option.h

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//
// option.h
//     Class and functions for parsing and storing command line options.
//
// Author:  Jens Wilberg, Lukas Aymans, Christoph Dalitz
// Date:    2018-08-30
// License: see ../LICENSE
//
 
#ifndef OPTION_H
#define OPTION_H
#include "util.h"
 
#include <cstddef>
#include <utility>
 
// class for handling all command line option
class Opt {
private:
   char *infile_name, *outfile_prefix;
   // output as gnuplot
   bool gnuplot;
   // csv file delimiter
   char delimiter;
   // csv file with header
   size_t skip;
   // verbosity level
   int verbose;
 
   // neighbour distance for smoothing
   double r;
   bool rdnn; // compute r with dnn
 
   // tested neighbours of triplet mid point
   size_t k;
   // max number of triplets to one mid point
   size_t n;
   // 1 - cos alpha, where alpha is the angle between the two triplet branches
   double a;
 
   // distance scale factor in metric
   double s;
   bool sdnn; // compute s with dnn
   // threshold for cdist in clustering
   double t;
   bool tauto; // auto generate t
   // maximum gap width
   double dmax;
   bool isdmax;   // dmax != none
   bool dmax_dnn; // use dnn for dmax
   // linkage method for clustering
   Linkage link;
 
   // min number of triplets per cluster
   size_t m;
 
   std::pair<double, bool> parse_argument(const char *str);
 
public:
   Opt();
   int parse_args(int argc, char **argv);
   // compute attributes which depend on dnn.
   void set_dnn(double dnn);
 
   void set_parameters(double _s, double _k, double _n, double _m, double _r, double _a, double _t);
 
   // read access functions
   const char *get_ifname();
   // get outfile name
   const char *get_ofprefix();
   bool needs_dnn();
   bool is_gnuplot();
   char get_delimiter();
   size_t get_skip();
   int get_verbosity();
   double get_r();
   size_t get_k();
   size_t get_n();
   double get_a();
   double get_s();
   bool is_tauto();
   double get_t();
   bool is_dmax();
   double get_dmax();
   Linkage get_linkage();
   size_t get_m();
};
 
#endif