| Allocate(int nResiduals) | NLLSMinimizable | |
| compute_current(double *k,int length, int rib_size) | TranslationModelMinimizable | [private] |
| ComputeES(double *parameters, double T) | NLLSMinimizable | [virtual] |
| ComputeResiduals(double *parameters) | TranslationModelMinimizable | [virtual] |
| eatwhite(ifstream &is) | TranslationModelMinimizable | [private] |
| efficiency | TranslationModelMinimizable | [private] |
| EntropyShift(double T) | TranslationModelMinimizable | [virtual] |
| F(double *parameters, double T) | TranslationModelMinimizable | [virtual] |
| F0(double *parameters, double T) | TranslationModelMinimizable | [virtual] |
| fm | TranslationModelMinimizable | [private] |
| fmerr | TranslationModelMinimizable | [private] |
| fp | TranslationModelMinimizable | [private] |
| fperr | TranslationModelMinimizable | [private] |
| geneticcode | TranslationModelMinimizable | [private] |
| GetEnergyLastComputed() | Minimizable | [inline, virtual] |
| GetEntropyLastComputed() | Minimizable | [inline, virtual] |
| GetNParameters() | TranslationModelMinimizable | [virtual] |
| GetNResiduals() | NLLSMinimizable | [inline] |
| GetResiduals() | NLLSMinimizable | [inline] |
| Gradient(double *parameters) | Minimizable | [inline, virtual] |
| Hessian(double *parameters) | Minimizable | [inline, virtual] |
| length | TranslationModelMinimizable | [private] |
| m_dEnergyLastComputed | Minimizable | [protected] |
| m_dEntropyLastComputed | Minimizable | [protected] |
| MAX_RNA_LENGTH | TranslationModelMinimizable | [private, static] |
| MAX_RNA_MOLS | TranslationModelMinimizable | [private, static] |
| MAX_STRING_LENGTH | TranslationModelMinimizable | [private, static] |
| NLLSMinimizable() | NLLSMinimizable | |
| nResiduals | NLLSMinimizable | [protected] |
| num_data_sets | TranslationModelMinimizable | [private] |
| num_genes | TranslationModelMinimizable | [private] |
| num_params | TranslationModelMinimizable | [private] |
| ObjectiveFunction(double *parameters) | NLLSMinimizable | [virtual] |
| residuals | NLLSMinimizable | [protected] |
| rib_size | TranslationModelMinimizable | [private] |
| RNAseq | TranslationModelMinimizable | [private] |
| SetNResiduals(int nResiduals) | NLLSMinimizable | [inline] |
| SumOfSquares() | NLLSMinimizable | |
| TINY | TranslationModelMinimizable | [private, static] |
| TranslationModelMinimizable(LocateInputFileDirectory *locate, const char *infilename, int ribosome_length) | TranslationModelMinimizable | |
| update_dens(double *n, double *k, double J, int N, int L) | TranslationModelMinimizable | [private] |
| ~NLLSMinimizable() | NLLSMinimizable | [virtual] |
| ~TranslationModelMinimizable() | TranslationModelMinimizable | |
