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34 lines
974 B
C++
34 lines
974 B
C++
// $Id: likelihoodComputationFactors.cpp 962 2006-11-07 15:13:34Z privmane $
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#include "definitions.h"
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#include "tree.h"
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#include "computeUpAlg.h"
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#include "likelihoodComputationFactors.h"
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#include <cmath>
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#include <cassert>
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using namespace likelihoodComputation;
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MDOUBLE likelihoodComputation::getLOG_LofPos(const int pos,
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const tree& et,
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const sequenceContainer& sc,
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const stochasticProcess& sp,
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const MDOUBLE gRate){ // when there is a global rate for this position
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// using the pij of stochastic process rather than pre computed pij's...
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vector<MDOUBLE> factors;
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computeUpAlg cup;
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suffStatGlobalHomPos ssc;
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cup.fillComputeUpSpecificGlobalRateFactors(et,sc,pos,sp,ssc,gRate,factors);
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doubleRep tmp = 0.0;
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for (int let = 0; let < sp.alphabetSize(); ++let) {
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doubleRep tmpLcat=
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ssc.get(et.getRoot()->id(),let)*
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sp.freq(let);;
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assert(tmpLcat>=0);
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tmp+=tmpLcat;
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}
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return log(tmp)-factors[et.getRoot()->id()]*log(10.0);
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}
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