Match Class Reference

#include <Match.h>

Inheritance diagram for Match:

List of all members.

Public Member Functions
	Match ()
	Match (const Match &m)
	Match (int qb, int qe, int tb, int te)
	~Match ()
Match &	operator= (const Match &m)
bool	operator< (const Match &m) const
bool	operator== (const Match &m) const
const Range &	queryRange () const
const Range &	targetRange () const
int	targetBegin () const
int	targetEnd () const
int	queryBegin () const
int	queryEnd () const
int	queryLength () const
int	targetLength () const
char	targetDirection () const
bool	onPlus () const
bool	onMinus () const
bool	targetOnPlus () const
bool	targetOnMinus () const
bool	isNull () const
int	qoverlap (const Match &m, bool sameDirection=true) const
int	toverlap (const Match &m, bool sameDirection=true) const
pair< int, int >	overlap (const Match &m, bool sd=true) const
pair< int, int >	overlay (const Match &m) const
pair< float, float >	overlayFraction (const Match &m) const
pair< float, float >	queryOverlapFraction (const Match &m, bool sameDirection=true) const
float	queryOverlapFractionMax (const Match &m, bool sameDirection=true) const
float	queryOverlapFractionMerge (const Match &m, bool sameDirection=true) const
pair< float, float >	targetOverlapFraction (const Match &m, bool sameDirection=true) const
float	targetOverlapFractionMax (const Match &m, bool sameDirection=true) const
float	targetOverlapFractionMerge (const Match &m, bool sameDirection=true) const
bool	contain (const Match &m, bool sameDirection=true) const
bool	qcontain (const Match &m, bool sd=true) const
bool	tcontain (const Match &m, bool sd=true) const
bool	similar (const Match &m, bool sd=true) const
bool	coveredBy (const Match &m, bool sd=true, float fraction=0.8) const
bool	plusContain (const Match &m) const
bool	qplustminusContain (const Match &m) const
int	queryDistance (const Match &m)
int	targetDistance (const Match &m)
pair< int, int >	combine (const Match &m)
void	setNull ()
void	setTargetRange (int b, int e)
void	set (int qb, int qe, int tb, int te)
ostream &	output (ostream &ous, const char delimiter[]="\t") const
string	asDelimitedString (const char delimiter[]=",") const
Protected Attributes
Range	q
Range	t
Friends
ostream &	operator<< (ostream &ous, const Match &m)

---

Detailed Description

describe one of the possibly many sequene matches from query to target q->t This should be a generic match, because different program may represent matches in slightly different ways.

This class will not store the query and target ids. A derived class will store this information.

---

Constructor & Destructor Documentation

Match::Match

(

)

[inline]

Build an empty Match

Match::Match

(

const Match &

m

)

[inline]

Match::Match	(	int	qb,
		int	qe,
		int	tb,
		int	te
	)			[inline]

Build a match object based on the ranges of match given.

Parameters:

	qb	query begin index inclusive
	qe	query end index inclusive
	tb	target begin index
	te	target end index Whether the index is 0 or 1-bases depends on the application.

Match::~Match

(

)

[inline]

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Member Function Documentation

Match & Match::operator=

(

const Match &

m

)

References q, and t.

Referenced by M8Match::operator=().

bool Match::operator<

(

const Match &

m

)

const

Match A is absolutely before B with no overlap.

Right now this oerator should only be meaningful to Matches that are both in the + direction | |------| | | A | | |------| | | |----| | | | | | B | | |----| \/------------------------> target When comparing matches A and B, A<B, where the horizontal direction is target, from small to large. The vertical dimension is the query axis, from top to buttom (small to large). Alternative definition is A.q.begin < B.q.begin and A.t.begin < B.t.begin

References Range::begin(), Range::end(), onPlus(), q, and t.

bool Match::operator==

(

const Match &

m

)

const [inline]

Test identical match

References q, and t.

const Range& Match::queryRange

(

)

const [inline]

returs a reference to a const range object

References q.

Referenced by M8MatchChain::add(), Blmodel::getExpectedTargetRange(), Tblastn::isFirstQueryMatch(), Tblastn::isLastQueryMatch(), M8MatchChain::M8MatchChain(), MatchQueryLessThan::operator()(), afterMatchQuery::operator()(), beforeMatchQuery::operator()(), cmpTargetDirectionalPtr::operator()(), cmpTargetPtr::operator()(), cmpQueryPtr::operator()(), operator<<(), Tblastn::overlapFirstQueryMatch(), Tblastn::overlapLastQueryMatch(), and Boxchain::queryOverlap().

const Range& Match::targetRange

(

)

const [inline]

References t.

Referenced by M8MatchChain::add(), Blmodel::getExpectedTargetRange(), main(), nextGoodModel(), cmpTargetDirectionalPtr::operator()(), cmpTargetPtr::operator()(), cmpQueryPtr::operator()(), and operator<<().

int Match::targetBegin

(

)

const [inline]

References Range::begin(), and t.

Referenced by Linkmatch::bestModel(), Blmodel::getExpectedTargetRange(), cmpMatchTbeginIntPtr::operator()(), cmpMatchTbeginInt::operator()(), Linkmatch::removeChain(), and Boxchain::targetBegin().

int Match::targetEnd

(

)

const [inline]

References Range::end(), and t.

Referenced by Linkmatch::bestModel(), Blmodel::getExpectedTargetRange(), cmpMatchTendIntPtr::operator()(), cmpMatchTendInt::operator()(), Linkmatch::removeChain(), and Boxchain::targetEnd().

int Match::queryBegin

(

)

const [inline]

References Range::begin(), and q.

Referenced by Blmodel::getExpectedTargetRange(), ltMatchQueryBeginPtr::operator()(), notlessMatchQueryBegin::operator()(), Boxchain::queryBegin(), Boxchain::queryCovered(), Blmodel::queryHasStart(), and Linkmatch::removeChain().

int Match::queryEnd

(

)

const [inline]

References Range::end(), and q.

Referenced by Blmodel::getExpectedTargetRange(), Boxchain::queryCovered(), Boxchain::queryEnd(), Blmodel::queryHasStop(), and Linkmatch::removeChain().

int Match::queryLength

(

)

const [inline]

Reimplemented in Blmodel.

References Range::length(), and q.

Referenced by Boxchain::querySeqCovered().

int Match::targetLength

(

)

const [inline]

Reimplemented in Blmodel.

References Range::length(), and t.

char Match::targetDirection

(

)

const [inline]

References Range::direction(), and t.

Referenced by Boxchain::direction().

bool Match::onPlus

(

)

const [inline]

This is a more generic function. Testing both query and target on the + direction.

References Range::direction(), q, and t.

Referenced by operator<().

bool Match::onMinus

(

)

const [inline]

References Range::direction(), q, and t.

bool Match::targetOnPlus

(

)

const [inline]

References Range::direction(), and t.

Referenced by Linkmatch::bestModel(), and Linkmatch::removeChain().

bool Match::targetOnMinus

(

)

const [inline]

References Range::direction(), and t.

bool Match::isNull

(

)

const [inline]

both query and target are NULL objects

References Range::isNull(), q, and t.

int Match::qoverlap	(	const Match &	m,
		bool	sameDirection = true
	)			const [inline]

query overlap amount

References Range::overlap(), and q.

int Match::toverlap	(	const Match &	m,
		bool	sameDirection = true
	)			const [inline]

target overlap amount

References Range::overlap(), and t.

pair<int, int> Match::overlap	(	const Match &	m,
		bool	sd = true
	)			const [inline]

it return the query,target overlap as a pair of integers return 0 if no overlap.

Parameters:

sd

has the same power as the parameter in the Range class. If set true, then overlap is computed only for Ranges in the same direction. Otherwise, return 0.

References Range::overlap(), q, and t.

Referenced by M8Match::combine().

pair<int, int> Match::overlay

(

const Match &

m

)

const [inline]

regardless of direction

References Range::overlay(), q, and t.

pair<float,float> Match::overlayFraction

(

const Match &

m

)

const [inline]

References Range::overlayFraction(), q, and t.

pair< float, float > Match::queryOverlapFraction	(	const Match &	m,
		bool	sameDirection = true
	)			const

return the query overlap fractions of this and m as compared to the queryRange for both objects. Compare to ...OverlapFractionMerge() methods that return only one number.

References Range::length(), Range::overlap(), and q.

Referenced by queryOverlapFractionMax().

float Match::queryOverlapFractionMax	(	const Match &	m,
		bool	sameDirection = true
	)			const [inline]

References queryOverlapFraction().

float Match::queryOverlapFractionMerge	(	const Match &	m,
		bool	sameDirection = true
	)			const [inline]

return the overlaping fraction of the query Ranges as compared to the merged Ranges of the two Ranges

return negative numbers if no overlap.

References Range::overlapFraction(), and q.

Referenced by MatchQueryLessThan::operator()(), and beforeMatchQuery::operator()().

pair< float, float > Match::targetOverlapFraction	(	const Match &	m,
		bool	sameDirection = true
	)			const

References Range::length(), Range::overlap(), and t.

Referenced by targetOverlapFractionMax().

float Match::targetOverlapFractionMax	(	const Match &	m,
		bool	sameDirection = true
	)			const [inline]

References targetOverlapFraction().

float Match::targetOverlapFractionMerge	(	const Match &	m,
		bool	sameDirection = true
	)			const [inline]

the overlap fraction compared the merged range The same function in Range class overlapFraction().

Parameter: sameDirection if true, then return 0 for target Ranges that are on the opposite strand.

References Range::overlapFraction(), and t.

Referenced by afterMatchQuery::operator()().

bool Match::contain	(	const Match &	m,
		bool	sameDirection = true
	)			const [inline]

if the sameDirection is true, the only the ranges are in the same directions are they compared. Test both query and target contain relation.

References Range::contain(), q, and t.

Referenced by Linkmatch::bestModel(), M8Match::contain(), and Linkmatch::removeChain().

bool Match::qcontain	(	const Match &	m,
		bool	sd = true
	)			const [inline]

References Range::contain(), and q.

bool Match::tcontain	(	const Match &	m,
		bool	sd = true
	)			const [inline]

References Range::contain(), and t.

bool Match::similar	(	const Match &	m,
		bool	sd = true
	)			const [inline]

References q, Range::similar(), and t.

bool Match::coveredBy	(	const Match &	m,
		bool	sd = true,
		float	fraction = 0.8
	)			const

References Range::length(), Range::overlap(), q, and t.

bool Match::plusContain

(

const Match &

m

)

const [inline]

both the query and the target are in the plus direction

References Range::plusContain(), q, and t.

bool Match::qplustminusContain

(

const Match &

m

)

const [inline]

References Range::minusContain(), Range::plusContain(), q, and t.

int Match::queryDistance

(

const Match &

m

)

[inline]

References Range::distance(), and q.

int Match::targetDistance

(

const Match &

m

)

[inline]

References Range::distance(), and t.

pair<int,int> Match::combine

(

const Match &

m

)

[inline]

merge query and target range separately, return the respective overlapping region for query and target in a pair<int, int>. This returned pair is directional sensitive. If the underlying Range is in oppositve direction, then the overlap is 0.

References Range::combine(), q, and t.

Referenced by M8Match::combine().

void Match::setNull

(

)

[inline]

References q, and t.

Referenced by Linkmatch::removeChain().

void Match::setTargetRange	(	int	b,
		int	e
	)			[inline]

References Range::set(), and t.

void Match::set	(	int	qb,
		int	qe,
		int	tb,
		int	te
	)			[inline]

References q, Range::set(), and t.

Referenced by Linkmatch::removeChain().

ostream& Match::output	(	ostream &	ous,
		const char	delimiter[] = "\t"
	)			const [inline]

for outpu to a tabular format

Reimplemented in M8Match.

References Range::output(), q, and t.

Referenced by operator<<(), and M8Match::output().

string Match::asDelimitedString

(

const char

delimiter[] = ","

)

const [inline]

could be used for SQL statements

Reimplemented in M8Match.

References Range::asDelimitedString(), q, and t.

Referenced by M8Match::asDelimitedString().

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	ous,
		const Match &	m
	)			[friend]

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Member Data Documentation

Range Match::q [protected]

Referenced by asDelimitedString(), combine(), M8Match::combine(), contain(), coveredBy(), isNull(), onMinus(), onPlus(), operator<(), operator=(), operator==(), output(), overlap(), overlay(), overlayFraction(), plusContain(), qcontain(), qoverlap(), qplustminusContain(), queryBegin(), queryDistance(), queryEnd(), queryLength(), queryOverlapFraction(), queryOverlapFractionMerge(), queryRange(), set(), setNull(), and similar().

Range Match::t [protected]

Referenced by asDelimitedString(), combine(), M8Match::combine(), contain(), coveredBy(), isNull(), onMinus(), onPlus(), operator<(), operator=(), operator==(), output(), overlap(), overlay(), overlayFraction(), plusContain(), qplustminusContain(), set(), setNull(), setTargetRange(), similar(), targetBegin(), targetDirection(), targetDistance(), targetEnd(), targetLength(), targetOnMinus(), targetOnPlus(), targetOverlapFraction(), targetOverlapFractionMerge(), targetRange(), tcontain(), and toverlap().

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

• seqaln/Utility/Match.h
• seqaln/Utility/Match.cpp