Data structure for storing a citation. More...

#include <Citation.hh>

Inheritance diagram for basic::citation_manager::Citation:

Public Member Functions
	Citation ()=default
	Constructor. More...

	Citation (std::string const &citation_as_string)
	Initialization constructor. More...

	Citation (Citation const &)=default
	Copy constructor. More...

	~Citation () override=default

CitationOP	clone () const

void	clear ()
	Completely clear the data in this citation. More...

void	initialize_from_string (std::string const &citation_as_string)
	Initializes from a string formatted as in the Rosetta database. See initialization constructor's description for an example. More...

void	add_primary_author (std::string const &given_names, std::string const &surname, std::string const &initials)
	Add a primary author. More...

void	add_co_author (std::string const &given_names, std::string const &surname, std::string const &initials)
	Add a co-author. More...

void	add_senior_author (std::string const &given_names, std::string const &surname, std::string const &initials)
	Add a primary author. More...

void	set_year_and_article (int const year_in, std::string const &article_title, std::string const &journal_title, std::string const &volume_issue_pages, std::string const &doi)
	Set the year, article title, journal title, and the string for the volume/issue/pages. More...

void	get_formatted_citation (std::ostream &outstream, CitationFormat const format=CitationFormat::DefaultStyle) const
	Get this citation as a string, in a particular format. More...

utility::vector1< AuthorNames > const &	primary_authors () const
	Access the list of primary authors. More...

utility::vector1< AuthorNames > const &	co_authors () const
	Access the list of coauthors. More...

utility::vector1< AuthorNames > const &	senior_authors () const
	Access the list of senior authors. More...

int	year () const
	Get the year. More...

std::string const &	article_title () const
	Get the article title. More...

std::string const &	journal_title () const
	Get the journal title. More...

std::string const &	volume_issue_pages () const
	Get the volume, issue, and pages. More...

std::string const &	doi () const
	Get the DOI. More...

Public Member Functions inherited from utility::VirtualBase
	VirtualBase ()=default
	Default constructor. More...

virtual	~VirtualBase ()=default
	The virtual destructor is one of the main reasons for the VirtualBase class. More...

	VirtualBase (VirtualBase const &)=default

	VirtualBase (VirtualBase &&)=default

VirtualBase &	operator= (VirtualBase const &)=default

VirtualBase &	operator= (VirtualBase &&)=default

Private Member Functions
void	get_default_formatted_citation (std::ostream &outstream) const
	Get the formatted citation, in default format. More...

void	get_nature_formatted_citation (std::ostream &outstream) const
	Get the formatted citation, in Nature format. More...

void	parse_authors (std::string const &section_name, utility::vector1< AuthorNames > &destination, utility::vector1< std::string > const &lines)
	Given a list of lines, parse out a list of author names from a block of the format: [BEGIN_SECTION_NAME] "Given names" "Surname" "Initials" "Given names" "Surname" "Initials" "Given names" "Surname" "Initials" [END_SECTION_NAME]. More...

void	parse_year (utility::vector1< std::string > const &lines)
	Given a list of lines, parse out an integer from a block of the format: [BEGIN_YEAR] 1982 [END_YEAR]. More...

void	parse_string_entry (std::string const &section_name, std::string &destination, utility::vector1< std::string > const &lines)
	Given a list of lines, parse out a string from a block of the format: [BEGIN_SECTION_NAME] The string to parse out [END_SECTION_NAME]. More...

Private Attributes
utility::vector1< AuthorNames >	primary_authors_

utility::vector1< AuthorNames >	co_authors_

utility::vector1< AuthorNames >	senior_authors_

int	year_ = 0

std::string	article_title_ = ""

std::string	journal_title_ = ""

std::string	volume_issue_pages_ = ""

std::string	doi_ = ""

Detailed Description

Data structure for storing a citation.

Constructor & Destructor Documentation

◆ Citation() [1/3]

basic::citation_manager::Citation::Citation ( )

default

Constructor.

◆ Citation() [2/3]

basic::citation_manager::Citation::Citation ( std::string const & citation_as_string )

Initialization constructor.

Initializes from input string. Below is an example of the format: [BEGIN_CITATION] [BEGIN_PRIMARY_AUTHORS] "Bobo" "Dang" "B" "Haifan" "Wu" "H" "Vikram Khipple" "Mulligan" "VK" [END_PRIMARY_AUTHORS] [BEGIN_COAUTHORS] "Marco" "Mravic" "M" "Yibing" "Wu" "Y" "Thomas" "Lemmin" "T" "Alexander" "Ford" "A" "Daniel-Adriano" "Silva" "D-A" "David" "Baker" "D" [END_COAUTHORS] [BEGIN_SENIOR_AUTHORS] "William" "DeGrado" "WF" [END_SENIOR_AUTHORS] [BEGIN_YEAR] 2017 [END_YEAR] [BEGIN_TITLE] De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures [END_TITLE] [BEGIN_JOURNAL] Proc Natl Acad Sci USA [END_JOURNAL] [BEGIN_VOLUME_ISSUE_PAGES] 114(41):10852–10857 [END_VOLUME_ISSUE_PAGES] [BEGIN_DOI] 10.1073/pnas.1710695114 [END_DOI] [END_CITATION]

References initialize_from_string().

◆ Citation() [3/3]

basic::citation_manager::Citation::Citation ( Citation const & )

default

Copy constructor.

◆ ~Citation()

basic::citation_manager::Citation::~Citation ( )

overridedefault

Member Function Documentation

◆ add_co_author()

void basic::citation_manager::Citation::add_co_author	(	std::string const &	given_names,
		std::string const &	surname,
		std::string const &	initials
	)

Add a co-author.

Must be added in order of appearance.

Note: If I were adding "John Fitzgerald Kennedy Jr.", I would set given_names="John Fitzgerald", surname="Kennedy", initials="JF Jr.".

References co_authors_.

◆ add_primary_author()

void basic::citation_manager::Citation::add_primary_author	(	std::string const &	given_names,
		std::string const &	surname,
		std::string const &	initials
	)

Add a primary author.

Must be added in order of appearance.

Note: If I were adding "James Tiberius Kirk", I would set given_names="James Tiberius", surname="Kirk", initials="JT".

References primary_authors_.

◆ add_senior_author()

void basic::citation_manager::Citation::add_senior_author	(	std::string const &	given_names,
		std::string const &	surname,
		std::string const &	initials
	)

Add a primary author.

Must be added in order of appearance.

Note: If I were adding "Mary-Kate Olsen", I would set given_names="Mary-Kate", surname="Olsen", initials="M-K".

References senior_authors_.

◆ article_title()

std::string const& basic::citation_manager::Citation::article_title ( ) const

inline

Get the article title.

References article_title_.

Referenced by set_year_and_article().

◆ clear()

void basic::citation_manager::Citation::clear ( )

Completely clear the data in this citation.

References article_title_, co_authors_, doi_, journal_title_, primary_authors_, senior_authors_, volume_issue_pages_, and year_.

Referenced by pyrosetta.bindings.pose.ResidueLabelAccessor::discard(), and initialize_from_string().

◆ clone()

CitationOP basic::citation_manager::Citation::clone ( ) const

◆ co_authors()

utility::vector1< AuthorNames > const& basic::citation_manager::Citation::co_authors ( ) const

inline

Access the list of coauthors.

References co_authors_.

◆ doi()

std::string const& basic::citation_manager::Citation::doi ( ) const

inline

Get the DOI.

References doi_.

Referenced by set_year_and_article().

◆ get_default_formatted_citation()

void basic::citation_manager::Citation::get_default_formatted_citation ( std::ostream & outstream ) const

private

Get the formatted citation, in default format.

References article_title_, conf::author, co_authors_, doi_, journal_title_, primary_authors_, senior_authors_, volume_issue_pages_, and year_.

Referenced by get_formatted_citation().

◆ get_formatted_citation()

void basic::citation_manager::Citation::get_formatted_citation	(	std::ostream &	outstream,
		CitationFormat const	format = `CitationFormat::DefaultStyle`
	)		const

Get this citation as a string, in a particular format.

References enumerate_junctions::default, basic::citation_manager::DefaultStyle, pyrosetta.tests.distributed.test_dask::format, get_default_formatted_citation(), get_nature_formatted_citation(), basic::citation_manager::NatureStyle, and utility_exit_with_message.

◆ get_nature_formatted_citation()

void basic::citation_manager::Citation::get_nature_formatted_citation ( std::ostream & outstream ) const

private

Get the formatted citation, in Nature format.

References article_title_, conf::author, co_authors_, doi_, journal_title_, primary_authors_, senior_authors_, volume_issue_pages_, and year_.

Referenced by get_formatted_citation().

◆ initialize_from_string()

void basic::citation_manager::Citation::initialize_from_string ( std::string const & citation_as_string )

Initializes from a string formatted as in the Rosetta database. See initialization constructor's description for an example.

Calls clear() before initializing.

References article_title_, clear(), co_authors_, doi_, errmsg(), journal_title_, solution_counts::lines, parse_authors(), parse_string_entry(), parse_year(), primary_authors_, runtime_assert_string_msg, senior_authors_, utility::split_by_newlines(), utility::strip(), and volume_issue_pages_.

Referenced by Citation().

◆ journal_title()

std::string const& basic::citation_manager::Citation::journal_title ( ) const

inline

Get the journal title.

References journal_title_.

Referenced by set_year_and_article().

◆ parse_authors()

void basic::citation_manager::Citation::parse_authors	(	std::string const &	section_name,
		utility::vector1< AuthorNames > &	destination,
		utility::vector1< std::string > const &	lines
	)

private

Given a list of lines, parse out a list of author names from a block of the format: [BEGIN_SECTION_NAME] "Given names" "Surname" "Initials" "Given names" "Surname" "Initials" "Given names" "Surname" "Initials" [END_SECTION_NAME].

Stores the result in destination.

References line, solution_counts::lines, utility::quoted_split(), runtime_assert_string_msg, and utility::strip().

Referenced by initialize_from_string().

◆ parse_string_entry()

void basic::citation_manager::Citation::parse_string_entry	(	std::string const &	section_name,
		std::string &	destination,
		utility::vector1< std::string > const &	lines
	)

private

Given a list of lines, parse out a string from a block of the format: [BEGIN_SECTION_NAME] The string to parse out [END_SECTION_NAME].

Stores the result in destination.

References line, solution_counts::lines, runtime_assert_string_msg, and utility::strip().

Referenced by initialize_from_string().

◆ parse_year()

void basic::citation_manager::Citation::parse_year ( utility::vector1< std::string > const & lines )

private

Given a list of lines, parse out an integer from a block of the format: [BEGIN_YEAR] 1982 [END_YEAR].

Stores the result in year_.

References line, solution_counts::lines, runtime_assert_string_msg, utility::strip(), and year_.

Referenced by initialize_from_string().

◆ primary_authors()

utility::vector1< AuthorNames > const& basic::citation_manager::Citation::primary_authors ( ) const

inline

Access the list of primary authors.

References primary_authors_.

◆ senior_authors()

utility::vector1< AuthorNames > const& basic::citation_manager::Citation::senior_authors ( ) const

inline

Access the list of senior authors.

References senior_authors_.

◆ set_year_and_article()

void basic::citation_manager::Citation::set_year_and_article	(	int const	year_in,
		std::string const &	article_title,
		std::string const &	journal_title,
		std::string const &	volume_issue_pages,
		std::string const &	doi
	)

Set the year, article title, journal title, and the string for the volume/issue/pages.

References article_title(), article_title_, doi(), doi_, journal_title(), journal_title_, runtime_assert_string_msg, volume_issue_pages(), volume_issue_pages_, and year_.

◆ volume_issue_pages()

std::string const& basic::citation_manager::Citation::volume_issue_pages ( ) const

inline

Get the volume, issue, and pages.

References volume_issue_pages_.

Referenced by set_year_and_article().

◆ year()

int basic::citation_manager::Citation::year ( ) const

inline

Get the year.

References year_.

Member Data Documentation

◆ article_title_

std::string basic::citation_manager::Citation::article_title_ = ""

private

Referenced by article_title(), clear(), get_default_formatted_citation(), get_nature_formatted_citation(), initialize_from_string(), and set_year_and_article().

◆ co_authors_

utility::vector1< AuthorNames > basic::citation_manager::Citation::co_authors_

private

Referenced by add_co_author(), clear(), co_authors(), get_default_formatted_citation(), get_nature_formatted_citation(), and initialize_from_string().

◆ doi_

std::string basic::citation_manager::Citation::doi_ = ""

private

Referenced by clear(), doi(), get_default_formatted_citation(), get_nature_formatted_citation(), initialize_from_string(), and set_year_and_article().

◆ journal_title_

std::string basic::citation_manager::Citation::journal_title_ = ""

private

Referenced by clear(), get_default_formatted_citation(), get_nature_formatted_citation(), initialize_from_string(), journal_title(), and set_year_and_article().

◆ primary_authors_

utility::vector1< AuthorNames > basic::citation_manager::Citation::primary_authors_

private

Referenced by add_primary_author(), clear(), get_default_formatted_citation(), get_nature_formatted_citation(), initialize_from_string(), and primary_authors().

◆ senior_authors_

utility::vector1< AuthorNames > basic::citation_manager::Citation::senior_authors_

private

Referenced by add_senior_author(), clear(), get_default_formatted_citation(), get_nature_formatted_citation(), initialize_from_string(), and senior_authors().

◆ volume_issue_pages_

std::string basic::citation_manager::Citation::volume_issue_pages_ = ""

private

Referenced by clear(), get_default_formatted_citation(), get_nature_formatted_citation(), initialize_from_string(), set_year_and_article(), and volume_issue_pages().

◆ year_

int basic::citation_manager::Citation::year_ = 0

private

Referenced by clear(), get_default_formatted_citation(), get_nature_formatted_citation(), parse_year(), set_year_and_article(), and year().

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

src/basic/citation_manager/Citation.hh
src/basic/citation_manager/Citation.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Citation() [1/3]

◆ Citation() [2/3]

◆ Citation() [3/3]

◆ ~Citation()

Member Function Documentation

◆ add_co_author()

◆ add_primary_author()

◆ add_senior_author()

◆ article_title()

◆ clear()

◆ clone()

◆ co_authors()

◆ doi()

◆ get_default_formatted_citation()

◆ get_formatted_citation()

◆ get_nature_formatted_citation()

◆ initialize_from_string()

◆ journal_title()

◆ parse_authors()

◆ parse_string_entry()

◆ parse_year()

◆ primary_authors()

◆ senior_authors()

◆ set_year_and_article()

◆ volume_issue_pages()

◆ year()

Member Data Documentation

◆ article_title_

◆ co_authors_

◆ doi_

◆ journal_title_

◆ primary_authors_

◆ senior_authors_

◆ volume_issue_pages_

◆ year_