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54 lines
1.6 KiB
C++
54 lines
1.6 KiB
C++
// $Id: optimizeBranchesJC_EM.cpp 370 2005-05-25 20:46:34Z ninio $
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#include <fstream>
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#include <iostream>
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#include <string>
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#include <iomanip>
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using namespace std;
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#include "nucJC.h"
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#include "sequence.h"
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#include "distribution.h"
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#include "stochasticProcess.h"
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#include "uniDistribution.h"
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#include "trivialAccelerator.h"
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#include "sequenceContainer.h"
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#include "nucleotide.h"
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#include "phylipFormat.h"
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#include "likelihoodComputation.h"
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#include "bblEM.h"
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// NOTE: YOU MUST CHANGE THE NAME OF THE string seqFile TO MATCH YOUR OWN LOCATION OF THE SEQUENCE FILE NAME!
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int main(int argc,char*argv[]) {
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cout<<"This program computes for the JC model, the likelihood of a given tree (when the branch lengths are given)."<<endl;
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string seqFile = "nuc7.phylip.txt";
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distribution *dist = new uniDistribution;
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replacementModel *probMod=new nucJC;
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pijAccelerator * pijAcc = new trivialAccelerator(probMod);
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stochasticProcess sp(dist, pijAcc);
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ifstream in(seqFile.c_str());
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if (!in) {errorMsg::reportError("unable to open input sequence file");}
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nucleotide myAlph;
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sequenceContainer original = phylipFormat::read(in,&myAlph);
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const string treeFileName = "startTree.txt";
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tree myT(treeFileName);
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cout<<"computing the log likelihood of the tree..."<<endl;
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MDOUBLE resL = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(myT,original,sp);
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cout<<" starting L = "<<resL<<endl;
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bblEM bblEM1(myT,original,sp,NULL,1000,0.05);
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resL = bblEM1.getTreeLikelihood();
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cout<<" end L, after bbl = "<<setprecision(12)<<resL<<endl;
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// ofstream out("tAfterBBL.txt");
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myT.output(cout);
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delete dist;
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delete probMod;
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return 0;
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}
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