Search Toolkit Book for CSeq_annot_SNP_Info

#include <objmgr/impl/snp_annot_info.hpp>

Inheritance diagram for CSeq_annot_SNP_Info:

Collaboration diagram for CSeq_annot_SNP_Info:

Public Types
typedef vector< SSNP_Info >	TSNP_Set

typedef TSNP_Set::const_iterator	const_iterator

typedef CRange< TSeqPos >	TRange

typedef vector< char >	TOctetString

Public Types inherited from CTSE_Info_Object
enum	ENeedUpdateAux { kNeedUpdate_bits = 8 }

enum	ENeedUpdate { fNeedUpdate_this = (1<<kNeedUpdate_bits)-1 , fNeedUpdate_children = fNeedUpdate_this<<kNeedUpdate_bits , fNeedUpdate_descr = 1<<0 , fNeedUpdate_annot = 1<<1 , fNeedUpdate_seq_data = 1<<2 , fNeedUpdate_core = 1<<3 , fNeedUpdate_assembly = 1<<4 , fNeedUpdate_bioseq = 1<<5 , fNeedUpdate_children_descr = fNeedUpdate_descr <<kNeedUpdate_bits , fNeedUpdate_children_annot = fNeedUpdate_annot <<kNeedUpdate_bits , fNeedUpdate_children_seq_data = fNeedUpdate_seq_data<<kNeedUpdate_bits , fNeedUpdate_children_core = fNeedUpdate_core <<kNeedUpdate_bits , fNeedUpdate_children_assembly = fNeedUpdate_assembly<<kNeedUpdate_bits , fNeedUpdate_children_bioseq = fNeedUpdate_bioseq <<kNeedUpdate_bits }

typedef map< CConstRef< CObject >, CRef< CObject > >	TObjectCopyMap

typedef int	TNeedUpdateFlags

typedef int	TChunkId

typedef vector< TChunkId >	TChunkIds

Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CSeq_annot_SNP_Info (void)

	CSeq_annot_SNP_Info (CSeq_annot &annot)

	CSeq_annot_SNP_Info (const CSeq_annot_SNP_Info &info)

	~CSeq_annot_SNP_Info (void)

const CSeq_annot_Info &	GetParentSeq_annot_Info (void) const

CSeq_annot_Info &	GetParentSeq_annot_Info (void)

const CSeq_entry_Info &	GetParentSeq_entry_Info (void) const

CSeq_entry_Info &	GetParentSeq_entry_Info (void)

void	x_ParentAttach (CSeq_annot_Info &parent)

void	x_ParentDetach (CSeq_annot_Info &parent)

void	x_UpdateAnnotIndexContents (CTSE_Info &tse)

void	x_UnmapAnnotObjects (CTSE_Info &tse)

void	x_DropAnnotObjects (CTSE_Info &tse)

bool	empty (void) const

size_t	size (void) const

const_iterator	begin (void) const

const_iterator	end (void) const

const_iterator	FirstIn (const TRange &range) const

const CSeq_id &	GetSeq_id (void) const

void	SetSeq_id (const CSeq_id &id)

void	SetGi (TGi gi)

void	OffsetGi (TIntId gi_offset)

size_t	GetSize (void) const

const SSNP_Info &	GetInfo (size_t index) const

size_t	GetIndex (const SSNP_Info &info) const

CSeq_annot &	GetRemainingSeq_annot (void)

void	Reset (void)

bool	HasLabel (size_t index) const

string	GetLabel (size_t index) const

void	x_AddSNP (const SSNP_Info &snp_info)

void	x_FinishParsing (void)

SSNP_Info::TCommentIndex	x_GetCommentIndex (const string &comment)

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

SSNP_Info::TAlleleIndex	x_GetAlleleIndex (const string &allele)

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

SSNP_Info::TQualityCodesIndex	x_GetQualityCodesIndex (const string &str)

SSNP_Info::TQualityCodesIndex	x_GetQualityCodesIndex (const TOctetString &os)

const string &	x_GetQualityCodesStr (SSNP_Info::TQualityCodesIndex index) const

void	x_GetQualityCodesOs (SSNP_Info::TQualityCodesIndex index, TOctetString &os) const

SSNP_Info::TExtraIndex	x_GetExtraIndex (const string &str)

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

const CIndexedStrings &	x_GetComments (void) const

const CIndexedStrings &	x_GetAlleles (void) const

const CIndexedStrings &	x_GetQualityCodesStr (void) const

const CIndexedOctetStrings &	x_GetQualityCodesOs (void) const

Public Member Functions inherited from CTSE_Info_Object
	CTSE_Info_Object (void)

	CTSE_Info_Object (const CTSE_Info_Object &src, TObjectCopyMap *copy_map)

virtual	~CTSE_Info_Object (void)

virtual const CBioObjectId &	GetBioObjectId (void) const

virtual void	SetBioObjectId (const CBioObjectId &id)

bool	HasDataSource (void) const

CDataSource &	GetDataSource (void) const

bool	HasTSE_Info (void) const

bool	BelongsToTSE_Info (const CTSE_Info &tse) const

const CTSE_Info &	GetTSE_Info (void) const

CTSE_Info &	GetTSE_Info (void)

bool	HasParent_Info (void) const

const CTSE_Info_Object &	GetBaseParent_Info (void) const

CTSE_Info_Object &	GetBaseParent_Info (void)

void	x_DSAttach (CDataSource &ds)

void	x_DSDetach (CDataSource &ds)

virtual void	x_DSAttachContents (CDataSource &ds)

virtual void	x_DSDetachContents (CDataSource &ds)

void	x_TSEAttach (CTSE_Info &tse)

void	x_TSEDetach (CTSE_Info &tse)

virtual void	x_TSEAttachContents (CTSE_Info &tse)

virtual void	x_TSEDetachContents (CTSE_Info &tse)

bool	x_DirtyAnnotIndex (void) const

void	x_SetDirtyAnnotIndex (void)

void	x_SetParentDirtyAnnotIndex (void)

void	x_ResetDirtyAnnotIndex (void)

virtual void	x_SetDirtyAnnotIndexNoParent (void)

virtual void	x_ResetDirtyAnnotIndexNoParent (void)

void	x_UpdateAnnotIndex (CTSE_Info &tse)

bool	x_NeedUpdate (ENeedUpdate flag) const

void	x_SetNeedUpdate (TNeedUpdateFlags flags)

virtual void	x_SetNeedUpdateParent (TNeedUpdateFlags flags)

void	x_Update (TNeedUpdateFlags flags) const

void	x_UpdateComplete (void) const

void	x_UpdateCore (void) const

void	x_LoadChunk (TChunkId chunk_id) const

void	x_LoadChunks (const TChunkIds &chunk_ids) const

virtual string	GetDescription (void) const

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Protected Member Functions
bool	x_CheckId (const CSeq_id &id)

void	x_DoUpdate (TNeedUpdateFlags flags)

Protected Member Functions inherited from CTSE_Info_Object
void	x_BaseParentAttach (CTSE_Info_Object &parent)

void	x_BaseParentDetach (CTSE_Info_Object &parent)

void	x_AttachObject (CTSE_Info_Object &object)

void	x_DetachObject (CTSE_Info_Object &object)

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Types
typedef CTSE_Info_Object	TParent

Private Member Functions
CSeq_annot_SNP_Info &	operator= (const CSeq_annot_SNP_Info &)

Private Attributes
CRef< CSeq_id >	m_Seq_id

TSNP_Set	m_SNP_Set

CIndexedStrings	m_Comments

CIndexedStrings	m_Alleles

CIndexedStrings	m_QualityCodesStr

CIndexedOctetStrings	m_QualityCodesOs

CIndexedStrings	m_Extra

CRef< CSeq_annot >	m_Seq_annot

Friends
class	CSeq_annot_Info

class	CSeq_annot_SNP_Info_Reader

struct	SSNP_Info

class	CSeq_feat_Handle

Additional Inherited Members
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Detailed Description

Definition at line 158 of file snp_annot_info.hpp.

Member Typedef Documentation

◆ const_iterator

typedef TSNP_Set::const_iterator CSeq_annot_SNP_Info::const_iterator

Definition at line 182 of file snp_annot_info.hpp.

◆ TOctetString

typedef vector<char> CSeq_annot_SNP_Info::TOctetString

Definition at line 217 of file snp_annot_info.hpp.

◆ TParent

typedef CTSE_Info_Object CSeq_annot_SNP_Info::TParent

private

Definition at line 160 of file snp_annot_info.hpp.

◆ TRange

typedef CRange<TSeqPos> CSeq_annot_SNP_Info::TRange

Definition at line 183 of file snp_annot_info.hpp.

◆ TSNP_Set

typedef vector<SSNP_Info> CSeq_annot_SNP_Info::TSNP_Set

Definition at line 181 of file snp_annot_info.hpp.

Constructor & Destructor Documentation

◆ CSeq_annot_SNP_Info() [1/3]

CSeq_annot_SNP_Info::CSeq_annot_SNP_Info ( void )

Definition at line 809 of file snp_annot_info.cpp.

◆ CSeq_annot_SNP_Info() [2/3]

CSeq_annot_SNP_Info::CSeq_annot_SNP_Info ( CSeq_annot & annot )

Definition at line 814 of file snp_annot_info.cpp.

◆ CSeq_annot_SNP_Info() [3/3]

CSeq_annot_SNP_Info::CSeq_annot_SNP_Info ( const CSeq_annot_SNP_Info & info )

Definition at line 820 of file snp_annot_info.cpp.

◆ ~CSeq_annot_SNP_Info()

CSeq_annot_SNP_Info::~CSeq_annot_SNP_Info ( void )

Definition at line 833 of file snp_annot_info.cpp.

Member Function Documentation

◆ begin()

CSeq_annot_SNP_Info::const_iterator CSeq_annot_SNP_Info::begin ( void ) const

inline

Definition at line 281 of file snp_annot_info.hpp.

References m_SNP_Set.

◆ empty()

bool CSeq_annot_SNP_Info::empty ( void ) const

inline

Definition at line 266 of file snp_annot_info.hpp.

References m_SNP_Set.

Referenced by GetPackedFeatAnnot().

◆ end()

CSeq_annot_SNP_Info::const_iterator CSeq_annot_SNP_Info::end ( void ) const

inline

Definition at line 289 of file snp_annot_info.hpp.

References m_SNP_Set.

Referenced by CAnnot_Collector::x_SearchObjects().

◆ FirstIn()

CSeq_annot_SNP_Info::const_iterator CSeq_annot_SNP_Info::FirstIn ( const TRange & range ) const

inline

Definition at line 297 of file snp_annot_info.hpp.

References m_SNP_Set, and compile_time_bits::range().

Referenced by CAnnot_Collector::x_SearchObjects().

◆ GetIndex()

size_t CSeq_annot_SNP_Info::GetIndex ( const SSNP_Info & info ) const

inline

Definition at line 424 of file snp_annot_info.hpp.

References _ASSERT, info, and m_SNP_Set.

◆ GetInfo()

const SSNP_Info & CSeq_annot_SNP_Info::GetInfo ( size_t index ) const

inline

Definition at line 416 of file snp_annot_info.hpp.

References _ASSERT, and m_SNP_Set.

Referenced by GetLabel(), CCreateFeat::GetOriginalFeat(), CAnnotObject_Ref::GetSNP_Info(), HasLabel(), and CSeq_feat_Handle::x_GetSNP_InfoAny().

◆ GetLabel()

string CSeq_annot_SNP_Info::GetLabel ( size_t index ) const

inline

Definition at line 439 of file snp_annot_info.hpp.

References GetInfo(), and SSNP_Info::GetLabel().

Referenced by CSeq_annot_Info::TableFeat_GetLabel().

◆ GetParentSeq_annot_Info() [1/2]

CSeq_annot_Info & CSeq_annot_SNP_Info::GetParentSeq_annot_Info ( void )

Definition at line 844 of file snp_annot_info.cpp.

References CTSE_Info_Object::GetBaseParent_Info().

◆ GetParentSeq_annot_Info() [2/2]

const CSeq_annot_Info & CSeq_annot_SNP_Info::GetParentSeq_annot_Info ( void ) const

Definition at line 838 of file snp_annot_info.cpp.

References CTSE_Info_Object::GetBaseParent_Info().

Referenced by GetParentSeq_entry_Info(), CAnnot_Collector::x_SearchObjects(), CSeq_annot_Info::x_SetSNP_annot_Info(), CSeq_annot_Info::x_TSEAttachContents(), x_UnmapAnnotObjects(), and x_UpdateAnnotIndexContents().

◆ GetParentSeq_entry_Info() [1/2]

CSeq_entry_Info & CSeq_annot_SNP_Info::GetParentSeq_entry_Info ( void )

Definition at line 856 of file snp_annot_info.cpp.

References GetParentSeq_annot_Info(), and CSeq_annot_Info::GetParentSeq_entry_Info().

◆ GetParentSeq_entry_Info() [2/2]

const CSeq_entry_Info & CSeq_annot_SNP_Info::GetParentSeq_entry_Info ( void ) const

Definition at line 850 of file snp_annot_info.cpp.

References GetParentSeq_annot_Info(), and CSeq_annot_Info::GetParentSeq_entry_Info().

◆ GetRemainingSeq_annot()

CSeq_annot & CSeq_annot_SNP_Info::GetRemainingSeq_annot ( void )

inline

Definition at line 311 of file snp_annot_info.hpp.

References m_Seq_annot.

Referenced by CSeq_annot_Info::x_SetSNP_annot_Info().

◆ GetSeq_id()

const CSeq_id & CSeq_annot_SNP_Info::GetSeq_id ( void ) const

inline

Definition at line 304 of file snp_annot_info.hpp.

References m_Seq_id.

Referenced by CAnnotObject_Ref::CAnnotObject_Ref(), CSeq_feat_Handle::GetSNPGi(), CSeq_feat_Handle::GetSNPSeq_id(), x_UnmapAnnotObjects(), x_UpdateAnnotIndexContents(), SSNP_Info::x_UpdateSeq_feat(), and CSeq_annot_SNP_Info_Reader::x_Write().

◆ GetSize()

size_t CSeq_annot_SNP_Info::GetSize ( void ) const

inline

Definition at line 409 of file snp_annot_info.hpp.

References m_SNP_Set.

◆ HasLabel()

bool CSeq_annot_SNP_Info::HasLabel ( size_t index ) const

inline

Definition at line 432 of file snp_annot_info.hpp.

References GetInfo(), and SSNP_Info::HasLabel().

Referenced by CSeq_annot_Info::TableFeat_HasLabel().

◆ OffsetGi()

void CSeq_annot_SNP_Info::OffsetGi ( TIntId gi_offset )

Definition at line 1071 of file snp_annot_info.cpp.

References CSeq_id_Base::GetGi(), GI_FROM, CSeq_id_Base::IsGi(), m_Seq_id, and CSeq_id_Base::SetGi().

◆ operator=()

CSeq_annot_SNP_Info& CSeq_annot_SNP_Info::operator= ( const CSeq_annot_SNP_Info & )

private

◆ Reset()

void CSeq_annot_SNP_Info::Reset ( void )

Definition at line 1094 of file snp_annot_info.cpp.

References CIndexedStrings::Clear(), CIndexedOctetStrings::Clear(), m_Alleles, m_Comments, m_Extra, m_QualityCodesOs, m_QualityCodesStr, m_Seq_annot, m_Seq_id, m_SNP_Set, and CRef< C, Locker >::Reset().

Referenced by CSeq_annot_SNP_Info_Reader::x_Read().

◆ SetGi()

void CSeq_annot_SNP_Info::SetGi ( TGi gi )

Definition at line 1064 of file snp_annot_info.cpp.

References m_Seq_id, and CSeq_id_Base::SetGi().

◆ SetSeq_id()

void CSeq_annot_SNP_Info::SetSeq_id ( const CSeq_id & id )

Definition at line 1058 of file snp_annot_info.cpp.

References m_Seq_id, and SerialClone().

Referenced by GetPackedFeatAnnot(), and CSeq_annot_SNP_Info_Reader::x_Read().

◆ size()

size_t CSeq_annot_SNP_Info::size ( void ) const

inline

Definition at line 273 of file snp_annot_info.hpp.

References m_SNP_Set.

◆ x_AddSNP()

void CSeq_annot_SNP_Info::x_AddSNP ( const SSNP_Info & snp_info )

inline

Definition at line 402 of file snp_annot_info.hpp.

References m_SNP_Set.

Referenced by x_ParseSNP_Info().

◆ x_CheckId()

bool CSeq_annot_SNP_Info::x_CheckId ( const CSeq_id & id )

inlineprotected

Definition at line 140 of file snp_annot_info.cpp.

References CSerialObject::Equals(), CSeq_id_Base::GetGi(), CSeq_id_Base::IsGi(), m_Seq_id, and SerialClone().

Referenced by SSNP_Info::ParseSeq_feat().

◆ x_DoUpdate()

void CSeq_annot_SNP_Info::x_DoUpdate ( TNeedUpdateFlags flags )

protectedvirtual

Reimplemented from CTSE_Info_Object.

Definition at line 894 of file snp_annot_info.cpp.

References flags, and CTSE_Info_Object::x_DoUpdate().

◆ x_DropAnnotObjects()

void CSeq_annot_SNP_Info::x_DropAnnotObjects ( CTSE_Info & tse )

Definition at line 889 of file snp_annot_info.cpp.

Referenced by CSeq_annot_Info::x_DropAnnotObjects().

◆ x_FinishParsing()

void CSeq_annot_SNP_Info::x_FinishParsing ( void )

Definition at line 1079 of file snp_annot_info.cpp.

References CIndexedStrings::ClearIndices(), CIndexedOctetStrings::ClearIndices(), m_Alleles, m_Comments, m_Extra, m_QualityCodesOs, m_QualityCodesStr, m_SNP_Set, ct::sort(), and CTSE_Info_Object::x_SetDirtyAnnotIndex().

◆ x_GetAllele()

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

inline

Definition at line 371 of file snp_annot_info.hpp.

References CIndexedStrings::GetString(), and m_Alleles.

Referenced by SSNP_Info::GetLabel(), CSeq_feat_Handle::GetSNPAllele(), and SSNP_Info::x_UpdateSeq_featData().

◆ x_GetAlleleIndex()

SSNP_Info::TAlleleIndex CSeq_annot_SNP_Info::x_GetAlleleIndex ( const string & allele )

Definition at line 1037 of file snp_annot_info.cpp.

References CIndexedStrings::GetIndex(), CIndexedStrings::IsEmpty(), SSNP_Info::kMax_AlleleIndex, and m_Alleles.

Referenced by SSNP_Info::ParseSeq_feat(), and x_ParseSNP_Info().

◆ x_GetAlleles()

const CIndexedStrings& CSeq_annot_SNP_Info::x_GetAlleles ( void ) const

inline

Definition at line 227 of file snp_annot_info.hpp.

References m_Alleles.

◆ x_GetComment()

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

inline

Definition at line 363 of file snp_annot_info.hpp.

References CIndexedStrings::GetString(), and m_Comments.

Referenced by CSeq_feat_Handle::GetSNPComment(), and SSNP_Info::x_UpdateSeq_featData().

◆ x_GetCommentIndex()

SSNP_Info::TCommentIndex CSeq_annot_SNP_Info::x_GetCommentIndex ( const string & comment )

inline

Definition at line 319 of file snp_annot_info.hpp.

References CIndexedStrings::GetIndex(), SSNP_Info::kMax_CommentIndex, and m_Comments.

Referenced by SSNP_Info::ParseSeq_feat().

◆ x_GetComments()

const CIndexedStrings& CSeq_annot_SNP_Info::x_GetComments ( void ) const

inline

Definition at line 224 of file snp_annot_info.hpp.

References m_Comments.

◆ x_GetExtra()

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

inline

Definition at line 395 of file snp_annot_info.hpp.

References CIndexedStrings::GetString(), and m_Extra.

Referenced by CSeq_feat_Handle::GetSNPExtra(), and SSNP_Info::x_UpdateSeq_featData().

◆ x_GetExtraIndex()

SSNP_Info::TExtraIndex CSeq_annot_SNP_Info::x_GetExtraIndex ( const string & str )

inline

Definition at line 330 of file snp_annot_info.hpp.

References CIndexedStrings::GetIndex(), SSNP_Info::kMax_ExtraIndex, m_Extra, and str().

Referenced by SSNP_Info::ParseSeq_feat().

◆ x_GetQualityCodesIndex() [1/2]

SSNP_Info::TQualityCodesIndex CSeq_annot_SNP_Info::x_GetQualityCodesIndex ( const string & str )

inline

Definition at line 341 of file snp_annot_info.hpp.

References CIndexedStrings::GetIndex(), SSNP_Info::kMax_QualityCodesIndex, m_QualityCodesStr, and str().

Referenced by SSNP_Info::ParseSeq_feat(), and x_ParseSNP_Info().

◆ x_GetQualityCodesIndex() [2/2]

SSNP_Info::TQualityCodesIndex CSeq_annot_SNP_Info::x_GetQualityCodesIndex ( const TOctetString & os )

inline

Definition at line 352 of file snp_annot_info.hpp.

References CIndexedOctetStrings::GetIndex(), SSNP_Info::kMax_QualityCodesIndex, and m_QualityCodesOs.

◆ x_GetQualityCodesOs() [1/2]

void CSeq_annot_SNP_Info::x_GetQualityCodesOs	(	SSNP_Info::TQualityCodesIndex	index,
		TOctetString &	os
	)		const

inline

Definition at line 386 of file snp_annot_info.hpp.

References CIndexedOctetStrings::GetString(), and m_QualityCodesOs.

Referenced by CSeq_feat_Handle::GetSNPQualityCodeOs(), and SSNP_Info::x_UpdateSeq_featData().

◆ x_GetQualityCodesOs() [2/2]

const CIndexedOctetStrings& CSeq_annot_SNP_Info::x_GetQualityCodesOs ( void ) const

inline

Definition at line 233 of file snp_annot_info.hpp.

References m_QualityCodesOs.

◆ x_GetQualityCodesStr() [1/2]

const string & CSeq_annot_SNP_Info::x_GetQualityCodesStr ( SSNP_Info::TQualityCodesIndex index ) const

inline

Definition at line 379 of file snp_annot_info.hpp.

References CIndexedStrings::GetString(), and m_QualityCodesStr.

Referenced by CSeq_feat_Handle::GetSNPQualityCodeStr(), and SSNP_Info::x_UpdateSeq_featData().

◆ x_GetQualityCodesStr() [2/2]

const CIndexedStrings& CSeq_annot_SNP_Info::x_GetQualityCodesStr ( void ) const

inline

Definition at line 230 of file snp_annot_info.hpp.

References m_QualityCodesStr.

◆ x_ParentAttach()

void CSeq_annot_SNP_Info::x_ParentAttach ( CSeq_annot_Info & parent )

Definition at line 862 of file snp_annot_info.cpp.

References CTSE_Info_Object::x_BaseParentAttach().

Referenced by CSeq_annot_Info::x_SetObject(), CSeq_annot_Info::x_SetSNP_annot_Info(), and CSeq_annot_Info::x_TSEAttachContents().

◆ x_ParentDetach()

void CSeq_annot_SNP_Info::x_ParentDetach ( CSeq_annot_Info & parent )

Definition at line 868 of file snp_annot_info.cpp.

References CTSE_Info_Object::x_BaseParentDetach().

◆ x_UnmapAnnotObjects()

void CSeq_annot_SNP_Info::x_UnmapAnnotObjects ( CTSE_Info & tse )

Definition at line 882 of file snp_annot_info.cpp.

References CSeq_id_Handle::GetHandle(), GetParentSeq_annot_Info(), GetSeq_id(), and CTSE_Info::x_UnmapSNP_Table().

Referenced by CSeq_annot_Info::x_UnmapAnnotObjects().

◆ x_UpdateAnnotIndexContents()

void CSeq_annot_SNP_Info::x_UpdateAnnotIndexContents ( CTSE_Info & tse )

virtual

Reimplemented from CTSE_Info_Object.

Definition at line 874 of file snp_annot_info.cpp.

References CSeq_id_Handle::GetHandle(), GetParentSeq_annot_Info(), GetSeq_id(), CTSE_Info::x_MapSNP_Table(), and CTSE_Info_Object::x_UpdateAnnotIndexContents().

Friends And Related Function Documentation

◆ CSeq_annot_Info

friend class CSeq_annot_Info

friend

Definition at line 245 of file snp_annot_info.hpp.

◆ CSeq_annot_SNP_Info_Reader

friend class CSeq_annot_SNP_Info_Reader

friend

Definition at line 246 of file snp_annot_info.hpp.

◆ CSeq_feat_Handle

friend class CSeq_feat_Handle

friend

Definition at line 248 of file snp_annot_info.hpp.

◆ SSNP_Info

friend struct SSNP_Info

friend

Definition at line 247 of file snp_annot_info.hpp.

Member Data Documentation

◆ m_Alleles

CIndexedStrings CSeq_annot_SNP_Info::m_Alleles

private

Definition at line 253 of file snp_annot_info.hpp.

Referenced by Reset(), x_FinishParsing(), x_GetAllele(), x_GetAlleleIndex(), x_GetAlleles(), CSeq_annot_SNP_Info_Reader::x_Read(), and CSeq_annot_SNP_Info_Reader::x_Write().

◆ m_Comments

CIndexedStrings CSeq_annot_SNP_Info::m_Comments

private

Definition at line 252 of file snp_annot_info.hpp.

Referenced by Reset(), x_FinishParsing(), x_GetComment(), x_GetCommentIndex(), x_GetComments(), CSeq_annot_SNP_Info_Reader::x_Read(), and CSeq_annot_SNP_Info_Reader::x_Write().

◆ m_Extra

CIndexedStrings CSeq_annot_SNP_Info::m_Extra

private

Definition at line 256 of file snp_annot_info.hpp.

Referenced by Reset(), x_FinishParsing(), x_GetExtra(), x_GetExtraIndex(), CSeq_annot_SNP_Info_Reader::x_Read(), and CSeq_annot_SNP_Info_Reader::x_Write().

◆ m_QualityCodesOs

CIndexedOctetStrings CSeq_annot_SNP_Info::m_QualityCodesOs

private

Definition at line 255 of file snp_annot_info.hpp.

Referenced by Reset(), x_FinishParsing(), x_GetQualityCodesIndex(), x_GetQualityCodesOs(), CSeq_annot_SNP_Info_Reader::x_Read(), and CSeq_annot_SNP_Info_Reader::x_Write().

◆ m_QualityCodesStr

CIndexedStrings CSeq_annot_SNP_Info::m_QualityCodesStr

private

Definition at line 254 of file snp_annot_info.hpp.

Referenced by Reset(), x_FinishParsing(), x_GetQualityCodesIndex(), x_GetQualityCodesStr(), CSeq_annot_SNP_Info_Reader::x_Read(), and CSeq_annot_SNP_Info_Reader::x_Write().

◆ m_Seq_annot

CRef<CSeq_annot> CSeq_annot_SNP_Info::m_Seq_annot

private

Definition at line 257 of file snp_annot_info.hpp.

Referenced by GetRemainingSeq_annot(), CSeq_annot_SNP_Info_Reader::Read(), Reset(), and CSeq_annot_SNP_Info_Reader::Write().

◆ m_Seq_id

CRef<CSeq_id> CSeq_annot_SNP_Info::m_Seq_id

private

Definition at line 250 of file snp_annot_info.hpp.

Referenced by GetSeq_id(), OffsetGi(), Reset(), SetGi(), SetSeq_id(), and x_CheckId().

◆ m_SNP_Set

TSNP_Set CSeq_annot_SNP_Info::m_SNP_Set

private

Definition at line 251 of file snp_annot_info.hpp.

Referenced by begin(), empty(), end(), FirstIn(), GetIndex(), GetInfo(), GetSize(), Reset(), size(), x_AddSNP(), x_FinishParsing(), CSeq_annot_SNP_Info_Reader::x_Read(), and CSeq_annot_SNP_Info_Reader::x_Write().

The documentation for this class was generated from the following files:

include/objmgr/impl/snp_annot_info.hpp
src/objmgr/snp_annot_info.cpp

Public Types

Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ const_iterator

◆ TOctetString

◆ TParent

◆ TRange

◆ TSNP_Set

Constructor & Destructor Documentation

◆ CSeq_annot_SNP_Info() [1/3]

◆ CSeq_annot_SNP_Info() [2/3]

◆ CSeq_annot_SNP_Info() [3/3]

◆ ~CSeq_annot_SNP_Info()

Member Function Documentation

◆ begin()

◆ empty()

◆ end()

◆ FirstIn()

◆ GetIndex()

◆ GetInfo()

◆ GetLabel()

◆ GetParentSeq_annot_Info() [1/2]

◆ GetParentSeq_annot_Info() [2/2]

◆ GetParentSeq_entry_Info() [1/2]

◆ GetParentSeq_entry_Info() [2/2]

◆ GetRemainingSeq_annot()

◆ GetSeq_id()

◆ GetSize()

◆ HasLabel()

◆ OffsetGi()

◆ operator=()

◆ Reset()

◆ SetGi()

◆ SetSeq_id()

◆ size()

◆ x_AddSNP()

◆ x_CheckId()

◆ x_DoUpdate()

◆ x_DropAnnotObjects()

◆ x_FinishParsing()

◆ x_GetAllele()

◆ x_GetAlleleIndex()

◆ x_GetAlleles()

◆ x_GetComment()

◆ x_GetCommentIndex()

◆ x_GetComments()

◆ x_GetExtra()

◆ x_GetExtraIndex()

◆ x_GetQualityCodesIndex() [1/2]

◆ x_GetQualityCodesIndex() [2/2]

◆ x_GetQualityCodesOs() [1/2]

◆ x_GetQualityCodesOs() [2/2]

◆ x_GetQualityCodesStr() [1/2]

◆ x_GetQualityCodesStr() [2/2]

◆ x_ParentAttach()

◆ x_ParentDetach()

◆ x_UnmapAnnotObjects()

◆ x_UpdateAnnotIndexContents()

Friends And Related Function Documentation

◆ CSeq_annot_Info

◆ CSeq_annot_SNP_Info_Reader

◆ CSeq_feat_Handle

◆ SSNP_Info

Member Data Documentation

◆ m_Alleles

◆ m_Comments

◆ m_Extra

◆ m_QualityCodesOs

◆ m_QualityCodesStr

◆ m_Seq_annot

◆ m_Seq_id

◆ m_SNP_Set