mmdb::math::Alignment Class Reference

#include <mmdb_math_align.h>

Inheritance diagram for mmdb::math::Alignment:

List of all members.

Public Member Functions
	Alignment ()
	Alignment (io::RPStream Object)
	~Alignment ()
void	SetAffineModel (realtype WGap, realtype WSpace)
void	SetScores (realtype SEqual, realtype SNEqual)
void	Align (cpstr S, cpstr T, ALIGN_METHOD Method=ALIGN_GLOBAL)
pstr	GetAlignedS ()
pstr	GetAlignedT ()
realtype	GetScore ()
char	GetSpace ()
realtype	GetSimilarity ()
realtype	GetSeqId ()
virtual void	OutputResults (io::RFile f, cpstr S, cpstr T)
void	read (io::RFile f)
void	write (io::RFile f)
Protected Member Functions
virtual void	InitAlignment ()
virtual void	FreeMemory ()
virtual realtype	Score (char A, char B)
void	BuildGATable (cpstr S, cpstr T, bool FreeSEnd, bool FreeTEnd)
void	BuildLATable (cpstr S, cpstr T)
void	Backtrace (cpstr S, cpstr T, int J, int I, bool StopAtZero)
void	AdjustEnds (cpstr S, cpstr T, int J, int I)
void	PrintVT (cpstr S, cpstr T)
Protected Attributes
char	Space
int	AlignKey
int	SLen
int	TLen
rmatrix	VT
rmatrix	ET
rmatrix	FT
pstr	AlgnS
pstr	AlgnT
realtype	VAchieved
realtype	SEq
realtype	SNEq
realtype	Wg
realtype	Ws

---

Constructor & Destructor Documentation

mmdb::math::Alignment::Alignment

(

)

mmdb::math::Alignment::Alignment

(

io::RPStream

Object )

mmdb::math::Alignment::~Alignment

(

)

---

Member Function Documentation

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

void mmdb::math::Alignment::Align	(	cpstr	S,
		cpstr	T,
		ALIGN_METHOD	Method = ALIGN_GLOBAL
	)

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

void mmdb::math::Alignment::BuildGATable	(	cpstr	S,
		cpstr	T,
		bool	FreeSEnd,
		bool	FreeTEnd
	)		[protected]

void mmdb::math::Alignment::BuildLATable	(	cpstr	S,
		cpstr	T
	)		[protected]

void mmdb::math::Alignment::FreeMemory

(

)

[protected, virtual]

pstr mmdb::math::Alignment::GetAlignedS

(

)

[inline]

pstr mmdb::math::Alignment::GetAlignedT

(

)

[inline]

realtype mmdb::math::Alignment::GetScore

(

)

[inline]

realtype mmdb::math::Alignment::GetSeqId

(

)

realtype mmdb::math::Alignment::GetSimilarity

(

)

char mmdb::math::Alignment::GetSpace

(

)

[inline]

void mmdb::math::Alignment::InitAlignment

(

)

[protected, virtual]

void mmdb::math::Alignment::OutputResults	(	io::RFile	f,
		cpstr	S,
		cpstr	T
	)		[virtual]

void mmdb::math::Alignment::PrintVT	(	cpstr	S,
		cpstr	T
	)		[protected]

void mmdb::math::Alignment::read

(

io::RFile

f )

realtype mmdb::math::Alignment::Score	(	char	A,
		char	B
	)		[protected, virtual]

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

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

void mmdb::math::Alignment::write

(

io::RFile

f )

---

Member Data Documentation

pstr mmdb::math::Alignment::AlgnS [protected]

pstr mmdb::math::Alignment::AlgnT [protected]

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

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

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

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

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

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

char mmdb::math::Alignment::Space [protected]

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

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

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

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

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

---

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

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