Alignsegex Class Reference

#include <alignseg.h>

Inheritance diagram for Alignsegex:

List of all members.

Public Member Functions
	Alignsegex ()
	Alignsegex (const int xx, const int yy, const int ll)
	Alignsegex (const Alignseg &as)
void	setPreviousNode (Alignsegex *as)
void	setPrevious (Alignsegex *as)
Alignsegex *	previous ()
bool	attachTo (Alignsegex *as, const int *xsc, const int *ysc, const Matrix *mtx)
void	setDefault ()
void	shrink (int sz, const int *xsc, const int *ysc, const Matrix *mt)
int	getMaxScore () const
void	setMaxScore (const int sc)
void	print (ostream &ous) const
void	addMaxScore (const int sc)
void	setConnectPath (const int p)
int	getConnectPath () const
Static Public Member Functions
static void	setParameters (int go, int ge, int gd)
Protected Attributes
Alignsegex *	prev
int	maxsc
int	connectpath
Static Protected Attributes
static int	gapopen = -3
static int	gapextend = -1
static int	gapaligndropoff = 12
Friends
ostream &	operator<< (ostream &ous, const Alignsegex &as)

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Constructor & Destructor Documentation

Alignsegex::Alignsegex

(

)

[inline]

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

Alignsegex::Alignsegex

(

const Alignseg &

as

)

[inline]

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Member Function Documentation

void Alignsegex::setPreviousNode

(

Alignsegex *

as

)

[inline]

References prev.

void Alignsegex::setPrevious

(

Alignsegex *

as

)

[inline]

References prev.

Referenced by Linkbox::connect().

Alignsegex* Alignsegex::previous

(

)

[inline]

References prev.

Referenced by Boxchain::Boxchain(), and Linkbox::removeChain().

bool Alignsegex::attachTo	(	Alignsegex *	as,
		const int *	xsc,
		const int *	ysc,
		const Matrix *	mtx
	)

If the best score obtained is greater than the gapalignmentdropoff and the original score. value then this node is attached to the given node, otherwise, the original value stays and no connection is made.

return true if a connectionis made.

References gapaligndropoff, gapextend, gapopen, Alignseg::getEndX(), Alignseg::getEndY(), Alignseg::getX(), Alignseg::getY(), maxsc, prev, Alignseg::score, Matrix::score(), Alignseg::x, and Alignseg::y.

void Alignsegex::setDefault

(

)

[inline]

References maxsc, prev, and Alignseg::score.

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

shrink from the end

Reimplemented from Alignseg.

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

int Alignsegex::getMaxScore

(

)

const [inline]

References maxsc.

Referenced by Linkbox::connect(), and ltAlignsegexEndYPtr::operator()().

void Alignsegex::setMaxScore

(

const int

sc

)

[inline]

References maxsc.

Referenced by Linkbox::connect().

void Alignsegex::print

(

ostream &

ous

)

const

References Alignseg::len, maxsc, Alignseg::score, Alignseg::x, and Alignseg::y.

void Alignsegex::addMaxScore

(

const int

sc

)

[inline]

References Alignseg::addScore(), and maxsc.

void Alignsegex::setConnectPath

(

const int

p

)

[inline]

References connectpath.

Referenced by Linkbox::connect().

int Alignsegex::getConnectPath

(

)

const [inline]

References connectpath.

Referenced by Boxchain::buildAlignment().

static void Alignsegex::setParameters	(	int	go,
		int	ge,
		int	gd
	)			[inline, static]

References gapaligndropoff, gapextend, and gapopen.

Referenced by main().

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Friends And Related Function Documentation

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

---

Member Data Documentation

Alignsegex* Alignsegex::prev [protected]

Referenced by attachTo(), previous(), setDefault(), setPrevious(), and setPreviousNode().

int Alignsegex::maxsc [protected]

Referenced by addMaxScore(), attachTo(), getMaxScore(), operator<<(), print(), setDefault(), setMaxScore(), and shrink().

int Alignsegex::connectpath [protected]

Referenced by getConnectPath(), and setConnectPath().

int Alignsegex::gapopen = -3 [static, protected]

Referenced by attachTo(), and setParameters().

int Alignsegex::gapextend = -1 [static, protected]

Referenced by attachTo(), and setParameters().

int Alignsegex::gapaligndropoff = 12 [static, protected]

Referenced by attachTo(), and setParameters().

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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