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Add scoring matrices and functions

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C. J. Howard 4 years ago
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4 changed files with 183 additions and 0 deletions
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  1. +54
    -0
      src/game/genetics/amino-acid.hpp
  2. +3
    -0
      src/game/genetics/genetics.hpp
  3. +105
    -0
      src/game/genetics/matrix.hpp
  4. +21
    -0
      src/game/genetics/protein.hpp

+ 54
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src/game/genetics/amino-acid.hpp View File

@ -0,0 +1,54 @@
/*
* Copyright (C) 2020 Christopher J. Howard
*
* This file is part of Antkeeper source code.
*
* Antkeeper source code is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Antkeeper source code is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Antkeeper source code. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef ANTKEEPER_GENETICS_AMINO_ACID_HPP
#define ANTKEEPER_GENETICS_AMINO_ACID_HPP
#include <type_traits>
namespace genetics {
namespace amino_acid {
/**
* Scores two amino acids using a substitution matrix.
*
* @param a IUPAC amino acid code of first amino acid.
* @param b IUPAC amino acid code of second amino acid.
* @param matrix Substitution matrix.
* @return Score of the two amino acids.
*/
template <class Matrix>
typename std::remove_all_extents<Matrix>::type score(char a, char b, const Matrix& matrix);
template <class Matrix>
typename std::remove_all_extents<Matrix>::type score(char a, char b, const Matrix& matrix)
{
int i = (a < 'A' || a > 'Z') ? ((a == '*') ? 26 : -1) : a - 'A';
int j = (b < 'A' || b > 'Z') ? ((b == '*') ? 26 : -1) : b - 'A';
if (i < 0 || j < 0)
return 0;
return matrix[i][j];
}
} // namspace amino_acid
} // namespace genetics
#endif // ANTKEEPER_GENETICS_AMINO_ACID_HPP

+ 3
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src/game/genetics/genetics.hpp View File

@ -20,9 +20,12 @@
#ifndef ANTKEEPER_GENETICS_HPP #ifndef ANTKEEPER_GENETICS_HPP
#define ANTKEEPER_GENETICS_HPP #define ANTKEEPER_GENETICS_HPP
#include "amino-acid.hpp"
#include "base.hpp" #include "base.hpp"
#include "codon.hpp" #include "codon.hpp"
#include "matrix.hpp"
#include "protein.hpp" #include "protein.hpp"
#include "sequence.hpp" #include "sequence.hpp"
#include "translation-table.hpp"
#endif // ANTKEEPER_GENETICS_HPP #endif // ANTKEEPER_GENETICS_HPP

+ 105
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src/game/genetics/matrix.hpp View File

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/*
* Copyright (C) 2020 Christopher J. Howard
*
* This file is part of Antkeeper source code.
*
* Antkeeper source code is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Antkeeper source code is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Antkeeper source code. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef ANTKEEPER_GENETICS_MATRIX_HPP
#define ANTKEEPER_GENETICS_MATRIX_HPP
namespace genetics {
namespace matrix {
/**
* BLOSUM62 substitution matrix.
*
* @see ftp://ftp.ncbi.nih.gov/blast/matrices/
*/
template <class T>
constexpr T blosum62[27][27] =
{
// A B C D E F G H I J K L M N O P Q R S T U V W X Y Z *
{ 4, -2, 0, -2, -1, -2, 0, -2, -1, 0, -1, -1, -1, -2, 0, -1, -1, -1, 1, 0, 0, 0, -3, 0, -2, -1, -4 }, // A
{ -2, 4, -3, 4, 1, -3, -1, 0, -3, 0, 0, -4, -3, 3, 0, -2, 0, -1, 0, -1, 0, -3, -4, -1, -3, 1, -4 }, // B
{ 0, -3, 9, -3, -4, -2, -3, -3, -1, 0, -3, -1, -1, -3, 0, -3, -3, -3, -1, -1, 0, -1, -2, -2, -2, -3, -4 }, // C
{ -2, 4, -3, 6, 2, -3, -1, -1, -3, 0, -1, -4, -3, 1, 0, -1, 0, -2, 0, -1, 0, -3, -4, -1, -3, 1, -4 }, // D
{ -1, 1, -4, 2, 5, -3, -2, 0, -3, 0, 1, -3, -2, 0, 0, -1, 2, 0, 0, -1, 0, -2, -3, -1, -2, 4, -4 }, // E
{ -2, -3, -2, -3, -3, 6, -3, -1, 0, 0, -3, 0, 0, -3, 0, -4, -3, -3, -2, -2, 0, -1, 1, -1, 3, -3, -4 }, // F
{ 0, -1, -3, -1, -2, -3, 6, -2, -4, 0, -2, -4, -3, 0, 0, -2, -2, -2, 0, -2, 0, -3, -2, -1, -3, -2, -4 }, // G
{ -2, 0, -3, -1, 0, -1, -2, 8, -3, 0, -1, -3, -2, 1, 0, -2, 0, 0, -1, -2, 0, -3, -2, -1, 2, 0, -4 }, // H
{ -1, -3, -1, -3, -3, 0, -4, -3, 4, 0, -3, 2, 1, -3, 0, -3, -3, -3, -2, -1, 0, 3, -3, -1, -1, -3, -4 }, // I
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, // J
{ -1, 0, -3, -1, 1, -3, -2, -1, -3, 0, 5, -2, -1, 0, 0, -1, 1, 2, 0, -1, 0, -2, -3, -1, -2, 1, -4 }, // K
{ -1, -4, -1, -4, -3, 0, -4, -3, 2, 0, -2, 4, 2, -3, 0, -3, -2, -2, -2, -1, 0, 1, -2, -1, -1, -3, -4 }, // L
{ -1, -3, -1, -3, -2, 0, -3, -2, 1, 0, -1, 2, 5, -2, 0, -2, 0, -1, -1, -1, 0, 1, -1, -1, -1, -1, -4 }, // M
{ -2, 3, -3, 1, 0, -3, 0, 1, -3, 0, 0, -3, -2, 6, 0, -2, 0, 0, 1, 0, 0, -3, -4, -1, -2, 0, -4 }, // N
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, // O
{ -1, -2, -3, -1, -1, -4, -2, -2, -3, 0, -1, -3, -2, -2, 0, 7, -1, -2, -1, -1, 0, -2, -4, -2, -3, -1, -4 }, // P
{ -1, 0, -3, 0, 2, -3, -2, 0, -3, 0, 1, -2, 0, 0, 0, -1, 5, 1, 0, -1, 0, -2, -2, -1, -1, 3, -4 }, // Q
{ -1, -1, -3, -2, 0, -3, -2, 0, -3, 0, 2, -2, -1, 0, 0, -2, 1, 5, -1, -1, 0, -3, -3, -1, -2, 0, -4 }, // R
{ 1, 0, -1, 0, 0, -2, 0, -1, -2, 0, 0, -2, -1, 1, 0, -1, 0, -1, 4, 1, 0, -2, -3, 0, -2, 0, -4 }, // S
{ 0, -1, -1, -1, -1, -2, -2, -2, -1, 0, -1, -1, -1, 0, 0, -1, -1, -1, 1, 5, 0, 0, -2, 0, -2, -1, -4 }, // T
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, // U
{ 0, -3, -1, -3, -2, -1, -3, -3, 3, 0, -2, 1, 1, -3, 0, -2, -2, -3, -2, 0, 0, 4, -3, -1, -1, -2, -4 }, // V
{ -3, -4, -2, -4, -3, 1, -2, -2, -3, 0, -3, -2, -1, -4, 0, -4, -2, -3, -3, -2, 0, -3, 11, -2, 2, -3, -4 }, // W
{ 0, -1, -2, -1, -1, -1, -1, -1, -1, 0, -1, -1, -1, -1, 0, -2, -1, -1, 0, 0, 0, -1, -2, -1, -1, -1, -4 }, // X
{ -2, -3, -2, -3, -2, 3, -3, 2, -1, 0, -2, -1, -1, -2, 0, -3, -1, -2, -2, -2, 0, -1, 2, -1, 7, -2, -4 }, // Y
{ -1, 1, -3, 1, 4, -3, -2, 0, -3, 0, 1, -3, -1, 0, 0, -1, 3, 0, 0, -1, 0, -2, -3, -1, -2, 4, -4 }, // Z
{ -4, -4, -4, -4, -4, -4, -4, -4, -4, 0, -4, -4, -4, -4, 0, -4, -4, -4, -4, -4, 0, -4, -4, -4, -4, -4, 1 } // *
};
/**
* BLOSUM80 substitution matrix.
*
* @see ftp://ftp.ncbi.nih.gov/blast/matrices/
*/
template <class T>
constexpr T blosum80[27][27] =
{
// A B C D E F G H I J K L M N O P Q R S T U V W X Y Z *
{ 7, -3, -1, -3, -2, -4, 0, -3, -3, 0, -1, -3, -2, -3, 0, -1, -2, -3, 2, 0, 0, -1, -5, -1, -4, -2, -8 }, // A
{ -3, 6, -6, 6, 1, -6, -2, -1, -6, 0, -1, -7, -5, 5, 0, -4, -1, -2, 0, -1, 0, -6, -8, -3, -5, 0, -8 }, // B
{ -1, -6, 13, -7, -7, -4, -6, -7, -2, 0, -6, -3, -3, -5, 0, -6, -5, -6, -2, -2, 0, -2, -5, -4, -5, -7, -8 }, // C
{ -3, 6, -7, 10, 2, -6, -3, -2, -7, 0, -2, -7, -6, 2, 0, -3, -1, -3, -1, -2, 0, -6, -8, -3, -6, 1, -8 }, // D
{ -2, 1, -7, 2, 8, -6, -4, 0, -6, 0, 1, -6, -4, -1, 0, -2, 3, -1, -1, -2, 0, -4, -6, -2, -5, 6, -8 }, // E
{ -4, -6, -4, -6, -6, 10, -6, -2, -1, 0, -5, 0, 0, -6, 0, -6, -5, -5, -4, -4, 0, -2, 0, -3, 4, -6, -8 }, // F
{ 0, -2, -6, -3, -4, -6, 9, -4, -7, 0, -3, -7, -5, -1, 0, -5, -4, -4, -1, -3, 0, -6, -6, -3, -6, -4, -8 }, // G
{ -3, -1, -7, -2, 0, -2, -4, 12, -6, 0, -1, -5, -4, 1, 0, -4, 1, 0, -2, -3, 0, -5, -4, -2, 3, 0, -8 }, // H
{ -3, -6, -2, -7, -6, -1, -7, -6, 7, 0, -5, 2, 2, -6, 0, -5, -5, -5, -4, -2, 0, 4, -5, -2, -3, -6, -8 }, // I
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, // J
{ -1, -1, -6, -2, 1, -5, -3, -1, -5, 0, 8, -4, -3, 0, 0, -2, 2, 3, -1, -1, 0, -4, -6, -2, -4, 1, -8 }, // K
{ -3, -7, -3, -7, -6, 0, -7, -5, 2, 0, -4, 6, 3, -6, 0, -5, -4, -4, -4, -3, 0, 1, -4, -2, -2, -5, -8 }, // L
{ -2, -5, -3, -6, -4, 0, -5, -4, 2, 0, -3, 3, 9, -4, 0, -4, -1, -3, -3, -1, 0, 1, -3, -2, -3, -3, -8 }, // M
{ -3, 5, -5, 2, -1, -6, -1, 1, -6, 0, 0, -6, -4, 9, 0, -4, 0, -1, 1, 0, 0, -5, -7, -2, -4, -1, -8 }, // N
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, // O
{ -1, -4, -6, -3, -2, -6, -5, -4, -5, 0, -2, -5, -4, -4, 0, 12, -3, -3, -2, -3, 0, -4, -7, -3, -6, -2, -8 }, // P
{ -2, -1, -5, -1, 3, -5, -4, 1, -5, 0, 2, -4, -1, 0, 0, -3, 9, 1, -1, -1, 0, -4, -4, -2, -3, 5, -8 }, // Q
{ -3, -2, -6, -3, -1, -5, -4, 0, -5, 0, 3, -4, -3, -1, 0, -3, 1, 9, -2, -2, 0, -4, -5, -2, -4, 0, -8 }, // R
{ 2, 0, -2, -1, -1, -4, -1, -2, -4, 0, -1, -4, -3, 1, 0, -2, -1, -2, 7, 2, 0, -3, -6, -1, -3, -1, -8 }, // S
{ 0, -1, -2, -2, -2, -4, -3, -3, -2, 0, -1, -3, -1, 0, 0, -3, -1, -2, 2, 8, 0, 0, -5, -1, -3, -2, -8 }, // T
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, // U
{ -1, -6, -2, -6, -4, -2, -6, -5, 4, 0, -4, 1, 1, -5, 0, -4, -4, -4, -3, 0, 0, 7, -5, -2, -3, -4, -8 }, // V
{ -5, -8, -5, -8, -6, 0, -6, -4, -5, 0, -6, -4, -3, -7, 0, -7, -4, -5, -6, -5, 0, -5, 16, -5, 3, -5, -8 }, // W
{ -1, -3, -4, -3, -2, -3, -3, -2, -2, 0, -2, -2, -2, -2, 0, -3, -2, -2, -1, -1, 0, -2, -5, -2, -3, -1, -8 }, // X
{ -4, -5, -5, -6, -5, 4, -6, 3, -3, 0, -4, -2, -3, -4, 0, -6, -3, -4, -3, -3, 0, -3, 3, -3, 11, -4, -8 }, // Y
{ -2, 0, -7, 1, 6, -6, -4, 0, -6, 0, 1, -5, -3, -1, 0, -2, 5, 0, -1, -2, 0, -4, -5, -1, -4, 6, -8 }, // Z
{ -8, -8, -8, -8, -8, -8, -8, -8, -8, 0, -8, -8, -8, -8, 0, -8, -8, -8, -8, -8, 0, -8, -8, -8, -8, -8, 1 } // *
};
} // namspace matrix
} // namespace genetics
#endif // ANTKEEPER_GENETICS_MATRIX_HPP

+ 21
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src/game/genetics/protein.hpp View File

@ -20,10 +20,31 @@
#ifndef ANTKEEPER_GENETICS_PROTEIN_HPP #ifndef ANTKEEPER_GENETICS_PROTEIN_HPP
#define ANTKEEPER_GENETICS_PROTEIN_HPP #define ANTKEEPER_GENETICS_PROTEIN_HPP
#include "amino-acid.hpp"
#include <type_traits>
namespace genetics { namespace genetics {
namespace protein { namespace protein {
/**
* Scores two proteins using a substitution matrix.
*
* @param first1,last1 Sequence of IUPAC amino acid codes which constitute the first protein.
* @param first2,last2 Sequence of IUPAC amino acid codes which constitute the second protein.
* @param matrix Substitution matrix.
* @return Score of the two proteins.
*/
template <class ForwardIt1, class ForwardIt2, class Matrix>
typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, ForwardIt2 last2, const Matrix& matrix);
template <class ForwardIt1, class ForwardIt2, class Matrix>
typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, ForwardIt2 last2, const Matrix& matrix)
{
typename std::remove_all_extents<Matrix>::type result = 0;
for (; first1 != last1 && first2 != last2; ++first1, ++first2)
result += amino_acid::score(*first1, *first2, matrix);
return result;
}
} // namespace protein } // namespace protein
} // namespace genetics } // namespace genetics

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