| AnnotationItem(const std::vector< RegionPrediction * > &, const DnaStr &, const DnaStr &) (defined in AnnotationItem) | AnnotationItem | |
| apair_t typedef (defined in AnnotationItem) | AnnotationItem | |
| bpair_t typedef (defined in AnnotationItem) | AnnotationItem | |
| checkOrf(const AnnotationItem *, const MatrixIdx &, int, int, const DnaStr &) (defined in AnnotationItem) | AnnotationItem | [static] |
| computeNonCodingScore() const (defined in AnnotationItem) | AnnotationItem | |
| dpUpdate(const AnnotationItem &, std::vector< scr_pr > &, bool) | AnnotationItem | |
| dpUpdate(std::vector< scr_pr > &, bool, bool) (defined in AnnotationItem) | AnnotationItem | |
| endScore(const CustomScore &, const AnnotationScore &, bool) const (defined in AnnotationItem) | AnnotationItem | |
| getBest(const MatrixIdx &) const (defined in AnnotationItem) | AnnotationItem | |
| getEnd3() const (defined in AnnotationItem) | AnnotationItem | [inline] |
| getEnd3AdjForStop(int model, dsu::Strand_t strnd) const (defined in AnnotationItem) | AnnotationItem | |
| getEnd5() const (defined in AnnotationItem) | AnnotationItem | [inline] |
| getEnd5AdjForStop(int model, dsu::Strand_t strnd) const (defined in AnnotationItem) | AnnotationItem | |
| getLeft() const (defined in AnnotationItem) | AnnotationItem | [inline] |
| getPred(int, dsu::Strand_t, dsu::side_t, int) const (defined in AnnotationItem) | AnnotationItem | |
| getPrevExonType(const MatrixIdx &) const (defined in AnnotationItem) | AnnotationItem | |
| getRegionPrediction() const (defined in AnnotationItem) | AnnotationItem | [inline] |
| getRght() const (defined in AnnotationItem) | AnnotationItem | [inline] |
| getSeq(dsu::Strand_t strnd) const (defined in AnnotationItem) | AnnotationItem | [inline] |
| getStrnd() const (defined in AnnotationItem) | AnnotationItem | [inline] |
| length() const (defined in AnnotationItem) | AnnotationItem | [inline] |
| print(std::ostream &, const CustomScore &) const (defined in AnnotationItem) | AnnotationItem | |
| strnd_frm_t typedef (defined in AnnotationItem) | AnnotationItem | |
| update(const MatrixIdx &, const MatrixIdx &, const int, const AnnotationScore &, const AnnotationItem &) (defined in AnnotationItem) | AnnotationItem | |
| update(const MatrixIdx &, const MatrixIdx &, const int, const AnnotationScore &) (defined in AnnotationItem) | AnnotationItem | |
| ~AnnotationItem() (defined in AnnotationItem) | AnnotationItem | [inline] |