SecondaryStructureChunk Class Reference

Public Member Functions
	SecondaryStructureChunk ()
	~SecondaryStructureChunk ()
void	set_start_seqpos (core::Size seqpos)
void	set_sequence (std::string sequence)
void	set_sequence (std::string full_sequence, core::Size start_seqpos, core::Size length)
void	set_ss (char ss)
void	append (SecondaryStructureChunk ss_chunk, std::string full_sequence)
core::Size	start_seqpos ()
core::Size	end_seqpos ()
core::Size	length ()
std::string const	sequence ()

Private Attributes
core::Size	sequence_position_start_
std::string	sequence_
char	ss_

Constructor & Destructor Documentation

SecondaryStructureChunk()

SecondaryStructureChunk::SecondaryStructureChunk ( )

inline

References sequence_, sequence_position_start_, and ss_.

~SecondaryStructureChunk()

SecondaryStructureChunk::~SecondaryStructureChunk ( )

inline

Member Function Documentation

append()

void SecondaryStructureChunk::append ( SecondaryStructureChunk  ss_chunk, std::string  full_sequence  )

inline

References end_seqpos(), set_sequence(), and start_seqpos().

end_seqpos()

core::Size SecondaryStructureChunk::end_seqpos ( )

inline

References length(), and sequence_position_start_.

Referenced by append().

length()

core::Size SecondaryStructureChunk::length ( )

inline

References sequence_.

Referenced by enumerate_junctions.Design::attach_valid(), end_seqpos(), enumerate_junctions.Design::output_string(), enumerate_junctions.Design::output_valid(), enumerate_junctions.DHR::print(), enumerate_junctions.Junction::print(), set_sequence(), enumerate_junctions.Junction::to_component(), enumerate_junctions.DHR::write_to_file(), and enumerate_junctions.Junction::write_to_file().

sequence()

std::string const SecondaryStructureChunk::sequence ( )

inline

References sequence_.

Referenced by pyrosetta.toolbox.py_jobdistributor.PyJobDistributor::job_complete(), pyrosetta.toolbox.py_jobdistributor.PyJobDistributor::output_decoy(), set_sequence(), and pyrosetta.toolbox.py_jobdistributor.PyJobDistributor::start_decoy().

set_sequence() [1/2]

void SecondaryStructureChunk::set_sequence ( std::string  full_sequence, core::Size  start_seqpos, core::Size  length  )

inline

References length(), sequence_, and start_seqpos().

set_sequence() [2/2]

void SecondaryStructureChunk::set_sequence ( std::string  sequence )

inline

References sequence(), and sequence_.

Referenced by append(), ChallengeMover::extract_ss_chunks_from_alignment_counts(), and extract_ss_chunks_from_seq().

set_ss()

void SecondaryStructureChunk::set_ss ( char  ss )

inline

References challenge::ss, and ss_.

set_start_seqpos()

void SecondaryStructureChunk::set_start_seqpos ( core::Size  seqpos )

inline

References sequence_position_start_.

Referenced by ChallengeMover::extract_ss_chunks_from_alignment_counts(), and extract_ss_chunks_from_seq().

start_seqpos()

core::Size SecondaryStructureChunk::start_seqpos ( )

inline

References sequence_position_start_.

Referenced by append(), ChallengeMover::extract_ss_chunks_from_alignment_counts(), extract_ss_chunks_from_seq(), and set_sequence().

Member Data Documentation

sequence_

std::string SecondaryStructureChunk::sequence_

private

Referenced by length(), SecondaryStructureChunk(), sequence(), and set_sequence().

sequence_position_start_

core::Size SecondaryStructureChunk::sequence_position_start_

private

Referenced by end_seqpos(), SecondaryStructureChunk(), set_start_seqpos(), and start_seqpos().

ss_

char SecondaryStructureChunk::ss_

private

Referenced by SecondaryStructureChunk(), and set_ss().

---

The documentation for this class was generated from the following file:

• src/apps/pilot/yfsong/challenge.cc