prime);

873

patched.append(old_3prime);

891 _ASSERT

(oldseqRow != updseqRow);

892 _ASSERT

(oldseqRow > -1 && updseqRow > -1);

904

upd_seq.

(0, aln_stop_upd + 1, new_5prime);

905

new_seq.append(new_5prime);

910

new_seq.append(old_3prime);

920

old_seq.

(0, aln_start, old_5prime);

921

new_seq.append(old_5prime);

926

new_seq.append(new_3prime);

936 if

(extension.empty()) {

940 const string

allowed(

"ATUCGRYSWKMBDHVN"

);

941 string

small_allowed(allowed);

945

valid_extension.reserve(extension.size());

946

copy_if(extension.begin(), extension.end(),

947

back_inserter(valid_extension),

948

[&allowed, &small_allowed](

const char

& c) {

return

(allowed.find(c) !=

NPOS

) || (small_allowed.find(c) !=

NPOS

); });

950 return

valid_extension;

956 if

(extension.empty()

963 if

(valid_extension.empty()) {

973

new_seq.assign(valid_extension);

974

new_seq.append(orig_seq);

976

new_seq.assign(orig_seq);

977

new_seq.append(valid_extension);

998 bool

updated(

false

);

1000

new_inst->

SetLength

(

static_cast<int>

(upd_str.size()));

1018

shifted_feat->

(feat);

1027 return

shifted_feat;

1035 if

((*it)->IsSetLoc()) {

1036 const CSeq_loc

& codebreak = (*it)->GetLoc();

1038

(*it)->SetLoc(*new_codebreak);

1060

shiftedLoc->

(sourceLoc);

1063 for

(; loc_it; ++loc_it) {

1087 if

(feat_it->GetLocation().IsInt()) {

1090 if

(start == 0 && stop ==

m_OldBsh

.GetBioseqLength() - 1) {

1146 if

(entry->

IsSeq

()) {

1161

CBioseq_set::TSeq_set::iterator it = seqset.begin();

1162 while

(it != seqset.end()) {

1164 if

((*it)->IsSeq() && (*it)->GetSeq().IsAa()) {

1165

it = seqset.erase(it);

1181 return m_OldBsh

.GetSeq_entry_Handle();

1190

oldSeh =

m_OldBsh

.GetSeq_entry_Handle();

1214

subtype.append(

" "

label

);

1241 return

(stop > aln_start && start <= aln_stop);

1244 return

(stop <= aln_start || start > aln_stop);

1262

mappedFeature->

SetLocation

().Assign(*mappedLoc);

1269 if

(

.IsSetExt() &&

1270 rna

.GetExt().IsTRNA() &&

1271 rna

.GetExt().GetTRNA().IsSetAnticodon()) {

1274

new_anticodon->

(

.GetExt().GetTRNA().GetAnticodon());

1276 rna

.SetExt().SetTRNA().SetAnticodon(*new_anticodon);

1283 if

((*it)->IsSetLoc()) {

1285

new_codebreak->

((*it)->GetLoc());

1287

(*it)->SetLoc(*new_codebreak);

1293 return

mappedFeature;

1313

mappedFeature->

SetLocation

().Assign(*mappedLoc);

1320 if

(

.IsSetExt() &&

1321 rna

.GetExt().IsTRNA() &&

1322 rna

.GetExt().GetTRNA().IsSetAnticodon()) {

1324 const CSeq_loc

& anticodon =

.GetExt().GetTRNA().GetAnticodon();

1326 rna

.SetExt().SetTRNA().SetAnticodon(*new_anticodon);

1333 if

((*it)->IsSetLoc()) {

1334 const CSeq_loc

& codebreak = (*it)->GetLoc();

1336

(*it)->SetLoc(*new_codebreak);

1342 return

mappedFeature;

1347 if

(!fh ||

row

< 0) {

1354 if

(loc_id_type != align_id_type) {

1360 copy

->SetLocation().SetId(alignId);

1363 if

(

.IsSetExt() &&

1364 rna

.GetExt().IsTRNA() &&

1365 rna

.GetExt().GetTRNA().IsSetAnticodon()) {

1366 rna

.SetExt().SetTRNA().SetAnticodon().SetId(alignId);

1369 else if

(

copy

->GetData().IsCdregion()) {

1373 if

((*it)->IsSetLoc()) {

1374

(*it)->SetLoc().SetId(alignId);

1404 "Could not form alignment between the subject sequence (old or update) and newly formed sequence"

);

1419

vector<CRef<CSeq_id> >& ids = denseg.

SetIds

();

1438 bool

deleteOld(

false

);

1440 if

(AreFeaturesDuplicates(**old_it, **imp_it)) {

1451

(*imp_it).Swap(fusedFeat);

1471

fusedFeat->

(feat_upd);

1474

FuseCommonFeatureFields(*fusedFeat, feat_old);

1481

FuseGenes(fusedGene, gene);

1489

FuseProteins(*fusedFeat, feat_old);

1496 rna

.IsSetExt() &&

.GetExt().IsName()) {

1498 string value

.GetExt().GetName();

1501

fusedRna.

SetExt

().SetName(orig_value);

1511

fusedFeat->

().SetRegion(origRegion);

1535 for

(

CFeat_CI

prot_it(old_protsh); prot_it; ++prot_it) {

1537

new_feat->

(*prot_it->GetSeq_feat());

1538

old_protfeats.push_back(new_feat);

1541 for

(

CFeat_CI

prot_it(fused_protsh); prot_it; ++prot_it) {

1543

new_feat->

(*prot_it->GetSeq_feat());

1544

upd_protfeats.push_back(new_feat);

1547

TFeatList::iterator old_it = old_protfeats.begin();

1548 bool

found_duplicate =

false

;

1549 while

(old_it != old_protfeats.end()) {

1550

TFeatList::iterator imp_it = upd_protfeats.begin();

1551 bool

deleteOld(

false

);

1552 while

(imp_it != upd_protfeats.end() && !deleteOld) {

1553 if

(AreProteinFeaturesDuplicates(**old_it, **imp_it)) {

1556

(*imp_it).Swap(fusedFeat);

1557

found_duplicate =

true

;

1564

old_it = old_protfeats.erase(old_it);

1574 if

(!found_duplicate) {

1589

newAnnot->

().SetFtable().push_back(feat);

1594

newAnnot->

().SetFtable().push_back(feat);

1605 bool

has_non_cds =

false

;

1612

seqAnnot->

().SetFtable().push_back(feat);

1613

has_non_cds =

true

;

1624

seqAnnot->

().SetFtable().push_back(feat);

1625

has_non_cds =

true

;

1666 bool

has_cds =

false

;

1680 if

(!eh.

()) {

1688 if

(!eh.

()) {

1696

CSeq_descr::Tdata::iterator desc_it = seq_descr.begin();

1697 while

(desc_it != seq_descr.end()) {

1698 if

((*desc_it)->IsSource() || (*desc_it)->IsPub()) {

1700

cpy->Assign(**desc_it);

1702

desc_it = seq_descr.erase(desc_it);

1717

setAnnot->

().SetFtable().push_back(feat);

1725

setAnnot->

().SetFtable().push_back(feat);

1735

setAnnot->

().SetFtable().push_back(feat);

1743

setAnnot->

().SetFtable().push_back(feat);

1807

new_protein->

(*prot_entry);

1853

cds->

SetProduct

().SetWhole().Assign(*product_id);

1883

new_protein->

(*prot_entry);

1895

cds->

SetProduct

().SetWhole().Assign(*product_id);

1913

bestId->

(*lcl_id);

1921 if

(

.IsSetExt() &&

1922 rna

.GetExt().IsTRNA() &&

1923 rna

.GetExt().GetTRNA().IsSetAnticodon()) {

1924 rna

.SetExt().SetTRNA().SetAnticodon().SetId(*bestId);

1931 if

((*it)->IsSetLoc()) {

1932

(*it)->SetLoc().SetId(*bestId);

1942 switch

((*desc_it)->Which()) {

1966 if

(entry->

IsSeq

()) {

1972

new_id->

((**it));

1978

CBioseq_set::TSeq_set::iterator it = seqset.begin();

1979 while

(it != seqset.end()) {

2001 if

(!annot.

IsFtable

())

continue

;

2016 if

(!protein || protein->

() || protein->

GetSeq

().

IsNa

() || !newId) {

2025 if

(!annot.

IsFtable

())

continue

;

2027

(*prot_feat)->SetLocation().SetId(*newId);

2046 if

(!eh.