Spec MatrixScore
A general scoring matrix.

Extends Score
All Extended Score
Defined in <seqan/score.h>
Signature template <typename TValue, typename TSeqValue, typename TSpec> class Score<TValue, ScoreMatrix<[TSeqValue[, TSpec]]> >;

Template Parameters

TValue The score value.
TSeqValue The alphabet type, defaults to AminoAcid.
TSpec Further specialization, defaults to Default.

Member Function Overview

Interface Function Overview

Interface Functions Inherited From Score

Interface Metafunction Overview

Interface Metafunctions Inherited From Score

Detailed Description

The TSpec argument can be used to obtain a predefined matrix. Specify one of the following tags:

ScoreSpecBlosum30, ScoreSpecBlosum45, ScoreSpecBlosum62, ScoreSpecBlosum80, ScoreSpecPam40, ScoreSpecPam120, ScoreSpecPam200, ScoreSpecPam250, ScoreSpecVtml200.

This will internally call setDefaultScoreMatrix.

In order to provide a more user-friendly access to the predefined scoring matrixes, typedefs exist: Blosum30, Blosum45, Blosum62, Blosum80, Pam40, Pam120, Pam200, Pam250 and Vtml200.

Member Functions Detail

MatrixScore::Score(gapExtend[, gapOpen]); MatrixScore::Score(fileName, gapExtend[, gapOpen]);

Constructor

Parameters

fileName Path to load the matrix from, type is char const *.
gapExtend Gap extension score, type is TValue.
gapOpen Gap open score, defaults to gapExtend, type is TValue.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Interface Functions Detail

void setDefaultScoreMatrix(score, tag);

Set the score matrix of a Score to one of the default matrixes.

Parameters

score The MatrixScore to update.
tag The tag to select the default matrix, see description below.

Remarks

The tag must be one of the following: Default, ScoreSpecBlosum30, ScoreSpecBlosum45, ScoreSpecBlosum62, ScoreSpecBlosum80, ScoreSpecPam40, ScoreSpecPam120, ScoreSpecPam200, ScoreSpecPam250, ScoreSpecVtml200.

If Default is used for tag then the matrix will be filled with default-constructed TValue values.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

void setScore(score, x, y, v);

Set the substitution score between to values.

Parameters

score The MatrixScore to set the value for.
x The substituted alphabet value.
y The alphabet value to substitute x for.
v The score value to set.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

int write(stream, scoreMatrix[, meta]);

Write a score matrix to a stream.

Parameters

stream Stream to write to.
scoreMatrix MatrixScore object.
meta Meta information is stored here.

Returns

int Status code, 0 on success, a different value on errors.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.