ed4_protein_2nd_structure.hxx

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#ifndef ED4_PROTEIN_2ND_STRUCTURE_HXX
#define ED4_PROTEIN_2ND_STRUCTURE_HXX

#ifndef AW_WINDOW_HXX
#include "aw_window.hxx"
#endif

// #define SHOW_PROGRESS ///< Print information about progress to screen (for finding and extending structures and resolving overlaps).

#define PFOLD_AWAR_ENABLE            "Pfold/enable"       
#define PFOLD_AWAR_SELECTED_SAI      "Pfold/selected_SAI" 
#define PFOLD_AWAR_PAIR_TEMPLATE     "Pfold/pairs/%s"     
#define PFOLD_AWAR_SYMBOL_TEMPLATE   "Pfold/symbols/%s"   
#define PFOLD_AWAR_SYMBOL_TEMPLATE_2 "Pfold/symbols2"     
#define PFOLD_AWAR_MATCH_METHOD      "Pfold/match_method" 
#define PFOLD_AWAR_SAI_FILTER        "Pfold/SAI_filter"   

// TODO: move static variables to .cpp file?

enum PFOLD_STRUCTURE {
    ALPHA_HELIX       = 0, 
    BETA_SHEET        = 1, 
    BETA_TURN         = 2, 
    STRUCTURE_SUMMARY = 3, 
//  THREE_TURN        = 4, ///< Three turn
//  FOUR_TURN         = 5, ///< Four turn
//  FIVE_TURN         = 6  ///< Five turn
};

struct name_value_pair {
    const char *name; 
    int        value; 
};

enum PFOLD_MATCH_TYPE {
    STRUCT_PERFECT_MATCH,  
    STRUCT_GOOD_MATCH,     
    STRUCT_MEDIUM_MATCH,   
    STRUCT_BAD_MATCH,      
    STRUCT_NO_MATCH,       
    STRUCT_UNKNOWN,        
    PFOLD_MATCH_TYPE_COUNT 
};

extern name_value_pair pfold_match_type_awars[];

#define PFOLD_PAIRS 6

extern char *pfold_pairs[PFOLD_PAIRS];

extern char *pfold_pair_chars[PFOLD_PAIRS];

#define PFOLD_PAIR_CHARS_2 "##++~~--  "

enum PFOLD_MATCH_METHOD {
    SECSTRUCT_SECSTRUCT,        
    SECSTRUCT_SEQUENCE,         
    SECSTRUCT_SEQUENCE_PREDICT, 
    PFOLD_MATCH_METHOD_COUNT    
};

#define cf_former(aa, strct) ((strct!=2) ? cf_parameters[aa][strct] : cf_parameters_norm[aa][strct])

#define cf_breaker(aa, strct) ((strct!=2) ? cf_parameters[aa][strct+2] : 0)


// General ED4 functions //////////////////////////////////////////////////////////////////////////////////////////////////////////



GB_ERROR ED4_pfold_calculate_secstruct_match(const unsigned char *structure_sai, const unsigned char *structure_cmp, int start, int end, char *result_buffer, PFOLD_MATCH_METHOD match_method = SECSTRUCT_SEQUENCE);

GB_ERROR ED4_pfold_set_SAI(char **protstruct, GBDATA *gb_main, const char *alignment_name, long *protstruct_len = NULp);


// AW related functions ///////////////////////////////////////////////////////////////////////////////////////////////

AW_window *ED4_pfold_create_props_window(AW_root *awr, const WindowCallback *refreshCallback);

#endif