#include <objtools/edit/gap_trim.hpp>

Inheritance diagram for CFeatGapInfo:

Collaboration diagram for CFeatGapInfo:

Public Types
typedef vector< CRef< CSeq_loc > >	TLocList

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
	CFeatGapInfo ()

	CFeatGapInfo (CSeq_feat_Handle sf)

	~CFeatGapInfo ()

void	CollectGaps (const CSeq_loc &feat_loc, CScope &scope)

void	CalculateRelevantIntervals (bool unknown_length, bool known_length, bool ns=false)

bool	HasKnown () const

bool	HasUnknown () const

bool	HasNs () const

bool	Trimmable () const

bool	Splittable () const

bool	ShouldRemove () const

void	Trim (CSeq_loc &loc, bool make_partial, CScope &scope)

TLocList	Split (const CSeq_loc &orig, bool in_intron, bool make_partial)

vector< CRef< CSeq_feat > >	AdjustForRelevantGapIntervals (bool make_partial, bool trim, bool split, bool in_intron, bool create_general_only=false)

CSeq_feat_Handle	GetFeature () const

bool	IsRelatedByCrossRef (const CFeatGapInfo &other) 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

Static Public Member Functions
static CRef< CBioseq >	AdjustProteinSeq (const CBioseq &seq, const CSeq_feat &feat, const CSeq_feat &orig_cds, CScope &scope)

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)

Protected Types
enum	EGapIntervalType { eGapIntervalType_unknown = 0 , eGapIntervalType_known , eGapIntervalType_n }

typedef pair< EGapIntervalType, pair< size_t, size_t > >	TGapInterval

typedef vector< TGapInterval >	TGapIntervalList

typedef vector< pair< size_t, size_t > >	TIntervalList

Protected Member Functions
void	x_AdjustOrigLabel (CSeq_feat &feat, size_t &id_offset, string &id_label, const string &qual)

void	x_AdjustCodebreaks (CSeq_feat &feat)

void	x_AdjustAnticodons (CSeq_feat &feat)

bool	x_UsableInterval (const TGapInterval &interval, bool unknown_length, bool known_length, bool ns)

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

Static Protected Member Functions
static void	x_AdjustFrame (CCdregion &cdregion, TSeqPos frame_adjust)

Protected Attributes
TGapIntervalList	m_Gaps

TIntervalList	m_InsideGaps

TIntervalList	m_LeftGaps

TIntervalList	m_RightGaps

TSeqPos	m_Start

TSeqPos	m_Stop

bool	m_Known

bool	m_Unknown

bool	m_Ns

CSeq_feat_Handle	m_Feature

Additional Inherited Members
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 65 of file gap_trim.hpp.

Member Typedef Documentation

◆ TGapInterval

typedef pair<EGapIntervalType, pair<size_t, size_t> > CFeatGapInfo::TGapInterval

protected

Definition at line 99 of file gap_trim.hpp.

◆ TGapIntervalList

typedef vector<TGapInterval> CFeatGapInfo::TGapIntervalList

protected

Definition at line 100 of file gap_trim.hpp.

◆ TIntervalList

typedef vector<pair<size_t, size_t> > CFeatGapInfo::TIntervalList

protected

Definition at line 103 of file gap_trim.hpp.

◆ TLocList

typedef vector< CRef<CSeq_loc> > CFeatGapInfo::TLocList

Definition at line 82 of file gap_trim.hpp.

Member Enumeration Documentation

◆ EGapIntervalType

enum CFeatGapInfo::EGapIntervalType

protected

Enumerator
eGapIntervalType_unknown
eGapIntervalType_known
eGapIntervalType_n

Definition at line 93 of file gap_trim.hpp.

Constructor & Destructor Documentation

◆ CFeatGapInfo() [1/2]

CFeatGapInfo::CFeatGapInfo ( )

inline

Definition at line 67 of file gap_trim.hpp.

◆ CFeatGapInfo() [2/2]

CFeatGapInfo::CFeatGapInfo ( CSeq_feat_Handle sf )

Definition at line 60 of file gap_trim.cpp.

◆ ~CFeatGapInfo()

CFeatGapInfo::~CFeatGapInfo ( )

inline

Definition at line 69 of file gap_trim.hpp.

Member Function Documentation

◆ AdjustForRelevantGapIntervals()

vector< CRef< CSeq_feat > > CFeatGapInfo::AdjustForRelevantGapIntervals	(	bool	make_partial,
		bool	trim,
		bool	split,
		bool	in_intron,
		bool	create_general_only = `false`
	)