SharedBFactorNetworkMinimizable.h Source File

00001 // SharedBFactorNetworkMinimizable.h: interface for the SharedBFactorNetworkMinimizable class.
00002 //
00004 
00005 #if !defined(AFX_SHAREDBFACTORNETWORKMINIMIZABLE_H__8F38BFB2_7B39_41DB_A979_3A20AD69180D__INCLUDED_)
00006 #define AFX_SHAREDBFACTORNETWORKMINIMIZABLE_H__8F38BFB2_7B39_41DB_A979_3A20AD69180D__INCLUDED_
00007 
00008 #if _MSC_VER > 1000
00009 #pragma once
00010 #endif // _MSC_VER > 1000
00011 
00012 #include <iomanip>
00013 #include <cmath>
00014 #include <assert.h>
00015 #include "SubjectObserver.h"
00016 #include "NLLSMinimizable.h"
00017 #include "Experiment.h"
00018 #include "ReactionMover.h"
00019 #include "CellAverageObserver.h"
00020 #include "ConversionFactor.h"
00021 #include "NetworkMinimizable.h"
00022 
00023 class SharedBFactorNetworkMinimizable : public NetworkMinimizable
00024 {
00025 public:
00026         // default construction gives no free parameters (nothing to optimize)
00027         SharedBFactorNetworkMinimizable();
00028         SharedBFactorNetworkMinimizable(std::vector<Experiment *> experiments,std::vector<CReactionMover *> reactionMovers,bool rateConstantsOptimizable,bool initialChemConcOptimizable,bool logsInObjectiveFunction,double timeSeriesWeight,double rateConstantsWeight,double initialChemConcWeight,int nCells=1);
00029         void Initialize(std::vector<Experiment *> experiments, std::vector<CReactionMover *> reactionMovers, int nCells, bool rateConstantsOptimizable, bool initialChemConcOptimizable, bool logsInObjectiveFunction, double timeSeriesWeight, double rateConstantsWeight, double initialChemConcWeight);
00030         virtual ~SharedBFactorNetworkMinimizable();
00031         // Get() functions
00032         Experiment *GetExperiment(int expNum) {return experiments[expNum];}
00033         CellAverageObserver *GetCellObserver(int coNum) {return cellObservers[coNum];}
00034         //double *GetParameters();
00035         double GetParameter(int parIndex);
00036         int GetNExp() {return this->nExp;}
00037         // overloaded from base classes
00038         int GetNParameters();
00039         double ComputeResiduals(double *parameters);
00040         virtual double ComputeES(double *parameters, double T);
00041 //      virtual double EntropyShift(double T);
00042         virtual double F(double *parameters, double T);
00043         virtual double F0(double *parameters, double T);
00044 private:
00045         std::vector<Experiment *> experiments;
00046         std::vector<CReactionMover *> reactionMovers;
00047         std::vector<CellAverageObserver *> cellObservers;
00048         std::vector<std::vector<double *> *> initialNetworkData;
00049         std::vector<std::vector<double *> *> currentNetworkData;
00050         int nExp;
00051 };
00052 
00053 #endif // !defined(AFX_SHAREDBFACTORNETWORKMINIMIZABLE_H__8F38BFB2_7B39_41DB_A979_3A20AD69180D__INCLUDED_)