https://github.com/trvrb/PACT
Revision ecd6e06f4b723156f42000731f4583201efd7d77 authored by Trevor Bedford on 15 October 2009, 02:53:14 UTC, committed by Trevor Bedford on 15 October 2009, 02:53:14 UTC
1 parent 98709f7
Tip revision: ecd6e06f4b723156f42000731f4583201efd7d77 authored by Trevor Bedford on 15 October 2009, 02:53:14 UTC
Improved compatibility with LAMARC trees (needed to ignore final enclosing parenthesis)
Improved compatibility with LAMARC trees (needed to ignore final enclosing parenthesis)
Tip revision: ecd6e06
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
*/
/*
This file is part of PACT.
PACT is free software: you can redistribute it and/or modify it under the terms of the GNU General
Public License as published by the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
PACT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
Public License for more details.
You should have received a copy of the GNU General Public License along with PACT. If not, see
<http://www.gnu.org/licenses/>.
*/
#ifndef PARAM_H
#define PARAM_H
#include <cmath>
#include <vector>
using std::vector;
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 renew_trunk;
vector<double> renew_trunk_values; // time
bool prune_to_trunk;
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_rule_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
Computing file changes ...