https://github.com/trvrb/PACT
Tip revision: 8ac38b4fe2e859c62cdf0c72a61d45a104762e66 authored by Trevor Bedford on 06 August 2015, 22:12:27 UTC
Update to print any-to-any migration rates in mig skyline.
Update to print any-to-any migration rates in mig skyline.
Tip revision: 8ac38b4
main.cpp
/*
(P)osterior (A)nalysis of (C)oalescent (T)rees
Copyright 2009-2013 Trevor Bedford <t.bedford@ed.ac.uk>
This program is designed to interpret and manipulate labeled evolutionary trees. Statistics
regarding the structured coalescent may be calculated.
*/
/* tree.hh: Copyright 2001-2006 Kasper Peeters <kasper.peeters@aei.mpg.de> */
/* rng.h, rng.cpp: Copyright 1997-2006 Ken Wilder */
/*
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/>.
*/
// Template class for standard library style tree
#include "tree.hh"
// Class for coalescent nodes within a tree object
#include "node.h"
// Extension of the tree class to deal specifically with coalescent trees
#include "coaltree.h"
// Collects a series of measurements, usually from multiple trees
#include "series.h"
// Input Migrate and Beast tree files and output Mathematica trees and tables of statistics
#include "io.h"
// Set default parameters and modify via parameter file
#include "param.h"
// Random number generator
#include "rng.h"
#include <iostream>
using std::cout;
using std::endl;
#include <stdexcept>
using std::runtime_error;
using std::out_of_range;
int main() {
try {
cout << "PACT 0.9.4 Copyright 2009-2013 Trevor Bedford" << endl << endl;
IO trees;
trees.treeManip();
trees.printTree();
trees.printStatistics();
trees.printTips();
trees.printSkylines();
trees.printPairs();
}
catch (runtime_error rex) {
cout << "<<< runtime_error >>>" << endl;
cout << rex.what() << endl;
}
catch (...) {
cout << "An exception occured, exiting" << endl;
}
return 0;
}