core::fragment::FragmentIO Class Reference

#include <FragmentIO.hh>

Public Member Functions
	FragmentIO ()
	FragmentIO (Size top, Size ncopies=1, bool bAnnotate=true)
FragSetOP	read_data (std::string const &filename)
	read a FragSet... note that this function caches the fragment set. i.e., if you read the same set from multiple positions in the code you get the same set. if you read a new file ... we'll check the cache for stale references and delete them. NOTE that this is using global data and is thread unsafe and is evil. More...
FragSetOP	read_data_from_stream (std::string const &filename, std::istream &data)
void	read_frames_from_file (std::string const &filename, FrameList &)
void	read_frames_from_stream (std::string const &filename, std::string const &firstline, std::istream &data, FrameList &)
void	write_data (std::string const &file, FragSet const &frags)
FragFactory &	get_frag_factory ()
void	set_top_frag_num (Size setting)
	Updates the number of distinct fragments to keep. More...
void	set_ncopies (Size setting)
	Updates the number of copies of each fragment to keep (default 1) More...
void	set_read_annotation (bool setting=true)
	Toggles between reading annotated (true) and non-annotated (false) More...
void	clean_frag_cache ()
	remove all FragSets that are not referenced outside the cache. More...

Private Types
typedef std::map< std::string, FragSetOP >	FragFileCache

Private Member Functions
void	read_next_frames (std::istream &data, std::string &next_line, FrameList &next_frames)
void	read_frag_data (std::istream &data, std::string &next_line, FrameList &next_frames)

Private Attributes
Size	top_
Size	ncopies_
bool	bAnnotate_

Static Private Attributes
static FragFactory	frag_factory_
static FragFileCache	frag_cache_

Member Typedef Documentation

FragFileCache

typedef std::map< std::string, FragSetOP > core::fragment::FragmentIO::FragFileCache

private

Constructor & Destructor Documentation

FragmentIO() [1/2]

core::fragment::FragmentIO::FragmentIO ( )

inline

FragmentIO() [2/2]

core::fragment::FragmentIO::FragmentIO ( Size  top, Size  ncopies = 1, bool  bAnnotate = true  )

inline

Member Function Documentation

clean_frag_cache()

void core::fragment::FragmentIO::clean_frag_cache

(

)

remove all FragSets that are not referenced outside the cache.

Referenced by protocols::abinitio::IterativeBase::increment_stage(), and read_data().

get_frag_factory()

FragFactory & core::fragment::FragmentIO::get_frag_factory

(

void

)

References frag_factory_.

read_data()

FragSetOP core::fragment::FragmentIO::read_data

(

std::string const &

filename

)

read a FragSet... note that this function caches the fragment set. i.e., if you read the same set from multiple positions in the code you get the same set. if you read a new file ... we'll check the cache for stale references and delete them. NOTE that this is using global data and is thread unsafe and is evil.

Open a file and construct a FragmentSet from its contents. Note that this function stores the constructed FragmentSet in GLOBAL DATA making it ABSOLUTELY TERRIBLE.

References clean_frag_cache(), protocols::abinitio::filename(), frag_cache_, read_data_from_stream(), and core::fragment::tr().

Referenced by protocols::abinitio::abscript::AbscriptMover::add_frags(), protocols::parser::FragmentReader::apply(), protocols::abinitio::decide_on_beta_jumping_from_frags(), protocols::abinitio::abscript::determine_frag_size(), protocols::abinitio::IterativeBase::gen_enumerate_pairings(), protocols::abinitio::IterativeBase::gen_resample_fragments(), protocols::hybridization::HybridizeProtocol::HybridizeProtocol(), protocols::hybridization::HybridizeProtocol::init(), protocols::hybridization::HybridizeProtocol::parse_my_tag(), protocols::abinitio::DomainAssembly::parse_my_tag(), protocols::abinitio::abscript::AbscriptLoopCloserCM::parse_my_tag(), protocols::abinitio::abscript::FragmentCM::parse_my_tag(), protocols::hybridization::CartesianSampler::parse_my_tag(), protocols::rbsegment_relax::ConfChangeMover::parse_my_tag(), protocols::struct_fragment::StructFragmentMover::read_frag_file(), protocols::topology_broker::read_frags(), protocols::loops::read_loop_fragments(), core::fragment::read_std_frags_from_cmd(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), protocols::abinitio::AbrelaxApplication::setup_fragments(), and protocols::abinitio::AbrelaxApplication::setup_jumps().

read_data_from_stream()

FragSetOP core::fragment::FragmentIO::read_data_from_stream	(	std::string const &	filename,
		std::istream &	data
	)

With the opened file, read the first line to determine the format of the fragment file, and then construct the appropriate FragmentSet. Note that this function does not store the fragment set in the abomination that is the frag_cache_

References bAnnotate_, protocols::abinitio::filename(), ncopies_, read_frames_from_stream(), protocols::kinmatch::str(), top_, and core::fragment::tr().

Referenced by core::fragment::FragmentSetLoader::create_resource(), and read_data().

read_frag_data()

void core::fragment::FragmentIO::read_frag_data ( std::istream &  data, std::string &  next_line, FrameList &  next_frames  )

private

References bAnnotate_, frag_factory_, core::fragment::FragFactory::frag_type(), ncopies_, top_, and core::fragment::tr().

Referenced by read_frames_from_stream().

read_frames_from_file()

void core::fragment::FragmentIO::read_frames_from_file	(	std::string const &	filename,
		FrameList &	frames
	)

References protocols::abinitio::filename(), read_frames_from_stream(), and core::fragment::tr().

Referenced by protocols::abinitio::AbrelaxApplication::insert_template_frags().

read_frames_from_stream()

void core::fragment::FragmentIO::read_frames_from_stream	(	std::string const &	filename,
		std::string const &	firstline,
		std::istream &	data,
		FrameList &	all_frames
	)

References bAnnotate_, ncopies_, read_frag_data(), read_next_frames(), top_, and core::fragment::tr().

Referenced by read_data_from_stream(), and read_frames_from_file().

read_next_frames()

void core::fragment::FragmentIO::read_next_frames ( std::istream &  data, std::string &  next_line, FrameList &  next_frames  )

private

References frag_factory_, core::fragment::FragFactory::frame(), and core::fragment::tr().

Referenced by read_frames_from_stream().

set_ncopies()

void core::fragment::FragmentIO::set_ncopies ( Size  setting )

inline

Updates the number of copies of each fragment to keep (default 1)

References ncopies_.

Referenced by protocols::topology_broker::read_frags().

set_read_annotation()

void core::fragment::FragmentIO::set_read_annotation ( bool  setting = true )

inline

Toggles between reading annotated (true) and non-annotated (false)

References bAnnotate_.

Referenced by protocols::topology_broker::read_frags().

set_top_frag_num()

void core::fragment::FragmentIO::set_top_frag_num ( Size  setting )

inline

Updates the number of distinct fragments to keep.

References top_.

Referenced by protocols::topology_broker::read_frags().

write_data()

void core::fragment::FragmentIO::write_data	(	std::string const &	file,
		FragSet const &	frags
	)

References core::fragment::FragSet::begin(), core::fragment::FragSet::end(), and core::conformation::membrane::out.

Referenced by protocols::abinitio::KinematicAbinitio::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::struct_fragment::StructFragmentMover::apply(), protocols::abinitio::IterativeBase::gen_resample_fragments(), and protocols::parser::FragSetLoader::load_data().

Member Data Documentation

bAnnotate_

bool core::fragment::FragmentIO::bAnnotate_

private

Referenced by read_data_from_stream(), read_frag_data(), read_frames_from_stream(), and set_read_annotation().

frag_cache_

FragmentIO::FragFileCache core::fragment::FragmentIO::frag_cache_

staticprivate

Referenced by read_data().

frag_factory_

FragFactory core::fragment::FragmentIO::frag_factory_

staticprivate

Referenced by get_frag_factory(), read_frag_data(), and read_next_frames().

ncopies_

Size core::fragment::FragmentIO::ncopies_

private

Referenced by read_data_from_stream(), read_frag_data(), read_frames_from_stream(), and set_ncopies().

top_

Size core::fragment::FragmentIO::top_

private

Referenced by read_data_from_stream(), read_frag_data(), read_frames_from_stream(), and set_top_frag_num().

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

• src/core/fragment/FragmentIO.hh
• src/core/fragment/FragmentIO.cc