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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/overlapping__features_8cpp_source.html below:

NCBI C++ ToolKit: src/misc/discrepancy/overlapping_features.cpp Source File

44 const auto

& cds =

context

.FeatCDS();

45 const auto

& trnas =

context

.FeatTRNAs();

47 bool

increase_count =

false

;

48 static size_t

bs_count = 0;

49 string

report_item_str =

"[n] coding region[s] [has] overlapping tRNAs[*"

+ to_string(++bs_count) +

"*]"

;

51 for

(

size_t i

= 0;

< cds.size();

++) {

52 const CSeq_loc

& loc_i = cds[

]->GetLocation();

53 bool

has_overlap =

false

;

54 string

cur_report_cds_trna_pair_str =

"Coding region overlaps tRNAs[*"

+ to_string(

) +

"*]"

;

56 for

(

size_t

j = 0; j < trnas.size(); j++) {

57 const CSeq_loc

& loc_j = trnas[j]->GetLocation();

61 if

(need_to_compare) {

62

ovlp =

context

.Compare(loc_i, loc_j);

65

increase_count =

true

;

83 static const string kCdsTrnaOverlapComment

"TAA stop codon is completed by the addition of 3' A residues to the mRNA"

;

100 const CSeq_loc

& loc_t =

->GetLocation();

104 if

(!(

.GetFrom() >=

.GetToOpen() ||

.GetFrom() >=

.GetToOpen())) {

105

ovlp_len =

.GetToOpen() -

.GetFrom();

107

other.

Reset

(&loc_t);

111

ovlp_len =

.GetToOpen() -

.GetFrom();

113

other.

Reset

(&loc_t);

133 if

(!br_loc->

GetId

()) {

140

br_loc->

SetInt

().SetId(*seq_id);

145

br_loc->

SetInt

().SetId(*seq_id);

146

br_loc->

SetInt

().SetFrom(rr.

GetTo

() - 2 + ovlp_len);

151

code_break->

SetLoc

().Assign(*br_loc);

152

code_break->

SetAa

().SetNcbieaa(

'*'

);

158 if

(comment.length()) {

164

new_cds->

SetData

().SetCdregion().SetCode_break().push_back(code_break);

165 context

.ReplaceSeq_feat(*obj, cds, *new_cds);

171

new_gene->

Assign

(*gene);

184 const string kCDSRNAExactMatch

"[n/2] coding region location[s] exactly match an RNA location"

;

196 bool

is_eukaryotic =

context

.IsEukaryotic(biosrc ? &biosrc->

GetSource

() :

nullptr

);

198 const auto

& cds =

context

.FeatCDS();

199 const auto

& rnas =

context

.Feat_RNAs();

200 for

(

const auto

& pRna : rnas) {

201 const CSeq_loc

& rna_loc = pRna->GetLocation();

209 for

(

const auto

* pCds : cds) {

210 const CSeq_loc

& cds_loc = pCds->GetLocation();

211 const auto

compare =

context

.Compare(cds_loc, rna_loc);

219 const auto

* pMrnaGene =

context

.GetGeneForFeature(*pMrna);

220 if

(pMrnaGene && (pMrnaGene ==

context

.GetGeneForFeature(*pCds))) {

222

pRnaGene =

context

.GetGeneForFeature(*pRna);

224 if

(pMrnaGene == pRnaGene) {

246 ENa_strand

cds_strand = pCds->GetLocation().GetStrand();

247 ENa_strand

rna_strand = pRna->GetLocation().GetStrand();

265

m_ReportItems = m_Objs.Export(*

this

false

)->GetSubitems();

271 const auto

& rrnas =

context

.FeatRRNAs();

272 for

(

size_t i

= 0;

< rrnas.size();

++) {

273 const CSeq_loc

& loc_i = rrnas[

]->GetLocation();

274 for

(

size_t

j =

+ 1; j < rrnas.size(); j++) {

275 const CSeq_loc

& loc_j = rrnas[j]->GetLocation();

277

m_Objs[

"[n] rRNA feature[s] overlap[S] another rRNA feature."

Add

context

.SeqFeatObjRef(*rrnas[

])).Add(*

context

.SeqFeatObjRef(*rrnas[j])).Fatal();

288 const auto

& genes =

context

.FeatGenes();

289 for

(

size_t i

= 0;

< genes.size();

++) {

290 const CSeq_loc

& loc_i = genes[

]->GetLocation();

292 for

(

size_t

j =

+ 1; j < genes.size(); j++) {

293 const CSeq_loc

& loc_j = genes[j]->GetLocation();

295

m_Objs[

"[n] gene[s] overlap[S] another gene on the same strand."

Add

context

.SeqFeatObjRef(*genes[

])).Add(*

context

.SeqFeatObjRef(*genes[j]));

306 const auto

& genes =

context

.FeatGenes();

307 for

(

size_t i

= 0;

< genes.size();

++) {

308 const CSeq_loc

& loc_i = genes[

]->GetLocation();

311 for

(

size_t

j =

+ 1; j < genes.size(); j++) {

312 const CSeq_loc

& loc_j = genes[j]->GetLocation();

315 if

(strand_i == strand_j) {

319

m_Objs[

"[n] gene[s] completely overlapped by other genes"

].Add(*

context

.SeqFeatObjRef(*genes[

]));

322

m_Objs[

"[n] gene[s] completely overlapped by other genes"

].Add(*

context

.SeqFeatObjRef(*genes[j]));

334 const auto

& genes =

context

.FeatGenes();

335 for

(

size_t i

= 0;

< genes.size();

++) {

336 const CSeq_loc

& loc_i = genes[

]->GetLocation();

338 for

(

size_t

j =

+ 1; j < genes.size(); j++) {

339 const CSeq_loc

& loc_j = genes[j]->GetLocation();

345

m_Objs[

"[n] genes match other genes in the same location, but on the opposite strand"

].Add(*

context

.SeqFeatObjRef(*genes[

])).Add(*

context

.SeqFeatObjRef(*genes[j]));

356 const auto

& pseudo =

context

.FeatPseudo();

357 const auto

& mrnas =

context

.FeatMRNAs();

358 for

(

size_t i

= 0;

< mrnas.size();

++) {

359 const CSeq_loc

& loc_i = mrnas[

]->GetLocation();

360 for

(

size_t

j = 0; j < pseudo.size(); j++) {

361 const CSeq_loc

& loc_j = pseudo[j]->GetLocation();

396 static const string kIntronExon

"[n] introns and exons are incorrectly positioned"

;

400 sort

(vex.begin(), vex.end(),

less

);

401 sort

(vint.begin(), vint.end(),

less

);

402 auto

Iex = vex.cbegin();

403 auto

Iint = vint.cbegin();

404 while

(Iex != vex.cend() && Iint != vint.cend()) {

427 const auto

& genes =

context

.FeatGenes();

428 const auto

& exons =

context

.FeatExons();

429 const auto

& introns =

context

.FeatIntrons();

430 if

(exons.empty() || introns.empty()) {

434

vector<const CSeq_feat*> vex;

435

vector<const CSeq_feat*> vint;

436

vex.insert(vex.end(), exons.cbegin(), exons.cend());

437

vint.insert(vint.end(), introns.cbegin(), introns.cend());

442 if

(gg->CanGetExcept_text() && gg->GetExcept_text() ==

"trans-splicing"

) {

447

vector<const CSeq_feat*> vex;

448

vector<const CSeq_feat*> vint;

467 static const string kGeneMisc

"[n] gene[s] overlap[S] with IGS misc features"

;

472 if

(gene->IsSetLocation() && gene->IsSetData() && gene->GetData().GetGene().IsSetLocus() &&

475 const CSeq_loc

& loc_gene = gene->GetLocation();

476 bool

gene_added =

false

;

479 if

(misc->IsSetLocation() && misc->IsSetComment() &&

NStr::FindNoCase

(misc->GetComment(),

"intergenic spacer"

) !=

NPOS

) {

480 const CSeq_loc

& loc_misc = misc->GetLocation();

499 const auto

& genes =

context

.FeatGenes();

500 const auto

& cds =

context

.FeatCDS();

501 const auto

& mrnas =

context

.FeatMRNAs();

503 const CGene_ref

& gref = gene->GetData().GetGene();

509 if

(

context

.GetGeneForFeature(*feat) == &*gene) {

516 if

(

context

.GetGeneForFeature(*feat) == &*gene) {

523

m_Objs[

"[n] gene[s] missing locus"

].Add(*

context

.SeqFeatObjRef(*gene, gene));

535

new_feat->

SetData

().SetGene().ResetDesc();

536 context

.ReplaceSeq_feat(*obj, *sf, *new_feat);

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

static void Add(TReportObjectList &list, TReportObjectSet &hash, CReportObj &obj, bool unique=true)

CReportNode & Ext(bool b=true)

CSeq_feat_EditHandle â.

namespace ncbi::objects::

#define DISCREPANCY_AUTOFIX(name)

#define DISCREPANCY_CASE(name, type, group, descr)

#define DISCREPANCY_SUMMARIZE(name)

std::ofstream out("events_result.xml")

main entry point for tests

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

ENa_strand GetStrand(void) const

Get the location's strand.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

TRange GetTotalRange(void) const

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

void SetPartialStop(bool val, ESeqLocExtremes ext)

CMappedFeat GetBestMrnaForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

CRef< CSeq_loc > Seq_loc_Subtract(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Subtract the second seq-loc from the first one.

@ eContains

First CSeq_loc contains second.

@ eSame

CSeq_locs contain each other.

@ eContained

First CSeq_loc contained by second.

@ eNoOverlap

CSeq_locs do not overlap or abut.

CConstRef< CSeq_feat > GetGeneForFeature(const CSeq_feat &feat, CScope &scope)

Finds gene for feature, but obeys SeqFeatXref directives.

void Remove(void) const

Remove the feature from Seq-annot.

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool CanGetLocus(void) const

Check if it is safe to call GetLocus method.

bool CanGetDesc(void) const

Check if it is safe to call GetDesc method.

const TLocus & GetLocus(void) const

Get the Locus member data.

void SetAa(TAa &value)

Assign a value to Aa data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetComment(const TComment &value)

Assign a value to Comment data member.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TComment & GetComment(void) const

Get the Comment member data.

const TGene & GetGene(void) const

Get the variant data.

bool CanGetComment(void) const

Check if it is safe to call GetComment method.

ENa_strand

strand of nucleic acid

const TSource & GetSource(void) const

Get the variant data.

constexpr auto sort(_Init &&init)

const string kCDSRNAContainstRNA

const string kCDSRNAOverlapNoContainSameStrand

const string kCDSRNAOverlapNoContain

const string kCDSRNAExactMatch

static const string kGeneMisc

static const string kCdsTrnaOverlapComment

static void CollectExonsIntrons(CReportNode &out, CDiscrepancyContext &context, vector< const CSeq_feat * > &vex, vector< const CSeq_feat * > &vint)

static bool less(const CSeq_feat *A, const CSeq_feat *B)

const string kCDSRNAOverlapNoContainOppStrand

const string kCDSRNAContains

const string kCDSRNAContainedIn

static const string kIntronExon

static const string kCDSoverlapTRNA

const string kCDSRNAAnyOverlap

static const sljit_gpr r1

static const sljit_gpr r2

float g0(Seg_Nsm *spn, Thd_Cxe *cxe)

float Overlap(iterator1 iter1, iterator1 end1, iterator2 iter2, iterator2 end2)

Overlap measure.

static CS_CONTEXT * context

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