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61 lines
1.6 KiB
C++
61 lines
1.6 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 "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 "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 "jcDistance.h"
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#include "distanceTable.h"
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#include "nj.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 JC model, the NJ tree."<<endl;
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string seqFile = "nuc7.phylip.txt";
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if (argc>1)
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seqFile=argv[1];
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distribution *dist = new uniDistribution;
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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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cout<<"computing the NJ tree..."<<endl;
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jcDistance likeDist1(myAlph.size());
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VVdouble disTab;
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vector<string> vNames;
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giveDistanceTable(&likeDist1,
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original,
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disTab,
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vNames);
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NJalg nj1;
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tree njTree = nj1.computeTree(disTab,vNames);
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// ofstream out("njTreeRes.txt");
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njTree.output(cout);
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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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return 0;
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}
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