TmMatches Class Reference

#include <tm_matches.hpp>

Public Member Functions
	TmMatches ()
	TmMatches (const SUFFIX_MARKER_TYPE exampleId, const SUFFIX_MARKER_TYPE exampleSize, const SUFFIX_MARKER_TYPE patternSize)
virtual	~TmMatches ()
double	getScore () const
std::vector< Interval >	getExampleIntervals () const
std::vector< Interval >	getPatternIntervals () const
SUFFIX_MARKER_TYPE	getExampleId () const
void	calculateSimpleScore ()
void	calculateScore ()
void	addExampleInterval (int start, int end)
void	addPatternInterval (int start, int end)

Detailed Description

Class used within Anubis search algorithm to store partial results. Holds information about mutual overlay of the pattern and found example.

Constructor & Destructor Documentation

TmMatches::TmMatches

(

)

Constructor.

TmMatches::TmMatches	(	const SUFFIX_MARKER_TYPE	exampleId,
		const SUFFIX_MARKER_TYPE	exampleSize,
		const SUFFIX_MARKER_TYPE	patternSize
	)

Constructor setting basic information.

Parameters

exampleId	id of found example
exampleSize	size of the found example
patternSize	size of the searched pattern

TmMatches::~TmMatches ( )

virtual

Destructor.

Member Function Documentation

void TmMatches::addExampleInterval	(	int	start,
		int	end
	)

Adds information about covering of example. If the new fragment intersects with any previous fragment, it is not added.

Parameters

start	start of the example overlay fragment
end	end of the example overlay fragment

void TmMatches::addPatternInterval	(	int	start,
		int	end
	)

Adds information about covering of pattern. If the new fragment intersects with any previous fragment, it is not added.

Parameters

start	start of the pattern overlay fragment
end	end of the pattern overlay fragment

void TmMatches::calculateScore

(

)

Calculates mutual overlay score in the scale [0,1]. Takes into account the number and the length of the fragments (the fewer fragments, the better). Score 1 - perfect score - is assigned when the whole pattern and the whole example are covered with only one fragment. Result of the computation is stored in the score field, use getScore() to retrieve it.

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void TmMatches::calculateSimpleScore

(

)

Calculates mutual overlay score in the scale [0,1]. Uses generalized Jaccard index for the computation. Score 1 - perfect score - is assigned when the whole pattern and the whole example are covered. Result of the computation is stored in the score field, use getScore() to retrieve it.

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SUFFIX_MARKER_TYPE TmMatches::getExampleId ( ) const

inline

Getter for example id.

Returns

example id

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std::vector<Interval> TmMatches::getExampleIntervals ( ) const

inline

Getter for the list of overlays of the example.

Returns

example overlays list

std::vector<Interval> TmMatches::getPatternIntervals ( ) const

inline

Getter for the list of overlays of the pattern.

Returns

pattern overlays list

double TmMatches::getScore ( ) const

inline

Getter for score of the mutual overlay.

Returns

score

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

• /home/rafalj/projects/concordia/concordia/concordia/tm_matches.hpp
• /home/rafalj/projects/concordia/concordia/concordia/tm_matches.cpp