In the CFastaFile.cpp, you will see the following two arrays. These two arrays define the order and index of characters in the embedded scoring matrices (refer to file CParams.cpp). You can customize your own scoring matrix by modifying the above two tables and a corresponding scoring matrix definition in the file CParams.cpp.
const char CFastaFile::amino_acids[MAX_AMINO_ACIDS] = {
'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H',
'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R',
'S', 'T', 'V', 'W', 'X', 'Y', 'Z'
};
const int CFastaFile::amino_acids_trans[256] = {
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, 0, 1, 2, 3, 4, 5, 6, 7, 8, -1, 9, 10, 11, 12, -1,
13, 14, 15, 16, 17, -1, 18, 19, 20, 21, 22, -1, -1, -1, -1, -1,
-1, 0, 1, 2, 3, 4, 5, 6, 7, 8, -1, 9, 10, 11, 12, -1,
13, 14, 15, 16, 17, -1, 18, 19, 20, 21, 22, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1
};