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TranslationModelMinimizable.h

Go to the documentation of this file.

#ifndef TRANSLATIONMODELMINIMIZABLE_H_INCLUDED
#define TRANSLATIONMODELMINIMIZABLE_H_INCLUDED

#include "GeneticCode.h"
#include "NLLSMinimizable.h"
#include <fstream>
#include <iostream>
#include <sstream>
#include <iomanip>
#include <cctype>
#include "LocateInputFileDirectory.h"
using namespace std;

class TranslationModelMinimizable : public NLLSMinimizable
{
public:
        TranslationModelMinimizable(LocateInputFileDirectory *locate, const char* infilename, int ribosome_length);
        ~TranslationModelMinimizable();
        double ComputeResiduals(double *parameters);
        double EntropyShift(double T);
        double F(double *parameters, double T);
        double F0(double *parameters, double T);
        int GetNParameters();  // returns number of parameters
private:
        ifstream& eatwhite(ifstream& is);
        double compute_current(double*k ,int length,int rib_size);
        void update_dens(double* n, double* k, double J, int N, int L);
        int rib_size;  // ribosome length (measured in codons)
        int num_params;
        int num_genes;  // number of genes to be used
        int num_data_sets;  // number of sets of fold change data (1 < num expt. conditions)                       
        // for expt data, 1st index is data set number and 2nd is gene number
        double** fm;  // mRNA fold changes
        double** fp;  // protein fold changes
        double** fmerr;  // errors in fm
        double** fperr;  // errors in fp
        Codon** RNAseq;  // codon sequence for each gene
        int* length;  // length of each gene sequence (# of codons)
        GeneticCode* geneticcode;  // info to read/decode genetic sequences
        double* efficiency;  // efficiency of tRNA binding for each codon (not currently in use)
        
        static const int MAX_STRING_LENGTH;
        static const double TINY;
        static const int MAX_RNA_MOLS;
        static const int MAX_RNA_LENGTH;

};

#endif

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