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34 lines
999 B
C++
34 lines
999 B
C++
// $Id: fromCountTableComponentToDistanceProp.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_PROP
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#define ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_PROP
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#include "definitions.h"
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#include "countTableComponent.h"
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#include "stochasticProcess.h"
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class fromCountTableComponentToDistanceProp {
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public:
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explicit fromCountTableComponentToDistanceProp(
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const vector<countTableComponentGam>& ctc,
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const vector<stochasticProcess> &sp,
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const MDOUBLE toll,
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const MDOUBLE brLenIntialGuess = 0.029);// =startingGuessForTreeBrLen
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void computeDistance();// return the likelihood
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MDOUBLE getDistance() { return _distance;} // return the distance.
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MDOUBLE getLikeDistance() { return _likeDistance;} // return the distance.
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private:
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const vector<stochasticProcess> & _sp;
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const vector<countTableComponentGam>& _ctc;
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MDOUBLE _toll;
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MDOUBLE _distance;
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MDOUBLE _likeDistance;
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int alphabetSize() {return (_ctc.empty()?0:_ctc[0].alphabetSize());}
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};
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#endif
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