AP_pro_a_nucs.hxx

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// =============================================================== //
//                                                                 //
//   File      : AP_pro_a_nucs.hxx                                 //
//   Purpose   :                                                   //
//                                                                 //
//   Institute of Microbiology (Technical University Munich)       //
//   http://www.arb-home.de/                                       //
//                                                                 //
// =============================================================== //

#ifndef AP_PRO_A_NUCS_HXX
#define AP_PRO_A_NUCS_HXX

#ifndef ARBDB_H
#include <arbdb.h>
#endif
#ifndef ARBTOOLS_H
#include <arbtools.h>
#endif


enum AP_BASES {
    AP_ILLEGAL = 0,

    AP_A   = 1,
    AP_C   = 2,
    AP_G   = 4,
    AP_T   = 8,
    AP_GAP = 16,      // known gap ('-')

    // -------------------- above are bit values, below combinations of them

    // @@@ define IUPAC here not in AP_pro_a_nucs.cxx@AP_create_dna_to_ap_bases

    AP_DOT = 31, // maybe gap, maybe some base (anything unknown, esp. '.', '?'; interpreted as dot)

    AP_MAX = 32 // amount of possible values
};

struct arb_r2a_pro_2_nucs : virtual Noncopyable {
    struct arb_r2a_pro_2_nucs *next;
    char                       nucbits[3]; // bitsets of nucs

    arb_r2a_pro_2_nucs();
    ~arb_r2a_pro_2_nucs();
};

struct arb_r2a_pro_2_nuc : virtual Noncopyable {
    char single_pro;
    int  index; // < 0x007fffff

    struct arb_r2a_pro_2_nucs *nucs;

    arb_r2a_pro_2_nuc();
    ~arb_r2a_pro_2_nuc();
};

struct AWT_PDP { // distance definition for one protein
    long patd[3];               // proteins at dist
    // every bit in patd[x] represents one protein (used bits: 0-23)
    // bit in patd[0] is set = > distance == 0
    // bit in patd[1] is set = > distance <= 1
    // bit in patd[2] is set = > distance <= 2

    char nucbits[3];            // bitsets of nucs
};

class AWT_translator;

class AWT_distance_meter : virtual Noncopyable {
    AWT_PDP *dist_[64];         // sets of proteins with special distance (64 > max_aa)

public:
    AWT_distance_meter(const AWT_translator *translator);
    ~AWT_distance_meter();

    const AWT_PDP *getDistance(int idx) const { return dist_[idx]; }
    AWT_PDP *getDistance(int idx)  { return dist_[idx]; }
};


class AWT_translator : virtual Noncopyable {
private:
    mutable AWT_distance_meter *distance_meter; // (mutable to allow lazy-evaluation)

    int                code_nr;    // arb (not embl)
    GB_HASH           *t2i_hash;   // hash table trin >> singlepro
    arb_r2a_pro_2_nuc *s2str[256]; // singlecode protein >> dna ...

    long *pro_2_bitset; // aa-index(!)   to bitset
    char *nuc_2_bitset; // dna-character to bitset

    unsigned char index_2_spro[64];      // 64 > max_aa

    int realmax_aa;             // number of real AA + stop codon
    int max_aa;                 // plus ambiguous codes

    void build_table(unsigned char pbase, const char *nuc);
    long *create_pro_to_bits() const;

public:

    AWT_translator(int arb_protein_code_nr);
    ~AWT_translator();

    const AWT_distance_meter *getDistanceMeter() const;
    AWT_distance_meter *getDistanceMeter() {
        return const_cast<AWT_distance_meter*>(const_cast<const AWT_translator*>(this)->getDistanceMeter());
    }

    int CodeNr() const { return code_nr; }
    const arb_r2a_pro_2_nuc *S2str(int index) const { return s2str[index]; }
    const arb_r2a_pro_2_nuc * const *S2strArray() const { return s2str; }

    long index2bitset(int index) const { return pro_2_bitset[index]; }
    unsigned char index2spro(int index) const { return index_2_spro[index]; }

    int RealmaxAA() const { return realmax_aa; }
    int MaxAA() const { return max_aa; } // incl. ambiguity codes

    char codon2aa(const char *codon) const {
        long spro = GBS_read_hash(t2i_hash, codon);
        return spro ? char(spro) : 'X';
    }

    char isStartOrStopCodon(const char *codon) const;
    char isStartCodon(const char *codon) const {
        char start = isStartOrStopCodon(codon);
        return start == '*' ? 0 : start; // ignore stop
    }
    char isStopCodon(const char *codon) const {
        char stop = isStartOrStopCodon(codon);
        return stop == 'M' ? 0 : stop; // ignore start
    }
};

#define AWAR_PROTEIN_TYPE "nt/protein_codon_type"

char *AP_create_dna_to_ap_bases(); // create dna 2 nuc_bitset

// ------------------------------

int AWT_default_protein_type(GBDATA *gb_main = NULp); // returns protein code selected in AWAR_PROTEIN_TYPE

AWT_translator *AWT_get_translator(int code_nr);                 // use explicit protein code
AWT_translator *AWT_get_user_translator(GBDATA *gb_main = NULp); // uses user setting for protein code from AWAR_PROTEIN_TYPE
// AWAR_PROTEIN_TYPE has to exist; the first call of AWT_get_user_translator needs 'gb_main' != 0

#else
#error AP_pro_a_nucs.hxx included twice
#endif // AP_PRO_A_NUCS_HXX