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... 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_

Member Typedef Documentation

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

private

Constructor & Destructor Documentation

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

inline

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

inline

Member Function Documentation

void core::fragment::FragmentIO::clean_frag_cache

(

)

remove all FragSets that are not referenced outside the cache.

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

Referenced by read_data().

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

(

void

)

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...

References bAnnotate_, clean_frag_cache(), frag_cache_, frags, getline(), utility::io::izstream::good(), ncopies_, tag, top_, core::fragment::tr, and utility_exit_with_message.

Referenced by read_data(), and core::fragment::read_std_frags_from_cmd().

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

References utility::io::izstream::fail(), utility::io::izstream::good(), read_data(), core::fragment::tr, and utility_exit_with_message.

void core::fragment::FragmentIO::read_data	(	std::istream &	data,
		FrameList &	all_frames
	)

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

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(), frame(), getline(), length, ncopies_, pdb_pos, tag, top_, and core::fragment::tr.

Referenced by read_data().

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(), getline(), tag, and core::fragment::tr.

Referenced by read_data().

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

inline

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

References ncopies_.

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

inline

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

References bAnnotate_.

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

inline

Updates the number of distinct fragments to keep.

References top_.

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

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

Member Data Documentation

bool core::fragment::FragmentIO::bAnnotate_

private

Referenced by read_data(), read_frag_data(), and set_read_annotation().

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

staticprivate

Referenced by clean_frag_cache(), and read_data().

FragFactory core::fragment::FragmentIO::frag_factory_

staticprivate

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

Size core::fragment::FragmentIO::ncopies_

private

Referenced by read_data(), read_frag_data(), and set_ncopies().

Size core::fragment::FragmentIO::top_

private

Referenced by read_data(), read_frag_data(), and set_top_frag_num().

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

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