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NCBI C++ ToolKit: include/objmgr/impl/snp_annot_info.hpp Source File

1 #ifndef SNP_ANNOT_INFO__HPP 2 #define SNP_ANNOT_INFO__HPP 73  void

ClearIndices(

void

);

78  return

m_Strings.empty();

82  return

m_Strings.size();

85  size_t

GetIndex(

const string

& s,

size_t

max_index);

89  return

m_Strings[index];

92  void

Resize(

size_t

new_size);

95  return

m_Strings[index];

115  void

ClearIndices(

void

);

120  return

m_Strings.empty();

124  return

m_ElementSize;

128  return

m_Strings.size();

132  size_t size

= GetTotalSize();

134  size

/= GetElementSize();

142  void

SetTotalString(

size_t

element_size, TOctetString& s);

144  size_t

GetIndex(

const

TOctetString& s,

size_t

max_index);

146  void

GetString(

size_t

index, TOctetString&)

const

;

177  void

x_UpdateAnnotIndexContents(

CTSE_Info

& tse);

178  void

x_UnmapAnnotObjects(

CTSE_Info

& tse);

179  void

x_DropAnnotObjects(

CTSE_Info

& tse);

185  bool empty

(

void

)

const

;

186  size_t size

(

void

)

const

;

192  const CSeq_id

& GetSeq_id(

void

)

const

;

193  void

SetSeq_id(

const CSeq_id

&

id

);

196  void

OffsetGi(

TIntId

gi_offset);

198  size_t

GetSize(

void

)

const

;

199  const SSNP_Info

& GetInfo(

size_t

index)

const

;

205  bool

HasLabel(

size_t

index)

const

;

206  string GetLabel

(

size_t

index)

const

;

209  void

x_AddSNP(

const SSNP_Info

& snp_info);

210  void

x_FinishParsing(

void

);

231  return

m_QualityCodesStr;

234  return

m_QualityCodesOs;

238  bool

x_CheckId(

const CSeq_id

&

id

);

240  void

x_DoUpdate(TNeedUpdateFlags

flags

);

size_t GetSize(void) const

size_t GetIndex(const TOctetString &s, size_t max_index)

size_t GetTotalSize(void) const

vector< char > TOctetString

unique_ptr< TIndices > m_Indices

void GetString(size_t index, TOctetString &) const

size_t GetElementSize(void) const

map< CTempString, size_t > TIndices

const TOctetString & GetTotalString(void) const

map< string, size_t > TIndices

string & SetString(size_t index)

vector< string > TStrings

size_t GetIndex(const string &s, size_t max_index)

const string & GetString(size_t index) const

unique_ptr< TIndices > m_Indices

size_t GetSize(void) const

bool HasLabel(size_t index) const

const CIndexedStrings & x_GetComments(void) const

vector< char > TOctetString

const CIndexedOctetStrings & x_GetQualityCodesOs(void) const

SSNP_Info::TQualityCodesIndex x_GetQualityCodesIndex(const string &str)

const CSeq_id & GetSeq_id(void) const

CIndexedStrings m_Alleles

const SSNP_Info & GetInfo(size_t index) const

const string & x_GetExtra(SSNP_Info::TExtraIndex index) const

TSNP_Set::const_iterator const_iterator

SSNP_Info::TExtraIndex x_GetExtraIndex(const string &str)

CIndexedStrings m_Comments

const CIndexedStrings & x_GetQualityCodesStr(void) const

CRef< CSeq_annot > m_Seq_annot

string GetLabel(size_t index) const

SSNP_Info::TCommentIndex x_GetCommentIndex(const string &comment)

CIndexedStrings m_QualityCodesStr

const string & x_GetComment(SSNP_Info::TCommentIndex index) const

CSeq_annot_SNP_Info & operator=(const CSeq_annot_SNP_Info &)

const CIndexedStrings & x_GetAlleles(void) const

size_t GetIndex(const SSNP_Info &info) const

const_iterator begin(void) const

vector< SSNP_Info > TSNP_Set

const string & x_GetAllele(SSNP_Info::TAlleleIndex index) const

void x_AddSNP(const SSNP_Info &snp_info)

CSeq_annot & GetRemainingSeq_annot(void)

const_iterator end(void) const

size_t GetSize(void) const

const_iterator FirstIn(const TRange &range) const

CIndexedOctetStrings m_QualityCodesOs

namespace ncbi::objects::

A very basic data-read interface.

A very basic data-write interface.

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

string GetLabel(const CSeq_id &id)

#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_XOBJMGR_EXPORT

TFrom GetFrom(void) const

Get the From member data.

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

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

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

string GetLabel(const CSeq_annot_SNP_Info &info) const

bool HasLabel(const CSeq_annot_SNP_Info &info) const

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