mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-27 23:00:25 +08:00
48 lines
1.3 KiB
C++
48 lines
1.3 KiB
C++
// $Id: semphy.cpp 1282 2006-12-05 11:03:10Z privmane $
|
|
|
|
#include "bootstrapProvider.h"
|
|
#include "mainSemphy.h"
|
|
#include "semphy_cmdline.h"
|
|
#include "errorMsg.h"
|
|
|
|
int main(int argc, char* argv[]) {
|
|
if (argc < 2) errorMsg::reportError("The program must get some parameters in the command line, use -h for help");
|
|
gengetopt_args_info args_info;
|
|
if (cmdline_parser(argc, argv, &args_info) != 0) {
|
|
errorMsg::reportError("error reading command line",1);
|
|
}
|
|
|
|
if (args_info.consurf_flag){
|
|
tree t_tmp;
|
|
{ // for ms1;
|
|
args_info.optimizeAlpha_flag = 0; // true
|
|
args_info.alpha_given = 0;
|
|
mainSemphy ms_tmp(args_info);
|
|
ms_tmp.computeNJtree();
|
|
t_tmp=ms_tmp.getTree();
|
|
}
|
|
args_info.optimizeAlpha_flag = 1; // true
|
|
args_info.alpha_given = 1;
|
|
mainSemphy ms2(args_info);
|
|
myLog::printArgv(1, argc, argv);
|
|
ms2.setTree(t_tmp);
|
|
ms2.optimizeAlphaOnly();
|
|
args_info.alpha_arg = static_cast<gammaDistribution*>(ms2.getStochasticProcess().distr())->getAlpha();
|
|
}
|
|
mainSemphy ms(args_info);
|
|
myLog::printArgv(1, argc, argv);
|
|
if (!args_info.BPonUserTree_given) {
|
|
// compute the ML tree for example.
|
|
ms.compute();
|
|
ms.output();
|
|
}
|
|
|
|
// computing the BP values
|
|
if (args_info.BPrepeats_given) {
|
|
bootstrapProvider bp(args_info);
|
|
bp.computeBP(ms);
|
|
bp.output(ms.out());
|
|
}
|
|
return 0;
|
|
}
|