mems::PairwiseScoringScheme Class Reference

#include <SubstitutionMatrix.h>

List of all members.

Public Member Functions
PairwiseScoringScheme &	operator= (const PairwiseScoringScheme &pss)
	PairwiseScoringScheme ()
	PairwiseScoringScheme (const score_t matrix[4][4], score_t gap_open, score_t gap_extend)
void	setMatrix (const score_t matrix[4][4])
Public Attributes
score_t	gap_extend
	gap extend penalty
score_t	gap_open
	gap open penalty
score_t	matrix [4][4]
	4x4 nucleotide substitution matrix

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Constructor & Destructor Documentation

mems::PairwiseScoringScheme::PairwiseScoringScheme (  const score_t  matrix[4][4], score_t  gap_open, score_t  gap_extend )  [inline]

Definition at line 44 of file SubstitutionMatrix.h. References gap_extend, gap_open, mems::score_t, and setMatrix().

mems::PairwiseScoringScheme::PairwiseScoringScheme (   )  [inline]

Definition at line 51 of file SubstitutionMatrix.h. References mems::default_gap_extend, mems::default_gap_open, and mems::hoxd_matrix.

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Member Function Documentation

PairwiseScoringScheme& mems::PairwiseScoringScheme::operator= (  const PairwiseScoringScheme &  pss  )  [inline]

Definition at line 52 of file SubstitutionMatrix.h. References gap_extend, gap_open, matrix, and setMatrix().

void mems::PairwiseScoringScheme::setMatrix (  const score_t  matrix[4][4]  )  [inline]

Definition at line 59 of file SubstitutionMatrix.h. References mems::score_t. Referenced by operator=(), and PairwiseScoringScheme().

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Member Data Documentation

score_t mems::PairwiseScoringScheme::gap_extend

gap extend penalty Definition at line 42 of file SubstitutionMatrix.h. Referenced by mems::computeGapScores(), and operator=().

score_t mems::PairwiseScoringScheme::gap_open

gap open penalty Definition at line 41 of file SubstitutionMatrix.h. Referenced by mems::computeGapScores(), and operator=().

score_t mems::PairwiseScoringScheme::matrix[4][4]

4x4 nucleotide substitution matrix Definition at line 40 of file SubstitutionMatrix.h. Referenced by mems::computeMatchScores(), and operator=().

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

• libMems/SubstitutionMatrix.h

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