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47 lines
1.2 KiB
C++
47 lines
1.2 KiB
C++
// $Id: postprint.cpp 409 2005-06-28 13:12:24Z ninio $
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#include "tree.h"
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#include "sequenceContainer.h"
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#include "mainSemphy.h"
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#include "njGamma.h"
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#include "logFile.h"
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#include "treeUtil.h"
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#include "likeDist.h"
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#include "someUtil.h"
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#include "codon.h"
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#include "recognizeFormat.h"
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#include "pDistance.h"
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#include "jcDistance.h"
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#include "likeDist.h"
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#include <iostream>
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#include <cassert>
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using namespace std;
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int main(int argc,char* argv[]) {
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if (argc < 2) errorMsg::reportError("The program must get some parameters in the command line, use -h for help");
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semphy_args_info args_info;
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if (semphy_cmdline_parser(argc, argv, &args_info) != 0) {
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errorMsg::reportError("error reading command line",1);
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}
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// check that we have all we need:
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if (!args_info.tree_given) {
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errorMsg::reportError("Must enter input tree",1);
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}
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mainSemphy ms(args_info);
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assert(ms.getStochasticProcess().categories() ==1);
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for (MDOUBLE f=0.005;f<5;f+=0.005){
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ms.setGlobalRate(f);
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ms.out()<<"global rate "<<f<<" "<< ms.getStochasticProcess().getGlobalRate()<<endl;
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ms.computeLikelihoodAndLikelihoodPerPosition();
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ms.printLikelihoodAndLikelihoodPerPosition();
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}
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return 0;
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}
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