add_pfam_domains(const std::string &domain_f) | MDAT::ProteinSequenceSet< MemoryType > | |
add_seq(ProteinSequence *seq) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
avg_size() const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | |
clean_up_domains(unsigned char options) | MDAT::ProteinSequenceSet< MemoryType > | |
clear() | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
delete_seqs(const std::map< std::string, bool > &names) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | virtual |
delete_seqs(std::vector< size_t > &indices) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | virtual |
dom_archis() | MDAT::ProteinSequenceSet< MemoryType > | inline |
dom_archis() const | MDAT::ProteinSequenceSet< MemoryType > | inline |
dom_archis(DomainArchitectureSet dom_arch) (defined in MDAT::ProteinSequenceSet< MemoryType >) | MDAT::ProteinSequenceSet< MemoryType > | inline |
domain_column_split(const ProteinSequenceSet< MemoryType > &set, SplitSet< ProteinSequenceSet< Default > > &splitSet) | MDAT::ProteinSequenceSet< MemoryType > | related |
domain_name(size_t i) const | MDAT::ProteinSequenceSet< MemoryType > | inline |
empty() const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
extract_architectures() | MDAT::ProteinSequenceSet< MemoryType > | |
file() const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
id() const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
id(int val) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
insert_gaps(const std::string &edit_string) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | |
keep_seqs(std::vector< size_t > &indices) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | virtual |
length() const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
n_architectures() const | MDAT::ProteinSequenceSet< MemoryType > | inline |
n_domains() const | MDAT::ProteinSequenceSet< MemoryType > | inline |
n_seqs() const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
operator[](unsigned int index) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
operator[](unsigned int index) const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
operator[](const std::string &seq_name) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
operator[](const std::string &seq_name) const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
ProteinSequenceSet() (defined in MDAT::ProteinSequenceSet< MemoryType >) | MDAT::ProteinSequenceSet< MemoryType > | inline |
ProteinSequenceSet(size_t id_val) (defined in MDAT::ProteinSequenceSet< MemoryType >) | MDAT::ProteinSequenceSet< MemoryType > | inline |
ProteinSequenceSet(const ProteinSequenceSet &)=delete (defined in MDAT::ProteinSequenceSet< MemoryType >) | MDAT::ProteinSequenceSet< MemoryType > | |
ProteinSequenceSet(ProteinSequenceSet &&)=default (defined in MDAT::ProteinSequenceSet< MemoryType >) | MDAT::ProteinSequenceSet< MemoryType > | |
read(const std::string &seq_f, const std::vector< std::string > &seq_names, bool check=false, short format=-1) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | virtual |
read(const std::string &seq_f, bool check=false, short format=-1) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inlinevirtual |
refine_boundaries() | MDAT::ProteinSequenceSet< MemoryType > | |
seq(unsigned int index) const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
seq_type() const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
seq_type(char seq_type_) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
SequenceSetBase() | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | |
SequenceSetBase(size_t value) (defined in MDAT::SequenceSetBase< ProteinSequence, MemoryType >) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | |
share(const SequenceSetBase< ProteinSequence, MemoryType > &set, size_t id) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
size() const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
sort(std::string type) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | |
splitByArchitecture(const ProteinSequenceSet< MemoryType > &set, std::vector< ProteinSequenceSet< MemoryType > > &architectureSplits) | MDAT::ProteinSequenceSet< MemoryType > | related |
to_lower() | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
to_upper() | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
transfer(SequenceSetBase< ProteinSequence, MemoryType > &set, size_t id) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
transfer(SequenceSetBase< ProteinSequence, MemoryType > &set) | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | inline |
value_type typedef | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | |
write(const std::string &seq_f, const std::string format) const | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | virtual |
write_domArchitecture(const std::string &out_f) const | MDAT::ProteinSequenceSet< MemoryType > | |
~SequenceSetBase() | MDAT::SequenceSetBase< ProteinSequence, MemoryType > | virtual |