add_seq(SequenceType *seq) | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
avg_size() const | MDAT::SequenceSetBase< SequenceType, MemoryType > | |
clear() | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
delete_seqs(const std::map< std::string, bool > &names) | MDAT::SequenceSetBase< SequenceType, MemoryType > | virtual |
delete_seqs(std::vector< size_t > &indices) | MDAT::SequenceSetBase< SequenceType, MemoryType > | virtual |
empty() const | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
file() const | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
id() const | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
id(int val) | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
insert_gaps(const std::string &edit_string) | MDAT::SequenceSetBase< SequenceType, MemoryType > | |
keep_seqs(std::vector< size_t > &indices) | MDAT::SequenceSetBase< SequenceType, MemoryType > | virtual |
length() const | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
n_seqs() const | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
operator<<(std::ostream &out, const SequenceSetBase< SeqType, MemType > &seqSet) | MDAT::SequenceSetBase< SequenceType, MemoryType > | friend |
operator[](unsigned int index) | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
operator[](unsigned int index) const | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
operator[](const std::string &seq_name) | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
operator[](const std::string &seq_name) const | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
read(const std::string &seq_f, const std::vector< std::string > &seq_names, bool check=false, short format=-1) | MDAT::SequenceSetBase< SequenceType, MemoryType > | virtual |
read(const std::string &seq_f, bool check=false, short format=-1) | MDAT::SequenceSetBase< SequenceType, MemoryType > | inlinevirtual |
seq(unsigned int index) const | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
seq_type() const | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
seq_type(char seq_type_) | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
SequenceSetBase() | MDAT::SequenceSetBase< SequenceType, MemoryType > | |
SequenceSetBase(size_t value) (defined in MDAT::SequenceSetBase< SequenceType, MemoryType >) | MDAT::SequenceSetBase< SequenceType, MemoryType > | |
share(const SequenceSetBase< SequenceType, MemoryType > &set, size_t id) | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
size() const | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
sort(std::string type) | MDAT::SequenceSetBase< SequenceType, MemoryType > | |
to_lower() | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
to_upper() | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
transfer(SequenceSetBase< SequenceType, MemoryType > &set, size_t id) | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
transfer(SequenceSetBase< SequenceType, MemoryType > &set) | MDAT::SequenceSetBase< SequenceType, MemoryType > | inline |
value_type typedef | MDAT::SequenceSetBase< SequenceType, MemoryType > | |
write(const std::string &seq_f, const std::string format) const | MDAT::SequenceSetBase< SequenceType, MemoryType > | virtual |
~SequenceSetBase() | MDAT::SequenceSetBase< SequenceType, MemoryType > | virtual |