| _matrix (defined in Annotation) | Annotation | [protected] |
| _negSeq (defined in Annotation) | Annotation | [protected] |
| _posSeq (defined in Annotation) | Annotation | [protected] |
| _theSeq (defined in Annotation) | Annotation | [protected] |
| aipair_t typedef (defined in Annotation) | Annotation | |
| Annotation(const string &theSequence, bool forceWholeGeneModel, int cutOff) | Annotation | [inline] |
| empty() const (defined in Annotation) | Annotation | [inline] |
| forceWholeGeneModel() const (defined in Annotation) | Annotation | [inline] |
| getBestStart(const CustomScore &) const | Annotation | |
| getGeneList(int &, const CustomScore &) const | Annotation | |
| getMatrix() const (defined in Annotation) | Annotation | [inline] |
| insert(const std::vector< RegionPrediction * > &, const CustomScore &) | Annotation | |
| print(std::ostream &, const CustomScore &) const (defined in Annotation) | Annotation | |
| scoreGeneList(std::list< GffFeature * > &flst, const CustomScore &cs) const (defined in Annotation) | Annotation | |
| scoreHelp(int end5, int end3, dsu::Strand_t strnd, int mid, const CustomScore &cs) const (defined in Annotation) | Annotation | |
| ~Annotation() (defined in Annotation) | Annotation | [inline] |