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46 lines
1.5 KiB
C++
46 lines
1.5 KiB
C++
#include <fstream>
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#include <iostream>
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#include <string>
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using namespace std;
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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 "gammaDistribution.h"
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#include "nucJC.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 "likeDist.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 HKY model, when two sequences are given, and the distance between these two sequences is known, the likelihood."<<endl;
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string seqFile = "s2l4_DNA.txt";
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distribution *dist = new gammaDistribution(4.0,8);
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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 MDOUBLE myToll = 0.0001;
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if (original.numberOfSeqs() != 2) {
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errorMsg::reportError("for this check, there suppose to be only 2 sequences",1);
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}
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sequence s1 = original[0];
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sequence s2 = original[1];
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likeDist likeDist1(sp,myToll);
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MDOUBLE resL = 0;
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MDOUBLE resD = likeDist1.giveDistance(s1,s2,NULL,&resL);
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cout<<" the likelihood of these 2 sequences is:"<<resL<<endl;
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cout<<" the ML distance between these 2 sequences is:"<<resD<<endl;
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delete dist;
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delete probMod;
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// system("PAUSE");
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return 0;
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}
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