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70 lines
2.1 KiB
C++
70 lines
2.1 KiB
C++
#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 "gammaDistribution.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 "bestHKYparam.h"
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#include "evaluateCharacterFreq.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, the ML estimate 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 gammaDistribution(1,8);
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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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// check
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vector<MDOUBLE> myFreq = evaluateCharacterFreq(original);
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for (int j=0; j < myFreq.size(); ++j) {
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cout<<" the freq of nuc "<<j<<" is: "<<myFreq[j]<<endl;
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}
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distribution *dist = new uniDistribution;
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replacementModel *probMod=new hky(myFreq[0],myFreq[1],myFreq[2],myFreq[3],2);
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pijAccelerator * pijAcc = new trivialAccelerator(probMod);
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stochasticProcess sp(dist, pijAcc);
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// end check
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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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bestHkyParamAndBBL bestHkyParamAndBBL1(myT,original,sp);
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resL = bestHkyParamAndBBL1.getBestL();
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MDOUBLE resAlpha = bestHkyParamAndBBL1.getBestHkyParam();
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cout<<"final likelihood: "<<resL<<endl;
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cout<<"best HKY parameter: "<<resAlpha<<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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//C:\tal\semphyCheck\nuc7.phylip.txt
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//C:\tal\semphyCheck\startTree.txt
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