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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/validerror__feat_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/validator/validerror_feat.cpp Source File

99 using namespace

sequence;

120 if

(!

|| m_Imp.ShouldSubdivide()) {

149

}

catch

(

const

exception& e) {

151 string

(

"Exception while validating feature. EXCEPTION: "

) +

184 "Coding region on TSA transcribed RNA should not be on the minus strand"

, feat);

205 "Invalid feature for a protein Bioseq."

, feat);

214 "Invalid feature for a nucleotide Bioseq."

, feat);

224 "Peptide processing feature should be remapped to the appropriate protein bioseq"

,

266 size_t

pos1 =

(inf_accession,

":"

);

267 size_t

pos2 =

(inf_accession,

"|"

);

268 size_t

pos = string::npos;

275 if

(pos == string::npos) {

278

prefix = inf_accession.substr(0, pos);

280

accession = inf_accession.substr(pos + 1);

290 if

(

.length() < 3) {

293 char

ch =

.c_str()[0];

294 if

(ch !=

'S'

&& ch !=

'E'

&& ch !=

'D'

)

return false

;

295

ch =

.c_str()[1];

296 if

(ch !=

'R'

)

return false

;

297

ch =

.c_str()[2];

298 if

(ch !=

'A'

&& ch !=

'P'

&& ch !=

'X'

&& ch !=

'R'

&& ch !=

'S'

&& ch !=

'Z'

)

return false

;

311 if

(!

(*it) && *it !=

'.'

) {

328 string

prefix, remainder;

330 bool

is_insd =

false

, is_refseq =

false

, is_blast =

false

;

339 if

(is_insd || is_refseq) {

340 if

(remainder.length() > 3) {

341 if

(remainder.c_str()[2] ==

'_'

) {

360 size_t

dot_pos =

(remainder,

"."

);

361 if

(dot_pos == string::npos ||

(remainder.substr(dot_pos + 1))) {

364 const string

& cps = remainder.substr(dot_pos + 1);

365 const char

*cp = cps.c_str();

366 while

(*cp != 0 &&

(*cp)) {

375 if

(acc_code == -5 || acc_code == -6) {

377

}

else if

(acc_code != 0) {

379

}

else if

(fetch_accession) {

386

}

else if

(is_blast && is_similar_to) {

388

}

else if

(is_similar_to) {

395 if

(

(remainder,

" "

) != string::npos) {

408

vector<string> accessions;

416

same_species =

false

;

419

same_species =

true

;

420

remainder = remainder.substr(14);

425

remainder = remainder.substr (1);

439

||

(prefix,

"similar to DNA sequence"

)

440

||

(prefix,

"similar to RNA sequence"

)

441

||

(prefix,

"similar to RNA sequence, mRNA"

)

442

||

(prefix,

"similar to RNA sequence, EST"

)

443

||

(prefix,

"similar to RNA sequence, other RNA"

)) {

458 string

prefix, remainder;

459 bool

same_species =

false

;

473 if

(same_species && !is_similar_to) {

478 for

(

size_t i

= 0;

i

< accessions.size();

i

++) {

489 const char

& ch = *str_itr;

494 if

(num_spaces > 3) {

496

}

else if

(num_spaces > 0){

514 bool

found_short =

false

;

518 TSeqPos

last_start = li.GetRange().GetFrom();

519 TSeqPos

last_stop = li.GetRange().GetTo();

521

last_id->

(li.GetSeq_id());

524 while

(li && !found_short) {

525 TSeqPos

this_start = li.GetRange().GetFrom();

526 TSeqPos

this_stop = li.GetRange().GetTo();

527 if

(

((

int

)this_start - (

int

)last_stop) < 11 ||

((

int

)this_stop - (

int

)last_start) < 11) {

528 if

(li.GetSeq_id().Equals(*last_id)) {

535 for

(

auto

id_it : last_bsh.

()) {

536 if

(id_it.GetSeqId()->Equals(li.GetSeq_id())) {

544

last_start = this_start;

545

last_stop = this_stop;

546

last_id->

(li.GetSeq_id());

582 bool

is_short =

false

;

584 if

(! m_Imp.IsIndexerVersion()) {

596

}

else if

(partial_right &&

633 if

((*it)->IsSetData() && (*it)->GetData().IsGene()

652 if

((*it)->IsSetId()) {

653 if

((*it)->GetId().Equals(

id

)) {

655

}

else if

((*it)->GetId().IsLocal()) {

658 if

(!far_feats.empty()) {

672 "Cross-referenced feature does not link reciprocally"

,

689 "CDS not contained within cross-referenced mRNA"

, feat);

696 "Feature gene xref does not match Feature ID cross-referenced gene feature"

,

704 "Cross-references are not between CDS and mRNA pair or between a gene and a CDS or mRNA (" 705

+ label1 +

","

+ label2 +

")"

,

711 "Cross-references are not between CDS and mRNA pair or between a gene and a CDS or mRNA (" 712

+ label1 +

","

+ label2 +

")"

,

717 "Cross-referenced feature does not link reciprocally"

,

725 "CDS not contained within cross-referenced mRNA"

, feat);

730 "Cross-referenced feature does not link reciprocally"

,

734 "Cross-referenced feature does not have its own cross-reference"

, feat);

754 for

(

auto

it = feat.

().begin(); it != feat.

().end(); it++) {

762 if

(!m_Imp.IsStandaloneAnnot() && !

) {

767 "SeqFeatXref with no id or data field"

, feat);

770

vector<CConstRef<CSeq_feat> > far_feats;

771 if

(m_Imp.IsStandaloneAnnot()) {

772 for

(

auto

it = m_Imp.GetSeqAnnot()->GetData().GetFtable().begin(); it != m_Imp.GetSeqAnnot()->GetData().GetFtable().end(); it++) {

774

far_feats.push_back(*it);

779 for

(

auto

it = far_handles.begin(); it != far_handles.end(); it++) {

780

far_feats.push_back(it->GetSeq_feat());

783 if

(far_feats.empty()) {

785 "Cross-referenced feature cannot be found"

,

788 for

(

auto

ff = far_feats.begin(); ff != far_feats.end(); ff++) {

792 if

(xref.

().

() != (*ff)->GetData().Which()) {

794 "SeqFeatXref contains both id and data, data type conflicts with data on feature with id"

,

802 "Cross-referenced feature cannot be found"

,

808 "Gene feature has gene cross-reference"

,

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

@ eErr_SEQ_FEAT_InvalidFeatureForNucleotide

@ eErr_SEQ_FEAT_InvalidFeatureForProtein

@ eErr_SEQ_FEAT_SeqFeatXrefFeatureMissing

@ eErr_SEQ_FEAT_InvalidForType

@ eErr_SEQ_FEAT_UnnecessaryGeneXref

@ eErr_INTERNAL_Exception

@ eErr_SEQ_FEAT_CDSonMinusStrandTranscribedRNA

@ eErr_SEQ_FEAT_SeqFeatXrefProblem

@ eErr_SEQ_FEAT_SeqFeatXrefNotReciprocal

@ eErr_SEQ_FEAT_CDSmRNAXrefLocationProblem

static bool IsLegalInferenceDatabase(const string &db)

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

static void GetPrefixAndRemainder(const string &inference, string &prefix, string &remainder)

static bool ProhibitXref(CSeqFeatData::ESubtype subtype1, CSeqFeatData::ESubtype subtype2)

ESubtype GetSubtype(void) const

string GetKey(EVocabulary vocab=eVocabulary_full) const

static bool AllowXref(CSeqFeatData::ESubtype subtype1, CSeqFeatData::ESubtype subtype2)

namespace ncbi::objects::

bool HasSeqFeatXref(const CSeqFeatXref::TId &id) const

const CGene_ref * GetGeneXref(void) const

See related function in util/feature.hpp.

static bool s_IsPseudo(const CSeq_feat &feat)

static bool s_GeneRefsAreEquivalent(const CGene_ref &g1, const CGene_ref &g2, string &label)

TSeq_feat_Handles GetFeaturesWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

vector< CSeq_feat_Handle > TSeq_feat_Handles

void ValidateSeqFeatXref(const CSeq_feat &feat)

~CValidError_feat() override

bool x_HasNonReciprocalXref(const CSeq_feat &feat, const CFeat_id &id, CSeqFeatData::ESubtype subtype)

CBioseq_Handle x_GetCachedBsh(const CSeq_loc &loc)

void ValidateSeqFeatContext(const CSeq_feat &feat, const CBioseq &seq)

static EInferenceValidCode ValidateInferenceAccession(string accession, bool fetch_accession, bool is_similar_to, CScope *scope=nullptr)

CValidError_feat(CValidError_imp &imp)

void ValidateOneFeatXrefPair(const CSeq_feat &feat, const CSeq_feat &far_feat)

bool IsIntronShort(const CSeq_feat &feat)

void SetTSE(CSeq_entry_Handle seh)

bool GetTSACDSOnMinusStrandErrors(const CSeq_feat &feat, const CBioseq &seq)

bool IsOverlappingGenePseudo(const CSeq_feat &feat)

static bool GetPrefixAndAccessionFromInferenceAccession(string inf_accession, string &prefix, string &accession)

bool DoesCDSHaveShortIntrons(const CSeq_feat &feat)

@ eInferenceValidCode_bad_prefix

@ eInferenceValidCode_spaces

@ eInferenceValidCode_bad_accession_version

@ eInferenceValidCode_comment

@ eInferenceValidCode_same_species_misused

@ eInferenceValidCode_empty

@ eInferenceValidCode_valid

@ eInferenceValidCode_bad_body

@ eInferenceValidCode_single_field

@ eInferenceValidCode_bad_accession

@ eInferenceValidCode_bad_accession_type

@ eInferenceValidCode_accession_version_not_public

@ eInferenceValidCode_unrecognized_database

void ValidateSeqFeat(const CSeq_feat &feat)

void x_ValidateSeqFeatExceptXref(const CSeq_feat &feat)

static EInferenceValidCode ValidateInference(string inference, bool fetch_accession, CScope *scope=nullptr)

static vector< string > GetAccessionsFromInferenceString(string inference, string &prefix, string &remainder, bool &same_species)

CBioseq_Handle GetBioseqHandleFromLocation(CScope *scope, const CSeq_loc &loc, const CTSE_Handle &tse)

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

static const char * str(char *buf, int n)

Public API for finding the gene(s) on a given feature using the same criteria as the flatfile generat...

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

@ eDiag_Fatal

Fatal error â guarantees exit(or abort)

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

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.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eSame

CSeq_locs contain each other.

@ eContained

First CSeq_loc contained by second.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TSeqPos GetBioseqLength(void) const

const CTSE_Handle & GetTSE_Handle(void) const

const TId & GetId(void) const

#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 list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

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

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

@ eNocase

Case insensitive compare.

static const char label[]

TId GetId(void) const

Get the variant data.

EProcessed

processing status

TProcessed GetProcessed(void) const

Get the Processed member data.

bool IsSetProcessed(void) const

Check if a value has been assigned to Processed data member.

@ eProcessed_signal_peptide

@ eProcessed_transit_peptide

const TData & GetData(void) const

Get the Data member data.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsProt(void) const

Check if variant Prot is selected.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

bool IsLocal(void) const

Check if variant Local is selected.

const TId & GetId(void) const

Get the Id member data.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

bool IsSetId(void) const

Check if a value has been assigned to Id data member.

bool IsSetPseudo(void) const

annotated on pseudogene? Check if a value has been assigned to Pseudo data member.

const TGene & GetGene(void) const

Get the variant data.

bool IsSetId(void) const

the feature copied Check if a value has been assigned to Id data member.

const TProt & GetProt(void) const

Get the variant data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

@ e_Txinit

transcription initiation

@ e_Rsite

restriction site (for maps really)

bool IsSetBiomol(void) const

Check if a value has been assigned to Biomol data member.

TTech GetTech(void) const

Get the Tech member data.

TBiomol GetBiomol(void) const

Get the Biomol member data.

bool IsSetTech(void) const

Check if a value has been assigned to Tech data member.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ eTech_tsa

transcriptome shotgun assembly

@ eBiomol_transcribed_RNA

transcribed RNA other than existing classes

@ e_Molinfo

info on the molecule and techniques

constexpr bool empty(list< Ts... >) noexcept

#define FOR_EACH_SEQFEATXREF_ON_SEQFEAT(Itr, Var)

FOR_EACH_SEQFEATXREF_ON_SEQFEAT EDIT_EACH_SEQFEATXREF_ON_SEQFEAT.

#define FOR_EACH_CHAR_IN_STRING(Itr, Var)

FOR_EACH_CHAR_IN_STRING EDIT_EACH_CHAR_IN_STRING.

CSingleFeatValidator * FeatValidatorFactory(const CSeq_feat &feat, CScope &scope, CValidError_imp &imp)

bool s_IsSraPrefix(string str)

static int ValidateAccessionFormat(string accession)

bool GeneXrefConflicts(const CSeq_feat &feat, const CSeq_feat &gene)

bool s_IsAllDigitsOrPeriods(string str)

bool s_HasId(const CSeq_feat &feat, const CSeqFeatXref::TId::TLocal &id)

bool FeaturePairIsTwoTypes(const CSeq_feat &feat1, const CSeq_feat &feat2, CSeqFeatData::ESubtype subtype1, CSeqFeatData::ESubtype subtype2)

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