💿🐜 Antkeeper source code
https://antkeeper.com
You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
86 lines
2.4 KiB
86 lines
2.4 KiB
/*
|
|
* Copyright (C) 2021 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/>.
|
|
*/
|
|
|
|
#include "codon.hpp"
|
|
|
|
namespace genetics {
|
|
namespace codon {
|
|
|
|
/**
|
|
* Returns the index of a nucleobase for use with a translation table.
|
|
*
|
|
* @param base IUPAC code of nucleobase, either `U`, `T`, `C`, `A`, or `G`.
|
|
* @return Index of the nucleobase, or a negative value if a non-standard nucleobase was supplied.
|
|
*/
|
|
static inline int base_index(char base)
|
|
{
|
|
switch (base)
|
|
{
|
|
case 'U':
|
|
case 'T':
|
|
return 0;
|
|
case 'C':
|
|
return 1;
|
|
case 'A':
|
|
return 2;
|
|
case 'G':
|
|
return 3;
|
|
}
|
|
|
|
return ~3;
|
|
}
|
|
|
|
/**
|
|
* Returns the index of a codon for use with a translation table.
|
|
*
|
|
* @param base1 IUPAC code of first nucleobase, either `U`, `T`, `C`, `A`, or `G`.
|
|
* @param base2 IUPAC code of second nucleobase, either `U`, `T`, `C`, `A`, or `G`.
|
|
* @param base3 IUPAC code of third nucleobase, either `U`, `T`, `C`, `A`, or `G`.
|
|
* @return Index of codon, or a negative value if a non-standard nucleobase was supplied.
|
|
*/
|
|
static inline int codon_index(char base1, char base2, char base3)
|
|
{
|
|
int i = base_index(base1);
|
|
int j = base_index(base2);
|
|
int k = base_index(base3);
|
|
return (i << 4) | (j << 2) | k;
|
|
}
|
|
|
|
inline char translate(char base1, char base2, char base3, const char* aas)
|
|
{
|
|
int index = codon_index(base1, base2, base3);
|
|
if (index < 0)
|
|
return '-';
|
|
return aas[index];
|
|
}
|
|
|
|
bool is_start(char base1, char base2, char base3, const char* starts)
|
|
{
|
|
char aa = translate(base1, base2, base3, starts);
|
|
return ((aa != '-') && (aa != '*'));
|
|
}
|
|
|
|
bool is_stop(char base1, char base2, char base3, const char* aas)
|
|
{
|
|
char aa = translate(base1, base2, base3, aas);
|
|
return (aa == '*');
|
|
}
|
|
|
|
} // namspace codon
|
|
} // namespace genetics
|