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CSeq_annot_SNP_Info Class Reference

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_InfoTSNP_Set
 
typedef TSNP_Set::const_iterator const_iterator
 
typedef CRange< TSeqPosTRange
 
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< TChunkIdTChunkIds
 
- 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< Uint8TCounter
 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_InfoGetParentSeq_annot_Info (void) const
 
CSeq_annot_InfoGetParentSeq_annot_Info (void)
 
const CSeq_entry_InfoGetParentSeq_entry_Info (void) const
 
CSeq_entry_InfoGetParentSeq_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_idGetSeq_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_InfoGetInfo (size_t index) const
 
size_t GetIndex (const SSNP_Info &info) const
 
CSeq_annotGetRemainingSeq_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 stringx_GetComment (SSNP_Info::TCommentIndex index) const
 
SSNP_Info::TAlleleIndex x_GetAlleleIndex (const string &allele)
 
const stringx_GetAllele (SSNP_Info::TAlleleIndex index) const
 
SSNP_Info::TQualityCodesIndex x_GetQualityCodesIndex (const string &str)
 
SSNP_Info::TQualityCodesIndex x_GetQualityCodesIndex (const TOctetString &os)
 
const stringx_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 stringx_GetExtra (SSNP_Info::TExtraIndex index) const
 
const CIndexedStringsx_GetComments (void) const
 
const CIndexedStringsx_GetAlleles (void) const
 
const CIndexedStringsx_GetQualityCodesStr (void) const
 
const CIndexedOctetStringsx_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 CBioObjectIdGetBioObjectId (void) const
 
virtual void SetBioObjectId (const CBioObjectId &id)
 
bool HasDataSource (void) const
 
CDataSourceGetDataSource (void) const
 
bool HasTSE_Info (void) const
 
bool BelongsToTSE_Info (const CTSE_Info &tse) const
 
const CTSE_InfoGetTSE_Info (void) const
 
CTSE_InfoGetTSE_Info (void)
 
bool HasParent_Info (void) const
 
const CTSE_Info_ObjectGetBaseParent_Info (void) const
 
CTSE_Info_ObjectGetBaseParent_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...
 
CObjectoperator= (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_Infooperator= (const CSeq_annot_SNP_Info &)
 

Private Attributes

CRef< CSeq_idm_Seq_id
 
TSNP_Set m_SNP_Set
 
CIndexedStrings m_Comments
 
CIndexedStrings m_Alleles
 
CIndexedStrings m_QualityCodesStr
 
CIndexedOctetStrings m_QualityCodesOs
 
CIndexedStrings m_Extra
 
CRef< CSeq_annotm_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

Definition at line 160 of file snp_annot_info.hpp.

◆ TRange

Definition at line 183 of file snp_annot_info.hpp.

◆ 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

◆ 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

◆ GetParentSeq_entry_Info() [1/2]

CSeq_entry_Info & CSeq_annot_SNP_Info::GetParentSeq_entry_Info ( void  )

◆ GetParentSeq_entry_Info() [2/2]

const CSeq_entry_Info & CSeq_annot_SNP_Info::GetParentSeq_entry_Info ( void  ) const

◆ 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

◆ 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)

◆ operator=()

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

◆ Reset()

void CSeq_annot_SNP_Info::Reset ( void  )

◆ 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

◆ 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  )

◆ x_GetAllele()

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

◆ x_GetAlleleIndex()

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

◆ 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

◆ x_GetCommentIndex()

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

◆ 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

◆ x_GetExtraIndex()

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

◆ x_GetQualityCodesIndex() [1/2]

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

◆ x_GetQualityCodesIndex() [2/2]

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

◆ x_GetQualityCodesOs() [1/2]

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

◆ 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

◆ 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)

◆ 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)

◆ x_UpdateAnnotIndexContents()

void CSeq_annot_SNP_Info::x_UpdateAnnotIndexContents ( CTSE_Info tse)
virtual

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

◆ m_Comments

CIndexedStrings CSeq_annot_SNP_Info::m_Comments
private

◆ m_Extra

CIndexedStrings CSeq_annot_SNP_Info::m_Extra
private

◆ m_QualityCodesOs

CIndexedOctetStrings CSeq_annot_SNP_Info::m_QualityCodesOs
private

◆ m_QualityCodesStr

CIndexedStrings CSeq_annot_SNP_Info::m_QualityCodesStr
private

◆ m_Seq_annot

CRef<CSeq_annot> CSeq_annot_SNP_Info::m_Seq_annot
private

◆ 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

The documentation for this class was generated from the following files:
Modified on Tue Apr 23 07:40:59 2024 by modify_doxy.py rev. 669887