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

SetTaxon3(make_shared<CTaxon3>());

shared_ptr<SValidatorContext> pContext):

(!

.empty() && remote) {

( !imp.

(se,

, scope) ) {

imp.

(se,

, scope);

stp = string::npos;

*ptr =

.c_str();

|| (*ptr ==

&& allowcomma)

|| (*ptr ==

&& (allowperiod || pos == stp))) {

tail =

.substr(pos);

last_is_bad =

;

badauthor = author.

();

last_is_bad =

;

(int_prv && !compar(*int_cur, *int_prv, scope)) {

*int_cur =

, *int_prv =

;

(; lit &&

; ++lit) {

(loc_choice) {

int_cur = &lit->GetInt();

= compar(*int_cur, *int_prv, &scope);

(lit->GetPacked_int(), this_int_cur, this_int_prv, &scope, compar);

}

(

exception& ) {

(strand1 == strand2);

(use_geo_loc_name) {

(xref.

().

().find(

) != string::npos) {

& db = xref.

();

src_db =

;

refseq_db =

;

(xref.

(refseq_db, src_db, correct_caps)) {

(is_biosource && !src_db) {

(refseq_db && is_refseq_or_gps) {

(refseq_db && !is_refseq_or_gps) {

User-defined methods of the data storage class.

@ eErr_SEQ_DESCR_LatLonWater

@ eErr_SEQ_DESCR_LatLonCountry

@ eErr_SEQ_DESCR_LatLonValue

@ eErr_SEQ_DESCR_LatLonGeoLocName

@ eErr_SEQ_DESCR_LatLonState

CValidator::CCacheImpl CCacheImpl

bool GetDBFlags(bool &is_refseq, bool &is_src, string &correct_caps) const

@Name_std.hpp User-defined methods of the data storage class.

Base class for all object manager exceptions.

@Pubdesc.hpp User-defined methods of the data storage class.

namespace ncbi::objects::

static bool NCBI_UseGeoLocNameForCountry(void)

@ eLatLonCountryErr_Value

@ eLatLonCountryErr_State

@ eLatLonCountryErr_Water

@ eLatLonCountryErr_Country

Template class for iteration on objects of class C (non-medifiable version)

static void SetSuppressionRules(const CUser_object &user, CValidError &errors)

bool IsValidStructuredComment(const CSeqdesc &desc)

size_t GetGeneCount(void) const

TSuppressed & SetSuppressed()

bool GetTSAConflictingBiomolTechErrors(const CSeq_entry_Handle &se)

bool Validate(const CSeq_entry &se, const CCit_sub *cs=nullptr, CScope *scope=nullptr)

const CValidatorEntryInfo & GetEntryInfo() const

size_t GetCumulativeInferenceCount(void) const

SValidatorContext & SetContext()

void SetProgressCallback(CValidator::TProgressCallback callback, void *user_data)

bool GetTSACDSOnMinusStrandErrors(const CSeq_entry_Handle &se)

bool GetTSANStretchErrors(const CSeq_entry_Handle &se)

size_t GetGeneXrefCount(void) const

CRef< CValidError > Validate(const CSeq_entry &se, CScope *scope=nullptr, Uint4 options=0)

CRef< CObjectManager > m_ObjMgr

CConstRef< CValidError > GetTSANStretchErrors(const CSeq_entry_Handle &se)

void x_SetEntryInfo(const TEntryInfo &info)

CConstRef< CValidError > GetTSACDSOnMinusStrandErrors(const CSeq_entry_Handle &se)

unique_ptr< CValidatorEntryInfo > m_pEntryInfo

static CRef< CCache > MakeEmptyCache()

TProgressCallback m_PrgCallback

static TDbxrefValidFlags IsValidDbxref(const CDbtag &xref, bool is_biosource, bool is_refseq_or_gps)

static bool BadCharsInAuthorFirstName(const string &str)

shared_ptr< SValidatorContext > m_pContext

static bool DoesSeqLocContainDuplicateIntervals(const CSeq_loc &loc, CScope &scope)

void SetProgressCallback(TProgressCallback callback, void *user_data=nullptr)

CConstRef< CValidError > GetTSAConflictingBiomolTechErrors(const CSeq_entry_Handle &se)

const TEntryInfo & GetEntryInfo() const

static bool BadCharsInAuthorInitials(const string &str)

static EErrType ConvertCode(CSubSource::ELatLonCountryErr errcode)

static bool DoesSeqLocContainAdjacentIntervals(const CSeq_loc &loc, CScope &scope)

static bool BadCharsInAuthorName(const string &str, bool allowcomma, bool allowperiod, bool last)

bool IsValidStructuredComment(const CSeqdesc &desc) const

shared_ptr< ITaxon3 > m_pOwnTaxon

CValidatorEntryInfo TEntryInfo

static string BadCharsInAuthor(const CName_std &author, bool &last_is_bad)

static bool IsSeqLocCorrectlyOrdered(const CSeq_loc &loc, CScope &scope)

static bool BadCharsInAuthorLastName(const string &str)

void SetTaxon3(shared_ptr< ITaxon3 > taxon)

bool IsSetEntryInfo() const

static taxupdate_func_t MakeTaxUpdateFunction(shared_ptr< ITaxon3 > taxon)

static bool BadCharsInAuthorSuffix(const string &str)

CValidator(CObjectManager &objmgr)

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

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

CCache(TSizeType capacity, THandler *handler=NULL)

Create cache object with the given capacity.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

TInst_Topology GetInst_Topology(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

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

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

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

Case-sensitive equality of a substring with another 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 enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to 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.

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

Author, Primary or Secondary Check if a value has been assigned to Name data member.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetDb(void) const

name of database or system Check if a value has been assigned to Db data member.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsSetSuffix(void) const

Jr, Sr, III Check if a value has been assigned to Suffix data member.

bool IsId(void) const

Check if variant Id is selected.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

const TInitials & GetInitials(void) const

Get the Initials member data.

bool IsName(void) const

Check if variant Name is selected.

const TDb & GetDb(void) const

Get the Db member data.

bool IsSetInitials(void) const

first + middle initials Check if a value has been assigned to Initials data member.

bool IsSetLast(void) const

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

const TStr & GetStr(void) const

Get the variant data.

const TSuffix & GetSuffix(void) const

Get the Suffix member data.

const TFirst & GetFirst(void) const

Get the First member data.

const TLast & GetLast(void) const

Get the Last member data.

const TName & GetName(void) const

Get the variant data.

bool IsSetFirst(void) const

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

TId GetId(void) const

Get the variant data.

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

const TId & GetId(void) const

Get the Id member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsSetStrand(void) const

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

TStrand GetStrand(void) const

Get the Strand member data.

TTo GetTo(void) const

Get the To member data.

E_Choice

Choice variants.

bool IsUser(void) const

Check if variant User is selected.

function< CRef< CTaxon3_reply >(const vector< CRef< COrg_ref > > &list)> taxupdate_func_t

bool ContainsSgml(const string &str)

bool x_CompareConsecutiveIntervals(const CPacked_seqint &packed_int, CConstRef< CSeq_interval > &int_cur, CConstRef< CSeq_interval > &int_prv, CScope *scope, CompareConsecutiveIntervalProc compar)

bool x_IsNotAdjacent(const CSeq_interval &int_cur, const CSeq_interval &int_prv, CScope *scope)

bool x_IsCorrectlyOrdered(const CSeq_interval &int_cur, const CSeq_interval &int_prv, CScope *scope)

bool CheckConsecutiveIntervals(const CSeq_loc &loc, CScope &scope, CompareConsecutiveIntervalProc compar)

bool(* CompareConsecutiveIntervalProc)(const CSeq_interval &int1, const CSeq_interval &int2, CScope *scope)

bool IsNotDuplicateInterval(const CSeq_interval &int1, const CSeq_interval &int2, CScope *scope)

bool x_SameStrand(const CSeq_interval &int1, const CSeq_interval &int2)

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