Lale Class Reference

#include <kzblast.h>

List of all members.

Public Member Functions
	Lale ()
	Lale (int ws, const BlastParameter &bp)
void	readQuery (const string &file)
void	buildfsa ()
void	showfsa (ostream &ous) const
list< Alignseg > &	findMatch (const bioseq &s)
int	extendhit (Alignseg &as, const int *tc, const int tclen)
void	showseg_debug (const Alignseg &as, const bioseq &ss) const
void	showmaxss_debug (const bioseq *tseq) const
bool	isComplete (const Alignseg &as, const bioseq &ss)
void	setMatrix (const Matrix &mt)
const Matrix *	getMatrix () const
const bioseq *	getQuery () const
Private Member Functions
void	mergeNeighbor (list< Alignseg > &segs, const int *qsc, const int *tsc)
Private Attributes
bioseq *	qseq
Matrix	mtx
BlastParameter	param
list< Alignseg >	maxss
ltrie *	fsa

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Detailed Description

Local Alignment by look up and extension LALE When this object is build it constructs a default BlastParameter object as member for useage. This parameter can be altered by setting to a new value.

Look up used a trie data structure.

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Constructor & Destructor Documentation

Lale::Lale

(

)

[inline]

Lale::Lale	(	int	ws,
		const BlastParameter &	bp
	)			[inline]

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Member Function Documentation

void Lale::readQuery

(

const string &

file

)

References bioseq::length(), qseq, and bioseq::read().

Referenced by main().

void Lale::buildfsa

(

)

[inline]

References ltrie::build(), fsa, mtx, BlastParameter::neighborFraction, BlastParameter::neighborThreshold, param, qseq, and bioseq::toString().

Referenced by main().

void Lale::showfsa

(

ostream &

ous

)

const [inline]

debug function

References fsa, and ltrie::showLeafs().

list< Alignseg > & Lale::findMatch

(

const bioseq &

s

)

find matches to the target sequence s

this method should return a data structure for further processing Lale is X, target is Y

References BlastParameter::extCutoff, extendhit(), ltrie::find(), fsa, bioseq::getcode(), isComplete(), bioseq::length(), maxss, mergeNeighbor(), mtx, intnode::next, param, lnode::pos, qseq, Matrix::score(), bioseq::toString(), intnode::value, BlastParameter::wordjoin, and BlastParameter::wordSize.

Referenced by main().

int Lale::extendhit	(	Alignseg &	as,
		const int *	tc,
		const int	tclen
	)

extend the hit Alignseg as. check to see the Alignseg has score > extCutoff then extend in both directions to see that the score reaches the max value

return 0 for not extended 1 extend end 2 extend start 3 extend both start and end

References Alignseg::addLength(), BlastParameter::extCutoff, BlastParameter::extDropoff, bioseq::getcode(), Alignseg::getLength(), Alignseg::getScore(), Alignseg::getX(), Alignseg::getY(), length, Matrix::lookup(), mtx, param, qseq, Alignseg::setScore(), Alignseg::setX(), and Alignseg::setY().

Referenced by findMatch().

void Lale::showseg_debug	(	const Alignseg &	as,
		const bioseq &	ss
	)			const

References Alignseg::getLength(), Alignseg::getX(), Alignseg::getY(), qseq, and bioseq::substring().

void Lale::showmaxss_debug

(

const bioseq *

tseq

)

const

References maxss, qseq, and bioseq::substring().

bool Lale::isComplete	(	const Alignseg &	as,
		const bioseq &	ss
	)

if it is complete, it will change the maxss to the only element that is complete

References Alignseg::getLength(), bioseq::length(), maxss, and qseq.

Referenced by findMatch().

void Lale::setMatrix

(

const Matrix &

mt

)

[inline]

References mtx.

const Matrix* Lale::getMatrix

(

)

const [inline]

References mtx.

Referenced by main().

const bioseq* Lale::getQuery

(

)

const [inline]

References qseq.

Referenced by main().

void Lale::mergeNeighbor	(	list< Alignseg > &	segs,
		const int *	qsc,
		const int *	tsc
	)			[private]

References mtx, and Matrix::score().

Referenced by findMatch().

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Member Data Documentation

bioseq* Lale::qseq [private]

Referenced by buildfsa(), extendhit(), findMatch(), getQuery(), isComplete(), readQuery(), showmaxss_debug(), and showseg_debug().

Matrix Lale::mtx [private]

Referenced by buildfsa(), extendhit(), findMatch(), getMatrix(), mergeNeighbor(), and setMatrix().

BlastParameter Lale::param [private]

Referenced by buildfsa(), extendhit(), and findMatch().

list<Alignseg> Lale::maxss [private]

Referenced by findMatch(), isComplete(), and showmaxss_debug().

ltrie* Lale::fsa [private]

Referenced by buildfsa(), findMatch(), and showfsa().

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

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