source: tags/initial/DIST/ph_matr.hxx

typedef enum {
        PH_TRANSFORMATION_NONE,
        PH_TRANSFORMATION_SIMILARITY,
        PH_TRANSFORMATION_JUKES_CANTOR,
        PH_TRANSFORMATION_FELSENSTEIN,

        PH_TRANSFORMATION_PAM,
        PH_TRANSFORMATION_CATEGORIES_HALL,
        PH_TRANSFORMATION_CATEGORIES_BARKER,
        PH_TRANSFORMATION_CATEGORIES_CHEMICAL,

        PH_TRANSFORMATION_HAESCH,
        PH_TRANSFORMATION_KIMURA,
        PH_TRANSFORMATION_OLSEN,
        PH_TRANSFORMATION_FELSENSTEIN_VOIGT,
        PH_TRANSFORMATION_OLSEN_VOIGT,
        PH_TRANSFORMATION_ML
} PH_TRANSFORMATION;

//extern const char *enum_trans_to_string[];

enum PH_MATRIX_TYPE {
        PH_MATRIX_FULL,
        PH_MATRIX_COMPRESSED };

class PHMATRIX;
class AW_root;

class ph_dummy {
        PHMATRIX *dummy;
        };

class PHENTRY {
        public:
        PHENTRY(GBDATA *gbd,class PHMATRIX *phmatri);
        PHENTRY(char *namei,class PHMATRIX *phmatri);
        ~PHENTRY(void);
        PHMATRIX *phmatrix;
        AP_sequence             *sequence;
        AP_sequence_parsimony   *sequence_parsimony;    // if exist ok
        AP_sequence_simple_protein *sequence_protein;
        long    seq_len;
        char    *name;
        char    *full_name;
        AP_FLOAT gc_bias;
        int     group_nr;                       // @@ OLIVER species belongs
                                                // to group number xxxx
};

typedef long PH_MUT_MATR[AP_MAX][AP_MAX];

enum PH_SAVE_TYPE {
        PH_SAVE_PHYLIP_COMP,
        PH_SAVE_READABLE
};

class PHMATRIX {
private:
    friend class PHENTRY;
    GBDATA *gb_main;
    GBDATA *gb_species_data;
    char        *use;
    long        seq_len;
    char        cancel_columns[256];
    AP_tree_root *tree_root;

    AW_root *aw_root;           // only link

    long        entries_mem_size;

public: 
    GB_BOOL     is_AA;
    PHENTRY     **entries;
    long        nentries;
    static PHMATRIX *ROOT;
    AP_smatrix *matrix;
    enum PH_MATRIX_TYPE matrix_type;

    PHMATRIX(GBDATA *gb_main,AW_root *awr);
    ~PHMATRIX(void);

    char *load(char *use,AP_filter *filter,AP_weights *weights,AP_smatrix *ratematrix, int all, GB_CSTR sort_tree_name);
    char *unload(void);
    const char *save(char *filename,enum PH_SAVE_TYPE type);

    void        clear(PH_MUT_MATR &hits);
    void        make_sym(PH_MUT_MATR &hits);
    void        rate_write(PH_MUT_MATR &hits,FILE *out);
    long        *create_helix_filter(BI_helix *helix,AP_filter *filter);
                                // 0 non helix 1 helix; compressed filter
    GB_ERROR calculate_rates(PH_MUT_MATR &hrates,PH_MUT_MATR &nrates,PH_MUT_MATR &pairs,long *filter);
    GB_ERROR haeschoe(const char *path);
    double      corr(double dist, double b, double & sigma);
    GB_ERROR calculate(AW_root *awr, char *cancel, double alpha, PH_TRANSFORMATION transformation);
    char *calculate_overall_freqs(double rel_frequencies[AP_MAX],char *cancel_columns);
    GB_ERROR calculate_pro(PH_TRANSFORMATION transformation);
    char *analyse(AW_root *aw_root);

    int search_group(GBT_TREE *node,GB_HASH *hash, long *groupcnt,char *groupname, PHENTRY **groups);           // @@ OLIVER
    char *compress(GBT_TREE *tree);
};


AW_window *create_save_matrix_window(AW_root *aw_root, char *base_name);