#include <FragmentIO.hh>

Collaboration diagram for core::fragment::FragmentIO:

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... More...

void	read_data (std::string const &filename, FrameList &)

void	read_data (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_

Detailed Description

Definition at line 57 of file FragmentIO.hh.

Member Typedef Documentation

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

private

Definition at line 58 of file FragmentIO.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 61 of file FragmentIO.hh.

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

inline

Definition at line 62 of file FragmentIO.hh.

Member Function Documentation

void core::fragment::FragmentIO::clean_frag_cache ( )

remove all FragSets that are not referenced outside the cache.

Definition at line 262 of file FragmentIO.cc.

References frag_cache_, and core::fragment::tr().

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

FragFactory & core::fragment::FragmentIO::get_frag_factory ( void )

Definition at line 99 of file FragmentIO.cc.

References frag_factory_.

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...

Definition at line 221 of file FragmentIO.cc.

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

Referenced by protocols::abinitio::decide_on_beta_jumping_from_frags(), protocols::abinitio::IterativeBase::gen_enumerate_pairings(), protocols::abinitio::IterativeBase::gen_resample_fragments(), protocols::hybridization::HybridizeProtocol::init(), protocols::abinitio::AbrelaxApplication::insert_template_frags(), protocols::seeded_abinitio::PlaceFragments::parse_my_tag(), protocols::abinitio::DomainAssembly::parse_my_tag(), protocols::hybridization::HybridizeProtocol::parse_my_tag(), read_data(), protocols::topology_broker::read_frags(), protocols::loops::read_loop_fragments(), and core::fragment::read_std_frags_from_cmd().