NeedlemanWunsch Class Reference

This class contains functions that are used to calculate the global alignment score of two amino acid sequences. This class uses the Needleman-Wunsch algorithm. For match and mismatch it uses a similarity scoring matrix. More...

#include <OpenMS/ANALYSIS/SEQUENCE/NeedlemanWunsch.h>

Collaboration diagram for NeedlemanWunsch:

Public Types
enum class	ScoringMatrix { identity , PAM30MS , SIZE_OF_SCORINGMATRIX }
	contains the valid matrices and the number of them More...

Public Member Functions
	NeedlemanWunsch (ScoringMatrix matrix, int penalty)
	Constructor that sets the scoring matrix and the gap penalty. More...
	NeedlemanWunsch ()=default
	Default constructor (scoring matrix PAM30MS and penalty 5) More...
	~NeedlemanWunsch ()=default
	Default destructor. More...
int	align (const String &seq1, const String &seq2)
	Calculates the similarity score of the global alignment of two amino acid sequences using Needleman-Wunsch- Algorithm. More...
void	setMatrix (const ScoringMatrix &matrix)
	sets the scoring matrix. Takes either a string or the enum ScoringMatrix. More...
void	setMatrix (const std::string &matrix)
void	setPenalty (const int penalty)
	sets the cost of gaps More...
ScoringMatrix	getMatrix () const
	returns the scoring matrix More...
int	getPenalty () const
	returns the gap penalty More...

Static Public Attributes
static const std::vector< std::string >	NamesOfScoringMatrices
	Names of valid matrices. More...

Private Attributes
int	gap_penalty_ = 5
	penalty for alignment score calculation More...
ScoringMatrix	my_matrix_ = ScoringMatrix::PAM30MS
	scoring matrix for the alignment score calculation More...
std::vector< int >	first_row_ {}
	alignment score calculation with two rows More...
std::vector< int >	second_row_ {}

Detailed Description

This class contains functions that are used to calculate the global alignment score of two amino acid sequences. This class uses the Needleman-Wunsch algorithm. For match and mismatch it uses a similarity scoring matrix.

Member Enumeration Documentation

ScoringMatrix

enum ScoringMatrix

strong

contains the valid matrices and the number of them

Enumerator
identity
PAM30MS
SIZE_OF_SCORINGMATRIX

Constructor & Destructor Documentation

NeedlemanWunsch() [1/2]

NeedlemanWunsch	(	ScoringMatrix	matrix,
		int	penalty
	)

Constructor that sets the scoring matrix and the gap penalty.

NeedlemanWunsch() [2/2]

NeedlemanWunsch ( )

default

Default constructor (scoring matrix PAM30MS and penalty 5)

~NeedlemanWunsch()

~NeedlemanWunsch ( )

default

Default destructor.

Member Function Documentation

align()

int align	(	const String &	seq1,
		const String &	seq2
	)

Calculates the similarity score of the global alignment of two amino acid sequences using Needleman-Wunsch- Algorithm.

getMatrix()

ScoringMatrix getMatrix

(

)

const

returns the scoring matrix

getPenalty()

int getPenalty

(

)

const

returns the gap penalty

setMatrix() [1/2]

void setMatrix

(

const ScoringMatrix &

matrix

)

sets the scoring matrix. Takes either a string or the enum ScoringMatrix.

Exceptions

Exception

illegal argument is thrown if the input is not a member of the valid matrices.

setMatrix() [2/2]

void setMatrix

(

const std::string &

matrix

)

setPenalty()

void setPenalty

(

const int

penalty

)

sets the cost of gaps

Member Data Documentation

first_row_

std::vector<int> first_row_ {}

private

alignment score calculation with two rows

gap_penalty_

int gap_penalty_ = 5

private

penalty for alignment score calculation

my_matrix_

ScoringMatrix my_matrix_ = ScoringMatrix::PAM30MS

private

scoring matrix for the alignment score calculation

NamesOfScoringMatrices

const std::vector<std::string> NamesOfScoringMatrices

static

Names of valid matrices.

second_row_

std::vector<int> second_row_ {}

private