gemmi::AlignmentScoring Struct Reference

#include <seqalign.hpp>

Static Public Member Functions
static const AlignmentScoring *	simple ()
static const AlignmentScoring *	partial_model ()
static const AlignmentScoring *	blosum62 ()

Public Attributes
int	match = 1
int	mismatch = -1
int	gapo = -1
int	gape = -1
int	good_gapo = 0
int	bad_gapo = -2
std::vector< std::int8_t >	score_matrix
std::vector< std::string >	matrix_encoding

Detailed Description

Definition at line 20 of file seqalign.hpp.

Member Function Documentation

simple()

static const AlignmentScoring * gemmi::AlignmentScoring::simple ( )

inlinestatic

Definition at line 31 of file seqalign.hpp.

partial_model()

static const AlignmentScoring * gemmi::AlignmentScoring::partial_model ( )

inlinestatic

Definition at line 36 of file seqalign.hpp.

blosum62()

static const AlignmentScoring * gemmi::AlignmentScoring::blosum62 ( )

inlinestatic

Definition at line 40 of file seqalign.hpp.

Member Data Documentation

match

int gemmi::AlignmentScoring::match = 1

Definition at line 21 of file seqalign.hpp.

mismatch

int gemmi::AlignmentScoring::mismatch = -1

Definition at line 22 of file seqalign.hpp.

gapo

int gemmi::AlignmentScoring::gapo = -1

Definition at line 23 of file seqalign.hpp.

gape

int gemmi::AlignmentScoring::gape = -1

Definition at line 24 of file seqalign.hpp.

good_gapo

int gemmi::AlignmentScoring::good_gapo = 0

Definition at line 26 of file seqalign.hpp.

bad_gapo

int gemmi::AlignmentScoring::bad_gapo = -2

Definition at line 27 of file seqalign.hpp.

score_matrix

std::vector<std::int8_t> gemmi::AlignmentScoring::score_matrix

Definition at line 28 of file seqalign.hpp.

matrix_encoding

std::vector<std::string> gemmi::AlignmentScoring::matrix_encoding

Definition at line 29 of file seqalign.hpp.

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

• include/gemmi/seqalign.hpp