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61 lines
2.2 KiB
C++
61 lines
2.2 KiB
C++
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#ifndef ___COMPUTE_POSTERIOR_EXPECTATION_OF_SUBSTITUTIONS
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#define ___COMPUTE_POSTERIOR_EXPECTATION_OF_SUBSTITUTIONS
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/*
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This is a father class where it implements the computePosteriorExpectationOfSubstitutions
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procedure for a reversible stochastic process. Its son, computePosteriorExpectationOfSubstitutions_nonReversibleSp
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implements the computePosteriorExpectationOfSubstitutions for a non-reversible stochastic process. The implementation
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difference is in two functions: computePosteriorOfChangeGivenTerminals and computePosterioGivenTerminalsPerBranch
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*/
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#include "definitions.h"
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#include "simulateJumps.h"
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#include "tree.h"
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#include "sequenceContainer.h"
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#include "stochasticProcess.h"
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#include "suffStatComponent.h"
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#include "computePijComponent.h"
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#include "simulateJumpsAbstract.h"
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class computePosteriorExpectationOfSubstitutions {
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public:
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explicit computePosteriorExpectationOfSubstitutions(const tree &tr, const sequenceContainer &sc, const stochasticProcess *sp);
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virtual ~computePosteriorExpectationOfSubstitutions(){};
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VVdouble computeExpectationAcrossTree(simulateJumpsAbstract &sim, //input given from simulation studies
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const VVVdouble &posteriorProbs, VVVdouble &expForBranch);
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VVdouble computePosteriorAcrossTree(simulateJumpsAbstract &sim, //input given from simulation studies
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const VVVdouble &posteriorProbsGivenTerminals,VVVdouble &probsForBranch);
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virtual void computePosteriorOfChangeGivenTerminals(VVVdouble &posteriorPerNodePer2States, int pos);
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private:
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MDOUBLE computePosteriorOfChangePerBranch(
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simulateJumpsAbstract &sim, //input given from simulation studies
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const VVVdouble &posteriorProbs,
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tree::nodeP node,
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int fromState, int toState);
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MDOUBLE computeExpectationOfChangePerBranch(
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simulateJumpsAbstract &sim, //input given from simulation studies
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const VVVdouble &posteriorProbsGivenTerminals,
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tree::nodeP node,
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int fromState, int toState);
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MDOUBLE computePosterioGivenTerminalsPerBranch (int nodeId,int sonState, int fatherState,suffStatGlobalHomPos &sscUp,
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suffStatGlobalHomPos &sscDown,computePijHom &pi, MDOUBLE &LLData, const string nodeName);
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protected:
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const tree &_tr;
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const sequenceContainer &_sc;
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const stochasticProcess *_sp;
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};
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#endif
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