ADENINE_BITS | AMOS::Sequence_t | [protected, static] |
BAC | AMOS::Read_t | [static] |
clear() | AMOS::Read_t | [virtual] |
compress(char seqchar, char qualchar) | AMOS::Sequence_t | [inline, protected, static] |
compress() | AMOS::Sequence_t | |
COMPRESS_BIT | AMOS::Sequence_t | [protected, static] |
CONTIG | AMOS::Read_t | [static] |
CYTOSINE_BITS | AMOS::Sequence_t | [protected, static] |
eid_m | AMOS::IBankable_t | [protected] |
END | AMOS::Read_t | [static] |
flags_m | AMOS::IBankable_t | [protected] |
getBase(Pos_t index) const | AMOS::Sequence_t | [inline] |
getBasePositions() const | AMOS::Read_t | [inline] |
getBasePositions() | AMOS::Read_t | [inline] |
getClearRange() | AMOS::Read_t | [inline] |
getComment() const | AMOS::Universal_t | [inline] |
getEID() const | AMOS::IBankable_t | [inline] |
getFragment() const | AMOS::Read_t | [inline] |
getFragmentPosition() | AMOS::Read_t | [inline] |
getIID() const | AMOS::IBankable_t | [inline] |
getLength() const | AMOS::Sequence_t | [inline] |
getNCode() const | AMOS::Read_t | [inline, virtual] |
getQualityClearRange() | AMOS::Read_t | [inline] |
getQualString() const | AMOS::Sequence_t | [inline] |
getQualString(Range_t range) const | AMOS::Sequence_t | |
getSeqString() const | AMOS::Sequence_t | [inline] |
getSeqString(Range_t range) const | AMOS::Sequence_t | |
getStatus() const | AMOS::Universal_t | [inline] |
getType() const | AMOS::Read_t | [inline] |
getVectorClearRange() | AMOS::Read_t | [inline] |
GUANINE_BITS | AMOS::Sequence_t | [protected, static] |
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] |
isCompressed() const | AMOS::Sequence_t | [inline] |
isFlagA() const | AMOS::IBankable_t | [inline] |
isFlagB() const | AMOS::IBankable_t | [inline] |
isModified() const | AMOS::IBankable_t | [inline] |
isRemoved() const | AMOS::IBankable_t | [inline] |
length_m | AMOS::Sequence_t | [protected] |
NCODE | AMOS::Read_t | [static] |
NULL_READ | AMOS::Read_t | [static] |
operator=(const Sequence_t &source) | AMOS::Sequence_t | |
OTHER | AMOS::Read_t | [static] |
QUAL_BITS | AMOS::Sequence_t | [protected, static] |
qual_m | AMOS::Sequence_t | [protected] |
Read_t() | AMOS::Read_t | [inline] |
Read_t(const Read_t &source) | AMOS::Read_t | [inline] |
readMessage(const Message_t &msg) | AMOS::Read_t | [virtual] |
readRecord(std::istream &fix, std::istream &var) | AMOS::Read_t | [protected, virtual] |
SEQ_BITS | AMOS::Sequence_t | [protected, static] |
seq_m | AMOS::Sequence_t | [protected] |
Sequence_t() | AMOS::Sequence_t | [inline] |
Sequence_t(const Sequence_t &source) | AMOS::Sequence_t | [inline] |
setBase(char seqchar, char qualchar, Pos_t index) | AMOS::Sequence_t | [inline] |
setBasePositions(const std::vector< int16_t > &bcp) | AMOS::Read_t | [inline] |
setClearRange(Range_t clear) | AMOS::Read_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] |
setFragment(ID_t frag) | AMOS::Read_t | [inline] |
setFragmentPosition(Pos_t pos) | AMOS::Read_t | [inline] |
setIID(ID_t iid) | AMOS::IBankable_t | [inline] |
setQualityClearRange(Range_t qclear) | AMOS::Read_t | [inline] |
setSequence(const char *seq, const char *qual) | AMOS::Sequence_t | |
setSequence(const std::string &seq, const std::string &qual) | AMOS::Sequence_t | |
setStatus(Status_t status) | AMOS::Universal_t | [inline] |
setType(ReadType_t type) | AMOS::Read_t | |
setVectorClearRange(Range_t vclear) | AMOS::Read_t | [inline] |
THYMINE_BITS | AMOS::Sequence_t | [protected, static] |
TRANSPOSON | AMOS::Read_t | [static] |
uncompress(uint8_t byte) | AMOS::Sequence_t | [inline, protected, static] |
uncompress() | AMOS::Sequence_t | |
Universal_t() | AMOS::Universal_t | [inline] |
Universal_t(const Universal_t &source) | AMOS::Universal_t | [inline] |
WALK | AMOS::Read_t | [static] |
writeMessage(Message_t &msg) const | AMOS::Read_t | [virtual] |
writeRecord(std::ostream &fix, std::ostream &var) const | AMOS::Read_t | [protected, virtual] |
~IBankable_t() | AMOS::IBankable_t | [inline, virtual] |
~IMessagable_t() | AMOS::IMessagable_t | [inline, virtual] |
~Read_t() | AMOS::Read_t | [inline] |
~Sequence_t() | AMOS::Sequence_t | [inline, virtual] |
~Universal_t() | AMOS::Universal_t | [inline, virtual] |