Alignseg Class Reference

#include <alignseg.h>

Inheritance diagram for Alignseg:

List of all members.

Public Member Functions
	Alignseg ()
	Alignseg (const int xx, const int yy, const int ll)
	Alignseg (const int xx, const int yy, const int ll, const int sc)
	Alignseg (const Alignseg &as)
int	distanceX (const Alignseg &as)
int	distanceY (const Alignseg &as)
bool	before (const Alignseg &as)
bool	before (const Alignseg *as)
int	diagonal () const
bool	sameDiagonal (const Alignseg &as)
bool	contain (const Alignseg &as) const
void	merge (const Alignseg &as)
bool	operator== (const Alignseg &as) const
int	getLength () const
int	getScore () const
void	setScore (const int sc)
int	getX () const
int	getEndX () const
int	getY () const
int	getEndY () const
void	setX (const int xx)
void	setY (const int yy)
void	setLength (const int l)
void	addLength (const int l)
void	addScore (const int sc)
int	YOverlap (const Alignseg &as) const
int	XOverlap (const Alignseg &as) const
void	shrink (int sz, const int *xsc, const int *ysc, const Matrix *mt)
Protected Attributes
int	x
int	y
int	len
int	score
Friends
ostream &	operator<< (ostream &ous, const Alignseg &as)

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Detailed Description

class Alignseg assume protein to protein or DNA to DNA alignment which is y=x+b

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Constructor & Destructor Documentation

Alignseg::Alignseg

(

)

[inline]

constructor where score is not considered

Alignseg::Alignseg	(	const int	xx,
		const int	yy,
		const int	ll
	)			[inline]

Alignseg::Alignseg	(	const int	xx,
		const int	yy,
		const int	ll,
		const int	sc
	)			[inline]

score is known

Alignseg::Alignseg

(

const Alignseg &

as

)

[inline]

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Member Function Documentation

int Alignseg::distanceX

(

const Alignseg &

as

)

[inline]

distance from end of this alignment to start of the next alignment segment, in X axis.

References len, and x.

int Alignseg::distanceY

(

const Alignseg &

as

)

[inline]

Distance defined in the Y-axix End to start distance

References len, and y.

bool Alignseg::before

(

const Alignseg &

as

)

[inline]

References getEndX(), getEndY(), getX(), and getY().

bool Alignseg::before

(

const Alignseg *

as

)

[inline]

References getEndX(), getEndY(), getX(), and getY().

int Alignseg::diagonal

(

)

const [inline]

References x, and y.

bool Alignseg::sameDiagonal

(

const Alignseg &

as

)

[inline]

References x, and y.

bool Alignseg::contain

(

const Alignseg &

as

)

const

Must be on the same diagonal

References len, x, and y.

void Alignseg::merge

(

const Alignseg &

as

)

Only make sense when merging aligns on the same diagonal It does not matter which one is in front of the other.

Always update this object! Does not care about the score. Mainly used for joining words.

References getEndX(), len, x, and y.

bool Alignseg::operator==

(

const Alignseg &

as

)

const [inline]

References len, x, and y.

int Alignseg::getLength

(

)

const [inline]

References len.

Referenced by Boxchain::buildAlignment(), Lale::extendhit(), Lale::isComplete(), ltAlignsegYXlen::operator()(), and Lale::showseg_debug().

int Alignseg::getScore

(

)

const [inline]

References score.

Referenced by Linkbox::connect(), Lale::extendhit(), and ltAlignsegexBeginYPtr::operator()().

void Alignseg::setScore

(

const int

sc

)

[inline]

References score.

Referenced by Lale::extendhit().

int Alignseg::getX

(

)

const [inline]

References x.

Referenced by Alignsegex::attachTo(), before(), Boxchain::buildAlignment(), Linkbox::connect(), Lale::extendhit(), ltAlignsegYXlen::operator()(), Linkbox::removeChain(), and Lale::showseg_debug().

int Alignseg::getEndX

(

)

const [inline]

References len, and x.

Referenced by Alignsegex::attachTo(), before(), Boxchain::buildAlignment(), Linkbox::connect(), merge(), Linkbox::removeChain(), and XOverlap().

int Alignseg::getY

(

)

const [inline]

References y.

Referenced by Alignsegex::attachTo(), before(), Boxchain::buildAlignment(), Linkbox::connect(), Lale::extendhit(), ltAlignsegexBeginYPtr::operator()(), ltAlignsegYXlen::operator()(), and Lale::showseg_debug().

int Alignseg::getEndY

(

)

const [inline]

References len, and y.

Referenced by Alignsegex::attachTo(), before(), Boxchain::buildAlignment(), Linkbox::connect(), ltAlignsegexEndYPtr::operator()(), and YOverlap().

void Alignseg::setX

(

const int

xx

)

[inline]

References x.

Referenced by Lale::extendhit().

void Alignseg::setY

(

const int

yy

)

[inline]

References y.

Referenced by Lale::extendhit().

void Alignseg::setLength

(

const int

l

)

[inline]

References len.

void Alignseg::addLength

(

const int

l

)

[inline]

increment the length by a value

References len.

Referenced by Lale::extendhit().

void Alignseg::addScore

(

const int

sc

)

[inline]

In Y direction, this object ends compared to the as object's start.

References score.

Referenced by Alignsegex::addMaxScore().

int Alignseg::YOverlap

(

const Alignseg &

as

)

const [inline]

References getEndY(), and y.

int Alignseg::XOverlap

(

const Alignseg &

as

)

const [inline]

References getEndX(), and x.

void Alignseg::shrink	(	int	sz,
		const int *	xsc,
		const int *	ysc,
		const Matrix *	mt
	)

Reimplemented in Alignsegex.

References len, Matrix::lookup(), score, x, and y.

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	ous,
		const Alignseg &	as
	)			[friend]

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Member Data Documentation

int Alignseg::x [protected]

Referenced by Alignsegex::attachTo(), contain(), diagonal(), distanceX(), getEndX(), getX(), merge(), operator<<(), operator==(), Alignsegex::print(), sameDiagonal(), setX(), Alignsegex::shrink(), shrink(), and XOverlap().

int Alignseg::y [protected]

Referenced by Alignsegex::attachTo(), contain(), diagonal(), distanceY(), getEndY(), getY(), merge(), operator<<(), operator==(), Alignsegex::print(), sameDiagonal(), setY(), Alignsegex::shrink(), shrink(), and YOverlap().

int Alignseg::len [protected]

Referenced by addLength(), contain(), distanceX(), distanceY(), getEndX(), getEndY(), getLength(), merge(), operator<<(), operator==(), Alignsegex::print(), setLength(), Alignsegex::shrink(), and shrink().

int Alignseg::score [protected]

Referenced by addScore(), Alignsegex::attachTo(), getScore(), operator<<(), Alignsegex::print(), Alignsegex::setDefault(), setScore(), Alignsegex::shrink(), and shrink().

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

• seqaln/src/blast/alignseg.h
• seqaln/src/blast/alignseg.cpp