| ADJACENCY_BIT | AMOS::Overlap_t | [protected, static] |
| ADJACENCY_BITS | AMOS::Overlap_t | [protected, static] |
| ANTINORMAL | AMOS::Overlap_t | [static] |
| ANTINORMAL_BITS | AMOS::Overlap_t | [protected, static] |
| clear() | AMOS::Overlap_t | [inline, virtual] |
| eid_m | AMOS::IBankable_t | [protected] |
| FLAGC_BIT | AMOS::Overlap_t | [protected, static] |
| flags_m | AMOS::IBankable_t | [protected] |
| flip() | AMOS::Overlap_t | |
| getAdjacency() const | AMOS::Overlap_t | |
| getAhang() const | AMOS::Overlap_t | [inline] |
| getBhang() const | AMOS::Overlap_t | [inline] |
| getComment() const | AMOS::Universal_t | [inline] |
| getEID() const | AMOS::IBankable_t | [inline] |
| getIID() const | AMOS::IBankable_t | [inline] |
| getNCode() const | AMOS::Overlap_t | [inline, virtual] |
| getReads() const | AMOS::Overlap_t | [inline] |
| getScore() const | AMOS::Overlap_t | [inline] |
| getStatus() const | AMOS::Universal_t | [inline] |
| IBankable_t() | AMOS::IBankable_t | [inline] |
| IBankable_t(const IBankable_t &source) | AMOS::IBankable_t | [inline] |
| iid_m | AMOS::IBankable_t | [protected] |
| IMessagable_t() | AMOS::IMessagable_t | [inline] |
| INNIE | AMOS::Overlap_t | [static] |
| INNIE_BITS | AMOS::Overlap_t | [protected, static] |
| isFlagA() const | AMOS::IBankable_t | [inline] |
| isFlagB() const | AMOS::IBankable_t | [inline] |
| isFlagC() const | AMOS::Overlap_t | [inline] |
| isModified() const | AMOS::IBankable_t | [inline] |
| isRemoved() const | AMOS::IBankable_t | [inline] |
| NCODE | AMOS::Overlap_t | [static] |
| NORMAL | AMOS::Overlap_t | [static] |
| NORMAL_BITS | AMOS::Overlap_t | [protected, static] |
| NULL_ADJACENCY | AMOS::Overlap_t | [static] |
| OUTIE | AMOS::Overlap_t | [static] |
| OUTIE_BITS | AMOS::Overlap_t | [protected, static] |
| Overlap_t() | AMOS::Overlap_t | [inline] |
| Overlap_t(const Overlap_t &source) | AMOS::Overlap_t | [inline] |
| readMessage(const Message_t &msg) | AMOS::Overlap_t | [virtual] |
| readRecord(std::istream &fix, std::istream &var) | AMOS::Overlap_t | [protected, virtual] |
| readRecordFix(std::istream &fix) | AMOS::Overlap_t | [protected, virtual] |
| setAdjacency(OverlapAdjacency_t adj) | AMOS::Overlap_t | |
| setAhang(Size_t aHang) | AMOS::Overlap_t | [inline] |
| setBhang(Size_t bHang) | AMOS::Overlap_t | [inline] |
| setComment(const std::string &comment) | AMOS::Universal_t | [inline] |
| setEID(const std::string &eid) | AMOS::IBankable_t | [inline] |
| setFlagA(bool flag) | AMOS::IBankable_t | [inline] |
| setFlagB(bool flag) | AMOS::IBankable_t | [inline] |
| setFlagC(bool flag) | AMOS::Overlap_t | [inline] |
| setIID(ID_t iid) | AMOS::IBankable_t | [inline] |
| setReads(std::pair< ID_t, ID_t > reads) | AMOS::Overlap_t | [inline] |
| setScore(uint32_t score) | AMOS::Overlap_t | [inline] |
| setStatus(Status_t status) | AMOS::Universal_t | [inline] |
| Universal_t() | AMOS::Universal_t | [inline] |
| Universal_t(const Universal_t &source) | AMOS::Universal_t | [inline] |
| writeMessage(Message_t &msg) const | AMOS::Overlap_t | [virtual] |
| writeRecord(std::ostream &fix, std::ostream &var) const | AMOS::Overlap_t | [protected, virtual] |
| ~IBankable_t() | AMOS::IBankable_t | [inline, virtual] |
| ~IMessagable_t() | AMOS::IMessagable_t | [inline, virtual] |
| ~Overlap_t() | AMOS::Overlap_t | [inline] |
| ~Universal_t() | AMOS::Universal_t | [inline, virtual] |
