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NCBI C++ ToolKit: src/objects/seqfeat/SeqFeatData.cpp Source File

(Non_std_residue, non_std_residue,

,

),

(signal_peptide, sig_peptide_aa,

,

),

(transit_peptide, transit_peptide_aa,

,

),

(propeptide, propeptide_aa,

,

)

(premsg, preRNA,

,

),

sc_ProtInfoPairs.find(

().GetProcessed());

(it != sc_ProtInfoPairs.end()) {

(it != sc_SiteInfoPairs.end()) {

sc_RnaInfoPairs.find(rna_type);

(it != sc_RnaInfoPairs.end()) {

& ext_name = (can_get_name

(ext_name ==

) {

}

(ext_name ==

) {

(it != sc_InfoPairs.end()) {

it = sm_FeatKeys.first.find(sName);

(it == sm_FeatKeys.first.end())

(sName ==

)

eSubtype_preRNA;

it = sm_FeatKeys.second.

(eSubtype);

(it == sm_FeatKeys.second.end())

iter = sx_MandatoryQuals.find(subtype);

(iter == sx_MandatoryQuals.end()) {

( e_Non_std_residue, eSubtype_non_std_residue, 92),

( e_Variation, eSubtype_variation_ref, 98),

<<

;

(

==

) {

<< setw(20) <<

<<

<< setw(30) <<

.m_Name <<

<< setw(3) <<

.m_Subtype <<

;

g_legal_quals;

it->second.test(qual);

iter = sc_QualPairs.first.

(qual);

(iter == sc_QualPairs.first.end())

iter->second;

iter = sc_QualPairs.second.find(qual);

(iter != sc_QualPairs.second.end())

iter->second;

iter = sc_QualPairs.second.find(qual);

(iter != sc_QualPairs.second.end())

{ iter->second,

};

<

_Ty,

_W

th>

constexpr

width = _Width;

table_t = std::array<TBitset, width>;

init_t = std::pair<_Ty, _Ty>;

non_empty_pair = std::pair<_Ty, TBitset>;

<

N>

constexpr TPairsMatrix(

init_t(&

)[

])

row_t = std::array<bool, width>;

init_matrix_t = std::array<row_t, width>;

init_matrix_t matrix{};

(

& rec :

)

matrix[rec.first][rec.second] =

;

matrix[rec.second][rec.first] =

;

m_table = assemble_table(matrix, std::make_index_sequence<width>{});

(

= 0;

< width; ++

)

(!m_table[

].

())

m_non_empty_indices[

++] =

;

m_non_empty_count =

;

constexpr

NonEmptyCount()

m_non_empty_count;

<

N>

(

std::array<non_empty_pair, N>&

, _Ty v1, _Ty

)

it = std::lower_bound(

.begin(),

.end(), v1, [](

left,

right)

return left.first < right;

(it !=

.end())

it->second.test(

);

(

table_t&

, _Ty v1, _Ty

)

<

N>

constexpr

select_bitsets()

select_bitsets(std::make_index_sequence<N>{});

constexpr

get_bitsets()

<

_Matrix,

...Ints>

constexpr

assemble_table(

_Matrix&

, std::index_sequence<Ints...>)

{ { TBitset{

[Ints]} ... } };

<

I>

constexpr non_empty_pair make_row()

{ _Ty(m_non_empty_indices[I]), m_table[m_non_empty_indices[I]] };

<

...Ints>

constexpr

select_bitsets(std::index_sequence<Ints...>)

-> std::array<non_empty_pair,

...(Ints) >

{ { make_row<Ints>() ... } };

std::array<size_t, width> m_non_empty_indices{};

m_non_empty_count{ 0 };

CAssembleSubTypePairs = TPairsMatrix<CSeqFeatData::ESubtype, CSeqFeatData::eSubtype_max>;

constexpr CAssembleSubTypePairs::init_t g_allowed_pairs[] = {

constexpr CAssembleSubTypePairs::init_t g_prohibited_pairs[] = {

constexpr CAssembleSubTypePairs g_allowed_init(g_allowed_pairs);

constexpr CAssembleSubTypePairs g_prohibited_init(g_prohibited_pairs);

constexpr

g_allowed_xrefs = g_allowed_init.get_bitsets();

constexpr

g_prohibited_xrefs = g_prohibited_init.get_bitsets();

constexpr

g_allowed_xrefs = g_allowed_init.select_bitsets<g_allowed_init.NonEmptyCount()>();

constexpr

g_prohibited_xrefs = g_prohibited_init.select_bitsets<g_prohibited_init.NonEmptyCount()>();

unique_ptr<CFeatList> theFeatList;

( !theFeatList.get() ) {

( !theFeatList.get() ) {

theFeatList.get();

unique_ptr<CBondList> theBondList;

( !theBondList.get() ) {

( !theBondList.get() ) {

theBondList.get();

unique_ptr<CSiteList> theSiteList;

( !theSiteList.get() ) {

( !theSiteList.get() ) {

theSiteList.get();

regulatory_subtypes_set.

(subtype) !=

regulatory_subtypes_set.

() );

FCreateSubtypeNameMap {

TSubtypeToNameMap * Create() {

( regulatory_subtypes_set.

() == p_new_map->size() );

TSubtypeNameElem sc_subtype_name_map[] = {

TSubtypeNameElem & subtype_name_elem =

sc_subtype_name_map[special_case_idx];

(*p_new_map)[subtype_name_elem.first] =

subtype_name_elem.second;

( regulatory_subtypes_set.

() == p_new_map->size() );

FCreateSubtypeNameMap::Create);

TSubtypeToNameMap::const_iterator find_iter =

sc_SubtypeToNameMap->find(subtype);

( find_iter != sc_SubtypeToNameMap->end() ) {

find_iter->second;

FCreateNameToSubtypeMap {

TNameToSubtypeMap * Create() {

& class_name =

(*p_new_map)[class_name] = *subtype_iter;

( p_new_map->size() == regulatory_subtypes_set.

() );

FCreateNameToSubtypeMap::Create);

TNameToSubtypeMap::const_iterator find_iter =

ms_NameToSubtypeMap->find(class_name);

( find_iter != ms_NameToSubtypeMap->end() ) {

find_iter->second;

vector<string> choices = {

,

,

,

,

,

,

,

,

,

,

,

,

vector<string> regulatory_class_values;

(regulatory_class_values.empty()) {

original =

;

(valid_val !=

) {

original !=

;

vector<string> choices = {

,

,

constexpr

discouraged_subtypes {

(discouraged_subtypes.test(subtype))

(discouraged_quals.test(qual))

config_item = *ci_it;

config_item = fm_it->second;

(; ci_it !=

(); ++ci_it) {

config_item = *ci_it;

(; ci_it !=

(); ++ci_it) {

(ci_it->GetStoragekey() ==

) {

config_item = *ci_it;

vector<string> keys;

(

= 0;

< config_item_size; ++

) {

iep->m_Subtype, iep->m_Name, iep->m_Name);

this_desc = iter->GetDescription();

parent_desc = this_desc;

( ! parent_desc.empty()) {

this_desc = parent_desc +

+ this_desc;

descs.push_back(this_desc);

string::size_type pos = 0;

((pos =

(str1,

, pos)) != NCBI_NS_STD::string::npos) {

(ci_it != sm_BondKeys.end ()) {

(ci_it != sm_BondKeys.end ()) {

bond_type = ci_it->second;

(ci_it == sm_BondKeys.end()) {

ci_it->second;

(ci_it != sm_SiteKeys.end ()) {

(ci_it != sm_SiteKeys.end ()) {

site_type = ci_it->second;

(ci_it == sm_SiteKeys.end()) {

ci_it->second;

regulatory_subtypes [] = {

, sc_RegulatorySubtypes, regulatory_subtypes);

sc_RegulatorySubtypes;

required =

;

(feat_subtype)

allowed =

;

(feat_subtype)

=

;

=

;

=

;

& productName)

vector<string> matchPhrases{

,

};

vector<string> containedPhrases{

,

};

(

& phrase: matchPhrases) {

(phrase == productName) {

(

& phrase: containedPhrases) {

(productName.find(phrase) != string::npos) {

MAKE_TWOWAY_CONST_MAP(sm_FeatKeys, ct::tagStrNocase, CSeqFeatData::ESubtype, { { "-10_signal", CSeqFeatData::eSubtype_10_signal }, { "-35_signal", CSeqFeatData::eSubtype_35_signal }, { "3'UTR", CSeqFeatData::eSubtype_3UTR }, { "3'clip", CSeqFeatData::eSubtype_3clip }, { "5'UTR", CSeqFeatData::eSubtype_5UTR }, { "5'clip", CSeqFeatData::eSubtype_5clip }, { "Bond", CSeqFeatData::eSubtype_bond }, { "CAAT_signal", CSeqFeatData::eSubtype_CAAT_signal }, { "CDS", CSeqFeatData::eSubtype_cdregion }, { "C_region", CSeqFeatData::eSubtype_C_region }, { "Cit", CSeqFeatData::eSubtype_pub }, { "CloneRef", CSeqFeatData::eSubtype_clone }, { "Comment", CSeqFeatData::eSubtype_comment }, { "D-loop", CSeqFeatData::eSubtype_D_loop }, { "D_segment", CSeqFeatData::eSubtype_D_segment }, { "GC_signal", CSeqFeatData::eSubtype_GC_signal }, { "Het", CSeqFeatData::eSubtype_het }, { "J_segment", CSeqFeatData::eSubtype_J_segment }, { "LTR", CSeqFeatData::eSubtype_LTR }, { "N_region", CSeqFeatData::eSubtype_N_region }, { "NonStdRes", CSeqFeatData::eSubtype_non_std_residue }, { "Num", CSeqFeatData::eSubtype_num }, { "Protein", CSeqFeatData::eSubtype_prot }, { "RBS", CSeqFeatData::eSubtype_RBS }, { "REFERENCE", CSeqFeatData::eSubtype_pub }, { "Region", CSeqFeatData::eSubtype_region }, { "Rsite", CSeqFeatData::eSubtype_rsite }, { "STS", CSeqFeatData::eSubtype_STS }, { "S_region", CSeqFeatData::eSubtype_S_region }, { "SecStr", CSeqFeatData::eSubtype_psec_str }, { "Site", CSeqFeatData::eSubtype_site }, { "Site-ref", CSeqFeatData::eSubtype_site_ref }, { "Src", CSeqFeatData::eSubtype_biosrc }, { "TATA_signal", CSeqFeatData::eSubtype_TATA_signal }, { "TxInit", CSeqFeatData::eSubtype_txinit }, { "User", CSeqFeatData::eSubtype_user }, { "V_region", CSeqFeatData::eSubtype_V_region }, { "V_segment", CSeqFeatData::eSubtype_V_segment }, { "VariationRef", CSeqFeatData::eSubtype_variation_ref }, { "Xref", CSeqFeatData::eSubtype_seq }, { "assembly_gap", CSeqFeatData::eSubtype_assembly_gap }, { "attenuator", CSeqFeatData::eSubtype_attenuator }, { "centromere", CSeqFeatData::eSubtype_centromere }, { "conflict", CSeqFeatData::eSubtype_conflict }, { "enhancer", CSeqFeatData::eSubtype_enhancer }, { "exon", CSeqFeatData::eSubtype_exon }, { "gap", CSeqFeatData::eSubtype_gap }, { "gene", CSeqFeatData::eSubtype_gene }, { "iDNA", CSeqFeatData::eSubtype_iDNA }, { "intron", CSeqFeatData::eSubtype_intron }, { "mRNA", CSeqFeatData::eSubtype_mRNA }, { "mat_peptide", CSeqFeatData::eSubtype_mat_peptide_aa }, { "mat_peptide_nt", CSeqFeatData::eSubtype_mat_peptide }, { "misc_RNA", CSeqFeatData::eSubtype_otherRNA }, { "misc_binding", CSeqFeatData::eSubtype_misc_binding }, { "misc_difference", CSeqFeatData::eSubtype_misc_difference }, { "misc_feature", CSeqFeatData::eSubtype_misc_feature }, { "misc_recomb", CSeqFeatData::eSubtype_misc_recomb }, { "misc_signal", CSeqFeatData::eSubtype_misc_signal }, { "misc_structure", CSeqFeatData::eSubtype_misc_structure }, { "mobile_element", CSeqFeatData::eSubtype_mobile_element }, { "modified_base", CSeqFeatData::eSubtype_modified_base }, { "ncRNA", CSeqFeatData::eSubtype_ncRNA }, { "old_sequence", CSeqFeatData::eSubtype_old_sequence }, { "operon", CSeqFeatData::eSubtype_operon }, { "oriT", CSeqFeatData::eSubtype_oriT }, { "polyA_signal", CSeqFeatData::eSubtype_polyA_signal }, { "polyA_site", CSeqFeatData::eSubtype_polyA_site }, { "precursor_RNA", CSeqFeatData::eSubtype_preRNA }, { "prim_transcript", CSeqFeatData::eSubtype_prim_transcript }, { "primer_bind", CSeqFeatData::eSubtype_primer_bind }, { "promoter", CSeqFeatData::eSubtype_promoter }, { "propeptide", CSeqFeatData::eSubtype_propeptide_aa }, { "propeptide_nt", CSeqFeatData::eSubtype_propeptide }, { "proprotein", CSeqFeatData::eSubtype_preprotein }, { "protein_bind", CSeqFeatData::eSubtype_protein_bind }, { "rRNA", CSeqFeatData::eSubtype_rRNA }, { "regulatory", CSeqFeatData::eSubtype_regulatory }, { "rep_origin", CSeqFeatData::eSubtype_rep_origin }, { "repeat_region", CSeqFeatData::eSubtype_repeat_region }, { "repeat_unit", CSeqFeatData::eSubtype_repeat_unit }, { "satellite", CSeqFeatData::eSubtype_satellite }, { "scRNA", CSeqFeatData::eSubtype_scRNA }, { "sig_peptide", CSeqFeatData::eSubtype_sig_peptide_aa }, { "sig_peptide_nt", CSeqFeatData::eSubtype_sig_peptide }, { "snRNA", CSeqFeatData::eSubtype_snRNA }, { "snoRNA", CSeqFeatData::eSubtype_snoRNA }, { "source", CSeqFeatData::eSubtype_biosrc }, { "stem_loop", CSeqFeatData::eSubtype_stem_loop }, { "tRNA", CSeqFeatData::eSubtype_tRNA }, { "telomere", CSeqFeatData::eSubtype_telomere }, { "terminator", CSeqFeatData::eSubtype_terminator }, { "tmRNA", CSeqFeatData::eSubtype_tmRNA }, { "transit_peptide", CSeqFeatData::eSubtype_transit_peptide_aa }, { "transit_peptide_nt", CSeqFeatData::eSubtype_transit_peptide }, { "unsure", CSeqFeatData::eSubtype_unsure }, { "variation", CSeqFeatData::eSubtype_variation }, { "virion", CSeqFeatData::eSubtype_virion } }) CSeqFeatData

vector< CSeqFeatData::E_Choice > TSubtypesTable

static CSafeStatic< TSubtypesTable > sx_SubtypesTable

string x_SpaceToDash(string str1)

#define ADD_XREF_PAIR(x, y)

#define SITE_INFO_PAIR(site, subtype, key_full, key_gb)

static const CBondList::TBondKey bond_key_to_subtype[]

static const CSiteList::TSiteKey site_key_to_subtype[]

SStaticPair< CProt_ref::EProcessed, CSeqFeatData::SFeatDataInfo > TProtInfoPair

static const SImportEntry *const kImportTableEnd

CStaticPairArrayMap< CRNA_ref::EType, CSeqFeatData::SFeatDataInfo > TRnaInfoMap

static const SFeatListItem sc_ConfigItemInit[]

CStaticPairArrayMap< CSeqFeatData::ESite, CSeqFeatData::SFeatDataInfo > TSiteInfoMap

#define RNA_INFO_PAIR(rna, subtype, key_full, key_gb)

static const SSubtypeInfo s_subtype_info[]

#define PROT_INFO_PAIR(proc, subtype, key_full, key_gb)

CStaticPairArrayMap< CProt_ref::EProcessed, CSeqFeatData::SFeatDataInfo > TProtInfoMap

SStaticPair< CSeqFeatData::ESite, CSeqFeatData::SFeatDataInfo > TSiteInfoPair

#define FEAT_INFO_PAIR(type, subtype, key_full, key_gb)

SStaticPair< CSeqFeatData::E_Choice, CSeqFeatData::SFeatDataInfo > TInfoPair

DEFINE_STATIC_ARRAY_MAP(TInfoMap, sc_InfoPairs, kInfoPairs)

CStaticPairArrayMap< CSeqFeatData::E_Choice, CSeqFeatData::SFeatDataInfo > TInfoMap

static atomic< bool > sx_SubtypesTableInitialized

#define SUBTYPE_INFO(type, subtype, value)

DEFINE_CLASS_STATIC_ARRAY_MAP(CBondList::TBondMap, CBondList::sm_BondKeys, bond_key_to_subtype)

static const size_t s_subtype_count

SStaticPair< CRNA_ref::EType, CSeqFeatData::SFeatDataInfo > TRnaInfoPair

static const TSiteInfoPair kSiteInfoPairs[]

static const TInfoPair kInfoPairs[]

DEFINE_STATIC_MUTEX(sx_InitTablesMutex)

static const TProtInfoPair kProtInfoPairs[]

static const TRnaInfoPair kRnaInfoPairs[]

static const SImportEntry kImportTable[]

CSeqFeatData::EBond GetBondType(string str) const

TBondMap::const_iterator const_iterator

bool IsBondName(string str) const

CFeatListItem - basic configuration data for one "feature" type.

string GetStoragekey() const

int m_Subtype

Feature subtype or eSubtype_any for default values.

string GetDescription() const

int m_Type

Feature type, or e_not_set for default values.

bool operator<(const CFeatListItem &rhs) const

CFeatListItem comparator to sort the set properly.

CConfigurableItems - a static list of items that can be configured.

const_iterator end() const

bool GetItemBySubtype(int subtype, CFeatListItem &config_item) const

void x_Init(void)

initialize our container of feature types and descriptions.

string GetStoragekey(int type, int subtype) const

Get the key used to store this type of feature.

TFeatTypeContainer m_FeatTypes

bool GetItemByKey(const string &key, CFeatListItem &config_item) const

string GetDescription(int type, int subtype) const

Get the displayable description of this type of feature.

vector< string > GetStoragekeys(int subtype) const

Get hierarchy of keys above this subtype, starting with "Master" example, eSubtype_gene,...

bool GetTypeSubType(const string &desc, int &type, int &subtype) const

Get the feature's type and subtype from its description.

TSubtypeMap m_FeatTypeMap

TFeatTypeContainer::const_iterator const_iterator

bool GetItem(int type, int subtype, CFeatListItem &config_item) const

can get all static information for one type/subtype.

bool GetItemByDescription(const string &desc, CFeatListItem &config_item) const

void GetDescriptions(vector< string > &descs, bool hierarchical=false) const

return a list of all the feature descriptions for a menu or other control.

const_iterator begin() const

bool TypeValid(int type, int subtype) const

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

static const string & GetRegulatoryClass(ESubtype subtype)

static bool ShouldRepresentAsGbqual(CSeqFeatData::ESubtype feat_subtype, const CGb_qual &qual)

bool IsLegalQualifier(EQualifier qual) const

Test wheather a certain qualifier is legal for the feature.

static bool IsDiscouragedQual(EQualifier qual)

static const TSubtypeSet & GetSetOfRegulatorySubtypes()

static EFeatureLocationAllowed AllowedFeatureLocation(ESubtype subtype)

EQualifier

List of available qualifiers for feature keys.

@ eQual_environmental_sample

@ eQual_recombination_class

@ eQual_UniProtKB_evidence

@ eQual_culture_collection

@ eQual_ribosomal_slippage

@ eQual_calculated_mol_wt

@ eQual_metagenome_source

@ eQual_mobile_element_type

@ eQual_artificial_location

static bool CanHaveGene(ESubtype subtype)

void PostRead(void) const

Invalidate subtype cache after deserialization.

static const TSubTypeQualifiersMap & s_GetLegalQualMap() noexcept

SFeatDataInfo m_FeatDataInfo

@ eFeatureLocationAllowed_NucOnly

@ eFeatureLocationAllowed_Error

@ eFeatureLocationAllowed_ProtOnly

@ eFeatureLocationAllowed_Any

static bool IsLegalProductNameForRibosomalSlippage(const string &product_name)

EVocabulary

ASCII representation of subtype (GenBank feature key, e.g.)

static const CSiteList * GetSiteList()

static bool AllowStrandBoth(ESubtype subtype)

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

ESubtype GetSubtype(void) const

static void s_InitSubtypesTable(void)

static bool RequireLocationIntervalsInBiologicalOrder(ESubtype subtype)

const TLegalQualifiers & GetLegalQualifiers(void) const

Get a list of all the legal qualifiers for the feature.

string GetKey(EVocabulary vocab=eVocabulary_full) const

const TQualifiers & GetMandatoryQualifiers(void) const

Get the list of all mandatory qualifiers for the feature.

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

Override Assign() to incorporate cache invalidation.

void x_InitFeatDataInfo(void) const

static bool FixRegulatoryClassValue(string &val)

static bool IsDiscouragedSubtype(ESubtype subtype)

static E_Choice GetTypeFromSubtype(ESubtype subtype)

static bool AllowAdjacentIntervals(ESubtype subtype)

static const vector< string > & GetRecombinationClassList()

static std::pair< EQualifier, CTempString > GetQualifierTypeAndValue(CTempString qual)

static const CFeatList * GetFeatList()

CSeqFeatData(void)

constructor

static bool FixImportKey(string &key)

void InvalidateCache(void) const

Combine invalidation of all cached values.

@ eSubtype_transit_peptide

@ eSubtype_misc_difference

@ eSubtype_misc_structure

@ eSubtype_bad

These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.

@ eSubtype_mobile_element

@ eSubtype_prim_transcript

@ eSubtype_transit_peptide_aa

@ eSubtype_non_std_residue

@ eSubtype_sig_peptide_aa

@ eSubtype_mat_peptide_aa

static EQualifier GetQualifierType(CTempString qual)

convert qual string to enumerated value

static const CBondList * GetBondList()

static CTempString GetQualifierAsString(EQualifier qual)

Convert a qualifier from an enumerated value to a string representation or empty if not found.

static ESubtype SubtypeNameToValue(CTempString sName)

Turn a string into its ESubtype which is NOT necessarily related to the identifier of the enum.

static CTempString SubtypeValueToName(ESubtype eSubtype)

Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum...

static bool IsRegulatory(ESubtype subtype)

static const vector< string > & GetRegulatoryClassList()

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

~CSeqFeatData(void)

destructor

Base class for all serializable objects.

bool IsSiteName(string str) const

TSiteMap::const_iterator const_iterator

CSeqFeatData::ESite GetSiteType(string str) const

const_iterator find(const key_type &key) const

Return a const_iterator pointing to the specified element, or to the end if the element is not found.

const_iterator end() const

Return the end of the controlled sequence.

size_type size() const

Return number of elements in the container.

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

TBase::const_iterator const_iterator

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

static constexpr const_bitset set_range(T _from, T _to)

const_iterator find(intermediate key) const

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

#define MAKE_CONST_MAP(name, type1, type2,...)

static void DLIST_NAME() init(DLIST_LIST_TYPE *list)

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

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

#define ITERATE_0_IDX(idx, up_to)

idx loops from 0 (inclusive) to up_to (exclusive)

constexpr size_t ArraySize(const Element(&)[Size])

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * release(void)

Release will release ownership of pointer to caller.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

ESerialRecursionMode

How to assign and compare child sub-objects of serial objects.

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

Set object to copy of another one.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Case-insensitive equality of a substring with another string.

size_type find(const CTempString match, size_type pos=0) const

Find the first instance of the entire matching string within the current string, beginning at an opti...

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.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

EProcessed

processing status

TType GetType(void) const

Get the Type member data.

EType

type of RNA feature

bool CanGetExt(void) const

Check if it is safe to call GetExt method.

const TName & GetName(void) const

Get the variant data.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsName(void) const

Check if variant Name is selected.

const TKey & GetKey(void) const

Get the Key member data.

E_Choice Which(void) const

Which variant is currently selected.

E_Choice

Choice variants.

bool IsSetQual(void) const

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

TSite GetSite(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

const TQual & GetQual(void) const

Get the Qual member data.

const TRna & GetRna(void) const

Get the variant data.

const TImp & GetImp(void) const

Get the variant data.

@ eSite_transmembrane_region

@ eSite_pyrrolidone_carboxylic_acid

@ eSite_gamma_carboxyglutamic_acid

@ eSite_oxidative_deamination

@ e_Het

cofactor, prosthetic grp, etc, bound to seq

@ e_not_set

No variant selected.

@ e_Region

named region (globin locus)

@ e_Seq

to annotate origin from another seq

@ e_Txinit

transcription initiation

@ e_Num

a numbering system

@ e_Pub

publication applies to this seq

@ e_User

user defined structure

@ e_Rsite

restriction site (for maps really)

@ e_Comment

just a comment

@ e_Non_std_residue

non-standard residue here in seq

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

std::false_type tagStrNocase

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

void Check(const string &value)

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

int strcmp(const char *str1, const char *str2)

std::istream & in(std::istream &in_, double &x_)

#define DEFINE_STATIC_ARRAY_MAP_WITH_COPY(Type, Var, Array)

CSeqFeatData::ESubtype m_Subtype

const char * m_Description

const char * m_StorageKey

CSeqFeatData::E_Choice m_Type

CSeqFeatData::ESubtype m_Subtype

CSeqFeatData::ESubtype m_Subtype

bool operator<(const SImportEntry &e) const

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

CSeqFeatData::E_Choice m_Type

CSeqFeatData::ESubtype m_Subtype

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