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NCBI C++ ToolKit: include/objtools/validator/validator.hpp Source File

1 #ifndef VALIDATOR___VALIDATOR__HPP 2 #define VALIDATOR___VALIDATOR__HPP 81

eVal_no_context = 0x2,

84

eVal_ovl_pep_err = 0x10,

85

eVal_seqsubmit_parent = 0x20,

86

eVal_need_isojta = 0x40,

87

eVal_validate_id_set = 0x80,

88

eVal_remote_fetch = 0x100,

89

eVal_far_fetch_mrna_products = 0x200,

90

eVal_far_fetch_cds_products = 0x400,

91

eVal_locus_tag_general_match = 0x800,

92

eVal_do_rubisco_test = 0x1000,

93

eVal_indexer_version = 0x2000,

94

eVal_use_entrez = 0x4000,

95

eVal_inference_accns = 0x8000,

96

eVal_ignore_exceptions = 0x10000,

97

eVal_report_splice_as_error = 0x20000,

98

eVal_latlon_check_state = 0x40000,

99

eVal_latlon_ignore_water = 0x80000,

100

eVal_genome_submission = 0x100000,

101

eVal_do_tax_lookup = 0x200000,

102

eVal_do_barcode_tests = 0x400000,

103

eVal_refseq_conventions = 0x800000,

104

eVal_collect_locus_tags = 0x1000000,

105

eVal_generate_golden_file = 0x2000000,

106

eVal_compare_vdjc_to_cds = 0x4000000,

107

eVal_ignore_inferences = 0x10000000,

108

eVal_force_inferences = 0x20000000,

109

eVal_new_strain_validation = 0x40000000,

118

shared_ptr<SValidatorContext> pContext);

120  void

SetTaxon3(shared_ptr<ITaxon3> taxon);

211  void

Validate(

const CPubdesc

& desc,

221  void

Validate(

const CSeqdesc

& desc,

227  bool

IsValidStructuredComment(

const CSeqdesc

& desc)

const

;

237  static bool

BadCharsInAuthorName(

const string

&

str

,

bool

allowcomma,

bool

allowperiod,

bool last

);

238  static bool

BadCharsInAuthorLastName(

const string

&

str

);

239  static bool

BadCharsInAuthorFirstName(

const string

&

str

);

240  static bool

BadCharsInAuthorInitials(

const string

&

str

);

241  static bool

BadCharsInAuthorSuffix(

const string

&

str

);

242  static string

BadCharsInAuthor(

const CName_std

& author,

bool

& last_is_bad);

243  static string

BadCharsInAuthor(

const CAuthor

& author,

bool

& last_is_bad);

245  static bool

IsSeqLocCorrectlyOrdered(

const CSeq_loc

& loc,

CScope

& scope);

246  static bool

DoesSeqLocContainAdjacentIntervals(

const CSeq_loc

& loc,

CScope

& scope);

247  static bool

DoesSeqLocContainDuplicateIntervals(

const CSeq_loc

& loc,

CScope

& scope);

267

m_Total(0), m_TotalDone(0),

268

m_Current(0), m_CurrentDone(0),

302

eRefSeqNotForSource = 64,

303

eBadCapitalization = 128,

312  bool

IsSetEntryInfo()

const

;

322  void

* m_UserData=

nullptr

;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CValidator::CCache CCache

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

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

namespace ncbi::objects::

CValidator::TProgressCallback m_PrgCallback

const CValidatorEntryInfo & GetEntryInfo() const

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

shared_ptr< SValidatorContext > m_pContext

CValidatorEntryInfo & x_SetEntryInfo()

Cache various information for one validation run.

size_t GetTotalDone() const

void * GetUserData() const

size_t GetCurrentDone() const

size_t GetCurrent() const

CRef< CObjectManager > m_ObjMgr

unique_ptr< CValidatorEntryInfo > m_pEntryInfo

CValidator & operator=(const CValidator &)=delete

shared_ptr< SValidatorContext > m_pContext

CValidator(const CValidator &)=delete

SValidatorContext & SetContext()

shared_ptr< ITaxon3 > m_pOwnTaxon

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)

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.

#define NCBI_VALIDATOR_EXPORT

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

Defines NCBI C++ diagnostic APIs, classes, and macros.


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