Search Toolkit Book for CAlnMixMatches

#include <objtools/alnmgr/alnmatch.hpp>

Inheritance diagram for CAlnMixMatches:

Collaboration diagram for CAlnMixMatches:

Public Types
enum	EAddFlags { fCalcScore = 0x01 , fForceTranslation = 0x02 , fPreserveRows = 0x04 }

typedef int(*	TCalcScoreMethod) (const string &s1, const string &s2, bool s1_is_prot, bool s2_is_prot, int gene_code1, int gene_code2)
	Typedefs. More...

typedef vector< CRef< CAlnMixMatch > >	TMatches

typedef int	TAddFlags

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
	CAlnMixMatches (CRef< CAlnMixSequences > &sequences, TCalcScoreMethod calc_score=0)
	Constructor. More...

const TMatches &	Get () const
	Container accessors. More...

TMatches &	Set ()

void	Add (const CDense_seg &ds, TAddFlags flags=0)
	"Add" a Dense-seg to the existing matches. More...

void	SortByScore ()
	Modifying algorithms. More...

void	SortByChainScore ()

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 Private Member Functions
static bool	x_CompareScores (const CRef< CAlnMixMatch > &match1, const CRef< CAlnMixMatch > &match2)

static bool	x_CompareChainScores (const CRef< CAlnMixMatch > &match1, const CRef< CAlnMixMatch > &match2)

Private Attributes
size_t	m_DsCnt

CRef< CScope >	m_Scope

TMatches	m_Matches

CRef< CAlnMixSequences >	m_AlnMixSequences

CAlnMixSequences::TSeqs &	m_Seqs

TCalcScoreMethod	x_CalculateScore

TAddFlags	m_AddFlags

bool &	m_ContainsAA

bool &	m_ContainsNA

Friends
class	CAlnMixMerger

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...

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

Detailed Description

Definition at line 48 of file alnmatch.hpp.

Member Typedef Documentation

◆ TAddFlags

typedef int CAlnMixMatches::TAddFlags

Definition at line 75 of file alnmatch.hpp.

◆ TCalcScoreMethod

typedef int(* CAlnMixMatches::TCalcScoreMethod) (const string &s1, const string &s2, bool s1_is_prot, bool s2_is_prot, int gene_code1, int gene_code2)

Typedefs.

Definition at line 53 of file alnmatch.hpp.

◆ TMatches

typedef vector<CRef<CAlnMixMatch> > CAlnMixMatches::TMatches

Definition at line 60 of file alnmatch.hpp.

Member Enumeration Documentation

◆ EAddFlags

enum CAlnMixMatches::EAddFlags

Enumerator
fCalcScore
fForceTranslation
fPreserveRows

Definition at line 62 of file alnmatch.hpp.

Constructor & Destructor Documentation

◆ CAlnMixMatches()

CAlnMixMatches::CAlnMixMatches	(	CRef< CAlnMixSequences > &	sequences,
		TCalcScoreMethod	calc_score = `0`
	)

Constructor.

Definition at line 49 of file alnmatch.cpp.

Member Function Documentation

◆ Add()

void CAlnMixMatches::Add	(	const CDense_seg &	ds,
		TAddFlags	flags = `0`
	)

"Add" a Dense-seg to the existing matches.

This would create and add new mathces that correspond to the relations in the given Dense-seg

Definition at line 97 of file alnmatch.cpp.

References _ASSERT, eNa_strand_minus, eNa_strand_plus, fCalcScore, fForceTranslation, flags, CDense_seg_Base::GetDim(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CAlnMixSeq::GetSeqString(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), int, len, m_AddFlags, m_AlnMixSequences, m_DsCnt, CAlnMixSequences::m_DsSeq, CAlnMixSeq::m_IsAA, m_Matches, CAlnMixSeq::m_Score, CAlnMixSeq::m_StrandScore, CAlnMixSeq::m_Width, match(), NCBI_THROW, NON_CONST_REVERSE_ITERATE, and x_CalculateScore.

Referenced by CAlnMix::Add().

◆ Get()

const TMatches& CAlnMixMatches::Get ( void ) const

inline

Container accessors.

Definition at line 84 of file alnmatch.hpp.

References m_Matches.

◆ Set()

TMatches& CAlnMixMatches::Set ( void )

inline

Definition at line 85 of file alnmatch.hpp.

References m_Matches.

◆ SortByChainScore()

void CAlnMixMatches::SortByChainScore ( )

Definition at line 90 of file alnmatch.cpp.

References m_Matches, and x_CompareChainScores().

Referenced by CAlnMix::Merge().

◆ SortByScore()

void CAlnMixMatches::SortByScore ( )

Modifying algorithms.

Definition at line 83 of file alnmatch.cpp.

References m_Matches, and x_CompareScores().

Referenced by CAlnMix::Merge().

◆ x_CompareChainScores()

bool CAlnMixMatches::x_CompareChainScores	(	const CRef< CAlnMixMatch > &	match1,
		const CRef< CAlnMixMatch > &	match2
	)

inlinestaticprivate

Definition at line 72 of file alnmatch.cpp.

Referenced by SortByChainScore().

◆ x_CompareScores()

bool CAlnMixMatches::x_CompareScores	(	const CRef< CAlnMixMatch > &	match1,
		const CRef< CAlnMixMatch > &	match2
	)

inlinestaticprivate

Definition at line 63 of file alnmatch.cpp.

Referenced by SortByScore().

Friends And Related Function Documentation

◆ CAlnMixMerger

friend class CAlnMixMerger

friend

Definition at line 101 of file alnmatch.hpp.

Member Data Documentation

◆ m_AddFlags

TAddFlags CAlnMixMatches::m_AddFlags

private

Definition at line 115 of file alnmatch.hpp.

Referenced by Add(), CAlnMixMerger::x_CreateDenseg(), and CAlnMixMerger::x_Merge().

◆ m_AlnMixSequences

CRef<CAlnMixSequences> CAlnMixMatches::m_AlnMixSequences

private

Definition at line 112 of file alnmatch.hpp.

Referenced by Add().

◆ m_ContainsAA

bool& CAlnMixMatches::m_ContainsAA

private

Definition at line 116 of file alnmatch.hpp.

Referenced by CAlnMixMerger::x_CreateDenseg(), and CAlnMixMerger::x_Merge().

◆ m_ContainsNA

bool& CAlnMixMatches::m_ContainsNA

private

Definition at line 117 of file alnmatch.hpp.

Referenced by CAlnMixMerger::x_CreateDenseg(), and CAlnMixMerger::x_Merge().

◆ m_DsCnt

size_t CAlnMixMatches::m_DsCnt

private

Definition at line 109 of file alnmatch.hpp.

Referenced by Add().

◆ m_Matches

TMatches CAlnMixMatches::m_Matches

private

Definition at line 111 of file alnmatch.hpp.

Referenced by Add(), Get(), Set(), SortByChainScore(), and SortByScore().

◆ m_Scope

CRef<CScope> CAlnMixMatches::m_Scope

private

Definition at line 110 of file alnmatch.hpp.

◆ m_Seqs

CAlnMixSequences::TSeqs& CAlnMixMatches::m_Seqs

private

Definition at line 113 of file alnmatch.hpp.

◆ x_CalculateScore

TCalcScoreMethod CAlnMixMatches::x_CalculateScore

private

Definition at line 114 of file alnmatch.hpp.

Referenced by Add().

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

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

Public Types

Public Member Functions

Static Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TAddFlags

◆ TCalcScoreMethod

◆ TMatches

Member Enumeration Documentation

◆ EAddFlags

Constructor & Destructor Documentation

◆ CAlnMixMatches()

Member Function Documentation

◆ Add()

◆ Get()

◆ Set()

◆ SortByChainScore()

◆ SortByScore()

◆ x_CompareChainScores()

◆ x_CompareScores()

Friends And Related Function Documentation

◆ CAlnMixMerger

Member Data Documentation

◆ m_AddFlags

◆ m_AlnMixSequences

◆ m_ContainsAA

◆ m_ContainsNA

◆ m_DsCnt

◆ m_Matches

◆ m_Scope

◆ m_Seqs

◆ x_CalculateScore