mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 06:30:25 +08:00
51 lines
1.3 KiB
C++
51 lines
1.3 KiB
C++
// $Id: posterior.cpp 674 2006-04-09 17:06:42Z ninio $
|
|
|
|
#include "tree.h"
|
|
#include "sequenceContainer.h"
|
|
#include "mainSemphy.h"
|
|
#include "njGamma.h"
|
|
#include "logFile.h"
|
|
#include "treeUtil.h"
|
|
#include "likeDist.h"
|
|
#include "someUtil.h"
|
|
|
|
#include <iostream>
|
|
#include <cassert>
|
|
using namespace std;
|
|
|
|
|
|
int main(int argc,char* argv[]) {
|
|
bool withoutBBL = false;
|
|
if (argc < 2) errorMsg::reportError("The program must get some parameters in the command line, use -h for help");
|
|
semphy_args_info args_info;
|
|
if (semphy_cmdline_parser(argc, argv, &args_info) != 0) {
|
|
errorMsg::reportError("error reading command line",1);
|
|
}
|
|
|
|
|
|
// check that we have all we need:
|
|
|
|
if (!args_info.tree_given) {
|
|
errorMsg::reportError("Must enter input tree",1);
|
|
}
|
|
if (!args_info.alpha_given) {
|
|
errorMsg::reportError("Must set gamma",1);
|
|
}
|
|
|
|
|
|
|
|
mainSemphy ms(args_info);
|
|
// see that we actually got gamma
|
|
assert(ms.getStochasticProcess().categories() >1);
|
|
for (int i=0;i<ms.getStochasticProcess().categories();++i)
|
|
LOG(3,<<"category["<<i<<"]="<<ms.getStochasticProcess().rates(i)<<endl);
|
|
if (withoutBBL == false) {
|
|
ms.optimizeBranchLengths(); // this will do both bbl and alpha.
|
|
}
|
|
|
|
VVdouble posteriorProbVV; // pos * rate
|
|
ms.extractPosteriorProb(posteriorProbVV);
|
|
ms.out()<<posteriorProbVV<<endl;
|
|
return 0;
|
|
}
|