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#include <fstream>
#include <iostream>
#include <string>
using namespace std;
#include "hky.h"
#include "sequence.h"
#include "distribution.h"
#include "stochasticProcess.h"
#include "uniDistribution.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 K2P model, when two sequences are given, the ML distance and its likelihood."<<endl;
string seqFile = "s2l4_DNA.txt";
distribution *dist = new uniDistribution;
replacementModel *probMod1=new hky(0.25,0.25,0.25,0.25,0.5);
pijAccelerator * pijAcc1 = new trivialAccelerator(probMod1);
replacementModel *probMod2=new hky(0.25,0.25,0.25,0.25,10);
pijAccelerator * pijAcc2 = new trivialAccelerator(probMod2);
stochasticProcess sp1(dist, pijAcc1);
stochasticProcess sp2(dist, pijAcc2);
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];
MDOUBLE resL1 = 0;
likeDist likeDist1(sp1,myToll);
MDOUBLE resD1 = likeDist1.giveDistance(s1,s2,NULL,&resL1);
cout<<endl<<"For Tr/Tv = 0.5" <<endl;
cout<<" the likelihood of these 2 sequences is:"<<resL1<<endl;
cout<<" the ML distance between these 2 sequences is:"<<resD1<<endl;
MDOUBLE resL2 = 0;
likeDist likeDist2(sp2,myToll);
MDOUBLE resD2 = likeDist2.giveDistance(s1,s2,NULL,&resL2);
cout<<endl<<"For Tr/Tv = 10" <<endl;
cout<<" the likelihood of these 2 sequences is:"<<resL2<<endl;
cout<<" the ML distance between these 2 sequences is:"<<resD2<<endl;
delete dist;
delete probMod1;
delete probMod2;
return 0;
}
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