---

TranslationModelMinimizable Class Reference

#include <TranslationModelMinimizable.h>

Inheritance diagram for TranslationModelMinimizable:

[legend]Collaboration diagram for TranslationModelMinimizable:

[legend]List of all members.

Public Methods
	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 ()
Private Methods
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)
Private Attributes
int	rib_size
int	num_params
int	num_genes
int	num_data_sets
double **	fm
double **	fp
double **	fmerr
double **	fperr
Codon **	RNAseq
int *	length
GeneticCode *	geneticcode
double *	efficiency
Static Private Attributes
const int	MAX_STRING_LENGTH = 100
const double	TINY = 1.0e-16
const int	MAX_RNA_MOLS = 2000
const int	MAX_RNA_LENGTH = 4000

---

Constructor & Destructor Documentation

TranslationModelMinimizable::TranslationModelMinimizable (  LocateInputFileDirectory *    locate, const char *    infilename, int    ribosome_length )

Definition at line 14 of file TranslationModelMinimizable.cpp. References NLLSMinimizable::Allocate, Anticodon, Codon, eatwhite, efficiency, fm, fmerr, fp, fperr, geneticcode, LocateInputFileDirectory::Get, GeneticCode::get_anticodon, GeneticCode::GetNumAnticodons, GeneticCode::GetNumCodons, length, MAX_RNA_LENGTH, MAX_RNA_MOLS, MAX_STRING_LENGTH, NLLSMinimizable::nResiduals, num_data_sets, num_genes, num_params, GeneticCode::read_seq, rib_size, RNAseq, NLLSMinimizable::SetNResiduals, stop, and uuu.

TranslationModelMinimizable::~TranslationModelMinimizable (    )

Definition at line 162 of file TranslationModelMinimizable.cpp. References efficiency, fm, fmerr, fp, fperr, geneticcode, length, num_data_sets, num_genes, and RNAseq.

---

Member Function Documentation

double TranslationModelMinimizable::compute_current (  double *    k, int    length, int    rib_size )  [private]

Definition at line 318 of file TranslationModelMinimizable.cpp. References TINY, and update_dens. Referenced by ComputeResiduals.

double TranslationModelMinimizable::ComputeResiduals (  double *    parameters )  [virtual]

Implements NLLSMinimizable. Definition at line 208 of file TranslationModelMinimizable.cpp. References compute_current, fm, fmerr, fp, fperr, geneticcode, GeneticCode::get_anticodon, GeneticCode::GetNumAnticodons, length, MAX_RNA_LENGTH, num_data_sets, num_genes, NLLSMinimizable::residuals, rib_size, RNAseq, and NLLSMinimizable::SumOfSquares. Referenced by F.

ifstream & TranslationModelMinimizable::eatwhite (  ifstream &    is )  [private]

Definition at line 431 of file TranslationModelMinimizable.cpp. Referenced by TranslationModelMinimizable.

double TranslationModelMinimizable::EntropyShift (  double    T )  [virtual]

Implements NLLSMinimizable. Definition at line 186 of file TranslationModelMinimizable.cpp.

double TranslationModelMinimizable::F (  double *    parameters, double    T )  [virtual]

Implements NLLSMinimizable. Definition at line 191 of file TranslationModelMinimizable.cpp. References ComputeResiduals.

double TranslationModelMinimizable::F0 (  double *    parameters, double    T )  [virtual]

Implements NLLSMinimizable. Definition at line 198 of file TranslationModelMinimizable.cpp.

int TranslationModelMinimizable::GetNParameters (    )  [virtual]

Implements Minimizable. Definition at line 203 of file TranslationModelMinimizable.cpp. References num_params.

void TranslationModelMinimizable::update_dens (  double *    n, double *    k, double    J, int    N, int    L )  [private]

Definition at line 410 of file TranslationModelMinimizable.cpp. Referenced by compute_current.

---

Member Data Documentation

double* TranslationModelMinimizable::efficiency [private]

Definition at line 40 of file TranslationModelMinimizable.h. Referenced by TranslationModelMinimizable, and ~TranslationModelMinimizable.

double** TranslationModelMinimizable::fm [private]

Definition at line 33 of file TranslationModelMinimizable.h. Referenced by ComputeResiduals, TranslationModelMinimizable, and ~TranslationModelMinimizable.

double** TranslationModelMinimizable::fmerr [private]

Definition at line 35 of file TranslationModelMinimizable.h. Referenced by ComputeResiduals, TranslationModelMinimizable, and ~TranslationModelMinimizable.

double** TranslationModelMinimizable::fp [private]

Definition at line 34 of file TranslationModelMinimizable.h. Referenced by ComputeResiduals, TranslationModelMinimizable, and ~TranslationModelMinimizable.

double** TranslationModelMinimizable::fperr [private]

Definition at line 36 of file TranslationModelMinimizable.h. Referenced by ComputeResiduals, TranslationModelMinimizable, and ~TranslationModelMinimizable.

GeneticCode* TranslationModelMinimizable::geneticcode [private]

Definition at line 39 of file TranslationModelMinimizable.h. Referenced by ComputeResiduals, TranslationModelMinimizable, and ~TranslationModelMinimizable.

int* TranslationModelMinimizable::length [private]

Definition at line 38 of file TranslationModelMinimizable.h. Referenced by ComputeResiduals, TranslationModelMinimizable, and ~TranslationModelMinimizable.

const int TranslationModelMinimizable::MAX_RNA_LENGTH = 4000 [static, private]

Definition at line 8 of file TranslationModelMinimizable.cpp. Referenced by ComputeResiduals, and TranslationModelMinimizable.

const int TranslationModelMinimizable::MAX_RNA_MOLS = 2000 [static, private]

Definition at line 10 of file TranslationModelMinimizable.cpp. Referenced by TranslationModelMinimizable.

const int TranslationModelMinimizable::MAX_STRING_LENGTH = 100 [static, private]

Definition at line 12 of file TranslationModelMinimizable.cpp. Referenced by TranslationModelMinimizable.

int TranslationModelMinimizable::num_data_sets [private]

Definition at line 31 of file TranslationModelMinimizable.h. Referenced by ComputeResiduals, TranslationModelMinimizable, and ~TranslationModelMinimizable.

int TranslationModelMinimizable::num_genes [private]

Definition at line 30 of file TranslationModelMinimizable.h. Referenced by ComputeResiduals, TranslationModelMinimizable, and ~TranslationModelMinimizable.

int TranslationModelMinimizable::num_params [private]

Definition at line 29 of file TranslationModelMinimizable.h. Referenced by GetNParameters, and TranslationModelMinimizable.

int TranslationModelMinimizable::rib_size [private]

Definition at line 28 of file TranslationModelMinimizable.h. Referenced by ComputeResiduals, and TranslationModelMinimizable.

Codon** TranslationModelMinimizable::RNAseq [private]

Definition at line 37 of file TranslationModelMinimizable.h. Referenced by ComputeResiduals, TranslationModelMinimizable, and ~TranslationModelMinimizable.

const double TranslationModelMinimizable::TINY = 1.0e-16 [static, private]

Definition at line 6 of file TranslationModelMinimizable.cpp. Referenced by compute_current.

---

The documentation for this class was generated from the following files:

• TranslationModelMinimizable.h
• TranslationModelMinimizable.cpp

---