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68 lines
2.0 KiB
C++
68 lines
2.0 KiB
C++
// $Id: semphyStep.h 702 2006-05-27 17:16:58Z ninio $
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#ifndef ___SEMPHY_STEP
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#define ___SEMPHY_STEP
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#include "suffStatComponent.h"
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#include "semphyDistance.h"
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#include "rearangeTree.h"
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#include "minSpanTree.h"
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#include "tree.h"
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#include "sequenceContainer.h"
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#include "computePijComponent.h"
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#include "stochasticProcess.h"
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class semphyStep {
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public:
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explicit semphyStep(
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tree& et,
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const tree* ctPtr,
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const sequenceContainer& sc,
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const stochasticProcess& sp,
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const computePijGam& pij0,
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const suffStatGlobalGam& cup,
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const suffStatGlobalGam& cdown,
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const bool useApproxCounts,
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const VdoubleRep& cprobAtEachPos,
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const VVdoubleRep & posteriorRateProbAtEachPos,
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const suffStatGlobalGam& computeMarginal,
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const Vdouble *weights,
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const MDOUBLE toll);
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void doNothing(void) const {};
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private:
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void computeSemphyStep();
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// void fillCpijUpDownExactMarginalProbAtEachPos();
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semphyDistance* computeQmatrix(const Vdouble* weight);
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MDOUBLE computeQstart(const semphyDistance* inSemDist) const;
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void addConstraintPenalty(VVdouble & penaltyTable);
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tree& _et;
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const tree* _ctPtr;
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const sequenceContainer& _sc;
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const stochasticProcess& _sp;
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const computePijGam& _pij0;
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const suffStatGlobalGam& _cup;
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const suffStatGlobalGam& _cdown;
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const bool _useApproxCounts;
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const VdoubleRep& _cprobAtEachPos;
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const VVdoubleRep & _posteriorRateProbAtEachPos;
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const suffStatGlobalGam& _computeMarginal;
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const Vdouble *_weights;
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const MDOUBLE _toll;
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// ouput to log file functions...
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void maybePrintPenaltyTableAndStartingTree(const VVdouble& penetlyTable) const;
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void maybePrintDistanceBetweenNodesTable(const semphyDistance* inSemDist) const;
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void maybePrintSpanTreeListAndQAfterSpanTree(const rearrangeTree::pairSet& inSet,const MDOUBLE score) const;
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void maybePrintTheTreeAfterRearrangeTree() const;
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void maybePrintQspanMinusQinit(const MDOUBLE qpan, const MDOUBLE qstart) const;
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void maybePrintTheTreeAfterCorrectToCanonialForm() const;
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};
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#endif
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