A class that receives lists of works to cite from Rosetta modules, then returns a list of all works to cite on demand. Threadsafe. More...

#include <CitationManager.hh>

Inheritance diagram for basic::citation_manager::CitationManager:

[legend]

Public Member Functions
void	clear_citations ()
	Clear all citations that have been collected. More...

void	add_citations (CitationCollectionList const &input)
	Add citations to the list of citations that have been collected. More...

void	add_citation (CitationCollectionBaseCOP const &input)
	Add a single citation to the citation manger. More...

void	write_all_citations_and_unpublished_author_info () const
	Write out all unpublished modules and citations to the CitationManager's tracer. More...

void	write_all_citations_and_unpublished_author_info_from_list_to_stream (CitationCollectionList const &list, std::ostream &outstream) const
	Write out all unpublished modules and citations in a CitationCollectionList to a given output stream. More...

CitationCOP	get_citation_by_doi (std::string const &doi) const
	Given a DOI string, get a Rosetta citation. More...

void	write_collected_citations (std::ostream &outstream, utility::vector1< CitationCollectionCOP > const &published, CitationFormat const citation_format=CitationFormat::DefaultStyle) const
	Get a summary of all the citations passed in the list. More...

void	write_unpublished_modules (std::ostream &outstream, utility::vector1< UnpublishedModuleInfoCOP > const &unpublished) const
	Write out a list of the unpublished modules. More...

Public Member Functions inherited from utility::SingletonBase< CitationManager >
	SingletonBase ()
	public constructor (the derived class must have a private constructor, of course). More...

Private Member Functions
	CitationManager ()
	Constructor triggers read from disk. More...

	CitationManager (CitationManager const &)=delete

CitationManager	operator= (CitationManager const &)=delete

void	load_rosetta_citations_from_database ()
	Load Rosetta citations from the Rosetta database, and populate the doi_rosetta_citation_map_. More...

void	populate_doi_rosetta_citation_map (std::string const &database_file_contents)
	Populate the doi_rosetta_citation_map_ from the contents of a database file. More...

void	split_citations (CitationCollectionList const &list, utility::vector1< CitationCollectionCOP > &published, utility::vector1< UnpublishedModuleInfoCOP > &unpublished) const
	Split the citations into published & unpublished vectors. More...

void	split_citations (utility::vector1< CitationCollectionCOP > &published, utility::vector1< UnpublishedModuleInfoCOP > &unpublished) const
	Split the citations into published & unpublished vectors. More...

Private Attributes
std::map< std::string, CitationCOP >	doi_rosetta_citation_map_
	A map of DOI->Rosetta citations. More...

CitationCollectionList	citation_list_
	A list of all the citations (and unpublished moduled) used so far. More...

Friends
class	utility::SingletonBase< CitationManager >

Additional Inherited Members
Static Public Member Functions inherited from utility::SingletonBase< CitationManager >
static CitationManager *	get_instance ()
	Safely instantiate a singleton class in a (possibly) multithreaded context. More...

Detailed Description

A class that receives lists of works to cite from Rosetta modules, then returns a list of all works to cite on demand. Threadsafe.

Constructor & Destructor Documentation

◆ CitationManager() [1/2]

basic::citation_manager::CitationManager::CitationManager ( )

private

Constructor triggers read from disk.

References load_rosetta_citations_from_database().

◆ CitationManager() [2/2]

basic::citation_manager::CitationManager::CitationManager ( CitationManager const & )

privatedelete

Member Function Documentation

◆ add_citation()

void basic::citation_manager::CitationManager::add_citation ( CitationCollectionBaseCOP const & input )

Add a single citation to the citation manger.

Note: Will not add if a duplicate

Threadsafe

References basic::citation_manager::CitationCollectionList::add(), citation_list_, and gaussian-sampling::input.

◆ add_citations()

void basic::citation_manager::CitationManager::add_citations ( CitationCollectionList const & input )

Add citations to the list of citations that have been collected.

Note: Only adds citations that have not been already added.

Threadsafe.

References basic::citation_manager::CitationCollectionList::add(), citation_list_, and gaussian-sampling::input.

◆ clear_citations()

void basic::citation_manager::CitationManager::clear_citations ( )

Clear all citations that have been collected.

Does not clear the map of DOI->Rosetta citation that was loaded from the Rosetta database.

Threadsafe.

References citation_list_.

◆ get_citation_by_doi()

CitationCOP basic::citation_manager::CitationManager::get_citation_by_doi ( std::string const & doi ) const

Given a DOI string, get a Rosetta citation.

Throws if the DOI string isn't in the list of Rosetta papers in the database.

References doi_rosetta_citation_map_, and utility_exit_with_message.

◆ load_rosetta_citations_from_database()

void basic::citation_manager::CitationManager::load_rosetta_citations_from_database ( )

private

Load Rosetta citations from the Rosetta database, and populate the doi_rosetta_citation_map_.

TRIGGERS READ FROM DISK. Threadsafe, but should only be done once!

References basic::Tracer::Debug, debug_assert, utility::file_contents(), lactamize::filename, basic::database::full_name(), populate_doi_rosetta_citation_map(), and basic::TR.

Referenced by CitationManager().

◆ operator=()

CitationManager basic::citation_manager::CitationManager::operator= ( CitationManager const & )

privatedelete

◆ populate_doi_rosetta_citation_map()

void basic::citation_manager::CitationManager::populate_doi_rosetta_citation_map ( std::string const & database_file_contents )

private

Populate the doi_rosetta_citation_map_ from the contents of a database file.

References basic::Tracer::Debug, debug_assert, doi_rosetta_citation_map_, errmsg(), line, solution_counts::lines, runtime_assert_string_msg, utility::split_by_newlines(), utility::strip(), and basic::TR.

Referenced by load_rosetta_citations_from_database().

◆ split_citations() [1/2]

void basic::citation_manager::CitationManager::split_citations	(	CitationCollectionList const &	list,
		utility::vector1< CitationCollectionCOP > &	published,
		utility::vector1< UnpublishedModuleInfoCOP > &	unpublished
	)		const

private

Split the citations into published & unpublished vectors.

Return by reference. Not threadsafe; list must be protected by a lock guard before calling this if there is the possibility that another thread could be acting on it.

References basic::options::OptionKeys::in::file::list, and utility_exit_with_message.

Referenced by write_all_citations_and_unpublished_author_info(), and write_all_citations_and_unpublished_author_info_from_list_to_stream().

◆ split_citations() [2/2]

void basic::citation_manager::CitationManager::split_citations	(	utility::vector1< CitationCollectionCOP > &	published,
		utility::vector1< UnpublishedModuleInfoCOP > &	unpublished
	)		const

private

Split the citations into published & unpublished vectors.

Return by reference. Threadsafe

Return by reference.

References citation_list_, basic::citation_manager::CitationCollectionList::citations(), basic::citation_manager::CitationCollectionList::empty(), and utility_exit_with_message.

◆ write_all_citations_and_unpublished_author_info()

void basic::citation_manager::CitationManager::write_all_citations_and_unpublished_author_info ( ) const

Write out all unpublished modules and citations to the CitationManager's tracer.

Write out all unpublished modules and citations to to the CitationManager's tracer.

References basic::Tracer::bgBlue, basic::Tracer::Bold, basic::Tracer::Reset, split_citations(), basic::TR, basic::Tracer::Underline, basic::Tracer::White, write_collected_citations(), and write_unpublished_modules().

◆ write_all_citations_and_unpublished_author_info_from_list_to_stream()

void basic::citation_manager::CitationManager::write_all_citations_and_unpublished_author_info_from_list_to_stream	(	CitationCollectionList const &	list,
		std::ostream &	outstream
	)		const

Write out all unpublished modules and citations in a CitationCollectionList to a given output stream.

References basic::options::OptionKeys::in::file::list, split_citations(), write_collected_citations(), and write_unpublished_modules().

◆ write_collected_citations()

void basic::citation_manager::CitationManager::write_collected_citations	(	std::ostream &	outstream,
		utility::vector1< CitationCollectionCOP > const &	published,
		CitationFormat const	citation_format = `CitationFormat::DefaultStyle`
	)		const

Get a summary of all the citations passed in the list.

Get a summary of all the citations that we've collected so far.

Note: This is ONLY a list of citations, in a given format, on separate lines, with header lines indicating the relevant module. This does NOT include an overall header explaining the context in which citations were collected.

Threadsafe.

Referenced by write_all_citations_and_unpublished_author_info(), and write_all_citations_and_unpublished_author_info_from_list_to_stream().

◆ write_unpublished_modules()

void basic::citation_manager::CitationManager::write_unpublished_modules	(	std::ostream &	outstream,
		utility::vector1< UnpublishedModuleInfoCOP > const &	unpublished
	)		const

Write out a list of the unpublished modules.

References pyrosetta.utility.array::module.

Referenced by write_all_citations_and_unpublished_author_info(), and write_all_citations_and_unpublished_author_info_from_list_to_stream().

Friends And Related Function Documentation

◆ utility::SingletonBase< CitationManager >

friend class utility::SingletonBase< CitationManager >

friend

Member Data Documentation

◆ citation_list_

CitationCollectionList basic::citation_manager::CitationManager::citation_list_

private

A list of all the citations (and unpublished moduled) used so far.

Referenced by add_citation(), add_citations(), clear_citations(), and split_citations().

◆ doi_rosetta_citation_map_

std::map< std::string, CitationCOP > basic::citation_manager::CitationManager::doi_rosetta_citation_map_

private

A map of DOI->Rosetta citations.

Referenced by get_citation_by_doi(), and populate_doi_rosetta_citation_map().

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

src/basic/citation_manager/CitationManager.hh
src/basic/citation_manager/CitationManager.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CitationManager() [1/2]

◆ CitationManager() [2/2]

Member Function Documentation

◆ add_citation()

◆ add_citations()

◆ clear_citations()

◆ get_citation_by_doi()

◆ load_rosetta_citations_from_database()

◆ operator=()

◆ populate_doi_rosetta_citation_map()

◆ split_citations() [1/2]

◆ split_citations() [2/2]

◆ write_all_citations_and_unpublished_author_info()

◆ write_all_citations_and_unpublished_author_info_from_list_to_stream()

◆ write_collected_citations()

◆ write_unpublished_modules()

Friends And Related Function Documentation

◆ utility::SingletonBase< CitationManager >

Member Data Documentation

◆ citation_list_

◆ doi_rosetta_citation_map_