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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/SeqFeatData_8hpp_source.html below:

NCBI C++ ToolKit: include/objects/seqfeat/SeqFeatData.hpp Source File

88 #ifndef OBJECTS_SEQFEAT_SEQFEATDATA_HPP 89 #define OBJECTS_SEQFEAT_SEQFEATDATA_HPP 126 string

GetKey(EVocabulary vocab = eVocabulary_full)

const

;

134

eSubtype_cdregion = 3,

136

eSubtype_preprotein = 5,

137

eSubtype_mat_peptide_aa = 6,

138

eSubtype_sig_peptide_aa = 7,

139

eSubtype_transit_peptide_aa = 8,

146

eSubtype_snoRNA = 15,

147

eSubtype_otherRNA = 16,

151

eSubtype_allele = 20,

152

eSubtype_attenuator = 21,

153

eSubtype_C_region = 22,

154

eSubtype_CAAT_signal = 23,

155

eSubtype_Imp_CDS = 24,

156

eSubtype_conflict = 25,

157

eSubtype_D_loop = 26,

158

eSubtype_D_segment = 27,

159

eSubtype_enhancer = 28,

161

eSubtype_EC_number = 30,

162

eSubtype_GC_signal = 31,

164

eSubtype_intron = 33,

165

eSubtype_J_segment = 34,

167

eSubtype_mat_peptide = 36,

168

eSubtype_misc_binding = 37,

169

eSubtype_misc_difference = 38,

170

eSubtype_misc_feature = 39,

171

eSubtype_misc_recomb = 40,

172

eSubtype_misc_RNA = 41,

173

eSubtype_misc_signal = 42,

174

eSubtype_misc_structure = 43,

175

eSubtype_modified_base = 44,

176

eSubtype_mutation = 45,

177

eSubtype_N_region = 46,

178

eSubtype_old_sequence = 47,

179

eSubtype_polyA_signal = 48,

180

eSubtype_polyA_site = 49,

181

eSubtype_precursor_RNA = 50,

182

eSubtype_prim_transcript = 51,

183

eSubtype_primer_bind = 52,

184

eSubtype_promoter = 53,

185

eSubtype_protein_bind = 54,

187

eSubtype_repeat_region = 56,

188

eSubtype_repeat_unit = 57,

189

eSubtype_rep_origin = 58,

190

eSubtype_S_region = 59,

191

eSubtype_satellite = 60,

192

eSubtype_sig_peptide = 61,

193

eSubtype_source = 62,

194

eSubtype_stem_loop = 63,

196

eSubtype_TATA_signal = 65,

197

eSubtype_terminator = 66,

198

eSubtype_transit_peptide = 67,

199

eSubtype_unsure = 68,

200

eSubtype_V_region = 69,

201

eSubtype_V_segment = 70,

202

eSubtype_variation = 71,

203

eSubtype_virion = 72,

208

eSubtype_10_signal = 77,

209

eSubtype_35_signal = 78,

211

eSubtype_operon = 80,

213

eSubtype_site_ref = 82,

214

eSubtype_region = 83,

215

eSubtype_comment = 84,

220

eSubtype_txinit = 89,

222

eSubtype_psec_str = 91,

223

eSubtype_non_std_residue = 92,

225

eSubtype_biosrc = 94,

229

eSubtype_variation_ref = 98,

230

eSubtype_mobile_element = 99,

231

eSubtype_centromere = 100,

232

eSubtype_telomere = 101,

233

eSubtype_assembly_gap = 102,

234

eSubtype_regulatory = 103,

235

eSubtype_propeptide = 104,

236

eSubtype_propeptide_aa = 105,

243 void

InvalidateSubtype(

void

)

const

;

246 void

InvalidateCache(

void

)

const

;

249 #define DEFINE_NCBI_SEQFEATDATA_VAL_SETTERS(x) \ 250 void Set##x(const T##x& v) { \ 252 Tparent::Set##x(v); \ 254 T##x& Set##x(void) { \ 256 return Tparent::Set##x(); \ 258 #define DEFINE_NCBI_SEQFEATDATA_SETTERS(x) \ 259 void Set##x(T##x& v) { \ 261 Tparent::Set##x(v); \ 263 T##x& Set##x(void) { \ 265 return Tparent::Set##x(); \ 277 void

SetComment(

void

) {

279

Tparent::SetComment();

294 #undef DEFINE_NCBI_SEQFEATDATA_SETTERS 295 #undef DEFINE_NCBI_SEQFEATDATA_VAL_SETTERS 302 void

PostRead(

void

)

const

;

319 static bool

CanHaveGene(

ESubtype

subtype);

474 bool

IsLegalQualifier(

EQualifier

qual)

const

;

482 const TQualifiers

& GetMandatoryQualifiers(

void

)

const

;

491 static

std::pair<EQualifier, CTempString> GetQualifierTypeAndValue(

CTempString

qual);

497 static bool

IsRegulatory(

ESubtype

subtype);

498 static const string

& GetRegulatoryClass(

ESubtype

subtype);

499 static ESubtype

GetRegulatoryClass(

const string

& class_name );

500 static const

vector<string>& GetRegulatoryClassList();

501 static bool

FixRegulatoryClassValue(

string

val

);

503 static const

vector<string>& GetRecombinationClassList();

505 static bool

IsDiscouragedSubtype(

ESubtype

subtype);

506 static bool

IsDiscouragedQual(

EQualifier

qual);

509

eFeatureLocationAllowed_Any = 0,

515 static

EFeatureLocationAllowed AllowedFeatureLocation(ESubtype subtype);

517 static bool

AllowStrandBoth(ESubtype subtype);

518 static bool

RequireLocationIntervalsInBiologicalOrder(ESubtype subtype);

519 static bool

AllowAdjacentIntervals(ESubtype subtype);

527 static bool

FixImportKey(

string

key

);

528 static bool

IsLegalProductNameForRibosomalSlippage(

const string

& product_name);

538 void

x_InitFeatDataInfo(

void

)

const

;

542 static void

s_InitSubtypesTable(

void

);

559

m_FeatDataInfo.

m_Subtype

= eSubtype_any;

573 return

IsLegalQualifier(

GetSubtype

(), qual);

587 return

GetMandatoryQualifiers(

GetSubtype

());

604

, m_Description(desc)

605

, m_StorageKey(

key

) {}

609 int

GetType()

const

;

611 string

GetDescription()

const

;

612 string

GetStoragekey()

const

;

631

{

return

m_Subtype; }

635

{

return

m_Description; }

639

{

return

m_StorageKey; }

657 bool

TypeValid(

int type

int

subtype)

const

;

661 bool

GetItemBySubtype(

int

subtype,

CFeatListItem

& config_item)

const

;

663 bool

GetItemByDescription(

const string

& desc,

CFeatListItem

& config_item)

const

;

664 bool

GetItemByKey(

const string

key

CFeatListItem

& config_item)

const

;

667 string

GetDescription(

int type

int

subtype)

const

;

671 bool

GetTypeSubType(

const string

& desc,

int

type

int

& subtype)

const

;

674 string

GetStoragekey(

int type

int

subtype)

const

;

676 string

GetStoragekey(

int

subtype)

const

;

681

vector<string> GetStoragekeys(

int

subtype)

const

;

685 void

GetDescriptions(

686

vector<string> &descs,

687 bool

hierarchical =

false 695 size_t size

()

const

;

713 return

m_FeatTypes.size();

720 return

m_FeatTypes.begin();

727 return

m_FeatTypes.end();

744 bool

IsBondName (

string str

)

const

;

753 size_t size

()

const

;

768 return

sm_BondKeys.size();

775 return

sm_BondKeys.begin();

782 return

sm_BondKeys.end();

799 bool

IsSiteName (

string str

)

const

;

808 size_t size

()

const

;

823 return

sm_SiteKeys.size();

830 return

sm_SiteKeys.begin();

837 return

sm_SiteKeys.end();

#define DEFINE_NCBI_SEQFEATDATA_VAL_SETTERS(x)

Override all setters to incorporate cache invalidation.

#define DEFINE_NCBI_SEQFEATDATA_SETTERS(x)

TBondMap::const_iterator const_iterator

void x_Init(void)

initialize our container of feature types and descriptions.

DECLARE_CLASS_STATIC_ARRAY_MAP(TBondMap, sm_BondKeys)

CStaticPairArrayMap< const char *, CSeqFeatData::EBond, PNocase_CStr > TBondMap

const_iterator end() const

const_iterator begin() const

SStaticPair< const char *, CSeqFeatData::EBond > TBondKey

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

string GetStoragekey() const

string m_StorageKey

a short string to use as a key or part of a key when storing a value by key/value string pairs.

string GetDescription() const

CFeatListItem(int type, int subtype, const char *desc, const char *key)

string m_Description

a string for display purposes.

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

const_iterator end() const

TFeatTypeContainer m_FeatTypes

map< int, CFeatListItem > TSubtypeMap

> all valid types and subtypes.

TSubtypeMap m_FeatTypeMap

TFeatTypeContainer::const_iterator const_iterator

const_iterator begin() const

set< CFeatListItem > TFeatTypeContainer

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

bool IsLegalQualifier(EQualifier qual) const

Test wheather a certain qualifier is legal for the feature.

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

SFeatDataInfo m_FeatDataInfo

@ eFeatureLocationAllowed_NucOnly

@ eFeatureLocationAllowed_Error

@ eFeatureLocationAllowed_ProtOnly

EVocabulary

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

const TLegalQualifiers & GetLegalQualifiers(void) const

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

const TQualifiers & GetMandatoryQualifiers(void) const

Get the list of all mandatory qualifiers for the feature.

void InvalidateCache(void) const

Combine invalidation of all cached values.

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.

CSeqFeatData_Base Tparent

Base class for all serializable objects.

void x_Init(void)

initialize our container of feature types and descriptions.

const_iterator begin() const

TSiteMap::const_iterator const_iterator

const_iterator end() const

CStaticPairArrayMap< const char *, CSeqFeatData::ESite, PNocase_CStr > TSiteMap

DECLARE_CLASS_STATIC_ARRAY_MAP(TSiteMap, sm_SiteKeys)

SStaticPair< const char *, CSeqFeatData::ESite > TSiteKey

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 ...

parent_type::const_iterator const_iterator

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

int GetSubtype(CFieldNamePanel *field_name_panel, string &ncRNA_class)

bool operator<(const CEquivRange &A, const CEquivRange &B)

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

ESerialRecursionMode

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

#define NCBISER_HAVE_POST_READ(Class)

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

Set object to copy of another one.

@ eRecursive

Recursively.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_SEQFEAT_EXPORT

E_Choice

Choice variants.

const struct ncbi::grid::netcache::search::fields::SIZE size

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

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

CSeqFeatData::ESubtype m_Subtype

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

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