Search Toolkit Book for CLocation_constraint

#include <objects/macro/Location_constraint.hpp>

Inheritance diagram for CLocation_constraint:

Collaboration diagram for CLocation_constraint:

Public Member Functions
	CLocation_constraint (void)

	~CLocation_constraint (void)

bool	Match (const CSeq_feat &feat, CConstRef< CSeq_feat > feat_to, CConstRef< CBioseq > feat_bioseq) const

bool	IsEmpty () const

Public Member Functions inherited from CLocation_constraint_Base
	CLocation_constraint_Base (void)

virtual	~CLocation_constraint_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetStrand (void) const
	Check if a value has been assigned to Strand data member. More...

bool	CanGetStrand (void) const
	Check if it is safe to call GetStrand method. More...

void	ResetStrand (void)
	Reset Strand data member. More...

void	SetDefaultStrand (void)
	Assign default value to Strand data member. More...

TStrand	GetStrand (void) const
	Get the Strand member data. More...

void	SetStrand (TStrand value)
	Assign a value to Strand data member. More...

TStrand &	SetStrand (void)
	Assign a value to Strand data member. More...

bool	IsSetSeq_type (void) const
	Check if a value has been assigned to Seq_type data member. More...

bool	CanGetSeq_type (void) const
	Check if it is safe to call GetSeq_type method. More...

void	ResetSeq_type (void)
	Reset Seq_type data member. More...

void	SetDefaultSeq_type (void)
	Assign default value to Seq_type data member. More...

TSeq_type	GetSeq_type (void) const
	Get the Seq_type member data. More...

void	SetSeq_type (TSeq_type value)
	Assign a value to Seq_type data member. More...

TSeq_type &	SetSeq_type (void)
	Assign a value to Seq_type data member. More...

bool	IsSetPartial5 (void) const
	Check if a value has been assigned to Partial5 data member. More...

bool	CanGetPartial5 (void) const
	Check if it is safe to call GetPartial5 method. More...

void	ResetPartial5 (void)
	Reset Partial5 data member. More...

void	SetDefaultPartial5 (void)
	Assign default value to Partial5 data member. More...

TPartial5	GetPartial5 (void) const
	Get the Partial5 member data. More...

void	SetPartial5 (TPartial5 value)
	Assign a value to Partial5 data member. More...

TPartial5 &	SetPartial5 (void)
	Assign a value to Partial5 data member. More...

bool	IsSetPartial3 (void) const
	Check if a value has been assigned to Partial3 data member. More...

bool	CanGetPartial3 (void) const
	Check if it is safe to call GetPartial3 method. More...

void	ResetPartial3 (void)
	Reset Partial3 data member. More...

void	SetDefaultPartial3 (void)
	Assign default value to Partial3 data member. More...

TPartial3	GetPartial3 (void) const
	Get the Partial3 member data. More...

void	SetPartial3 (TPartial3 value)
	Assign a value to Partial3 data member. More...

TPartial3 &	SetPartial3 (void)
	Assign a value to Partial3 data member. More...

bool	IsSetLocation_type (void) const
	Check if a value has been assigned to Location_type data member. More...

bool	CanGetLocation_type (void) const
	Check if it is safe to call GetLocation_type method. More...

void	ResetLocation_type (void)
	Reset Location_type data member. More...

void	SetDefaultLocation_type (void)
	Assign default value to Location_type data member. More...

TLocation_type	GetLocation_type (void) const
	Get the Location_type member data. More...

void	SetLocation_type (TLocation_type value)
	Assign a value to Location_type data member. More...

TLocation_type &	SetLocation_type (void)
	Assign a value to Location_type data member. More...

bool	IsSetEnd5 (void) const
	Check if a value has been assigned to End5 data member. More...

bool	CanGetEnd5 (void) const
	Check if it is safe to call GetEnd5 method. More...

void	ResetEnd5 (void)
	Reset End5 data member. More...

const TEnd5 &	GetEnd5 (void) const
	Get the End5 member data. More...

void	SetEnd5 (TEnd5 &value)
	Assign a value to End5 data member. More...

TEnd5 &	SetEnd5 (void)
	Assign a value to End5 data member. More...

bool	IsSetEnd3 (void) const
	Check if a value has been assigned to End3 data member. More...

bool	CanGetEnd3 (void) const
	Check if it is safe to call GetEnd3 method. More...

void	ResetEnd3 (void)
	Reset End3 data member. More...

const TEnd3 &	GetEnd3 (void) const
	Get the End3 member data. More...

void	SetEnd3 (TEnd3 &value)
	Assign a value to End3 data member. More...

TEnd3 &	SetEnd3 (void)
	Assign a value to End3 data member. More...

virtual void	Reset (void)
	Reset the whole object. More...

Public Member Functions inherited from CSerialObject
	CSerialObject (void)

virtual	~CSerialObject (void)

virtual const CTypeInfo *	GetThisTypeInfo (void) const =0

virtual void	Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Set object to copy of another one. More...

virtual bool	Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
	Check if both objects contain the same values. More...

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

void	ThrowUnassigned (TMemberIndex index) const

void	ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const

bool	HasNamespaceName (void) const
	Check if object data type has namespace name. More...

const string &	GetNamespaceName (void) const
	Get namespace name. More...

bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...

const string &	GetNamespacePrefix (void) const
	Get namespace prefix. 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...

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

Private Types
typedef CLocation_constraint_Base	Tparent

Private Member Functions
	CLocation_constraint (const CLocation_constraint &value)

CLocation_constraint &	operator= (const CLocation_constraint &value)

bool	x_DoesStrandMatchConstraint (const CSeq_loc &loc) const

bool	x_DoesBioseqMatchSequenceType (CConstRef< CBioseq > bioseq, const ESeqtype_constraint &seq_type) const

bool	x_DoesLocationMatchPartialnessConstraint (const CSeq_loc &loc) const

bool	x_DoesLocationMatchTypeConstraint (const CSeq_loc &seq_loc) const

bool	x_DoesLocationMatchDistanceConstraint (CConstRef< CBioseq > bioseq_hl, const CSeq_loc &loc) const

Additional Inherited Members
Public Types inherited from CLocation_constraint_Base
enum class	E_memberIndex { e__allMandatory = 0 , e_strand , e_seq_type , e_partial5 , e_partial3 , e_location_type , e_end5 , e_end3 }

typedef EStrand_constraint	TStrand

typedef ESeqtype_constraint	TSeq_type

typedef EPartial_constraint	TPartial5

typedef EPartial_constraint	TPartial3

typedef ELocation_type_constraint	TLocation_type

typedef CLocation_pos_constraint	TEnd5

typedef CLocation_pos_constraint	TEnd3

typedef Tparent::CMemberIndex< E_memberIndex, 8 >	TmemberIndex

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...

Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)

static void	SetVerifyDataGlobal (ESerialVerifyData verify)

static string	UnassignedString (void)

static CStringUTF8	UnassignedStringUTF8 (void)

static char	UnassignedByte (void)

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 CSerialObject
static const char *	ms_UnassignedStr = "<unassigned>"

static const char	ms_UnassignedByte = char(0xcd)

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

Definition at line 55 of file Location_constraint.hpp.

Member Typedef Documentation

◆ Tparent

typedef CLocation_constraint_Base CLocation_constraint::Tparent

private

Definition at line 57 of file Location_constraint.hpp.

Constructor & Destructor Documentation

◆ CLocation_constraint() [1/2]

CLocation_constraint::CLocation_constraint ( void )

inline

Definition at line 85 of file Location_constraint.hpp.

◆ ~CLocation_constraint()

CLocation_constraint::~CLocation_constraint ( void )

Definition at line 56 of file Location_constraint.cpp.

◆ CLocation_constraint() [2/2]

CLocation_constraint::CLocation_constraint ( const CLocation_constraint & value )

private

Member Function Documentation

◆ IsEmpty()

bool CLocation_constraint::IsEmpty ( void ) const

Definition at line 60 of file Location_constraint.cpp.

Referenced by Match().

◆ Match()

bool CLocation_constraint::Match	(	const CSeq_feat &	feat,
		CConstRef< CSeq_feat >	feat_to,
		CConstRef< CBioseq >	feat_bioseq
	)		const

Definition at line 197 of file Location_constraint.cpp.

References CConstRef< C, Locker >::Empty(), eStrand_constraint_any, CSeq_feat_Base::GetLocation(), CLocation_constraint_Base::GetSeq_type(), CLocation_constraint_Base::GetStrand(), CBioseq::IsAa(), IsEmpty(), x_DoesBioseqMatchSequenceType(), x_DoesLocationMatchDistanceConstraint(), x_DoesLocationMatchPartialnessConstraint(), x_DoesLocationMatchTypeConstraint(), and x_DoesStrandMatchConstraint().

Referenced by x_DoesLocationMatchDistanceConstraint().

◆ operator=()

CLocation_constraint& CLocation_constraint::operator= ( const CLocation_constraint & value )

private

◆ x_DoesBioseqMatchSequenceType()

bool CLocation_constraint::x_DoesBioseqMatchSequenceType	(	CConstRef< CBioseq >	bioseq,
		const ESeqtype_constraint &	seq_type
	)		const

private

Definition at line 97 of file Location_constraint.cpp.

References eSeqtype_constraint_any, eSeqtype_constraint_nuc, eSeqtype_constraint_prot, CBioseq::IsAa(), and CBioseq::IsNa().

Referenced by Match().

◆ x_DoesLocationMatchDistanceConstraint()

bool CLocation_constraint::x_DoesLocationMatchDistanceConstraint	(	CConstRef< CBioseq >	bioseq_hl,
		const CSeq_loc &	loc
	)		const

private

Definition at line 157 of file Location_constraint.cpp.

References CLocation_constraint_Base::CanGetEnd3(), CLocation_constraint_Base::CanGetEnd5(), eExtreme_Positional, eNa_strand_minus, CLocation_constraint_Base::GetEnd3(), CLocation_constraint_Base::GetEnd5(), CBioseq::GetLength(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CLocation_constraint_Base::IsSetEnd3(), CLocation_constraint_Base::IsSetEnd5(), CSeq_loc::IsSetStrand(), and Match().

Referenced by Match().

◆ x_DoesLocationMatchPartialnessConstraint()

bool CLocation_constraint::x_DoesLocationMatchPartialnessConstraint ( const CSeq_loc & loc ) const

private

Definition at line 107 of file Location_constraint.cpp.

References eExtreme_Biological, ePartial_constraint_complete, ePartial_constraint_partial, CLocation_constraint_Base::GetPartial3(), CLocation_constraint_Base::GetPartial5(), CSeq_loc::IsPartialStart(), and CSeq_loc::IsPartialStop().

Referenced by Match().

◆ x_DoesLocationMatchTypeConstraint()

bool CLocation_constraint::x_DoesLocationMatchTypeConstraint ( const CSeq_loc & seq_loc ) const

private

Definition at line 120 of file Location_constraint.cpp.

References CSeq_loc_Base::e_Null, eLocation_type_constraint_any, eLocation_type_constraint_joined, eLocation_type_constraint_ordered, eLocation_type_constraint_single_interval, and CLocation_constraint_Base::GetLocation_type().

Referenced by Match().

◆ x_DoesStrandMatchConstraint()

bool CLocation_constraint::x_DoesStrandMatchConstraint ( const CSeq_loc & loc ) const

private

Definition at line 74 of file Location_constraint.cpp.

References CSeq_loc_Base::e_not_set, eNa_strand_minus, eStrand_constraint_any, eStrand_constraint_minus, eStrand_constraint_plus, CLocation_constraint_Base::GetStrand(), CSeq_loc::GetStrand(), and CSeq_loc_Base::Which().

Referenced by Match().

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

include/objects/macro/Location_constraint.hpp
src/objects/macro/Location_constraint.cpp

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Tparent

Constructor & Destructor Documentation

◆ CLocation_constraint() [1/2]

◆ ~CLocation_constraint()

◆ CLocation_constraint() [2/2]

Member Function Documentation

◆ IsEmpty()

◆ Match()

◆ operator=()

◆ x_DoesBioseqMatchSequenceType()

◆ x_DoesLocationMatchDistanceConstraint()

◆ x_DoesLocationMatchPartialnessConstraint()

◆ x_DoesLocationMatchTypeConstraint()

◆ x_DoesStrandMatchConstraint()