Default IAlnSeqId implementation based on CSeq_id_Handle. More...

#include <objtools/alnmgr/aln_seqid.hpp>

Inheritance diagram for CAlnSeqId:

Collaboration diagram for CAlnSeqId:

Public Member Functions
	CAlnSeqId (const CSeq_id &id)
	Constructor. More...

virtual const CSeq_id &	GetSeqId (void) const
	Get CSeq_id. More...

virtual string	AsString (void) const
	Sequence label - same as CSeq_id_Handle::AsString() More...

virtual bool	operator== (const IAlnSeqId &id) const
	Comparison operators. More...

virtual bool	operator!= (const IAlnSeqId &id) const

virtual bool	operator< (const IAlnSeqId &id) const

virtual void	SetBioseqHandle (const CBioseq_Handle &handle)
	Store bioseq handle for the id. More...

virtual TMol	GetSequenceType (void) const
	Check sequence type. More...

virtual int	GetBaseWidth (void) const
	Base Width - 1 = nucleotide, 3 = protein. More...

virtual void	SetBaseWidth (int base_width)
	Set base width for the sequence. More...

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

Public Member Functions inherited from CSeq_id_Handle
	CSeq_id_Handle (void)

	CSeq_id_Handle (const CSeq_id_Info *info, TPacked packed=0, TVariant variant=0)

	CSeq_id_Handle (ENull)

bool	operator== (const CSeq_id_Handle &handle) const

bool	operator!= (const CSeq_id_Handle &handle) const

bool	operator< (const CSeq_id_Handle &handle) const

bool	operator== (const CSeq_id &id) const

int	CompareOrdered (const CSeq_id_Handle &id) const
	Compare ids in a defined order (see CSeq_id::CompareOrdered()) More...

	DECLARE_OPERATOR_BOOL_REF (m_Info)
	Check if the handle is a valid or an empty one. More...

void	Reset (void)
	Reset the handle (remove seq-id reference) More...

bool	HaveMatchingHandles (void) const

bool	HaveReverseMatch (void) const

bool	HaveMatchingHandles (EAllowWeakMatch allow_weak_match) const

bool	HaveReverseMatch (EAllowWeakMatch allow_weak_match) const

void	GetMatchingHandles (TMatches &matches) const

void	GetReverseMatchingHandles (TMatches &matches) const

void	GetMatchingHandles (TMatches &matches, EAllowWeakMatch allow_weak_match) const

void	GetReverseMatchingHandles (TMatches &matches, EAllowWeakMatch allow_weak_match) const

bool	MatchesTo (const CSeq_id_Handle &h) const
	True if *this matches to h. More...

bool	IsBetter (const CSeq_id_Handle &h) const
	True if "this" is a better bioseq than "h". More...

string	AsString (void) const

CSeq_id::E_Choice	Which (void) const

bool	IsPacked (void) const

TPacked	GetPacked (void) const

bool	IsSetVariant (void) const

TVariant	GetVariant (void) const

bool	IsGi (void) const

TGi	GetGi (void) const

bool	IsAccVer (void) const

unsigned	GetHash (void) const

CSeq_id::EAccessionInfo	IdentifyAccession (void) const

CConstRef< CSeq_id >	GetSeqId (void) const

CConstRef< CSeq_id >	GetSeqIdOrNull (void) const

CSeq_id_Mapper &	GetMapper (void) const

void	Swap (CSeq_id_Handle &idh)

bool	IsAllowedSNPScaleLimit (CSeq_id::ESNPScaleLimit scale_limit) const

const CSeq_id_Info *	x_GetInfo (void) const

Public Member Functions inherited from IAlnSeqId
bool	IsProtein (void) const

bool	IsNucleotide (void) const

virtual	~IAlnSeqId (void)
	Virtual destructor. More...

Private Attributes
CConstRef< CSeq_id >	m_Seq_id

CBioseq_Handle	m_BioseqHandle

TMol	m_Mol

int	m_BaseWidth

Additional Inherited Members
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 Types inherited from CSeq_id_Handle
typedef CSeq_id_Info::TPacked	TPacked

typedef CSeq_id_Info::TVariant	TVariant

typedef set< CSeq_id_Handle >	TMatches

Public Types inherited from IAlnSeqId
typedef CSeq_inst::TMol	TMol

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 Member Functions inherited from CSeq_id_Handle
static CSeq_id_Handle	GetHandle (const CSeq_id &id)
	Normal way of getting a handle, works for any seq-id. More...

static CSeq_id_Handle	GetHandle (const string &str_id)
	Construct CSeq_id from string representation and return handle for it. More...

static CSeq_id_Handle	GetHandle (TGi gi)
	Faster way to create a handle for a gi. More...

static CSeq_id_Handle	GetGiHandle (TGi gi)
	Faster way to create a handle for a gi. More...

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...

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

Detailed Description

Default IAlnSeqId implementation based on CSeq_id_Handle.

See also: CAlnSeqIdConverter; CAlnSeqIdsExtract

Definition at line 112 of file aln_seqid.hpp.

Constructor & Destructor Documentation

◆ CAlnSeqId()

CAlnSeqId::CAlnSeqId ( const CSeq_id & id )

inline

Constructor.

Definition at line 119 of file aln_seqid.hpp.

Member Function Documentation

◆ AsString()

string CAlnSeqId::AsString ( void ) const

virtual

Sequence label - same as CSeq_id_Handle::AsString()

Implements IAlnSeqId.

Definition at line 60 of file aln_seqid.cpp.

References CSeq_id_Handle::AsString().

◆ GetBaseWidth()

int CAlnSeqId::GetBaseWidth ( void ) const

virtual

Base Width - 1 = nucleotide, 3 = protein.

Implements IAlnSeqId.

Definition at line 94 of file aln_seqid.cpp.

References m_BaseWidth.

◆ GetSeqId()

const CSeq_id & CAlnSeqId::GetSeqId ( void ) const

virtual

Get CSeq_id.

Implements IAlnSeqId.

Definition at line 55 of file aln_seqid.cpp.

References m_Seq_id.

◆ GetSequenceType()

IAlnSeqId::TMol CAlnSeqId::GetSequenceType ( void ) const

virtual

Check sequence type.

Implements IAlnSeqId.

Definition at line 75 of file aln_seqid.cpp.

References CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_not_set, CSeq_id::fAcc_nuc, CSeq_id::fAcc_prot, CSeq_id_Handle::IdentifyAccession(), m_BaseWidth, and m_Mol.

◆ operator!=()

bool CAlnSeqId::operator!= ( const IAlnSeqId & id ) const

virtual

Implements IAlnSeqId.

Definition at line 114 of file aln_seqid.cpp.

References CSeq_id_Handle::operator!=().

◆ operator<()

bool CAlnSeqId::operator< ( const IAlnSeqId & id ) const

virtual

Implements IAlnSeqId.

Definition at line 119 of file aln_seqid.cpp.

◆ operator==()

bool CAlnSeqId::operator== ( const IAlnSeqId & id ) const

virtual

Comparison operators.

Implements IAlnSeqId.

Definition at line 109 of file aln_seqid.cpp.

References CSeq_id_Handle::operator==().

◆ SetBaseWidth()

void CAlnSeqId::SetBaseWidth ( int base_width )

virtual

Set base width for the sequence.

Implements IAlnSeqId.

Definition at line 99 of file aln_seqid.cpp.

References _ASSERT, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_not_set, IAlnSeqId::IsNucleotide(), IAlnSeqId::IsProtein(), m_BaseWidth, and m_Mol.

◆ SetBioseqHandle()

void CAlnSeqId::SetBioseqHandle ( const CBioseq_Handle & handle )

virtual

Store bioseq handle for the id.

Definition at line 65 of file aln_seqid.cpp.

References CBioseq_Handle::GetSequenceType(), CSeq_inst::IsAa(), m_BaseWidth, m_BioseqHandle, and m_Mol.

Member Data Documentation

◆ m_BaseWidth

int CAlnSeqId::m_BaseWidth

private

Definition at line 151 of file aln_seqid.hpp.

Referenced by GetBaseWidth(), GetSequenceType(), SetBaseWidth(), and SetBioseqHandle().

◆ m_BioseqHandle

CBioseq_Handle CAlnSeqId::m_BioseqHandle

private

Definition at line 149 of file aln_seqid.hpp.

Referenced by SetBioseqHandle().

◆ m_Mol

TMol CAlnSeqId::m_Mol

mutableprivate

Definition at line 150 of file aln_seqid.hpp.

Referenced by GetSequenceType(), SetBaseWidth(), and SetBioseqHandle().

◆ m_Seq_id

CConstRef<CSeq_id> CAlnSeqId::m_Seq_id

private

Definition at line 148 of file aln_seqid.hpp.

Referenced by GetSeqId().

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

include/objtools/alnmgr/aln_seqid.hpp
src/objtools/alnmgr/aln_seqid.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CAlnSeqId()

Member Function Documentation

◆ AsString()

◆ GetBaseWidth()

◆ GetSeqId()

◆ GetSequenceType()

◆ operator!=()

◆ operator<()

◆ operator==()

◆ SetBaseWidth()

◆ SetBioseqHandle()

Member Data Documentation

◆ m_BaseWidth

◆ m_BioseqHandle

◆ m_Mol

◆ m_Seq_id