source: branches/stable/SL/SEQUENCE/AP_seq_protein.hxx

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

#ifndef AP_SEQ_PROTEIN_HXX
#define AP_SEQ_PROTEIN_HXX

#ifndef AP_SEQUENCE_HXX
#include <AP_sequence.hxx>
#endif
#ifndef DOWNCAST_H
#include <downcast.h>
#endif

enum AP_PROTEINS {
    APP_ILLEGAL = 0,

    APP_A    = (1 <<  0),       // Ala
    APP_C    = (1 <<  1),       // Cys
    APP_D    = (1 <<  2),       // Asp
    APP_E    = (1 <<  3),       // Glu
    APP_F    = (1 <<  4),       // Phe
    APP_G    = (1 <<  5),       // Gly
    APP_H    = (1 <<  6),       // His
    APP_I    = (1 <<  7),       // Ile
    APP_K    = (1 <<  8),       // Lys
    APP_L    = (1 <<  9),       // Leu
    APP_M    = (1 << 10),       // Met
    APP_N    = (1 << 11),       // Asn
    APP_P    = (1 << 12),       // Pro
    APP_Q    = (1 << 13),       // Gln
    APP_R    = (1 << 14),       // Arg
    APP_S    = (1 << 15),       // Ser
    APP_T    = (1 << 16),       // Thr
    APP_V    = (1 << 17),       // Val
    APP_W    = (1 << 18),       // Trp
    APP_Y    = (1 << 19),       // Tyr
    APP_STAR = (1 << 20),       // *
    APP_GAP  = (1 << 21),       // known gap ('-')

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

    APP_X   = (APP_GAP-1),      // Xaa (any real codon)
    APP_DOT = APP_X | APP_GAP,  // maybe a codon, maybe a gap

    APP_B = APP_D | APP_N,      // Asx ( = Asp | Asn )
    APP_Z = APP_E | APP_Q,      // Glx ( = Glu | Gln )
    APP_J = APP_I | APP_L,      // Xle ( = Ile | Leu )

    APP_MAX = (APP_GAP<<1)-1,
};

class AP_sequence_protein FINAL_TYPE : public AP_combinableSeq { // derived from a Noncopyable
    AP_PROTEINS *seq_prot;
    AP_PROTEINS *mut1; // combination of sequences reachable with up to 1 nucleotide mutation per codon
    AP_PROTEINS *mut2; // combination of sequences reachable with up to 2 nucleotide mutations per codons
    // Note: ANY protein or a gap is reachable with up to 3 mutations per codon

    AP_FLOAT count_weighted_bases() const OVERRIDE;
    void set(const char *isequence) OVERRIDE;
    void unset() OVERRIDE;

    const AP_PROTEINS *get_mut1() const { lazy_load_sequence(); ap_assert(mut1); return mut1; }
    const AP_PROTEINS *get_mut2() const { lazy_load_sequence(); ap_assert(mut2); return mut2; }

public:
    AP_sequence_protein(const AliView *aliview);
    ~AP_sequence_protein() OVERRIDE;

    const AP_PROTEINS *get_sequence() const { lazy_load_sequence(); ap_assert(seq_prot); return seq_prot; }

    AP_combinableSeq *dup() const OVERRIDE; // used to get the real new element
    Mutations combine_seq(const AP_combinableSeq *lefts, const AP_combinableSeq *rights, char *mutation_per_site = NULp) OVERRIDE;
    Mutations mutations_if_combined_with(const AP_combinableSeq *other) OVERRIDE;
    void partial_match(const AP_combinableSeq *part, long *overlap, long *penalty) const OVERRIDE;
    uint32_t checksum() const OVERRIDE;
    int cmp_combined(const AP_combinableSeq *other) const OVERRIDE;
};



#else
#error AP_seq_protein.hxx included twice
#endif // AP_SEQ_PROTEIN_HXX