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charchar-maps.h
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#include <iostream>
#include <map>
using namespace std;
// DNA: Map containing specific base:base alignment scores.
// Purine -> Purine or Pyrimidine -> Pyrimidine swaps produce a smaller penalty
map<pair<char,char>, int> bbScores {
{{'A','A'}, 10},
{{'A','G'}, -1},
{{'A','C'}, -3},
{{'A','T'}, -4},
{{'G','A'}, -1},
{{'G','G'}, 7},
{{'G','C'}, -5},
{{'G','T'}, -3},
{{'C','A'}, -3},
{{'C','G'}, -5},
{{'C','C'}, 9},
{{'C','T'}, 0},
{{'T','A'}, -4},
{{'T','G'}, -3},
{{'T','C'}, 0},
{{'T','T'}, 8},
};
// Protein: BLOSUM62 Map containing specific amino-acid:amino-acid alignment scores.
map<pair<char,char>, int> aaScores {
{{'A','A'}, 4},
{{'R','A'}, -1},
{{'R','R'}, 5},
{{'N','A'}, -2},
{{'N','R'}, 0},
{{'N','N'}, 6},
{{'D','A'}, -2},
{{'D','R'}, -2},
{{'D','N'}, 1},
{{'D','D'}, 6},
{{'C','A'}, 0},
{{'C','R'}, -3},
{{'C','N'}, -3},
{{'C','D'}, -3},
{{'C','C'}, 9},
{{'Q','A'}, -1},
{{'Q','R'}, 1},
{{'Q','N'}, 0},
{{'Q','D'}, 0},
{{'Q','C'}, -3},
{{'Q','Q'}, 5},
{{'E','A'}, -1},
{{'E','R'}, 0},
{{'E','N'}, 0},
{{'E','D'}, 2},
{{'E','C'}, -4},
{{'E','Q'}, 2},
{{'E','E'}, 5},
{{'G','A'}, 0},
{{'G','R'}, -2},
{{'G','N'}, 0},
{{'G','D'}, -1},
{{'G','C'}, -3},
{{'G','Q'}, -2},
{{'G','E'}, -2},
{{'G','G'}, 6},
{{'H','A'}, -2},
{{'H','R'}, 0},
{{'H','N'}, 1},
{{'H','D'}, -1},
{{'H','C'}, -3},
{{'H','Q'}, 0},
{{'H','E'}, 0},
{{'H','G'}, -2},
{{'H','H'}, 8},
{{'I','A'}, -1},
{{'I','R'}, -3},
{{'I','N'}, -3},
{{'I','D'}, -3},
{{'I','C'}, -1},
{{'I','Q'}, -3},
{{'I','E'}, -3},
{{'I','G'}, -4},
{{'I','H'}, -3},
{{'I','I'}, 4},
{{'L','A'}, -1},
{{'L','R'}, -2},
{{'L','N'}, -3},
{{'L','D'}, -4},
{{'L','C'}, -1},
{{'L','Q'}, -2},
{{'L','E'}, -3},
{{'L','G'}, -4},
{{'L','H'}, -3},
{{'L','I'}, 2},
{{'L','L'}, 4},
{{'K','A'}, -1},
{{'K','R'}, 2},
{{'K','R'}, 0},
{{'K','R'}, -1},
{{'K','R'}, -3},
{{'K','R'}, 1},
{{'K','R'}, 1},
{{'K','R'}, -2},
{{'K','R'}, -1},
{{'K','R'}, -3},
{{'K','R'}, -2},
{{'K','K'}, 5},
{{'M','A'}, -1},
{{'M','R'}, -1},
{{'M','N'}, -2},
{{'M','D'}, -3},
{{'M','C'}, -1},
{{'M','Q'}, 0},
{{'M','E'}, -2},
{{'M','G'}, -3},
{{'M','H'}, -2},
{{'M','I'}, 1},
{{'M','L'}, 2},
{{'M','K'}, -1},
{{'M','M'}, 5},
{{'F','A'}, -2},
{{'F','R'}, -3},
{{'F','N'}, -3},
{{'F','D'}, -3},
{{'F','C'}, -2},
{{'F','Q'}, -3},
{{'F','E'}, -3},
{{'F','G'}, -3},
{{'F','H'}, -1},
{{'F','I'}, 0},
{{'F','L'}, 0},
{{'F','K'}, -3},
{{'F','M'}, 0},
{{'F','F'}, 6},
{{'P','A'}, -1},
{{'P','R'}, -2},
{{'P','N'}, -2},
{{'P','D'}, -1},
{{'P','C'}, -3},
{{'P','Q'}, -1},
{{'P','E'}, -1},
{{'P','G'}, -2},
{{'P','H'}, -2},
{{'P','I'}, -3},
{{'P','L'}, -3},
{{'P','K'}, -1},
{{'P','M'}, -2},
{{'P','F'}, -4},
{{'P','P'}, 7},
{{'S','A'}, 1},
{{'S','R'}, -1},
{{'S','N'}, 1},
{{'S','D'}, 0},
{{'S','C'}, -1},
{{'S','Q'}, 0},
{{'S','E'}, 0},
{{'S','G'}, 0},
{{'S','H'}, -1},
{{'S','I'}, -2},
{{'S','L'}, -2},
{{'S','K'}, 0},
{{'S','M'}, -1},
{{'S','F'}, -2},
{{'S','P'}, -1},
{{'S','S'}, 4},
{{'T','A'}, 0},
{{'T','R'}, -1},
{{'T','N'}, 0},
{{'T','D'}, -1},
{{'T','C'}, -1},
{{'T','Q'}, -1},
{{'T','E'}, -1},
{{'T','G'}, -2},
{{'T','H'}, -2},
{{'T','I'}, -1},
{{'T','L'}, -1},
{{'T','K'}, -1},
{{'T','M'}, -1},
{{'T','F'}, -2},
{{'T','P'}, -1},
{{'T','S'}, 1},
{{'T','T'}, 5},
{{'W','A'}, -3},
{{'W','R'}, -3},
{{'W','N'}, -4},
{{'W','D'}, -4},
{{'W','C'}, -2},
{{'W','Q'}, -2},
{{'W','E'}, -3},
{{'W','G'}, -2},
{{'W','H'}, -2},
{{'W','I'}, -3},
{{'W','L'}, -2},
{{'W','K'}, -3},
{{'W','M'}, -1},
{{'W','F'}, 1},
{{'W','P'}, -4},
{{'W','S'}, -3},
{{'W','T'}, -2},
{{'W','W'}, 11},
{{'Y','A'}, -2},
{{'Y','R'}, -2},
{{'Y','N'}, -2},
{{'Y','D'}, -3},
{{'Y','C'}, -2},
{{'Y','Q'}, -1},
{{'Y','E'}, -2},
{{'Y','G'}, -3},
{{'Y','H'}, 2},
{{'Y','I'}, -1},
{{'Y','L'}, -1},
{{'Y','K'}, -2},
{{'Y','M'}, -1},
{{'Y','F'}, 3},
{{'Y','P'}, -3},
{{'Y','S'}, -2},
{{'Y','T'}, -2},
{{'Y','W'}, 2},
{{'Y','Y'}, 7},
{{'V','A'}, 0},
{{'V','R'}, -3},
{{'V','N'}, -3},
{{'V','D'}, -3},
{{'V','C'}, -1},
{{'V','Q'}, -2},
{{'V','E'}, -2},
{{'V','G'}, -3},
{{'V','H'}, -3},
{{'V','I'}, 3},
{{'V','L'}, 1},
{{'V','K'}, -2},
{{'V','M'}, 1},
{{'V','F'}, -1},
{{'V','P'}, -2},
{{'V','S'}, -2},
{{'V','T'}, 0},
{{'V','W'}, -3},
{{'V','Y'}, -1},
{{'V','V'}, 4},
};