| bufferSize | StochHMM::sequenceStream | private |
| clear() | StochHMM::sequence | |
| complement() | StochHMM::sequence | |
| digitize() | StochHMM::sequence | |
| exDefDefined() | StochHMM::sequence | inline |
| get_index(size_t position, int order, std::pair< Index, Index > &word_index) | StochHMM::sequence | |
| getAttrib() | StochHMM::sequence | inline |
| getDigitalSeq() | StochHMM::sequence | inline |
| getExDef() | StochHMM::sequence | inline |
| getFasta(std::ifstream &, track *) | StochHMM::sequenceStream | |
| StochHMM::sequence::getFasta(std::ifstream &file) | StochHMM::sequence | inline |
| StochHMM::sequence::getFasta(std::ifstream &, track *, stateInfo *) | StochHMM::sequence | |
| getFastq(std::ifstream &, track *) | StochHMM::sequence | |
| getHeader() | StochHMM::sequence | inline |
| getLength() | StochHMM::sequence | inline |
| getMask(size_t) | StochHMM::sequence | |
| getMaskedFasta(std::ifstream &, track *) | StochHMM::sequence | |
| getMaxMask() | StochHMM::sequence | inline |
| getReal(std::ifstream &file) | StochHMM::sequence | inline |
| getReal(std::ifstream &file, track *trk) | StochHMM::sequence | inline |
| getReal(std::ifstream &, track *, stateInfo *) | StochHMM::sequence | |
| getSymbol(size_t) const | StochHMM::sequence | |
| getTrack() | StochHMM::sequence | inline |
| getUndigitized() | StochHMM::sequence | inline |
| operator=(const sequence &) | StochHMM::sequence | |
| operator[](size_t index) | StochHMM::sequence | inline |
| previousSeq | StochHMM::sequenceStream | private |
| print() | StochHMM::sequence | inline |
| readingFile | StochHMM::sequenceStream | private |
| realValue(size_t) | StochHMM::sequence | |
| resetSeq() | StochHMM::sequenceStream | private |
| retain | StochHMM::sequenceStream | private |
| retainSize | StochHMM::sequenceStream | private |
| reverse() | StochHMM::sequence | |
| reverseComplement() | StochHMM::sequence | |
| sequence() | StochHMM::sequence | |
| sequence(bool) | StochHMM::sequence | |
| sequence(std::vector< double > *, track *) | StochHMM::sequence | |
| sequence(std::string &, track *) | StochHMM::sequence | |
| sequence(char *, track *) | StochHMM::sequence | |
| sequence(const sequence &) | StochHMM::sequence | |
| sequenceStream() | StochHMM::sequenceStream | |
| sequenceStream(bool) | StochHMM::sequenceStream | |
| sequenceStream(std::vector< double > *, track *) | StochHMM::sequenceStream | |
| sequenceStream(char *, track *) | StochHMM::sequenceStream | |
| sequenceStream(std::string &, track *) | StochHMM::sequenceStream | |
| sequenceStream(size_t, size_t) | StochHMM::sequenceStream | |
| sequenceStream(size_t, size_t, bool) | StochHMM::sequenceStream | |
| sequenceStream(size_t, size_t, std::vector< double > *, track *) | StochHMM::sequenceStream | |
| sequenceStream(size_t, size_t, std::string &, track *) | StochHMM::sequenceStream | |
| sequenceStream(size_t, size_t, char *, track *) | StochHMM::sequenceStream | |
| seqValue(size_t) | StochHMM::sequence | |
| setAttrib(double attr) | StochHMM::sequence | inline |
| setBuffer(size_t buff) | StochHMM::sequenceStream | inline |
| setHeader(std::string &head) | StochHMM::sequence | inline |
| setRealSeq(std::vector< double > *, track *) | StochHMM::sequence | |
| setRetain(size_t ret) | StochHMM::sequenceStream | inline |
| setSeq(std::string &, track *) | StochHMM::sequence | |
| setTrack(track *tr) | StochHMM::sequence | inline |
| shuffle() | StochHMM::sequence | |
| size() | StochHMM::sequence | inline |
| stringify() | StochHMM::sequence | |
| undigitize() | StochHMM::sequence | |
| ~sequence() | StochHMM::sequence | |
1.8.1