NeedlemanWunsch Class Reference

Global-alignment similarity score for two amino-acid sequences using the Needleman-Wunsch algorithm. More...

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

Collaboration diagram for NeedlemanWunsch:

Public Types
enum class	ScoringMatrix { identity , PAM30MS , SIZE_OF_SCORINGMATRIX }
	Substitution matrices bundled with this class. More...

Public Member Functions
	NeedlemanWunsch (ScoringMatrix matrix, int penalty)
	Construct with a chosen scoring matrix and gap penalty.
	NeedlemanWunsch ()=default
	Default constructor.
	~NeedlemanWunsch ()=default
	Destructor.
int	align (const std::string &seq1, const std::string &seq2)
	Compute the Needleman-Wunsch similarity score of seq1 vs. seq2.
void	setMatrix (const ScoringMatrix &matrix)
	Select the scoring matrix used by align.
void	setMatrix (const std::string &matrix)
	Select the scoring matrix by name; the accepted names are listed in NamesOfScoringMatrices.
void	setPenalty (const int penalty)
	Set the linear gap penalty subtracted per gap step.
ScoringMatrix	getMatrix () const
	Currently selected scoring matrix.
int	getPenalty () const
	Currently configured gap penalty.

Static Public Attributes
static const std::vector< std::string >	NamesOfScoringMatrices
	Lookup table for setMatrix(const std::string&); current entries: "identity", "PAM30MS".

Private Attributes
int	gap_penalty_ = 5
	Linear gap penalty.
ScoringMatrix	my_matrix_ = ScoringMatrix::PAM30MS
	Currently selected scoring matrix.
std::vector< int >	first_row_ {}
	First row of the two-row rolling buffer used by align.
std::vector< int >	second_row_ {}
	Second row of the two-row rolling buffer used by align.

Detailed Description

Global-alignment similarity score for two amino-acid sequences using the Needleman-Wunsch algorithm.

Computes the score (not the alignment itself) of the best global alignment of two amino-acid sequences against a substitution matrix plus a linear gap penalty. The implementation uses a two-row rolling buffer.

Note

The implementation indexes the substitution matrix by c - 'A', so the input strings must contain only uppercase ASCII letters in [A-Z]. Characters J, O, and U have INT16_MAX rows/columns in both bundled matrices and effectively forbid any alignment involving them. Lowercase or non-ASCII characters lead to out-of-bounds reads.

Member Enumeration Documentation

ScoringMatrix

enum class ScoringMatrix

strong

Substitution matrices bundled with this class.

Enumerator
identity	+1 on the diagonal, 0 elsewhere; J / O / U columns and rows are forbidden (INT16_MAX).
PAM30MS	PAM30 matrix extended for MS-style substitutions (default).
SIZE_OF_SCORINGMATRIX	Number of valid matrices.

Constructor & Destructor Documentation

NeedlemanWunsch() [1/2]

NeedlemanWunsch	(	ScoringMatrix	matrix,
		int	penalty
	)

Construct with a chosen scoring matrix and gap penalty.

Parameters

[in]	matrix	Scoring matrix to use.
[in]	penalty	Linear gap penalty (subtracted per gap step).

NeedlemanWunsch() [2/2]

NeedlemanWunsch ( )

default

Default constructor.

Uses ScoringMatrix::PAM30MS and a gap penalty of 5.

~NeedlemanWunsch()

~NeedlemanWunsch ( )

default

Destructor.

Member Function Documentation

align()

int align	(	const std::string &	seq1,
		const std::string &	seq2
	)

Compute the Needleman-Wunsch similarity score of seq1 vs. seq2.

Uses the currently selected scoring matrix and gap penalty. The sequences must contain only uppercase [A-Z] characters; see the class brief for the constraints.

Parameters

[in]	seq1	First amino-acid sequence.
[in]	seq2	Second amino-acid sequence.

Returns

Score of the best global alignment.

getMatrix()

ScoringMatrix getMatrix

(

)

const

Currently selected scoring matrix.

Returns

The scoring matrix passed to the last setMatrix call (or the default PAM30MS if setMatrix has not been called).

getPenalty()

int getPenalty

(

)

const

Currently configured gap penalty.

Returns

The penalty passed to the last setPenalty call (or the default 5 if setPenalty has not been called).

setMatrix() [1/2]

void setMatrix

(

const ScoringMatrix &

matrix

)

Select the scoring matrix used by align.

Parameters

[in]

matrix

Scoring matrix to use.

setMatrix() [2/2]

void setMatrix

(

const std::string &

matrix

)

Select the scoring matrix by name; the accepted names are listed in NamesOfScoringMatrices.

Parameters

[in]

matrix

Matrix name (currently "identity" or "PAM30MS").

Exceptions

Exception::IllegalArgument

when matrix is not one of the names in NamesOfScoringMatrices. The error message lists the valid names.

setPenalty()

void setPenalty

(

const int

penalty

)

Set the linear gap penalty subtracted per gap step.

Parameters

[in]

penalty

Gap penalty (typically positive); the algorithm subtracts penalty from the score for each gap step.

Member Data Documentation

first_row_

std::vector<int> first_row_ {}

private

First row of the two-row rolling buffer used by align.

gap_penalty_

int gap_penalty_ = 5

private

Linear gap penalty.

my_matrix_

ScoringMatrix my_matrix_ = ScoringMatrix::PAM30MS

private

Currently selected scoring matrix.

NamesOfScoringMatrices

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

static

Lookup table for setMatrix(const std::string&); current entries: "identity", "PAM30MS".

second_row_

std::vector<int> second_row_ {}

private

Second row of the two-row rolling buffer used by align.