mmdb::math::Alignment1 Class Reference

#include <mmdb_math_align.h>

Inheritance diagram for mmdb::math::Alignment1:

List of all members.

Public Member Functions
	Alignment1 ()
	Alignment1 (io::RPStream Object)
	~Alignment1 ()
void	SetAffineModel (realtype WGap, realtype WSpace)
void	SetScores (realtype SEqual, realtype SNEqual)
void	Align (ivector S, int SLength, ivector T, int TLength, ALIGN_METHOD Method=ALIGN_GLOBAL)
ivector	GetAlignedS ()
ivector	GetAlignedT ()
int	GetAlignLength ()
realtype	GetScore ()
realtype	GetSimilarity ()
virtual void	OutputResults (io::RFile f, ivector S, int lenS, ivector T, int lenT)
void	read (io::RFile f)
void	write (io::RFile f)
Protected Member Functions
virtual void	InitAlignment1 ()
virtual void	FreeMemory ()
virtual realtype	Score (int A, int B)
void	BuildGATable (ivector S, ivector T, bool FreeSEnds, bool FreeTEnds)
void	BuildLATable (ivector S, ivector T)
void	Backtrace (ivector S, ivector T, int J, int I, bool StopAtZero)
void	AdjustEnds (ivector S, ivector T, int J, int I)
void	PrintVT (ivector S, ivector T)
Protected Attributes
int	Space
int	AlignKey
int	SLen
int	TLen
int	AlgnLen
rmatrix	VT
rmatrix	ET
rmatrix	FT
ivector	AlgnS
ivector	AlgnT
realtype	VAchieved
realtype	SEq
realtype	SNEq
realtype	Wg
realtype	Ws

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Constructor & Destructor Documentation

mmdb::math::Alignment1::Alignment1

(

)

mmdb::math::Alignment1::Alignment1

(

io::RPStream

Object )

mmdb::math::Alignment1::~Alignment1

(

)

---

Member Function Documentation

void mmdb::math::Alignment1::AdjustEnds	(	ivector	S,
		ivector	T,
		int	J,
		int	I
	)		[protected]

void mmdb::math::Alignment1::Align	(	ivector	S,
		int	SLength,
		ivector	T,
		int	TLength,
		ALIGN_METHOD	Method = ALIGN_GLOBAL
	)

void mmdb::math::Alignment1::Backtrace	(	ivector	S,
		ivector	T,
		int	J,
		int	I,
		bool	StopAtZero
	)		[protected]

void mmdb::math::Alignment1::BuildGATable	(	ivector	S,
		ivector	T,
		bool	FreeSEnds,
		bool	FreeTEnds
	)		[protected]

void mmdb::math::Alignment1::BuildLATable	(	ivector	S,
		ivector	T
	)		[protected]

void mmdb::math::Alignment1::FreeMemory

(

)

[protected, virtual]

ivector mmdb::math::Alignment1::GetAlignedS

(

)

[inline]

ivector mmdb::math::Alignment1::GetAlignedT

(

)

[inline]

int mmdb::math::Alignment1::GetAlignLength

(

)

[inline]

realtype mmdb::math::Alignment1::GetScore

(

)

[inline]

realtype mmdb::math::Alignment1::GetSimilarity

(

)

void mmdb::math::Alignment1::InitAlignment1

(

)

[protected, virtual]

void mmdb::math::Alignment1::OutputResults	(	io::RFile	f,
		ivector	S,
		int	lenS,
		ivector	T,
		int	lenT
	)		[virtual]

void mmdb::math::Alignment1::PrintVT	(	ivector	S,
		ivector	T
	)		[protected]

void mmdb::math::Alignment1::read

(

io::RFile

f )

realtype mmdb::math::Alignment1::Score	(	int	A,
		int	B
	)		[protected, virtual]

void mmdb::math::Alignment1::SetAffineModel	(	realtype	WGap,
		realtype	WSpace
	)

void mmdb::math::Alignment1::SetScores	(	realtype	SEqual,
		realtype	SNEqual
	)

void mmdb::math::Alignment1::write

(

io::RFile

f )

---

Member Data Documentation

int mmdb::math::Alignment1::AlgnLen [protected]

ivector mmdb::math::Alignment1::AlgnS [protected]

ivector mmdb::math::Alignment1::AlgnT [protected]

int mmdb::math::Alignment1::AlignKey [protected]

rmatrix mmdb::math::Alignment1::ET [protected]

rmatrix mmdb::math::Alignment1::FT [protected]

realtype mmdb::math::Alignment1::SEq [protected]

int mmdb::math::Alignment1::SLen [protected]

realtype mmdb::math::Alignment1::SNEq [protected]

int mmdb::math::Alignment1::Space [protected]

int mmdb::math::Alignment1::TLen [protected]

realtype mmdb::math::Alignment1::VAchieved [protected]

rmatrix mmdb::math::Alignment1::VT [protected]

realtype mmdb::math::Alignment1::Wg [protected]

realtype mmdb::math::Alignment1::Ws [protected]

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

• src/mmdb_math_align.h
• src/mmdb_math_align.cpp