| BasicDNATable() | mems::SortedMerList | [static] |
| binary_seq_len | mems::SortedMerList | [protected] |
| bsearch(const struct bmer &query_mer, const gnSeqI start, const gnSeqI end) | mems::SortedMerList | [protected, virtual] |
| CalculateMaxMerSize() const | mems::SortedMerList | [protected, virtual] |
| Clear() | mems::SortedMerList | [virtual] |
| Create(const genome::gnSequence &seq, const uint64 seed) | mems::SortedMerList | [virtual] |
| CreateBasicDNATable() | mems::SortedMerList | [protected, static] |
| CreateProteinTable() | mems::SortedMerList | [protected, static] |
| Description() const | mems::SortedMerList | [virtual] |
| FillDnaSeedSML(const genome::gnSequence &seq, std::vector< bmer > &sml_array) | mems::SortedMerList | [virtual] |
| FillDnaSML(const genome::gnSequence &seq, std::vector< bmer > &sml_array) | mems::SortedMerList | [protected, virtual] |
| FillSML(gnSeqC *seq_buf, gnSeqI seq_len, boolean circular, std::vector< bmer > &sml_array) | mems::SortedMerList | [protected, virtual] |
| FillSML(const genome::gnSequence &seq, std::vector< bmer > &sml_array) | mems::SortedMerList | [protected, virtual] |
| FillSML(gnSeqI seq_len, std::vector< gnSeqI > &sml_array) | mems::SortedMerList | [protected, virtual] |
| Find(const std::string &query_seq, gnSeqI &result) | mems::SortedMerList | [virtual] |
| FindAll(const std::string &query_seq, std::vector< gnSeqI > result) | mems::SortedMerList | [virtual] |
| FindMer(const uint64 query_mer, gnSeqI &result) | mems::SortedMerList | [virtual] |
| GetBSequence(uint32 *dest, const gnSeqI len, const gnSeqI offset) | mems::SortedMerList | [virtual] |
| GetDnaMer(gnSeqI offset) const | mems::SortedMerList | [protected, virtual] |
| GetDnaSeedMer(gnSeqI offset) const | mems::SortedMerList | [virtual] |
| GetHeader() const | mems::SortedMerList | [virtual] |
| GetID() const | mems::SortedMerList | [virtual] |
| GetMer(gnSeqI position) const | mems::SortedMerList | [virtual] |
| GetMerMask() const | mems::SortedMerList | [virtual] |
| GetMerMaskSize() const | mems::SortedMerList | [virtual] |
| GetSeedMask() const | mems::SortedMerList | [virtual] |
| GetSeedMer(gnSeqI offset) const | mems::SortedMerList | [virtual] |
| header | mems::SortedMerList | [protected] |
| IsCircular() const | mems::SortedMerList | [virtual] |
| Length() const | mems::SortedMerList | |
| mask_size | mems::SortedMerList | [protected] |
| mer_mask | mems::SortedMerList | [protected] |
| Merge(SortedMerList &sa, SortedMerList &sa2)=0 | mems::SortedMerList | [pure virtual] |
| operator=(const SortedMerList &sa) | mems::SortedMerList | |
| operator[](gnSeqI index)=0 | mems::SortedMerList | [pure virtual] |
| ProteinTable() | mems::SortedMerList | [static] |
| Read(std::vector< bmer > &readVector, gnSeqI size, gnSeqI offset)=0 | mems::SortedMerList | [pure virtual] |
| RevCompMer(uint64 mer_a, int mer_length) const | mems::SortedMerList | [virtual] |
| Seed() const | mems::SortedMerList | [virtual] |
| seed_mask | mems::SortedMerList | [protected] |
| SeedLength() const | mems::SortedMerList | [virtual] |
| SeedWeight() const | mems::SortedMerList | [virtual] |
| sequence | mems::SortedMerList | [protected] |
| SetDescription(const std::string &d) | mems::SortedMerList | [virtual] |
| SetID(const sarID_t d) | mems::SortedMerList | [virtual] |
| SetMerMaskSize(uint32 mer_size) | mems::SortedMerList | [virtual] |
| SetSequence(gnSeqC *seq_buf, gnSeqI seq_len) | mems::SortedMerList | [protected, virtual] |
| ShiftWords(uint32 *data, uint32 length, int32 bits) | mems::SortedMerList | [protected, virtual] |
| SMLLength() const | mems::SortedMerList | |
| SortedMerList() | mems::SortedMerList | |
| SortedMerList(const SortedMerList &sa) | mems::SortedMerList | |
| translate(uint8 *dest, const gnSeqC *src, const gnSeqI len) const | mems::SortedMerList | [protected, virtual] |
| translate32(uint32 *dest, const gnSeqC *src, const gnSeqI len) const | mems::SortedMerList | [protected, virtual] |
| UniqueMerCount() | mems::SortedMerList | [virtual] |
| ~SortedMerList() | mems::SortedMerList | |
