| _cutOff (defined in Options) | Options | |
| _dtFile (defined in Options) | Options | |
| _exonDistrFile (defined in Options) | Options | |
| _forceModels (defined in Options) | Options | |
| _hmmFile (defined in Options) | Options | |
| _matrixFile (defined in Options) | Options | |
| _outputGeneModelFile (defined in Options) | Options | |
| _subEnd3 (defined in Options) | Options | |
| _subEnd5 (defined in Options) | Options | |
| _train (defined in Options) | Options | |
| _trainOffSet (defined in Options) | Options | |
| _vecFile (defined in Options) | Options | |
| createInstance(int argc, char **argv, const string &id) (defined in Options) | Options | [inline, static] |
| doTraining() const (defined in Options) | Options | [inline] |
| getInstance() (defined in Options) | Options | [inline, static] |
| isExonDistr() const | Options | [inline] |
| isLinComb() const (defined in Options) | Options | [inline] |
| isVerbose() const (defined in Options) | Options | [inline] |
| m_evidenceListFile (defined in Options) | Options | |
| m_fastaFile (defined in Options) | Options | |
| main(int, char **) | Options | [friend] |
| Options(int argc, char **argv, const string &) (defined in Options) | Options | [protected] |
| quit (defined in Options) | Options | |
| setIntronFalse() (defined in Options) | Options | [inline] |
| useIntron() const (defined in Options) | Options | [inline] |