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#include <fstream>
#include <iostream>
#include <string>
#include <iomanip>
using namespace std;
#include "nucJC.h"
#include "sequence.h"
#include "distribution.h"
#include "stochasticProcess.h"
#include "gammaDistribution.h"
#include "trivialAccelerator.h"
#include "sequenceContainer.h"
#include "nucleotide.h"
#include "phylipFormat.h"
#include "likelihoodComputation.h"
#include "bblEM.h"
// NOTE: YOU MUST CHANGE THE NAME OF THE string seqFile TO MATCH YOUR OWN LOCATION OF THE SEQUENCE FILE NAME!
int main(int argc,char*argv[]) {
cout<<"This program computes for the JC model, the likelihood of a given tree (when the branch lengths are given)."<<endl;
string seqFile = "nuc7.phylip.txt";
distribution *dist = new gammaDistribution(1,8);
replacementModel *probMod=new nucJC;
pijAccelerator * pijAcc = new trivialAccelerator(probMod);
stochasticProcess sp(dist, pijAcc);
ifstream in(seqFile.c_str());
if (!in) {errorMsg::reportError("unable to open input sequence file");}
nucleotide myAlph;
sequenceContainer original = phylipFormat::read(in,&myAlph);
const string treeFileName = "startTree.txt";
tree myT(treeFileName);
cout<<"computing the log likelihood of the tree..."<<endl;
MDOUBLE resL = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(myT,original,sp);
cout<<" starting L = "<<resL<<endl;
bblEM bblEM1(myT,original,sp,NULL,1000,0.05);
resL = bblEM1.getTreeLikelihood();
cout<<" end L, after bbl = "<<setprecision(12)<<resL<<endl;
//ofstream out("tAfterBBL.txt");
myT.output(cout);
delete dist;
delete probMod;
//system("PAUSE");
return 0;
}
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