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40 lines
1.3 KiB
C++
40 lines
1.3 KiB
C++
// $Id: fromCountTableComponentToDistance.h 4471 2008-07-17 15:38:50Z cohenofi $
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#ifndef ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE__FIX_ROOT
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#define ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE__FIX_ROOT
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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 "unObservableData.h"
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static const MDOUBLE startingGuessForTreeBrLen = 0.029;
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class fromCountTableComponentToDistancefixRoot {
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public:
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explicit fromCountTableComponentToDistancefixRoot(
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const vector<countTableComponentGam>& ctc,
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const stochasticProcess &sp,
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const MDOUBLE toll,
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const MDOUBLE brLenIntialGuess, // =startingGuessForTreeBrLen
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unObservableData* unObservableData_p);
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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 stochasticProcess & _sp;
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const vector<countTableComponentGam>& _ctc; //_ctc[letterAtRoot][rate][alph][alph]
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MDOUBLE _toll;
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MDOUBLE _distance;
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MDOUBLE _likeDistance;
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unObservableData* _unObservableData_p;
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// int alphabetSize() {return _ctc.alphabetSize();}
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int alphabetSize() {return _ctc[0].alphabetSize();}
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};
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#endif
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