utility::options::OptionCollection Class Reference

Program options collection. More...

#include <OptionCollection.hh>

Public Member Functions
	OptionCollection ()
	Default constructor. More...
	~OptionCollection ()
	Destructor. More...
void	add_built_in_options ()
	Add the built-in options. More...
BooleanOption &	add (BooleanOptionKey const &key, std::string const &description)
	Add a BooleanOption. More...
IntegerOption &	add (IntegerOptionKey const &key, std::string const &description)
	Add an IntegerOption. More...
RealOption &	add (RealOptionKey const &key, std::string const &description)
	Add a RealOption. More...
StringOption &	add (StringOptionKey const &key, std::string const &description)
	Add a StringOption. More...
FileOption &	add (FileOptionKey const &key, std::string const &description)
	Add a FileOption. More...
PathOption &	add (PathOptionKey const &key, std::string const &description)
	Add a PathOption. More...
BooleanVectorOption &	add (BooleanVectorOptionKey const &key, std::string const &description)
	Add a BooleanVectorOption. More...
IntegerVectorOption &	add (IntegerVectorOptionKey const &key, std::string const &description)
	Add an IntegerVectorOption. More...
RealVectorOption &	add (RealVectorOptionKey const &key, std::string const &description)
	Add a RealVectorOption. More...
ResidueChainVectorOption &	add (ResidueChainVectorOptionKey const &key, std::string const &description)
	Add an ResidueChainVectorOption. More...
StringVectorOption &	add (StringVectorOptionKey const &key, std::string const &description)
	Add a StringVectorOption. More...
FileVectorOption &	add (FileVectorOptionKey const &key, std::string const &description)
	Add a FileVectorOption. More...
PathVectorOption &	add (PathVectorOptionKey const &key, std::string const &description)
	Add a PathVectorOption. More...
BooleanOption &	add (BooleanOption const &option)
	Add a BooleanOption. More...
IntegerOption &	add (IntegerOption const &option)
	Add an IntegerOption. More...
RealOption &	add (RealOption const &option)
	Add a RealOption. More...
StringOption &	add (StringOption const &option)
	Add a StringOption. More...
FileOption &	add (FileOption const &option)
	Add a FileOption. More...
PathOption &	add (PathOption const &option)
	Add a PathOption. More...
template<typename T >
AnyOption< T > &	add (AnyOption< T > const &option)
	Add an AnyOption. More...
BooleanVectorOption &	add (BooleanVectorOption const &option)
	Add a BooleanVectorOption. More...
IntegerVectorOption &	add (IntegerVectorOption const &option)
	Add an IntegerVectorOption. More...
RealVectorOption &	add (RealVectorOption const &option)
	Add a RealVectorOption. More...
ResidueChainVectorOption &	add (ResidueChainVectorOption const &option)
	Add an ResidueChainVectorOption. More...
StringVectorOption &	add (StringVectorOption const &option)
	Add a StringVectorOption. More...
FileVectorOption &	add (FileVectorOption const &option)
	Add a FileVectorOption. More...
PathVectorOption &	add (PathVectorOption const &option)
	Add a PathVectorOption. More...
template<typename T >
AnyVectorOption< T > &	add (AnyVectorOption< T > const &option)
	Add an AnyVectorOption. More...
void	check_specs () const
	Check for problems in the option specifications. More...
void	load (const std::vector< std::string > &args, bool const free_args)
	Load the user-specified option values. More...
void	load (int const argc, char *const argv[], bool const free_args=false)
	Load the user-specified option values. More...
void	load (std::string executable_name, ValueStrings &arg_strings, bool const free_args)
	Load the user-specified option values. More...
void	load_options_from_file (std::string const &file_string, std::string const &cid="")
	Load all options in a flags file. More...
void	load_options_from_file_exception (std::string const &file_string, std::string const &cid="")
	same as load_options_from_file, but throws exception instead of call to std::exit More...
void	load_options_from_stream (std::istream &stream, std::string const &file_string="STREAM", std::string const &cid="")
	Load all options in a flags file. More...
void	check_values () const
	Check for problems in the option values. More...
void	show_help (std::ostream &stream)
	Show all the options and their descriptions. More...
void	show_option_help (OptionKey const &, std::string &group, std::ostream &stream)
	Show one option and it description. More...
void	show_help_hier (std::ostream &stream)
	Show all the options and their descriptions in a hierarchy format. More...
void	show_option_help_hier (OptionKey const &, std::string &group, std::ostream &stream)
	Show one option and it description in a hierarchy format. More...
void	show_user (std::ostream &stream) const
	Show the user-specified options and their values. More...
void	show_all (std::ostream &stream) const
	Show all the options and their values. More...
void	show_all_hier (std::ostream &stream) const
	Show all the options and their values in a hierarchy format. More...
void	show_table_text (std::ostream &stream) const
	Show the options definitions table in text format. More...
void	show_table_Wiki (std::ostream &stream) const
	Show the options definitions table in Wiki format. More...
void	show_accessed_options (std::ostream &stream) const
	Show accessed list of options. More...
void	show_inaccessed_user_options (std::ostream &stream) const
	Show inaccessed user-specified options. More...
void	show_unused_options (std::ostream &stream) const
	Show options that were user-specified, but not yet accessed. Differs from show_inaccessed_user_options() mainly by formatting And how the options are accessed. (This one should be destructor safe.) More...
std::string	get_argv () const
	Returns a copy of the concatenated argv strings that were initialized in load(). More...
bool	has (BooleanOptionKey const &key) const
	Is there an option with a BooleanOptionKey? More...
bool	has (IntegerOptionKey const &key) const
	Is there an option with an IntegerOptionKey? More...
bool	has (RealOptionKey const &key) const
	Is there an option with a RealOptionKey? More...
bool	has (StringOptionKey const &key) const
	Is there an option with a StringOptionKey? More...
bool	has (FileOptionKey const &key) const
	Is there an option with a FileOptionKey? More...
bool	has (PathOptionKey const &key) const
	Is there an option with a PathOptionKey? More...
bool	has (AnyOptionKey const &key) const
	Is there an option with an AnyOptionKey? More...
bool	has (BooleanVectorOptionKey const &key) const
	Is there an option with a BooleanVectorOptionKey? More...
bool	has (IntegerVectorOptionKey const &key) const
	Is there an option with an IntegerVectorOptionKey? More...
bool	has (RealVectorOptionKey const &key) const
	Is there an option with a RealVectorOptionKey? More...
bool	has (ResidueChainVectorOptionKey const &key) const
	Is there an option with an IntegerVectorOptionKey? More...
bool	has (StringVectorOptionKey const &key) const
	Is there an option with a StringVectorOptionKey? More...
bool	has (FileVectorOptionKey const &key) const
	Is there an option with a FileVectorOptionKey? More...
bool	has (PathVectorOptionKey const &key) const
	Is there an option with a PathVectorOptionKey? More...
bool	has (AnyVectorOptionKey const &key) const
	Is there an option with an AnyVectorOptionKey? More...
bool	has (OptionKey const &key) const
	Is there an option with an OptionKey? More...
BooleanOption const &	option (BooleanOptionKey const &key) const
	Option by BooleanOptionKey. More...
BooleanOption &	option (BooleanOptionKey const &key)
	Option by BooleanOptionKey. More...
IntegerOption const &	option (IntegerOptionKey const &key) const
	Option by IntegerOptionKey. More...
IntegerOption &	option (IntegerOptionKey const &key)
	Option by IntegerOptionKey. More...
RealOption const &	option (RealOptionKey const &key) const
	Option by RealOptionKey. More...
RealOption &	option (RealOptionKey const &key)
	Option by RealOptionKey. More...
StringOption const &	option (StringOptionKey const &key) const
	Option by StringOptionKey. More...
StringOption &	option (StringOptionKey const &key)
	Option by StringOptionKey. More...
FileOption const &	option (FileOptionKey const &key) const
	Option by FileOptionKey. More...
FileOption &	option (FileOptionKey const &key)
	Option by FileOptionKey. More...
PathOption const &	option (PathOptionKey const &key) const
	Option by PathOptionKey. More...
PathOption &	option (PathOptionKey const &key)
	Option by PathOptionKey. More...
Option const &	option (AnyOptionKey const &key) const
	Option by AnyOptionKey. More...
Option &	option (AnyOptionKey const &key)
	Option by AnyOptionKey. More...
template<typename OptionType >
OptionType const &	option (AnyOptionKey const &key) const
	Option by AnyOptionKey with option type template argument. More...
template<typename OptionType >
OptionType &	option (AnyOptionKey const &key)
	Option by AnyOptionKey with option type template argument. More...
BooleanVectorOption const &	option (BooleanVectorOptionKey const &key) const
	VectorOption by BooleanVectorOptionKey. More...
BooleanVectorOption &	option (BooleanVectorOptionKey const &key)
	VectorOption by BooleanVectorOptionKey. More...
IntegerVectorOption const &	option (IntegerVectorOptionKey const &key) const
	VectorOption by IntegerVectorOptionKey. More...
IntegerVectorOption &	option (IntegerVectorOptionKey const &key)
	VectorOption by IntegerVectorOptionKey. More...
RealVectorOption const &	option (RealVectorOptionKey const &key) const
	VectorOption by RealVectorOptionKey. More...
RealVectorOption &	option (RealVectorOptionKey const &key)
	VectorOption by RealVectorOptionKey. More...
StringVectorOption const &	option (StringVectorOptionKey const &key) const
	VectorOption by StringVectorOptionKey. More...
StringVectorOption &	option (StringVectorOptionKey const &key)
	VectorOption by StringVectorOptionKey. More...
FileVectorOption const &	option (FileVectorOptionKey const &key) const
	VectorOption by FileVectorOptionKey. More...
FileVectorOption &	option (FileVectorOptionKey const &key)
	VectorOption by FileVectorOptionKey. More...
PathVectorOption const &	option (PathVectorOptionKey const &key) const
	VectorOption by PathVectorOptionKey. More...
PathVectorOption &	option (PathVectorOptionKey const &key)
	VectorOption by PathVectorOptionKey. More...
VectorOption const &	option (AnyVectorOptionKey const &key) const
	VectorOption by AnyVectorOptionKey. More...
VectorOption &	option (AnyVectorOptionKey const &key)
	VectorOption by AnyVectorOptionKey. More...
template<typename VectorOptionType >
VectorOptionType const &	option (AnyVectorOptionKey const &key) const
	VectorOption by AnyVectorOptionKey with option type template argument. More...
template<typename VectorOptionType >
VectorOptionType &	option (AnyVectorOptionKey const &key)
	VectorOption by AnyVectorOptionKey with option type template argument. More...
Option const &	option (OptionKey const &key) const
	Option by OptionKey. More...
Option &	option (OptionKey const &key)
	Option by OptionKey. More...
template<typename OptionType >
OptionType const &	option (OptionKey const &key) const
	Option by OptionKey with option type template argument. More...
template<typename OptionType >
OptionType &	option (OptionKey const &key)
	Option by OptionKey with option type template argument. More...
BooleanOption const &	operator[] (BooleanOptionKey const &key) const
	OptionCollection[ BooleanOptionKey ]. More...
BooleanOption &	operator[] (BooleanOptionKey const &key)
	OptionCollection[ BooleanOptionKey ]. More...
IntegerOption const &	operator[] (IntegerOptionKey const &key) const
	OptionCollection[ IntegerOptionKey ]. More...
IntegerOption &	operator[] (IntegerOptionKey const &key)
	OptionCollection[ IntegerOptionKey ]. More...
RealOption const &	operator[] (RealOptionKey const &key) const
	OptionCollection[ RealOptionKey ]. More...
RealOption &	operator[] (RealOptionKey const &key)
	OptionCollection[ RealOptionKey ]. More...
StringOption const &	operator[] (StringOptionKey const &key) const
	OptionCollection[ StringOptionKey ]. More...
StringOption &	operator[] (StringOptionKey const &key)
	OptionCollection[ StringOptionKey ]. More...
FileOption const &	operator[] (FileOptionKey const &key) const
	OptionCollection[ FileOptionKey ]. More...
FileOption &	operator[] (FileOptionKey const &key)
	OptionCollection[ FileOptionKey ]. More...
PathOption const &	operator[] (PathOptionKey const &key) const
	OptionCollection[ PathOptionKey ]. More...
PathOption &	operator[] (PathOptionKey const &key)
	OptionCollection[ PathOptionKey ]. More...
Option const &	operator[] (AnyOptionKey const &key) const
	OptionCollection[ AnyOptionKey ]. More...
Option &	operator[] (AnyOptionKey const &key)
	OptionCollection[ AnyOptionKey ]. More...
template<typename OptionType >
OptionType const &	operator[] (AnyOptionKey const &key) const
	OptionCollection[ AnyOptionKey ] with option type template argument. More...
template<typename OptionType >
OptionType &	operator[] (AnyOptionKey const &key)
	OptionCollection[ AnyOptionKey ] with option type template argument. More...
BooleanVectorOption const &	operator[] (BooleanVectorOptionKey const &key) const
	OptionCollection[ BooleanVectorOptionKey ]. More...
BooleanVectorOption &	operator[] (BooleanVectorOptionKey const &key)
	OptionCollection[ BooleanVectorOptionKey ]. More...
IntegerVectorOption const &	operator[] (IntegerVectorOptionKey const &key) const
	OptionCollection[ IntegerVectorOptionKey ]. More...
IntegerVectorOption &	operator[] (IntegerVectorOptionKey const &key)
	OptionCollection[ IntegerVectorOptionKey ]. More...
RealVectorOption const &	operator[] (RealVectorOptionKey const &key) const
	OptionCollection[ RealVectorOptionKey ]. More...
RealVectorOption &	operator[] (RealVectorOptionKey const &key)
	OptionCollection[ RealVectorOptionKey ]. More...
ResidueChainVectorOption const &	operator[] (ResidueChainVectorOptionKey const &key) const
	OptionCollection[ ResidueChainVectorOptionKey ]. More...
ResidueChainVectorOption &	operator[] (ResidueChainVectorOptionKey const &key)
	OptionCollection[ ResidueChainVectorOptionKey ]. More...
StringVectorOption const &	operator[] (StringVectorOptionKey const &key) const
	OptionCollection[ StringVectorOptionKey ]. More...
StringVectorOption &	operator[] (StringVectorOptionKey const &key)
	OptionCollection[ StringVectorOptionKey ]. More...
FileVectorOption const &	operator[] (FileVectorOptionKey const &key) const
	OptionCollection[ FileVectorOptionKey ]. More...
FileVectorOption &	operator[] (FileVectorOptionKey const &key)
	OptionCollection[ FileVectorOptionKey ]. More...
PathVectorOption const &	operator[] (PathVectorOptionKey const &key) const
	OptionCollection[ PathVectorOptionKey ]. More...
PathVectorOption &	operator[] (PathVectorOptionKey const &key)
	OptionCollection[ PathVectorOptionKey ]. More...
VectorOption const &	operator[] (AnyVectorOptionKey const &key) const
	OptionCollection[ AnyVectorOptionKey ]. More...
VectorOption &	operator[] (AnyVectorOptionKey const &key)
	OptionCollection[ AnyVectorOptionKey ]. More...
template<typename VectorOptionType >
VectorOptionType const &	operator[] (AnyVectorOptionKey const &key) const
	OptionCollection[ AnyVectorOptionKey ] with option type template argument. More...
template<typename VectorOptionType >
VectorOptionType &	operator[] (AnyVectorOptionKey const &key)
	OptionCollection[ AnyVectorOptionKey ] with option type template argument. More...
Option const &	operator[] (OptionKey const &key) const
	OptionCollection[ OptionKey ]. More...
Option &	operator[] (OptionKey const &key)
	OptionCollection[ OptionKey ]. More...
template<typename OptionType >
OptionType const &	operator[] (OptionKey const &key) const
	OptionCollection[ OptionKey ] with option type template argument. More...
template<typename OptionType >
OptionType &	operator[] (OptionKey const &key)
	OptionCollection[ OptionKey ] with option type template argument. More...
BooleanOption const &	operator() (BooleanOptionKey const &key, bool check_restricted_access=true) const
	Option by BooleanOptionKey. More...
BooleanOption &	operator() (BooleanOptionKey const &key, bool check_restricted_access=true)
	Option by BooleanOptionKey. More...
IntegerOption const &	operator() (IntegerOptionKey const &key, bool check_restricted_access=true) const
	Option by IntegerOptionKey. More...
IntegerOption &	operator() (IntegerOptionKey const &key, bool check_restricted_access=true)
	Option by IntegerOptionKey. More...
RealOption const &	operator() (RealOptionKey const &key, bool check_restricted_access=true) const
	Option by RealOptionKey. More...
RealOption &	operator() (RealOptionKey const &key, bool check_restricted_access=true)
	Option by RealOptionKey. More...
StringOption const &	operator() (StringOptionKey const &key, bool check_restricted_access=true) const
	Option by StringOptionKey. More...
StringOption &	operator() (StringOptionKey const &key, bool check_restricted_access=true)
	Option by StringOptionKey. More...
FileOption const &	operator() (FileOptionKey const &key, bool check_restricted_access=true) const
	Option by FileOptionKey. More...
FileOption &	operator() (FileOptionKey const &key, bool check_restricted_access=true)
	Option by FileOptionKey. More...
PathOption const &	operator() (PathOptionKey const &key, bool check_restricted_access=true) const
	Option by PathOptionKey. More...
PathOption &	operator() (PathOptionKey const &key, bool check_restricted_access=true)
	Option by PathOptionKey. More...
Option const &	operator() (AnyOptionKey const &key, bool check_restricted_access=true) const
	Option by AnyOptionKey. More...
Option &	operator() (AnyOptionKey const &key, bool check_restricted_access=true)
	Option by AnyOptionKey. More...
template<typename OptionType >
OptionType const &	operator() (AnyOptionKey const &key, bool check_restricted_access=true) const
	Option by AnyOptionKey with option type template argument. More...
template<typename OptionType >
OptionType &	operator() (AnyOptionKey const &key, bool check_restricted_access=true)
	Option by AnyOptionKey with option type template argument. More...
BooleanVectorOption const &	operator() (BooleanVectorOptionKey const &key, bool check_restricted_access=true) const
	VectorOption by BooleanVectorOptionKey. More...
BooleanVectorOption &	operator() (BooleanVectorOptionKey const &key, bool check_restricted_access=true)
	VectorOption by BooleanVectorOptionKey. More...
IntegerVectorOption const &	operator() (IntegerVectorOptionKey const &key, bool check_restricted_access=true) const
	VectorOption by IntegerVectorOptionKey. More...
IntegerVectorOption &	operator() (IntegerVectorOptionKey const &key, bool check_restricted_access=true)
	VectorOption by IntegerVectorOptionKey. More...
RealVectorOption const &	operator() (RealVectorOptionKey const &key, bool check_restricted_access=true) const
	VectorOption by RealVectorOptionKey. More...
RealVectorOption &	operator() (RealVectorOptionKey const &key, bool check_restricted_access=true)
	VectorOption by RealVectorOptionKey. More...
ResidueChainVectorOption const &	operator() (ResidueChainVectorOptionKey const &key, bool check_restricted_access=true) const
	VectorOption by ResidueChainVectorOptionKey. More...
ResidueChainVectorOption &	operator() (ResidueChainVectorOptionKey const &key, bool check_restricted_access=true)
	VectorOption by ResidueChainVectorOptionKey. More...
StringVectorOption const &	operator() (StringVectorOptionKey const &key, bool check_restricted_access=true) const
	VectorOption by StringVectorOptionKey. More...
StringVectorOption &	operator() (StringVectorOptionKey const &key, bool check_restricted_access=true)
	VectorOption by StringVectorOptionKey. More...
FileVectorOption const &	operator() (FileVectorOptionKey const &key, bool check_restricted_access=true) const
	VectorOption by FileVectorOptionKey. More...
FileVectorOption &	operator() (FileVectorOptionKey const &key, bool check_restricted_access=true)
	VectorOption by FileVectorOptionKey. More...
PathVectorOption const &	operator() (PathVectorOptionKey const &key, bool check_restricted_access=true) const
	VectorOption by PathVectorOptionKey. More...
PathVectorOption &	operator() (PathVectorOptionKey const &key, bool check_restricted_access=true)
	VectorOption by PathVectorOptionKey. More...
VectorOption const &	operator() (AnyVectorOptionKey const &key, bool check_restricted_access=true) const
	VectorOption by AnyVectorOptionKey. More...
VectorOption &	operator() (AnyVectorOptionKey const &key, bool check_restricted_access=true)
	VectorOption by AnyVectorOptionKey. More...
template<typename VectorOptionType >
VectorOptionType const &	operator() (AnyVectorOptionKey const &key, bool check_restricted_access=true) const
	VectorOption by AnyVectorOptionKey with option type template argument. More...
template<typename VectorOptionType >
VectorOptionType &	operator() (AnyVectorOptionKey const &key, bool check_restricted_access=true)
	VectorOption by AnyVectorOptionKey with option type template argument. More...
Option const &	operator() (OptionKey const &key, bool check_restricted_access=true) const
	Option by OptionKey. More...
Option &	operator() (OptionKey const &key, bool check_restricted_access=true)
	Option by OptionKey. More...
template<typename OptionType >
OptionType const &	operator() (OptionKey const &key, bool check_restricted_access=true) const
	Option by OptionKey with option type template argument. More...
template<typename OptionType >
OptionType &	operator() (OptionKey const &key, bool check_restricted_access=true)
	Option by OptionKey with option type template argument. More...

Static Public Member Functions
static void	add_relevant (const OptionKey &key)
	add OptionKey to list of application relevant options More...
static bool	is_relevant (OptionKey const &key)
	Checks if option has been registered as relevant. More...
static std::string	space_prefixed (std::string const &s, int const n=1)
	Space-prefixed string except blank if string is empty. More...
static std::string	tab_prefixed (std::string const &s, int const n=1)
	Tab-prefixed string except blank if string is empty. More...
static void	check_key (OptionKey const &key)
	Check that a key's identifiers are legal. More...
static void	check_key (Option const &option)
	Check that an option's identifiers are legal. More...
static std::string	find_key_cl (std::string const &key_string, std::string const &cid, bool const top)
	Find a user-specified option key in a command line context. More...
static std::string	find_key_file (std::string const &key_string, std::string const &cid, bool const top)
static std::string::size_type	n_part (std::string const &s)
	Number of parts in an option id. More...
static std::string::size_type	n_part_prefix_match (std::string const &s, std::string const &t)
	Number of prefix parts of two ids that match. More...
static std::string	prefix (std::string const &s, int const n=1)
	Prefix of an option id with a specified number of parts. More...
static std::string	suffix (std::string const &s, int const n=1)
	Suffix of an option id with a specified number of parts. More...
static std::string &	trim (std::string &s, int const n=1)
	Trim a specified number of parts from the suffix of an option id. More...
static std::string	trimmed (std::string const &s, int const n=1)
	Prefix of an option id with a specified number of suffix parts removed. More...
static std::string	cleaned (std::string const &s)
	Cleaned option id with repeat colons condensed. More...
static std::string	merged (std::string const &s, std::string const &t)
	Merged option ids with the minimal suffix-prefix overlap, if any, removed. More...
static std::string	wrapped (std::string const &s, std::string::size_type const indent=10, std::string::size_type const width=80, std::string const &header_for_extra_lines="")
	String wrapped and indented. More...
static void	set_show_accessed_options_flag (bool v)
	modify 'show_accessed_options' flag; More...
static void	set_show_unused_options_flag (bool v)
	modify 'show_unused_options' flag; More...

Private Types
enum	OptionTypes {   UNKNOWN_OPTION, BOOLEAN_OPTION, INTEGER_OPTION, REAL_OPTION,   STRING_OPTION, FILE_OPTION, PATH_OPTION, ANY_OPTION,   BOOLEAN_VECTOR_OPTION, INTEGER_VECTOR_OPTION, REAL_VECTOR_OPTION, RESIDUE_CHAIN_VECTOR_OPTION,   STRING_VECTOR_OPTION, FILE_VECTOR_OPTION, PATH_VECTOR_OPTION, ANY_VECTOR_OPTION }
	Option types enumeration. More...
typedef std::list< std::string >	ValueStrings
typedef utility::keys::SmallKeyVector < BooleanOptionKey, BooleanOption >	Booleans
typedef utility::keys::SmallKeyVector < IntegerOptionKey, IntegerOption >	Integers
typedef utility::keys::SmallKeyVector < RealOptionKey, RealOption >	Reals
typedef utility::keys::SmallKeyVector < StringOptionKey, StringOption >	Strings
typedef utility::keys::SmallKeyVector < FileOptionKey, FileOption >	Files
typedef utility::keys::SmallKeyVector < PathOptionKey, PathOption >	Paths
typedef utility::keys::SmallKeyVector < AnyOptionKey, VariantOption < ScalarOption > >	Anys
typedef utility::keys::SmallKeyVector < BooleanVectorOptionKey, BooleanVectorOption >	BooleanVectors
typedef utility::keys::SmallKeyVector < IntegerVectorOptionKey, IntegerVectorOption >	IntegerVectors
typedef utility::keys::SmallKeyVector < RealVectorOptionKey, RealVectorOption >	RealVectors
typedef utility::keys::SmallKeyVector < ResidueChainVectorOptionKey, ResidueChainVectorOption >	ResidueChainVectors
typedef utility::keys::SmallKeyVector < StringVectorOptionKey, StringVectorOption >	StringVectors
typedef utility::keys::SmallKeyVector < FileVectorOptionKey, FileVectorOption >	FileVectors
typedef utility::keys::SmallKeyVector < PathVectorOptionKey, PathVectorOption >	PathVectors
typedef utility::keys::SmallKeyVector < AnyVectorOptionKey, VariantOption< VectorOption > >	AnyVectors
typedef utility::keys::SmallKeyVector < OptionKey, OptionTypes >	All

Private Member Functions
void	load_option_cl (std::string const &arg_string, ValueStrings &arg_strings, std::string const &pid)
	Load a user-specified option argument from a command line. More...
void	load_option_from_file (std::string const &arg_string, ValueStrings &arg_strings, std::string const &pid)
	Load one option from user specified file. More...
void	load_option_file (std::string const &arg_string, ValueStrings &val_strings, std::string &cid, bool const cl_context=false)
void	set_option_value_cl (std::string const &key_id, ValueStrings &arg_strings)
	Set a user-specified option value from a command line. More...
void	set_option_value_file (std::string const &key_id, ValueStrings &val_strings)

Private Attributes
Booleans	booleans_
	Boolean options. More...
Integers	integers_
	Integer options. More...
Reals	reals_
	Real options. More...
Strings	strings_
	String options. More...
Files	files_
	File options. More...
Paths	paths_
	Path options. More...
Anys	anys_
	Any value type options. More...
BooleanVectors	boolean_vectors_
	Boolean vector options. More...
IntegerVectors	integer_vectors_
	Integer vector options. More...
RealVectors	real_vectors_
	Real vector options. More...
ResidueChainVectors	residue_chain_vectors_
	Residue/chain vector options. More...
StringVectors	string_vectors_
	String vector options. More...
FileVectors	file_vectors_
	File vector options. More...
PathVectors	path_vectors_
	Path vector options. More...
AnyVectors	any_vectors_
	Any value type vector options. More...
All	all_
	All options (non-owning pointers) More...
std::string	argv_copy_
	keep a copy of argv around in case people want to get at it elsewhere in the code. More...

Static Private Attributes
static std::vector< OptionKey const * >	relevant_
	global list of application relevant options More...
static bool	show_accessed_options_ = false
	Flag indicating that list of accessed option should be printed when destructor of OptionCollection is called. This flag is false by default. More...
static bool	show_unused_options_ = false
	Flag indicating that list of user specified but inaccessed options should be printed when destructor of OptionCollection is called. This flag is false by default. More...

Friends
std::ostream &	operator<< (std::ostream &stream, OptionCollection const &options)
	Output to stream. More...

Detailed Description

Program options collection.

Member Typedef Documentation

typedef utility::keys::SmallKeyVector< OptionKey, OptionTypes > utility::options::OptionCollection::All

private

typedef utility::keys::SmallKeyVector< AnyOptionKey, VariantOption< ScalarOption > > utility::options::OptionCollection::Anys

private

typedef utility::keys::SmallKeyVector< AnyVectorOptionKey, VariantOption< VectorOption > > utility::options::OptionCollection::AnyVectors

private

typedef utility::keys::SmallKeyVector< BooleanOptionKey, BooleanOption > utility::options::OptionCollection::Booleans

private

typedef utility::keys::SmallKeyVector< BooleanVectorOptionKey, BooleanVectorOption > utility::options::OptionCollection::BooleanVectors

private

typedef utility::keys::SmallKeyVector< FileOptionKey, FileOption > utility::options::OptionCollection::Files

private

typedef utility::keys::SmallKeyVector< FileVectorOptionKey, FileVectorOption > utility::options::OptionCollection::FileVectors

private

typedef utility::keys::SmallKeyVector< IntegerOptionKey, IntegerOption > utility::options::OptionCollection::Integers

private

typedef utility::keys::SmallKeyVector< IntegerVectorOptionKey, IntegerVectorOption > utility::options::OptionCollection::IntegerVectors

private

typedef utility::keys::SmallKeyVector< PathOptionKey, PathOption > utility::options::OptionCollection::Paths

private

typedef utility::keys::SmallKeyVector< PathVectorOptionKey, PathVectorOption > utility::options::OptionCollection::PathVectors

private

typedef utility::keys::SmallKeyVector< RealOptionKey, RealOption > utility::options::OptionCollection::Reals

private

typedef utility::keys::SmallKeyVector< RealVectorOptionKey, RealVectorOption > utility::options::OptionCollection::RealVectors

private

typedef utility::keys::SmallKeyVector< ResidueChainVectorOptionKey, ResidueChainVectorOption > utility::options::OptionCollection::ResidueChainVectors

private

typedef utility::keys::SmallKeyVector< StringOptionKey, StringOption > utility::options::OptionCollection::Strings

private

typedef utility::keys::SmallKeyVector< StringVectorOptionKey, StringVectorOption > utility::options::OptionCollection::StringVectors

private

typedef std::list< std::string > utility::options::OptionCollection::ValueStrings

private

Member Enumeration Documentation

enum utility::options::OptionCollection::OptionTypes

private

Option types enumeration.

Enumerator
UNKNOWN_OPTION
BOOLEAN_OPTION
INTEGER_OPTION
REAL_OPTION
STRING_OPTION
FILE_OPTION
PATH_OPTION
ANY_OPTION
BOOLEAN_VECTOR_OPTION
INTEGER_VECTOR_OPTION
REAL_VECTOR_OPTION
RESIDUE_CHAIN_VECTOR_OPTION
STRING_VECTOR_OPTION
FILE_VECTOR_OPTION
PATH_VECTOR_OPTION
ANY_VECTOR_OPTION

Constructor & Destructor Documentation

utility::options::OptionCollection::OptionCollection ( )

inline

Default constructor.

utility::options::OptionCollection::~OptionCollection

(

)

Destructor.

References utility::io::oc::cout, show_accessed_options(), show_accessed_options_, show_unused_options(), and show_unused_options_.

Member Function Documentation

BooleanOption& utility::options::OptionCollection::add ( BooleanOptionKey const &  key, std::string const &  description  )

inline

Add a BooleanOption.

References all_, BOOLEAN_OPTION, booleans_, and check_key().

Referenced by add_built_in_options(), add_rosetta_options_0(), add_rosetta_options_1(), add_rosetta_options_10(), add_rosetta_options_11(), add_rosetta_options_12(), add_rosetta_options_13(), add_rosetta_options_14(), add_rosetta_options_15(), add_rosetta_options_2(), add_rosetta_options_3(), add_rosetta_options_4(), add_rosetta_options_5(), add_rosetta_options_6(), add_rosetta_options_7(), add_rosetta_options_8(), add_rosetta_options_9(), and main().

IntegerOption& utility::options::OptionCollection::add ( IntegerOptionKey const &  key, std::string const &  description  )

inline

Add an IntegerOption.

References all_, check_key(), INTEGER_OPTION, and integers_.

RealOption& utility::options::OptionCollection::add ( RealOptionKey const &  key, std::string const &  description  )

inline

Add a RealOption.

References all_, check_key(), REAL_OPTION, and reals_.

StringOption& utility::options::OptionCollection::add ( StringOptionKey const &  key, std::string const &  description  )

inline

Add a StringOption.

References all_, check_key(), STRING_OPTION, and strings_.

FileOption& utility::options::OptionCollection::add ( FileOptionKey const &  key, std::string const &  description  )

inline

Add a FileOption.

References all_, check_key(), FILE_OPTION, and files_.

PathOption& utility::options::OptionCollection::add ( PathOptionKey const &  key, std::string const &  description  )

inline

Add a PathOption.

References all_, check_key(), PATH_OPTION, and paths_.

BooleanVectorOption& utility::options::OptionCollection::add ( BooleanVectorOptionKey const &  key, std::string const &  description  )

inline

Add a BooleanVectorOption.

References all_, BOOLEAN_VECTOR_OPTION, boolean_vectors_, and check_key().

IntegerVectorOption& utility::options::OptionCollection::add ( IntegerVectorOptionKey const &  key, std::string const &  description  )

inline

Add an IntegerVectorOption.

References all_, check_key(), INTEGER_VECTOR_OPTION, and integer_vectors_.

RealVectorOption& utility::options::OptionCollection::add ( RealVectorOptionKey const &  key, std::string const &  description  )

inline

Add a RealVectorOption.

References all_, check_key(), REAL_VECTOR_OPTION, and real_vectors_.

ResidueChainVectorOption& utility::options::OptionCollection::add ( ResidueChainVectorOptionKey const &  key, std::string const &  description  )

inline

Add an ResidueChainVectorOption.

References all_, check_key(), RESIDUE_CHAIN_VECTOR_OPTION, and residue_chain_vectors_.

StringVectorOption& utility::options::OptionCollection::add ( StringVectorOptionKey const &  key, std::string const &  description  )

inline

Add a StringVectorOption.

References all_, check_key(), STRING_VECTOR_OPTION, and string_vectors_.

FileVectorOption& utility::options::OptionCollection::add ( FileVectorOptionKey const &  key, std::string const &  description  )

inline

Add a FileVectorOption.

References all_, check_key(), FILE_VECTOR_OPTION, and file_vectors_.

PathVectorOption& utility::options::OptionCollection::add ( PathVectorOptionKey const &  key, std::string const &  description  )

inline

Add a PathVectorOption.

References all_, check_key(), PATH_VECTOR_OPTION, and path_vectors_.

BooleanOption& utility::options::OptionCollection::add ( BooleanOption const &  option )

inline

Add a BooleanOption.

References all_, BOOLEAN_OPTION, booleans_, check_key(), and utility::options::ScalarOption_T_< K, T >::key().

IntegerOption& utility::options::OptionCollection::add ( IntegerOption const &  option )

inline

Add an IntegerOption.

References all_, check_key(), INTEGER_OPTION, integers_, and utility::options::ScalarOption_T_< K, T >::key().

RealOption& utility::options::OptionCollection::add ( RealOption const &  option )

inline

Add a RealOption.

References all_, check_key(), utility::options::ScalarOption_T_< K, T >::key(), REAL_OPTION, and reals_.

StringOption& utility::options::OptionCollection::add ( StringOption const &  option )

inline

Add a StringOption.

References all_, check_key(), utility::options::ScalarOption_T_< K, T >::key(), STRING_OPTION, and strings_.

FileOption& utility::options::OptionCollection::add ( FileOption const &  option )

inline

Add a FileOption.

References all_, check_key(), FILE_OPTION, files_, and utility::options::ScalarOption_T_< K, T >::key().

PathOption& utility::options::OptionCollection::add ( PathOption const &  option )

inline

Add a PathOption.

References all_, check_key(), utility::options::ScalarOption_T_< K, T >::key(), PATH_OPTION, and paths_.

template<typename T >

AnyOption< T >& utility::options::OptionCollection::add ( AnyOption< T > const &  option )

inline

Add an AnyOption.

References all_, ANY_OPTION, anys_, check_key(), and utility::options::ScalarOption_T_< AnyOptionKey, T >::key().

BooleanVectorOption& utility::options::OptionCollection::add ( BooleanVectorOption const &  option )

inline

Add a BooleanVectorOption.

References all_, BOOLEAN_VECTOR_OPTION, boolean_vectors_, check_key(), and utility::options::VectorOption_T_< K, T >::key().

IntegerVectorOption& utility::options::OptionCollection::add ( IntegerVectorOption const &  option )

inline

Add an IntegerVectorOption.

References all_, check_key(), INTEGER_VECTOR_OPTION, integer_vectors_, and utility::options::VectorOption_T_< K, T >::key().

RealVectorOption& utility::options::OptionCollection::add ( RealVectorOption const &  option )

inline

Add a RealVectorOption.

References all_, check_key(), utility::options::VectorOption_T_< K, T >::key(), REAL_VECTOR_OPTION, and real_vectors_.

ResidueChainVectorOption& utility::options::OptionCollection::add ( ResidueChainVectorOption const &  option )

inline

Add an ResidueChainVectorOption.

References all_, check_key(), utility::options::VectorOption_T_< K, T >::key(), RESIDUE_CHAIN_VECTOR_OPTION, and residue_chain_vectors_.

StringVectorOption& utility::options::OptionCollection::add ( StringVectorOption const &  option )

inline

Add a StringVectorOption.

References all_, check_key(), utility::options::VectorOption_T_< K, T >::key(), STRING_VECTOR_OPTION, and string_vectors_.

FileVectorOption& utility::options::OptionCollection::add ( FileVectorOption const &  option )

inline

Add a FileVectorOption.

References all_, check_key(), FILE_VECTOR_OPTION, file_vectors_, and utility::options::VectorOption_T_< K, T >::key().

PathVectorOption& utility::options::OptionCollection::add ( PathVectorOption const &  option )

inline

Add a PathVectorOption.

References all_, check_key(), utility::options::VectorOption_T_< K, T >::key(), PATH_VECTOR_OPTION, and path_vectors_.

template<typename T >

AnyVectorOption< T >& utility::options::OptionCollection::add ( AnyVectorOption< T > const &  option )

inline

Add an AnyVectorOption.

References all_, ANY_VECTOR_OPTION, any_vectors_, check_key(), and utility::options::VectorOption_T_< AnyVectorOptionKey, T >::key().

void utility::options::OptionCollection::add_built_in_options

(

)

Add the built-in options.

References add(), basic::options::OptionKeys::out::path::all, check_specs(), utility::options::ScalarOption_T_< K, T >::def(), utility::options::OptionKeys::options::exit, app.delta_score_per_mutation::help, utility::options::ScalarOption_T_< K, T >::legal(), options, app.pyrosetta_toolkit.modules.SQLPDB::table, utility::options::OptionKeys::options::table::text, basic::options::OptionKeys::inout::dbms::user, and utility::options::OptionKeys::options::table::Wiki.

Referenced by basic::options::initialize().

static void utility::options::OptionCollection::add_relevant ( const OptionKey &  key )

inlinestatic

add OptionKey to list of application relevant options

References relevant_.

Referenced by main(), and register_options().

void utility::options::OptionCollection::check_key ( OptionKey const &  key )

static

Check that a key's identifiers are legal.

References utility::keys::AutoKey< O, S, C >::code(), utility::keys::AutoKey< O, S, C >::id(), utility::keys::AutoKey< O, S, C >::identifier(), ObjexxFCL::is_double(), and suffix().

Referenced by add().

void utility::options::OptionCollection::check_key ( Option const &  option )

static

Check that an option's identifiers are legal.

References utility::options::Option::code(), utility::options::Option::id(), utility::options::Option::identifier(), ObjexxFCL::is_double(), and suffix().

void utility::options::OptionCollection::check_specs

(

)

const

Check for problems in the option specifications.

References begin, basic::options::OptionKeys::cutoutdomain::end, has(), key, option(), and utility::options::std_exit_wrapper().

Referenced by add_built_in_options(), and basic::options::initialize().

void utility::options::OptionCollection::check_values

(

)

const

Check for problems in the option values.

References begin, basic::options::OptionKeys::cutoutdomain::end, has(), key, option(), and utility::options::std_exit_wrapper().

Referenced by load().

std::string utility::options::OptionCollection::cleaned ( std::string const &  s )

static

Cleaned option id with repeat colons condensed.

References basic::options::OptionKeys::in::file::t.

Referenced by load_option_cl(), load_option_file(), and merged().

std::string utility::options::OptionCollection::find_key_cl ( std::string const &  key_string, std::string const &  cid, bool const  top  )

static

Find a user-specified option key in a command line context.

Note

Searches up the context to find a match

References begin, utility::keys::AutoKey< O, S, C >::code(), basic::options::OptionKeys::cutoutdomain::end, has, utility::keys::AutoKey< O, S, C >::id(), utility::keys::AutoKey< O, S, C >::identifier(), is_relevant(), key, merged(), n_part(), n_part_prefix_match(), suffix(), and trim().

Referenced by basic::options::key(), load_option_cl(), and load_option_file().

std::string utility::options::OptionCollection::find_key_file ( std::string const &  key_string, std::string const &  cid, bool const  top  )

static

References has, and merged().

Referenced by load_option_file().

std::string utility::options::OptionCollection::get_argv

(

)

const

Returns a copy of the concatenated argv strings that were initialized in load().

References argv_copy_.

bool utility::options::OptionCollection::has ( BooleanOptionKey const &  key ) const

inline

Is there an option with a BooleanOptionKey?

References booleans_, and utility::keys::SmallKeyVector< K, T >::has().

Referenced by check_specs(), check_values(), load_options_from_stream(), main(), utility::options::operator<<(), set_option_value_cl(), set_option_value_file(), show_all(), show_all_hier(), show_inaccessed_user_options(), show_option_help(), show_option_help_hier(), show_table_text(), show_table_Wiki(), and show_user().

bool utility::options::OptionCollection::has ( IntegerOptionKey const &  key ) const

inline

Is there an option with an IntegerOptionKey?

References utility::keys::SmallKeyVector< K, T >::has(), and integers_.

bool utility::options::OptionCollection::has ( RealOptionKey const &  key ) const

inline

Is there an option with a RealOptionKey?

References utility::keys::SmallKeyVector< K, T >::has(), and reals_.

bool utility::options::OptionCollection::has ( StringOptionKey const &  key ) const

inline

Is there an option with a StringOptionKey?

References utility::keys::SmallKeyVector< K, T >::has(), and strings_.

bool utility::options::OptionCollection::has ( FileOptionKey const &  key ) const

inline

Is there an option with a FileOptionKey?

References files_, and utility::keys::SmallKeyVector< K, T >::has().

bool utility::options::OptionCollection::has ( PathOptionKey const &  key ) const

inline

Is there an option with a PathOptionKey?

References utility::keys::SmallKeyVector< K, T >::has(), and paths_.

bool utility::options::OptionCollection::has ( AnyOptionKey const &  key ) const

inline

Is there an option with an AnyOptionKey?

References anys_, and utility::keys::SmallKeyVector< K, T >::has().

bool utility::options::OptionCollection::has ( BooleanVectorOptionKey const &  key ) const

inline

Is there an option with a BooleanVectorOptionKey?

References boolean_vectors_, and utility::keys::SmallKeyVector< K, T >::has().

bool utility::options::OptionCollection::has ( IntegerVectorOptionKey const &  key ) const

inline

Is there an option with an IntegerVectorOptionKey?

References utility::keys::SmallKeyVector< K, T >::has(), and integer_vectors_.

bool utility::options::OptionCollection::has ( RealVectorOptionKey const &  key ) const

inline

Is there an option with a RealVectorOptionKey?

References utility::keys::SmallKeyVector< K, T >::has(), and real_vectors_.

bool utility::options::OptionCollection::has ( ResidueChainVectorOptionKey const &  key ) const

inline

Is there an option with an IntegerVectorOptionKey?

References utility::keys::SmallKeyVector< K, T >::has(), and residue_chain_vectors_.

bool utility::options::OptionCollection::has ( StringVectorOptionKey const &  key ) const

inline

Is there an option with a StringVectorOptionKey?

References utility::keys::SmallKeyVector< K, T >::has(), and string_vectors_.

bool utility::options::OptionCollection::has ( FileVectorOptionKey const &  key ) const

inline

Is there an option with a FileVectorOptionKey?

References file_vectors_, and utility::keys::SmallKeyVector< K, T >::has().

bool utility::options::OptionCollection::has ( PathVectorOptionKey const &  key ) const

inline

Is there an option with a PathVectorOptionKey?

References utility::keys::SmallKeyVector< K, T >::has(), and path_vectors_.

bool utility::options::OptionCollection::has ( AnyVectorOptionKey const &  key ) const

inline

Is there an option with an AnyVectorOptionKey?

References any_vectors_, and utility::keys::SmallKeyVector< K, T >::has().

bool utility::options::OptionCollection::has ( OptionKey const &  key ) const

inline

Is there an option with an OptionKey?

References all_, and utility::keys::SmallKeyVector< K, T >::has().

bool utility::options::OptionCollection::is_relevant ( OptionKey const &  key )

static

Checks if option has been registered as relevant.

Checks is option has been registered as relevant.

References utility::keys::AutoKey< O, S, C >::id(), and relevant_.

Referenced by find_key_cl().

void utility::options::OptionCollection::load	(	const std::vector< std::string > &	args,
		bool const	free_args
	)

Load the user-specified option values.

References argv_copy_.

Referenced by load().

void utility::options::OptionCollection::load	(	int const	argc,
		char *const	argv[],
		bool const	free_args = false
	)

Load the user-specified option values.

References argv_copy_, and load().

void utility::options::OptionCollection::load	(	std::string	executable_name,
		ValueStrings &	arg_strings,
		bool const	free_args
	)

Load the user-specified option values.

References basic::options::OptionKeys::out::path::all, check_values(), utility::io::oc::cout, utility::options::OptionKeys::options::exit, app.delta_score_per_mutation::help, ObjexxFCL::is_double(), load_option_cl(), load_option_from_file(), load_options_from_file(), utility::excn::EXCN_Msg_Exception::msg(), option(), options, show_all_hier(), show_help_hier(), show_table_text(), show_table_Wiki(), show_user(), utility::options::std_exit_wrapper(), app.pyrosetta_toolkit.modules.SQLPDB::table, utility::options::OptionKeys::options::table::text, ObjexxFCL::trim(), basic::options::OptionKeys::inout::dbms::user, and utility::options::OptionKeys::options::table::Wiki.

void utility::options::OptionCollection::load_option_cl ( std::string const &  arg_string, ValueStrings &  arg_strings, std::string const &  pid  )

private

Load a user-specified option argument from a command line.

References cleaned(), find_key_cl(), set_option_value_cl(), ObjexxFCL::stripped_whitespace(), and top.

Referenced by load(), and load_option_from_file().

void utility::options::OptionCollection::load_option_file ( std::string const &  arg_string, ValueStrings &  val_strings, std::string &  cid, bool const  cl_context = false  )

private

References cleaned(), find_key_cl(), find_key_file(), load_option_from_file(), set_option_value_file(), ObjexxFCL::stripped_whitespace(), and top.

Referenced by load_options_from_stream().

void utility::options::OptionCollection::load_option_from_file ( std::string const &  arg_string, ValueStrings &  arg_strings, std::string const &  pid  )

private

Load one option from user specified file.

References ObjexxFCL::getline(), load_option_cl(), utility::excn::EXCN_Msg_Exception::msg(), app.delta_score_per_mutation::res, and utility::split_to_list().

Referenced by load(), and load_option_file().

void utility::options::OptionCollection::load_options_from_file	(	std::string const &	file_string,
		std::string const &	cid = ""
	)

Load all options in a flags file.

References load_options_from_file_exception(), and utility::excn::EXCN_Msg_Exception::msg().

Referenced by load(), load_options_from_stream(), LigandDockBenchmark::setUp(), and LigandDockScriptBenchmark::setUp().

void utility::options::OptionCollection::load_options_from_file_exception	(	std::string const &	file_string,
		std::string const &	cid = ""
	)

same as load_options_from_file, but throws exception instead of call to std::exit

Load all options in a flags file.

References load_options_from_stream().

Referenced by load_options_from_file().

void utility::options::OptionCollection::load_options_from_stream	(	std::istream &	stream,
		std::string const &	file_string = "STREAM",
		std::string const &	cid = ""
	)

Load all options in a flags file.

References demo.D060_Folding::f, ObjexxFCL::getline(), ObjexxFCL::has(), has(), ObjexxFCL::is_any_of(), basic::options::OptionKeys::frags::j, ObjexxFCL::len_trim_whitespace(), line, load_option_file(), load_options_from_file(), quote, utility::replace_environment_variables(), ObjexxFCL::SPACE(), ObjexxFCL::strip_whitespace(), ObjexxFCL::stripped_whitespace(), ObjexxFCL::TAB(), ObjexxFCL::trim(), and ObjexxFCL::WHITESPACE().

Referenced by load_options_from_file_exception().

std::string utility::options::OptionCollection::merged ( std::string const &  s, std::string const &  t  )

static

Merged option ids with the minimal suffix-prefix overlap, if any, removed.

References cleaned(), min(), n_part(), basic::options::OptionKeys::out::file::o, prefix(), suffix(), basic::options::OptionKeys::in::file::t, and trimmed().

Referenced by find_key_cl(), and find_key_file().

std::string::size_type utility::options::OptionCollection::n_part ( std::string const &  s )

static

Number of parts in an option id.

Referenced by find_key_cl(), merged(), n_part_prefix_match(), prefix(), show_all_hier(), show_option_help_hier(), show_table_text(), suffix(), trim(), and trimmed().

std::string::size_type utility::options::OptionCollection::n_part_prefix_match ( std::string const &  s, std::string const &  t  )

static

Number of prefix parts of two ids that match.

References min(), n_part(), and prefix().

Referenced by find_key_cl().

BooleanOption const& utility::options::OptionCollection::operator() ( BooleanOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

Option by BooleanOptionKey.

References booleans_, utility::options::Option::check_restricted_access(), and option().

BooleanOption& utility::options::OptionCollection::operator() ( BooleanOptionKey const &  key, bool  check_restricted_access = true  )

inline

Option by BooleanOptionKey.

References booleans_, utility::options::Option::check_restricted_access(), and option().

IntegerOption const& utility::options::OptionCollection::operator() ( IntegerOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

Option by IntegerOptionKey.

References utility::options::Option::check_restricted_access(), integers_, and option().

IntegerOption& utility::options::OptionCollection::operator() ( IntegerOptionKey const &  key, bool  check_restricted_access = true  )

inline

Option by IntegerOptionKey.

References utility::options::Option::check_restricted_access(), integers_, and option().

RealOption const& utility::options::OptionCollection::operator() ( RealOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

Option by RealOptionKey.

References utility::options::Option::check_restricted_access(), option(), and reals_.

RealOption& utility::options::OptionCollection::operator() ( RealOptionKey const &  key, bool  check_restricted_access = true  )

inline

Option by RealOptionKey.

References utility::options::Option::check_restricted_access(), option(), and reals_.

StringOption const& utility::options::OptionCollection::operator() ( StringOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

Option by StringOptionKey.

References utility::options::Option::check_restricted_access(), option(), and strings_.

StringOption& utility::options::OptionCollection::operator() ( StringOptionKey const &  key, bool  check_restricted_access = true  )

inline

Option by StringOptionKey.

References utility::options::Option::check_restricted_access(), option(), and strings_.

FileOption const& utility::options::OptionCollection::operator() ( FileOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

Option by FileOptionKey.

References utility::options::Option::check_restricted_access(), files_, and option().

FileOption& utility::options::OptionCollection::operator() ( FileOptionKey const &  key, bool  check_restricted_access = true  )

inline

Option by FileOptionKey.

References utility::options::Option::check_restricted_access(), files_, and option().

PathOption const& utility::options::OptionCollection::operator() ( PathOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

Option by PathOptionKey.

References utility::options::Option::check_restricted_access(), option(), and paths_.

PathOption& utility::options::OptionCollection::operator() ( PathOptionKey const &  key, bool  check_restricted_access = true  )

inline

Option by PathOptionKey.

References utility::options::Option::check_restricted_access(), option(), and paths_.

Option const& utility::options::OptionCollection::operator() ( AnyOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

Option by AnyOptionKey.

References anys_, utility::options::Option::check_restricted_access(), and option().

Option& utility::options::OptionCollection::operator() ( AnyOptionKey const &  key, bool  check_restricted_access = true  )

inline

Option by AnyOptionKey.

References anys_, utility::options::Option::check_restricted_access(), and option().

template<typename OptionType >

OptionType const& utility::options::OptionCollection::operator() ( AnyOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

Option by AnyOptionKey with option type template argument.

References anys_, and option().

template<typename OptionType >

OptionType& utility::options::OptionCollection::operator() ( AnyOptionKey const &  key, bool  check_restricted_access = true  )

inline

Option by AnyOptionKey with option type template argument.

References anys_, and option().

BooleanVectorOption const& utility::options::OptionCollection::operator() ( BooleanVectorOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

VectorOption by BooleanVectorOptionKey.

References boolean_vectors_, utility::options::Option::check_restricted_access(), and option().

BooleanVectorOption& utility::options::OptionCollection::operator() ( BooleanVectorOptionKey const &  key, bool  check_restricted_access = true  )

inline

VectorOption by BooleanVectorOptionKey.

References boolean_vectors_, utility::options::Option::check_restricted_access(), and option().

IntegerVectorOption const& utility::options::OptionCollection::operator() ( IntegerVectorOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

VectorOption by IntegerVectorOptionKey.

References utility::options::Option::check_restricted_access(), integer_vectors_, and option().

IntegerVectorOption& utility::options::OptionCollection::operator() ( IntegerVectorOptionKey const &  key, bool  check_restricted_access = true  )

inline

VectorOption by IntegerVectorOptionKey.

References utility::options::Option::check_restricted_access(), integer_vectors_, and option().

RealVectorOption const& utility::options::OptionCollection::operator() ( RealVectorOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

VectorOption by RealVectorOptionKey.

References utility::options::Option::check_restricted_access(), option(), and real_vectors_.

RealVectorOption& utility::options::OptionCollection::operator() ( RealVectorOptionKey const &  key, bool  check_restricted_access = true  )

inline

VectorOption by RealVectorOptionKey.

References utility::options::Option::check_restricted_access(), option(), and real_vectors_.

ResidueChainVectorOption const& utility::options::OptionCollection::operator() ( ResidueChainVectorOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

VectorOption by ResidueChainVectorOptionKey.

References utility::options::Option::check_restricted_access(), option(), and residue_chain_vectors_.

ResidueChainVectorOption& utility::options::OptionCollection::operator() ( ResidueChainVectorOptionKey const &  key, bool  check_restricted_access = true  )

inline

VectorOption by ResidueChainVectorOptionKey.

References utility::options::Option::check_restricted_access(), option(), and residue_chain_vectors_.

StringVectorOption const& utility::options::OptionCollection::operator() ( StringVectorOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

VectorOption by StringVectorOptionKey.

References utility::options::Option::check_restricted_access(), option(), and string_vectors_.

StringVectorOption& utility::options::OptionCollection::operator() ( StringVectorOptionKey const &  key, bool  check_restricted_access = true  )

inline

VectorOption by StringVectorOptionKey.

References utility::options::Option::check_restricted_access(), option(), and string_vectors_.

FileVectorOption const& utility::options::OptionCollection::operator() ( FileVectorOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

VectorOption by FileVectorOptionKey.

References utility::options::Option::check_restricted_access(), file_vectors_, and option().

FileVectorOption& utility::options::OptionCollection::operator() ( FileVectorOptionKey const &  key, bool  check_restricted_access = true  )

inline

VectorOption by FileVectorOptionKey.

References utility::options::Option::check_restricted_access(), file_vectors_, and option().

PathVectorOption const& utility::options::OptionCollection::operator() ( PathVectorOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

VectorOption by PathVectorOptionKey.

References utility::options::Option::check_restricted_access(), option(), and path_vectors_.

PathVectorOption& utility::options::OptionCollection::operator() ( PathVectorOptionKey const &  key, bool  check_restricted_access = true  )

inline

VectorOption by PathVectorOptionKey.

References utility::options::Option::check_restricted_access(), option(), and path_vectors_.

VectorOption const& utility::options::OptionCollection::operator() ( AnyVectorOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

VectorOption by AnyVectorOptionKey.

References any_vectors_, utility::options::Option::check_restricted_access(), and option().

VectorOption& utility::options::OptionCollection::operator() ( AnyVectorOptionKey const &  key, bool  check_restricted_access = true  )

inline

VectorOption by AnyVectorOptionKey.

References any_vectors_, utility::options::Option::check_restricted_access(), and option().

template<typename VectorOptionType >

VectorOptionType const& utility::options::OptionCollection::operator() ( AnyVectorOptionKey const &  key, bool  check_restricted_access = true  ) const

inline

VectorOption by AnyVectorOptionKey with option type template argument.

References any_vectors_, and option().

template<typename VectorOptionType >

VectorOptionType& utility::options::OptionCollection::operator() ( AnyVectorOptionKey const &  key, bool  check_restricted_access = true  )

inline

VectorOption by AnyVectorOptionKey with option type template argument.

References any_vectors_, and option().

Option const& utility::options::OptionCollection::operator() ( OptionKey const &  key, bool  check_restricted_access = true  ) const

inline

Option by OptionKey.

References all_, ANY_OPTION, ANY_VECTOR_OPTION, any_vectors_, anys_, utility::keys::SmallKeyVector< K, T >::begin(), BOOLEAN_OPTION, BOOLEAN_VECTOR_OPTION, boolean_vectors_, booleans_, utility::io::oc::cerr, utility::down_cast(), FILE_OPTION, FILE_VECTOR_OPTION, file_vectors_, files_, utility::keys::SmallKeyVector< K, T >::has(), INTEGER_OPTION, INTEGER_VECTOR_OPTION, integer_vectors_, integers_, key, option(), PATH_OPTION, PATH_VECTOR_OPTION, path_vectors_, paths_, REAL_OPTION, REAL_VECTOR_OPTION, real_vectors_, reals_, RESIDUE_CHAIN_VECTOR_OPTION, residue_chain_vectors_, runtime_assert, STRING_OPTION, STRING_VECTOR_OPTION, string_vectors_, strings_, and UNKNOWN_OPTION.

Option& utility::options::OptionCollection::operator() ( OptionKey const &  key, bool  check_restricted_access = true  )

inline

Option by OptionKey.

References all_, ANY_OPTION, ANY_VECTOR_OPTION, any_vectors_, anys_, utility::keys::SmallKeyVector< K, T >::begin(), BOOLEAN_OPTION, BOOLEAN_VECTOR_OPTION, boolean_vectors_, booleans_, utility::io::oc::cerr, utility::down_cast(), FILE_OPTION, FILE_VECTOR_OPTION, file_vectors_, files_, utility::keys::SmallKeyVector< K, T >::has(), INTEGER_OPTION, INTEGER_VECTOR_OPTION, integer_vectors_, integers_, key, option(), PATH_OPTION, PATH_VECTOR_OPTION, path_vectors_, paths_, REAL_OPTION, REAL_VECTOR_OPTION, real_vectors_, reals_, RESIDUE_CHAIN_VECTOR_OPTION, residue_chain_vectors_, runtime_assert, STRING_OPTION, STRING_VECTOR_OPTION, string_vectors_, strings_, and UNKNOWN_OPTION.

template<typename OptionType >

OptionType const& utility::options::OptionCollection::operator() ( OptionKey const &  key, bool  check_restricted_access = true  ) const

inline

Option by OptionKey with option type template argument.

References utility::down_cast(), and key.

template<typename OptionType >

OptionType& utility::options::OptionCollection::operator() ( OptionKey const &  key, bool  check_restricted_access = true  )

inline

Option by OptionKey with option type template argument.

References utility::down_cast(), and key.

BooleanOption const& utility::options::OptionCollection::operator[] ( BooleanOptionKey const &  key ) const

inline

OptionCollection[ BooleanOptionKey ].

References booleans_, utility::options::Option::check_restricted_access(), and option().

Referenced by operator[](), and option().

BooleanOption& utility::options::OptionCollection::operator[] ( BooleanOptionKey const &  key )

inline

OptionCollection[ BooleanOptionKey ].

References booleans_, utility::options::Option::check_restricted_access(), and option().

IntegerOption const& utility::options::OptionCollection::operator[] ( IntegerOptionKey const &  key ) const

inline

OptionCollection[ IntegerOptionKey ].

References utility::options::Option::check_restricted_access(), integers_, and option().

IntegerOption& utility::options::OptionCollection::operator[] ( IntegerOptionKey const &  key )

inline

OptionCollection[ IntegerOptionKey ].

References utility::options::Option::check_restricted_access(), integers_, and option().

RealOption const& utility::options::OptionCollection::operator[] ( RealOptionKey const &  key ) const

inline

OptionCollection[ RealOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and reals_.

RealOption& utility::options::OptionCollection::operator[] ( RealOptionKey const &  key )

inline

OptionCollection[ RealOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and reals_.

StringOption const& utility::options::OptionCollection::operator[] ( StringOptionKey const &  key ) const

inline

OptionCollection[ StringOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and strings_.

StringOption& utility::options::OptionCollection::operator[] ( StringOptionKey const &  key )

inline

OptionCollection[ StringOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and strings_.

FileOption const& utility::options::OptionCollection::operator[] ( FileOptionKey const &  key ) const

inline

OptionCollection[ FileOptionKey ].

References utility::options::Option::check_restricted_access(), files_, and option().

FileOption& utility::options::OptionCollection::operator[] ( FileOptionKey const &  key )

inline

OptionCollection[ FileOptionKey ].

References utility::options::Option::check_restricted_access(), files_, and option().

PathOption const& utility::options::OptionCollection::operator[] ( PathOptionKey const &  key ) const

inline

OptionCollection[ PathOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and paths_.

PathOption& utility::options::OptionCollection::operator[] ( PathOptionKey const &  key )

inline

OptionCollection[ PathOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and paths_.

Option const& utility::options::OptionCollection::operator[] ( AnyOptionKey const &  key ) const

inline

OptionCollection[ AnyOptionKey ].

References anys_, utility::options::Option::check_restricted_access(), and option().

Option& utility::options::OptionCollection::operator[] ( AnyOptionKey const &  key )

inline

OptionCollection[ AnyOptionKey ].

References anys_, utility::options::Option::check_restricted_access(), and option().

template<typename OptionType >

OptionType const& utility::options::OptionCollection::operator[] ( AnyOptionKey const &  key ) const

inline

OptionCollection[ AnyOptionKey ] with option type template argument.

References anys_, and option().

template<typename OptionType >

OptionType& utility::options::OptionCollection::operator[] ( AnyOptionKey const &  key )

inline

OptionCollection[ AnyOptionKey ] with option type template argument.

References anys_, and option().

BooleanVectorOption const& utility::options::OptionCollection::operator[] ( BooleanVectorOptionKey const &  key ) const

inline

OptionCollection[ BooleanVectorOptionKey ].

References boolean_vectors_, utility::options::Option::check_restricted_access(), and option().

BooleanVectorOption& utility::options::OptionCollection::operator[] ( BooleanVectorOptionKey const &  key )

inline

OptionCollection[ BooleanVectorOptionKey ].

References boolean_vectors_, utility::options::Option::check_restricted_access(), and option().

IntegerVectorOption const& utility::options::OptionCollection::operator[] ( IntegerVectorOptionKey const &  key ) const

inline

OptionCollection[ IntegerVectorOptionKey ].

References utility::options::Option::check_restricted_access(), integer_vectors_, and option().

IntegerVectorOption& utility::options::OptionCollection::operator[] ( IntegerVectorOptionKey const &  key )

inline

OptionCollection[ IntegerVectorOptionKey ].

References utility::options::Option::check_restricted_access(), integer_vectors_, and option().

RealVectorOption const& utility::options::OptionCollection::operator[] ( RealVectorOptionKey const &  key ) const

inline

OptionCollection[ RealVectorOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and real_vectors_.

RealVectorOption& utility::options::OptionCollection::operator[] ( RealVectorOptionKey const &  key )

inline

OptionCollection[ RealVectorOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and real_vectors_.

ResidueChainVectorOption const& utility::options::OptionCollection::operator[] ( ResidueChainVectorOptionKey const &  key ) const

inline

OptionCollection[ ResidueChainVectorOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and residue_chain_vectors_.

ResidueChainVectorOption& utility::options::OptionCollection::operator[] ( ResidueChainVectorOptionKey const &  key )

inline

OptionCollection[ ResidueChainVectorOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and residue_chain_vectors_.

StringVectorOption const& utility::options::OptionCollection::operator[] ( StringVectorOptionKey const &  key ) const

inline

OptionCollection[ StringVectorOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and string_vectors_.

StringVectorOption& utility::options::OptionCollection::operator[] ( StringVectorOptionKey const &  key )

inline

OptionCollection[ StringVectorOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and string_vectors_.

FileVectorOption const& utility::options::OptionCollection::operator[] ( FileVectorOptionKey const &  key ) const

inline

OptionCollection[ FileVectorOptionKey ].

References utility::options::Option::check_restricted_access(), file_vectors_, and option().

FileVectorOption& utility::options::OptionCollection::operator[] ( FileVectorOptionKey const &  key )

inline

OptionCollection[ FileVectorOptionKey ].

References utility::options::Option::check_restricted_access(), file_vectors_, and option().

PathVectorOption const& utility::options::OptionCollection::operator[] ( PathVectorOptionKey const &  key ) const

inline

OptionCollection[ PathVectorOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and path_vectors_.

PathVectorOption& utility::options::OptionCollection::operator[] ( PathVectorOptionKey const &  key )

inline

OptionCollection[ PathVectorOptionKey ].

References utility::options::Option::check_restricted_access(), option(), and path_vectors_.

VectorOption const& utility::options::OptionCollection::operator[] ( AnyVectorOptionKey const &  key ) const

inline

OptionCollection[ AnyVectorOptionKey ].

References any_vectors_, utility::options::Option::check_restricted_access(), and option().

VectorOption& utility::options::OptionCollection::operator[] ( AnyVectorOptionKey const &  key )

inline

OptionCollection[ AnyVectorOptionKey ].

References any_vectors_, utility::options::Option::check_restricted_access(), and option().

template<typename VectorOptionType >

VectorOptionType const& utility::options::OptionCollection::operator[] ( AnyVectorOptionKey const &  key ) const

inline

OptionCollection[ AnyVectorOptionKey ] with option type template argument.

References any_vectors_, and option().

template<typename VectorOptionType >

VectorOptionType& utility::options::OptionCollection::operator[] ( AnyVectorOptionKey const &  key )

inline

OptionCollection[ AnyVectorOptionKey ] with option type template argument.

References any_vectors_, and option().

Option const& utility::options::OptionCollection::operator[] ( OptionKey const &  key ) const

inline

OptionCollection[ OptionKey ].

References all_, ANY_OPTION, ANY_VECTOR_OPTION, any_vectors_, anys_, utility::keys::SmallKeyVector< K, T >::begin(), BOOLEAN_OPTION, BOOLEAN_VECTOR_OPTION, boolean_vectors_, booleans_, utility::io::oc::cerr, utility::down_cast(), FILE_OPTION, FILE_VECTOR_OPTION, file_vectors_, files_, utility::keys::SmallKeyVector< K, T >::has(), INTEGER_OPTION, INTEGER_VECTOR_OPTION, integer_vectors_, integers_, key, option(), PATH_OPTION, PATH_VECTOR_OPTION, path_vectors_, paths_, REAL_OPTION, REAL_VECTOR_OPTION, real_vectors_, reals_, RESIDUE_CHAIN_VECTOR_OPTION, residue_chain_vectors_, runtime_assert, STRING_OPTION, STRING_VECTOR_OPTION, string_vectors_, strings_, and UNKNOWN_OPTION.

Option& utility::options::OptionCollection::operator[] ( OptionKey const &  key )

inline

OptionCollection[ OptionKey ].

References all_, ANY_OPTION, ANY_VECTOR_OPTION, any_vectors_, anys_, utility::keys::SmallKeyVector< K, T >::begin(), BOOLEAN_OPTION, BOOLEAN_VECTOR_OPTION, boolean_vectors_, booleans_, utility::io::oc::cerr, utility::down_cast(), FILE_OPTION, FILE_VECTOR_OPTION, file_vectors_, files_, utility::keys::SmallKeyVector< K, T >::has(), INTEGER_OPTION, INTEGER_VECTOR_OPTION, integer_vectors_, integers_, key, option(), PATH_OPTION, PATH_VECTOR_OPTION, path_vectors_, paths_, REAL_OPTION, REAL_VECTOR_OPTION, real_vectors_, reals_, RESIDUE_CHAIN_VECTOR_OPTION, residue_chain_vectors_, runtime_assert, STRING_OPTION, STRING_VECTOR_OPTION, string_vectors_, strings_, and UNKNOWN_OPTION.

template<typename OptionType >

OptionType const& utility::options::OptionCollection::operator[] ( OptionKey const &  key ) const

inline

OptionCollection[ OptionKey ] with option type template argument.

References utility::down_cast(), and operator[]().

template<typename OptionType >

OptionType& utility::options::OptionCollection::operator[] ( OptionKey const &  key )

inline

OptionCollection[ OptionKey ] with option type template argument.

References utility::down_cast(), and operator[]().

BooleanOption const& utility::options::OptionCollection::option ( BooleanOptionKey const &  key ) const

inline

Option by BooleanOptionKey.

References operator[]().

Referenced by check_specs(), check_values(), basic::options::int2afteroption(), basic::options::intafteroption(), load(), operator()(), utility::options::operator<<(), operator[](), basic::options::optional_positive_intafteroption(), basic::options::real2afteroption(), basic::options::real3afteroption(), basic::options::realafteroption(), set_option_value_cl(), set_option_value_file(), show_all(), show_all_hier(), show_inaccessed_user_options(), show_option_help(), show_option_help_hier(), show_table_text(), show_table_Wiki(), show_user(), and basic::options::stringafteroption().

BooleanOption& utility::options::OptionCollection::option ( BooleanOptionKey const &  key )

inline

Option by BooleanOptionKey.

References operator[]().

IntegerOption const& utility::options::OptionCollection::option ( IntegerOptionKey const &  key ) const

inline

Option by IntegerOptionKey.

References operator[]().

IntegerOption& utility::options::OptionCollection::option ( IntegerOptionKey const &  key )

inline

Option by IntegerOptionKey.

References operator[]().

RealOption const& utility::options::OptionCollection::option ( RealOptionKey const &  key ) const

inline

Option by RealOptionKey.

References operator[]().

RealOption& utility::options::OptionCollection::option ( RealOptionKey const &  key )

inline

Option by RealOptionKey.

References operator[]().

StringOption const& utility::options::OptionCollection::option ( StringOptionKey const &  key ) const

inline

Option by StringOptionKey.

References operator[]().

StringOption& utility::options::OptionCollection::option ( StringOptionKey const &  key )

inline

Option by StringOptionKey.

References operator[]().

FileOption const& utility::options::OptionCollection::option ( FileOptionKey const &  key ) const

inline

Option by FileOptionKey.

References operator[]().

FileOption& utility::options::OptionCollection::option ( FileOptionKey const &  key )

inline

Option by FileOptionKey.

References operator[]().

PathOption const& utility::options::OptionCollection::option ( PathOptionKey const &  key ) const

inline

Option by PathOptionKey.

References operator[]().

PathOption& utility::options::OptionCollection::option ( PathOptionKey const &  key )

inline

Option by PathOptionKey.

References operator[]().

Option const& utility::options::OptionCollection::option ( AnyOptionKey const &  key ) const

inline

Option by AnyOptionKey.

References operator[]().

Option& utility::options::OptionCollection::option ( AnyOptionKey const &  key )

inline

Option by AnyOptionKey.

References operator[]().

template<typename OptionType >

OptionType const& utility::options::OptionCollection::option ( AnyOptionKey const &  key ) const

inline

Option by AnyOptionKey with option type template argument.

References key.

template<typename OptionType >

OptionType& utility::options::OptionCollection::option ( AnyOptionKey const &  key )

inline

Option by AnyOptionKey with option type template argument.

References key.

BooleanVectorOption const& utility::options::OptionCollection::option ( BooleanVectorOptionKey const &  key ) const

inline

VectorOption by BooleanVectorOptionKey.

References operator[]().

BooleanVectorOption& utility::options::OptionCollection::option ( BooleanVectorOptionKey const &  key )

inline

VectorOption by BooleanVectorOptionKey.

References operator[]().

IntegerVectorOption const& utility::options::OptionCollection::option ( IntegerVectorOptionKey const &  key ) const

inline

VectorOption by IntegerVectorOptionKey.

References operator[]().

IntegerVectorOption& utility::options::OptionCollection::option ( IntegerVectorOptionKey const &  key )

inline

VectorOption by IntegerVectorOptionKey.

References operator[]().

RealVectorOption const& utility::options::OptionCollection::option ( RealVectorOptionKey const &  key ) const

inline

VectorOption by RealVectorOptionKey.

References operator[]().

RealVectorOption& utility::options::OptionCollection::option ( RealVectorOptionKey const &  key )

inline

VectorOption by RealVectorOptionKey.

References operator[]().

StringVectorOption const& utility::options::OptionCollection::option ( StringVectorOptionKey const &  key ) const

inline

VectorOption by StringVectorOptionKey.

References operator[]().

StringVectorOption& utility::options::OptionCollection::option ( StringVectorOptionKey const &  key )

inline

VectorOption by StringVectorOptionKey.

References operator[]().

FileVectorOption const& utility::options::OptionCollection::option ( FileVectorOptionKey const &  key ) const

inline

VectorOption by FileVectorOptionKey.

References operator[]().

FileVectorOption& utility::options::OptionCollection::option ( FileVectorOptionKey const &  key )

inline

VectorOption by FileVectorOptionKey.

References operator[]().

PathVectorOption const& utility::options::OptionCollection::option ( PathVectorOptionKey const &  key ) const

inline

VectorOption by PathVectorOptionKey.

References operator[]().

PathVectorOption& utility::options::OptionCollection::option ( PathVectorOptionKey const &  key )

inline

VectorOption by PathVectorOptionKey.

References operator[]().

VectorOption const& utility::options::OptionCollection::option ( AnyVectorOptionKey const &  key ) const

inline

VectorOption by AnyVectorOptionKey.

References operator[]().

VectorOption& utility::options::OptionCollection::option ( AnyVectorOptionKey const &  key )

inline

VectorOption by AnyVectorOptionKey.

References operator[]().

template<typename VectorOptionType >

VectorOptionType const& utility::options::OptionCollection::option ( AnyVectorOptionKey const &  key ) const

inline

VectorOption by AnyVectorOptionKey with option type template argument.

References key.

template<typename VectorOptionType >

VectorOptionType& utility::options::OptionCollection::option ( AnyVectorOptionKey const &  key )

inline

VectorOption by AnyVectorOptionKey with option type template argument.

References key.

Option const& utility::options::OptionCollection::option ( OptionKey const &  key ) const

inline

Option by OptionKey.

References operator[]().

Option& utility::options::OptionCollection::option ( OptionKey const &  key )

inline

Option by OptionKey.

References operator[]().

template<typename OptionType >

OptionType const& utility::options::OptionCollection::option ( OptionKey const &  key ) const

inline

Option by OptionKey with option type template argument.

References key.

template<typename OptionType >

OptionType& utility::options::OptionCollection::option ( OptionKey const &  key )

inline

Option by OptionKey with option type template argument.

References key.

std::string utility::options::OptionCollection::prefix ( std::string const &  s, int const  n = 1  )

static

Prefix of an option id with a specified number of parts.

References n_part(), runtime_assert, and basic::options::OptionKeys::in::file::s.

Referenced by yaml.scanner.Scanner::check_document_end(), yaml.scanner.Scanner::check_document_start(), merged(), n_part_prefix_match(), yaml.scanner.Scanner::scan_anchor(), yaml.scanner.Scanner::scan_block_scalar(), yaml.scanner.Scanner::scan_directive_name(), yaml.scanner.Scanner::scan_flow_scalar(), yaml.scanner.Scanner::scan_yaml_directive_number(), show_all(), show_all_hier(), show_option_help(), show_option_help_hier(), show_table_text(), show_table_Wiki(), and show_user().

void utility::options::OptionCollection::set_option_value_cl ( std::string const &  key_id, ValueStrings &  arg_strings  )

private

Set a user-specified option value from a command line.

Set a user-specified option value from a command line note Decides whether to use value strings and erases the ones used.

References utility::options::Option::can_hold_another(), utility::options::Option::cl_value(), has, has(), utility::keys::AutoKey< O, S, C >::id(), ObjexxFCL::is_any_of(), utility::options::Option::is_cl_value(), key, utility::options::VectorOption::n(), utility::options::VectorOption::n_lower(), option(), runtime_assert, utility::options::OptionKey::scalar(), and utility::options::OptionKey::vector().

Referenced by load_option_cl().

void utility::options::OptionCollection::set_option_value_file ( std::string const &  key_id, ValueStrings &  val_strings  )

private

References utility::options::ScalarOption_T_< K, T >::cl_value(), has, has(), utility::keys::AutoKey< O, S, C >::id(), key, utility::options::VectorOption::n(), utility::options::VectorOption::n_lower(), option(), runtime_assert, utility::options::OptionKey::scalar(), and utility::options::OptionKey::vector().

Referenced by load_option_file().

static void utility::options::OptionCollection::set_show_accessed_options_flag ( bool  v )

inlinestatic

modify 'show_accessed_options' flag;

References show_accessed_options_, and test.T850_SubClassing::v.

static void utility::options::OptionCollection::set_show_unused_options_flag ( bool  v )

inlinestatic

modify 'show_unused_options' flag;

References show_unused_options_, and test.T850_SubClassing::v.

void utility::options::OptionCollection::show_accessed_options

(

std::ostream &

stream

)

const

Show accessed list of options.

References utility::keys::SmallKeyVector< K, T >::begin(), boolean_vectors_, booleans_, utility::keys::SmallKeyVector< K, T >::end(), file_vectors_, files_, integer_vectors_, integers_, path_vectors_, paths_, real_vectors_, reals_, utility::options::show_accessed_options_T(), string_vectors_, and strings_.

Referenced by ~OptionCollection().

void utility::options::OptionCollection::show_all

(

std::ostream &

stream

)

const

Show all the options and their values.

References begin, basic::options::OptionKeys::cutoutdomain::end, utility::options::Option::equals_string(), has(), utility::options::Option::id(), key, option(), and prefix().

void utility::options::OptionCollection::show_all_hier

(

std::ostream &

stream

)

const

Show all the options and their values in a hierarchy format.

References begin, basic::options::OptionKeys::cutoutdomain::end, utility::options::Option::equals_string(), has(), utility::options::Option::id(), key, basic::options::OptionKeys::in::file::l, n_part(), option(), prefix(), and suffix().

Referenced by load().

void utility::options::OptionCollection::show_help

(

std::ostream &

stream

)

Show all the options and their descriptions.

References begin, basic::options::OptionKeys::cutoutdomain::end, key, relevant_, and show_option_help().

void utility::options::OptionCollection::show_help_hier

(

std::ostream &

stream

)

Show all the options and their descriptions in a hierarchy format.

References ObjexxFCL::format::A(), begin, COL1, COL2, COL3, basic::options::OptionKeys::cutoutdomain::end, BuildPackagedBindings::format, key, ObjexxFCL::format::LJ(), relevant_, ObjexxFCL::format::RJ(), and show_option_help_hier().

Referenced by load().

void utility::options::OptionCollection::show_inaccessed_user_options

(

std::ostream &

stream

)

const

Show inaccessed user-specified options.

Show the user-specified options and their values.

References begin, basic::options::OptionKeys::cutoutdomain::end, has(), utility::options::Option::id(), utility::options::Option::is_been_accessed(), key, option(), utility::options::Option::set_accessed(), utility::options::Option::user(), and utility::options::Option::value_string().

void utility::options::OptionCollection::show_option_help	(	OptionKey const &	key,
		std::string &	group,
		std::ostream &	stream
	)

Show one option and it description.

References utility::options::Option::default_string(), utility::options::Option::description(), has(), utility::options::Option::id(), utility::options::Option::legal_string(), min(), option(), prefix(), space_prefixed(), and wrapped().

Referenced by show_help().

void utility::options::OptionCollection::show_option_help_hier	(	OptionKey const &	key,
		std::string &	group,
		std::ostream &	stream
	)

Show one option and it description in a hierarchy format.

References ObjexxFCL::format::A(), COL1, COL2, COL3, utility::options::Option::description(), BuildPackagedBindings::format, has(), utility::options::Option::id(), n_part(), option(), prefix(), ObjexxFCL::format::RJ(), suffix(), utility::options::Option::type_string(), utility::options::Option::value_string(), and wrapped().

Referenced by show_help_hier().

void utility::options::OptionCollection::show_table_text

(

std::ostream &

stream

)

const

Show the options definitions table in text format.

References begin, utility::options::Option::default_string(), utility::options::Option::description(), basic::options::OptionKeys::cutoutdomain::end, has(), utility::options::Option::id(), key, basic::options::OptionKeys::in::file::l, utility::options::Option::legal_string(), n_part(), option(), prefix(), suffix(), and utility::options::Option::type_string().

Referenced by load().

void utility::options::OptionCollection::show_table_Wiki

(

std::ostream &

stream

)

const

Show the options definitions table in Wiki format.

Note

Based on Sergey Lyskov's Python Wiki table generator code

References begin, utility::options::Option::default_string(), utility::options::Option::description(), basic::options::OptionKeys::cutoutdomain::end, has(), utility::options::Option::id(), key, utility::options::Option::legal_string(), option(), prefix(), suffix(), and utility::options::Option::type_string().

Referenced by load().

void utility::options::OptionCollection::show_unused_options

(

std::ostream &

stream

)

const

Show options that were user-specified, but not yet accessed. Differs from show_inaccessed_user_options() mainly by formatting And how the options are accessed. (This one should be destructor safe.)

References utility::keys::SmallKeyVector< K, T >::begin(), boolean_vectors_, booleans_, utility::keys::SmallKeyVector< K, T >::end(), file_vectors_, files_, integer_vectors_, integers_, path_vectors_, paths_, real_vectors_, reals_, utility::options::show_unused_options_T(), string_vectors_, and strings_.

Referenced by ~OptionCollection().

void utility::options::OptionCollection::show_user

(

std::ostream &

stream

)

const

Show the user-specified options and their values.

References begin, basic::options::OptionKeys::cutoutdomain::end, has(), utility::options::Option::id(), utility::options::Option::is_been_accessed(), key, option(), prefix(), utility::options::Option::set_accessed(), utility::options::Option::user(), and utility::options::Option::value_string().

Referenced by load().

static std::string utility::options::OptionCollection::space_prefixed ( std::string const &  s, int const  n = 1  )

inlinestatic

Space-prefixed string except blank if string is empty.

References basic::options::OptionKeys::in::file::s.

Referenced by show_option_help().

std::string utility::options::OptionCollection::suffix ( std::string const &  s, int const  n = 1  )

static

Suffix of an option id with a specified number of parts.

References n_part(), runtime_assert, and basic::options::OptionKeys::in::file::s.

Referenced by check_key(), find_key_cl(), merged(), show_all_hier(), show_option_help_hier(), show_table_text(), and show_table_Wiki().

static std::string utility::options::OptionCollection::tab_prefixed ( std::string const &  s, int const  n = 1  )

inlinestatic

Tab-prefixed string except blank if string is empty.

References basic::options::OptionKeys::in::file::s.

std::string & utility::options::OptionCollection::trim ( std::string &  s, int const  n = 1  )

static

Trim a specified number of parts from the suffix of an option id.

References n_part(), runtime_assert, and basic::options::OptionKeys::in::file::s.

Referenced by find_key_cl().

std::string utility::options::OptionCollection::trimmed ( std::string const &  s, int const  n = 1  )

static

Prefix of an option id with a specified number of suffix parts removed.

References n_part(), runtime_assert, and basic::options::OptionKeys::in::file::s.

Referenced by merged().

std::string utility::options::OptionCollection::wrapped ( std::string const &  s, std::string::size_type const  indent = 10, std::string::size_type const  width = 80, std::string const &  header_for_extra_lines = ""  )

static

String wrapped and indented.

References basic::options::OptionKeys::score::fiber_diffraction::b, ObjexxFCL::is_any_of(), basic::options::OptionKeys::in::file::l, min(), runtime_assert, basic::options::OptionKeys::in::file::s, numeric::statistics::w(), and basic::options::OptionKeys::mp::visualize::width.

Referenced by show_option_help(), and show_option_help_hier().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  stream, OptionCollection const &  options  )

friend

Output to stream.

Member Data Documentation

All utility::options::OptionCollection::all_

private

All options (non-owning pointers)

Referenced by add(), has(), operator()(), and operator[]().

AnyVectors utility::options::OptionCollection::any_vectors_

private

Any value type vector options.

Referenced by add(), has(), operator()(), and operator[]().

Anys utility::options::OptionCollection::anys_

private

Any value type options.

Referenced by add(), has(), operator()(), and operator[]().

std::string utility::options::OptionCollection::argv_copy_

private

keep a copy of argv around in case people want to get at it elsewhere in the code.

Referenced by get_argv(), and load().

BooleanVectors utility::options::OptionCollection::boolean_vectors_

private

Boolean vector options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

Booleans utility::options::OptionCollection::booleans_

private

Boolean options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

FileVectors utility::options::OptionCollection::file_vectors_

private

File vector options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

Files utility::options::OptionCollection::files_

private

File options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

IntegerVectors utility::options::OptionCollection::integer_vectors_

private

Integer vector options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

Integers utility::options::OptionCollection::integers_

private

Integer options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

PathVectors utility::options::OptionCollection::path_vectors_

private

Path vector options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

Paths utility::options::OptionCollection::paths_

private

Path options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

RealVectors utility::options::OptionCollection::real_vectors_

private

Real vector options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

Reals utility::options::OptionCollection::reals_

private

Real options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

std::vector< OptionKey const * > utility::options::OptionCollection::relevant_

staticprivate

global list of application relevant options

Referenced by add_relevant(), is_relevant(), show_help(), and show_help_hier().

ResidueChainVectors utility::options::OptionCollection::residue_chain_vectors_

private

Residue/chain vector options.

Referenced by add(), has(), operator()(), and operator[]().

bool utility::options::OptionCollection::show_accessed_options_ = false

staticprivate

Flag indicating that list of accessed option should be printed when destructor of OptionCollection is called. This flag is false by default.

Flag indicating that list of accessed option should be printed when destructor of OptionCollection is called.

Referenced by set_show_accessed_options_flag(), and ~OptionCollection().

bool utility::options::OptionCollection::show_unused_options_ = false

staticprivate

Flag indicating that list of user specified but inaccessed options should be printed when destructor of OptionCollection is called. This flag is false by default.

Flag indicating that list of user set but not accessed option should be printed when destructor of OptionCollection is called.

Referenced by set_show_unused_options_flag(), and ~OptionCollection().

StringVectors utility::options::OptionCollection::string_vectors_

private

String vector options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

Strings utility::options::OptionCollection::strings_

private

String options.

Referenced by add(), has(), operator()(), operator[](), show_accessed_options(), and show_unused_options().

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

• src/utility/options/OptionCollection.hh
• src/utility/options/OptionCollection.cc