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#include <fstream>
#include <iostream>
#include <string>
using namespace std;
#include "sequence.h"
#include "distribution.h"
#include "stochasticProcess.h"
#include "uniDistribution.h"
#include "nucJC.h"
#include "trivialAccelerator.h"
#include "sequenceContainer.h"
#include "nucleotide.h"
#include "phylipFormat.h"
#include "likeDist.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, when two sequences are given, and the distance between these two sequences is known, the likelihood."<<endl;
string seqFile = "s2l4_DNA.txt";
distribution *dist = new uniDistribution;
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 MDOUBLE myToll = 0.0001;
if (original.numberOfSeqs() != 2) {
errorMsg::reportError("for this check, there suppose to be only 2 sequences",1);
}
sequence s1 = original[0];
sequence s2 = original[1];
likeDist likeDist1(sp,myToll);
MDOUBLE resL = 0;
MDOUBLE resD = likeDist1.giveDistance(s1,s2,NULL,&resL);
cout<<" the likelihood of these 2 sequences is:"<<resL<<endl;
cout<<" the ML distance between these 2 sequences is:"<<resD<<endl;
delete dist;
delete probMod;
return 0;
}
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