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40 lines
1.2 KiB
C++
40 lines
1.2 KiB
C++
// $Id: fromCountTableComponentToDistance2USSRV.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_2_USSRV
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#define ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_2_USSRV
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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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#include "ussrvModel.h"
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#include "likeDist2USSRV.h"
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static const MDOUBLE startingGuessForTreeBrLen = 0.029;
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class fromCountTableComponentToDistance2USSRV {
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public:
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explicit fromCountTableComponentToDistance2USSRV(
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const countTableComponentGam& ctcBase,
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const countTableComponentHom& ctcSSRV,
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const ussrvModel& model,
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MDOUBLE toll,
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MDOUBLE brLenIntialGuess);// =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 ussrvModel & _model;
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const countTableComponentGam& _ctcBase;
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const countTableComponentHom& _ctcSSRV;
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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.alphabetSize();}
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};
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#endif //___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_2_USSRV
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