mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 07:10:24 +08:00
70 lines
2.1 KiB
C++
70 lines
2.1 KiB
C++
#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 "uniDistribution.h"
|
|
#include "trivialAccelerator.h"
|
|
#include "sequenceContainer.h"
|
|
#include "nucleotide.h"
|
|
#include "phylipFormat.h"
|
|
#include "likelihoodComputation.h"
|
|
#include "bestHKYparam.h"
|
|
#include "evaluateCharacterFreq.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 HKY model, the ML estimate of a given tree (when the branch lengths are given)."<<endl;
|
|
string seqFile = "nuc7.phylip.txt";
|
|
// distribution *dist = new gammaDistribution(1,8);
|
|
ifstream in(seqFile.c_str());
|
|
if (!in) {errorMsg::reportError("unable to open input sequence file");}
|
|
nucleotide myAlph;
|
|
sequenceContainer original = phylipFormat::read(in,&myAlph);
|
|
|
|
// check
|
|
|
|
vector<MDOUBLE> myFreq = evaluateCharacterFreq(original);
|
|
for (int j=0; j < myFreq.size(); ++j) {
|
|
cout<<" the freq of nuc "<<j<<" is: "<<myFreq[j]<<endl;
|
|
}
|
|
|
|
distribution *dist = new uniDistribution;
|
|
replacementModel *probMod=new hky(myFreq[0],myFreq[1],myFreq[2],myFreq[3],2);
|
|
pijAccelerator * pijAcc = new trivialAccelerator(probMod);
|
|
stochasticProcess sp(dist, pijAcc);
|
|
|
|
|
|
|
|
// end check
|
|
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;
|
|
bestHkyParamAndBBL bestHkyParamAndBBL1(myT,original,sp);
|
|
|
|
resL = bestHkyParamAndBBL1.getBestL();
|
|
MDOUBLE resAlpha = bestHkyParamAndBBL1.getBestHkyParam();
|
|
cout<<"final likelihood: "<<resL<<endl;
|
|
cout<<"best HKY parameter: "<<resAlpha<<endl;
|
|
// ofstream out("tAfterBBL.txt");
|
|
myT.output(cout);
|
|
|
|
delete dist;
|
|
delete probMod;
|
|
return 0;
|
|
}
|
|
|
|
//C:\tal\semphyCheck\nuc7.phylip.txt
|
|
//C:\tal\semphyCheck\startTree.txt
|