https://github.com/trvrb/PACT
Revision 19b0ca3fe22c54589f980b091443b62b97dca589 authored by Trevor Bedford on 12 October 2009, 18:51:53 UTC, committed by Trevor Bedford on 12 October 2009, 18:51:53 UTC
1 parent fbd0e54
Tip revision: 19b0ca3fe22c54589f980b091443b62b97dca589 authored by Trevor Bedford on 12 October 2009, 18:51:53 UTC
Filling out skyline UI.
Filling out skyline UI.
Tip revision: 19b0ca3
param.h
/* param.h
Copyright 2009 Trevor Bedford <bedfordt@umich.edu>
This contains all the global variables used by pact, can be modified later if necessary
*/
#ifndef PARAM_H
#define PARAM_H
#include <cmath>
#include <vector>
using std::vector;
#define INF pow(double(10),double(100)) // 10^100 (~infinity)
class Parameters {
public:
Parameters(); // constructor, imports parameters from in.param if available
void print(); // prints parameter listing
bool manip(); // are any tree manipulation parameters true?
bool summary(); // are any summary parameters true?
bool tips();
bool skyline(); // are any skyline parameters true?
// PARAMETERS
bool push_times_back;
vector<double> push_times_back_values; // start, stop
bool prune_to_trunk;
vector<double> prune_to_trunk_values; // time back
bool prune_to_label;
vector<double> prune_to_label_values; // label
bool trim_ends;
vector<double> trim_ends_values; // start, stop
bool section_tree;
vector<double> section_tree_values; // start, window, step
bool time_slice;
vector<double> time_slice_values; // time
bool print_hp_tree;
bool summary_tmrca;
bool summary_length;
bool summary_proportions;
bool summary_coal_rates;
bool summary_mig_rates;
bool summary_diversity;
bool summary_fst;
bool summary_tajima_d;
bool tips_time_to_trunk;
vector<double> skyline_values; // start, stop, step
bool skyline_tmrca;
bool skyline_length;
bool skyline_proportions;
bool skyline_coal_rates;
bool skyline_mig_rates;
bool skyline_diversity;
bool skyline_fst;
bool skyline_tajima_d;
private:
void importLine(string); // reads a string and attempts to extract parameters from it
};
#endif
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