NucleotideCode.h

/*  This file is part of Victor.

    Victor 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.

    Victor 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 Victor.  If not, see <http://www.gnu.org/licenses/>.
 */


#ifndef __Nucleotide_CODE_H__
#define __Nucleotide_CODE_H__

// Includes

#include <string>
#include <Debug.h>


enum NucleotideCode {
    ADENINE = 0,
    THYMINE,
    CYTOSINE,
    GUANINE,
    URACIL,
    XX, //  Corresponds to unknown Nucleotide type 
    Nucleotide_CODE_SIZE // number of Nucleotide types
};

inline
bool
isKnownNucleotide(NucleotideCode code) {
    return !(code == XX);
}

inline
NucleotideCode
nucleotideOneLetterTranslator(char name) {
    DUMP(name);
    if (name == ' ') {
        return XX;
    }
    if (name == 'X') {
        return XX;
    }
    if (name == 'A') {
        return ADENINE;
    } else if (name == 'T') {
        return THYMINE;
    } else if (name == 'C') {
        return CYTOSINE;
    } else if (name == 'G') {
        return GUANINE;
    } else if (name == 'U') {
        return URACIL;
    }

    return XX; // Nucleotide type name is unknown
}

inline
NucleotideCode
nucleotideThreeLetterTranslator(const string& name) {
    DUMP(name);
    if (name == "") {
        return XX;
    }
    if (name == "X") {
        return XX;
    }
    if (name == "A") {
        return ADENINE;
    } else if (name == "T") {
        return THYMINE;
    } else if (name == "C") {
        return CYTOSINE;
    } else if (name == "G") {
        return GUANINE;
    } else if (name == "U") {
        return URACIL;
    } else if (name == "DA") {
        return ADENINE;
    } else if (name == "DT") {
        return THYMINE;
    } else if (name == "DC") {
        return CYTOSINE;
    } else if (name == "DG") {
        return GUANINE;
    } else if (name == "DU") {
        return URACIL;
    }

    return XX; // Nucleotide type name is unknown
}

inline string nucleotideThreeLetterTranslator(NucleotideCode code) {
    switch (code) {
        case XX:
            return "X";
        case ADENINE:
            return "A";
        case THYMINE:
            return "T";
        case CYTOSINE:
            return "C";
        case GUANINE:
            return "G";
        case URACIL:
            return "U";
        case Nucleotide_CODE_SIZE:
            ERROR("NucleotideTranslator(NucleotideCode code): unknown code", exception);
    }

    ERROR("NucleotideTranslator(NucleotideCode code): unknown code", eXXXception);

    return "X";
}

inline string nucleotideOneLetter2ThreeLetter(char oneLetter) {
    NucleotideCode code;
    code = nucleotideOneLetterTranslator(oneLetter);
    return nucleotideThreeLetterTranslator(code);
}

inline char nucleotideThreeLetter2OneLetter(const string& threeLetter) {
    NucleotideCode code;
    code = nucleotideThreeLetterTranslator(threeLetter);
    return nucleotideOneLetterTranslator(code);
}

inline NucleotideCode& operator++(NucleotideCode& ac, int) {
    return ac = ((ac == XX) ? ADENINE : NucleotideCode(ac + 1));
}

inline NucleotideCode& operator--(NucleotideCode& ac, int) {
    return ac = ((ac == ADENINE) ? XX : NucleotideCode(ac - 1));
}

#endif /* __Nucleotide_CODE_H__ */