argparse.hpp

 
#ifndef ARGPARSE_H
#define ARGPARSE_H
 
#include <stdio.h>
#include <string>
#include <configparser.hpp>
// argument defaults
 
#define PROGNAME                 "cawlign"
#define DEFAULT_DATA_TYPE        nucleotide
#define DEFAULT_GENETIC_CODE     "universal"
#define DEFAULT_REFERENCE        "HXB2_pol"
#define DEFAULT_SCORING          "Nucleotide-BLAST"
#define DEFAULT_SPACE            quadratic
#define DEFAULT_LOCAL_TYPE       trim
#define DEFAULT_OUTPUT_FORMAT    refmap
#define DEFAULT_RC_TYPE          none
 
#include "stringBuffer.h"
 
#ifndef VERSION_NUMBER
    #define VERSION_NUMBER            "0.2.0"
#endif
 
#ifndef LIBRARY_PATH
    #define LIBRARY_PATH            "/usr/local/share/cawlign/"
#endif
 
#define SCORES_SUBPATH        "scoring"
#define REF_SUBPATH           "references"
#define GENETIC_CODES_SUBPATH "genetic_codes"
 
namespace argparse
{
  
    enum data_t {
      nucleotide,
      codon,
      protein
    };
 
    enum local_t {
      trim,
      global,
      local
    };
 
    enum space_t {
        quadratic,
        linear
    };
 
    enum out_format_t {
        refmap,
        refalign,
        pairwise
    };
 
    enum rc_t {
        none,
        silent,
        annotated
    };
 
   class args_t {
    public:
 
        FILE            * output,
                        * reference,
                        * input;
       
        ConfigParser    * scores;
             
        data_t          data_type;
        local_t         local_option;
        space_t         space_type;
        out_format_t    out_format;
        rc_t            reverse_complement;
        ConfigParser    * genetic_code;
        
        bool            quiet;
        bool            affine;
        bool            include_reference;
       
       StringBuffer*   memory_ref;
 
        
        args_t( int, const char ** );
        ~args_t();
        
    private:
        void parse_input        ( const char * );
        void parse_reference    ( const char * );
        void parse_output       ( const char * );
        void parse_scores       ( const char * );
        void parse_quiet        ( void );
        void parse_affine       ( void );
        void parse_include_ref  ( void );
        void parse_rc           ( const char * );
        void parse_space_t      ( const char * );
        void parse_data_t       ( const char * );
        void parse_local_t      ( const char * );
        void parse_out_format_t ( const char * );
        void parse_genetic_code ( const char * );
 
        std::string code_name;
 
    };
 
    void ERROR_NO_USAGE ( const char * msg, ... );
 
    // defined in argparse.cpp
    std::ifstream check_file_path_stream (const char* path, const char * subpath);
}
 
#endif // ARGPARSE_H