ToolOptions Class Reference

Inheritance diagram for ToolOptions:

Collaboration diagram for ToolOptions:

Public Member Functions
void	addGeneric (po::options_description &o)
	Appends generic options (those that the user can see)
string	print () const
	Returns a string listing the encapsulated options, suitable for logging.
void	addGeneric (po::options_description &o)
	Appends generic options (those that the user can see)
void	addGeneric (po::options_description &o)
	Appends generic options (those that the user can see)
bool	postConditions (po::variables_map &vm)
	Post-processing of options returning true if there were no problems, otherwise false.
void	addGeneric (po::options_description &o)
	Appends generic options (those that the user can see)
void	addHidden (po::options_description &o)
	Appends hidden options (these generally match positional)
void	addPositional (po::positional_options_description &p)
	Appends positional options.
bool	check (po::variables_map &map)
	Validates passed options, returning true if there is a problem or false if not.
bool	postConditions (po::variables_map &map)
	Post-processing of options returning true if there were no problems, otherwise false.
string	help () const
	Returns a slice of the example command-line in the help output.
string	print () const
	Returns a string listing the encapsulated options, suitable for logging.
void	addGeneric (po::options_description &o)
	Appends generic options (those that the user can see)
string	print () const
	Returns a string listing the encapsulated options, suitable for logging.
bool	postConditions (po::variables_map &map)
	Post-processing of options returning true if there were no problems, otherwise false.
void	addGeneric (po::options_description &o)
	Appends generic options (those that the user can see)
string	print () const
	Returns a string listing the encapsulated options, suitable for logging.
bool	postConditions (po::variables_map &map)
	Post-processing of options returning true if there were no problems, otherwise false.
void	addGeneric (po::options_description &o)
	Appends generic options (those that the user can see)
string	print () const
	Returns a string listing the encapsulated options, suitable for logging.

Public Attributes
string	atom_selection
string	solvent_selection
double	cutoff
string	fit_radius_str
string	fit_area_str
double	esp_radius
double	esp_area
double	weight
bool	close_solvent
string	esp_file
uint	seed
uint	solvent_size
string	protein_selection
string	lipid_selection
uint	maxdt
uint	threshold
bool	reimage
double	xmin
double	xmax
double	ymin
double	ymax
uint	xbins
uint	ybins
string	calc_type
string	reference_filename
string	align_selection
string	target_selection
CalcType	type
bool	upper_only
bool	lower_only
bool	has_align
string	modeltype
string	bond_atom_selection
int	max_offset
bool	group_centroids
bool	residue_centroids
bool	com
float	bondlength
string	timeseries
double	min_dist
double	max_dist
bool	by_molecule
bool	by_fragment
int	num_bins
double	suiteness_cutoff

Member Function Documentation

addGeneric() [1/7]

void ToolOptions::addGeneric ( po::options_description & opts )

inlinevirtual

Appends generic options (those that the user can see)

Reimplemented from loos::OptionsFramework::OptionsPackage.

addGeneric() [2/7]

void ToolOptions::addGeneric ( po::options_description & opts )

inlinevirtual

Appends generic options (those that the user can see)

Reimplemented from loos::OptionsFramework::OptionsPackage.

addGeneric() [3/7]

void ToolOptions::addGeneric ( po::options_description & opts )

inlinevirtual

Appends generic options (those that the user can see)

Reimplemented from loos::OptionsFramework::OptionsPackage.

addGeneric() [4/7]

void ToolOptions::addGeneric ( po::options_description & opts )

inlinevirtual

Appends generic options (those that the user can see)

Reimplemented from loos::OptionsFramework::OptionsPackage.

addGeneric() [5/7]

void ToolOptions::addGeneric ( po::options_description & opts )

inlinevirtual

Appends generic options (those that the user can see)

Reimplemented from loos::OptionsFramework::OptionsPackage.

addGeneric() [6/7]

void ToolOptions::addGeneric ( po::options_description & opts )

inlinevirtual

Appends generic options (those that the user can see)

Reimplemented from loos::OptionsFramework::OptionsPackage.

addGeneric() [7/7]

void ToolOptions::addGeneric ( po::options_description & opts )

inlinevirtual

Appends generic options (those that the user can see)

Reimplemented from loos::OptionsFramework::OptionsPackage.

addHidden()

void ToolOptions::addHidden ( po::options_description & opts )

inlinevirtual

Appends hidden options (these generally match positional)

Reimplemented from loos::OptionsFramework::OptionsPackage.

addPositional()

void ToolOptions::addPositional ( po::positional_options_description & opts )

inlinevirtual

Appends positional options.

Reimplemented from loos::OptionsFramework::OptionsPackage.

check()

bool ToolOptions::check ( po::variables_map & map )

inlinevirtual

Validates passed options, returning true if there is a problem or false if not.

check() is typically used to validate positional options. For example, if you tool needs a command line that looks like:

* tool [options] min-value max-value number-of-bins
* 

then check() would verify that min-value, max-value, and number-of-bins were passed on the command-line. Another example is where there are mutually-exclusive options. This would be checked by check().

Reimplemented from loos::OptionsFramework::OptionsPackage.

help()

string ToolOptions::help ( ) const

inlinevirtual

Returns a slice of the example command-line in the help output.

This is used specifically for positional options. If your tool has a command line that looks like:

* tool [options] min-value max-value selection
* 

The required arguments min-value, max-value, and selection are actually "hidden" options and will not be printed out when boost::program_options generates its help message. The AggregateOptions class will build the full command line for the help message by using the help() methods from each OptionsPackage, printing out something like the above on the command line as part of the help output.

Reimplemented from loos::OptionsFramework::OptionsPackage.

postConditions() [1/4]

bool ToolOptions::postConditions ( po::variables_map & map )

inlinevirtual

Post-processing of options returning true if there were no problems, otherwise false.

postConditions() is called after options parsing and validation is complete. This is a mechanism for a subclass to do additional processing with the options it has been provided. For example, a model option subclass might read in the specified model and copy coordinates from an optionally specified file.

Note that the return value from postConditions() is the opposite of check(). Here, a true is returned if there are no problems.

Reimplemented from loos::OptionsFramework::OptionsPackage.

postConditions() [2/4]

bool ToolOptions::postConditions ( po::variables_map & map )

inlinevirtual

Post-processing of options returning true if there were no problems, otherwise false.

postConditions() is called after options parsing and validation is complete. This is a mechanism for a subclass to do additional processing with the options it has been provided. For example, a model option subclass might read in the specified model and copy coordinates from an optionally specified file.

Note that the return value from postConditions() is the opposite of check(). Here, a true is returned if there are no problems.

Reimplemented from loos::OptionsFramework::OptionsPackage.

postConditions() [3/4]

bool ToolOptions::postConditions ( po::variables_map & map )

inlinevirtual

Post-processing of options returning true if there were no problems, otherwise false.

postConditions() is called after options parsing and validation is complete. This is a mechanism for a subclass to do additional processing with the options it has been provided. For example, a model option subclass might read in the specified model and copy coordinates from an optionally specified file.

Note that the return value from postConditions() is the opposite of check(). Here, a true is returned if there are no problems.

Reimplemented from loos::OptionsFramework::OptionsPackage.

postConditions() [4/4]

bool ToolOptions::postConditions ( po::variables_map & map )

inlinevirtual

Post-processing of options returning true if there were no problems, otherwise false.

postConditions() is called after options parsing and validation is complete. This is a mechanism for a subclass to do additional processing with the options it has been provided. For example, a model option subclass might read in the specified model and copy coordinates from an optionally specified file.

Note that the return value from postConditions() is the opposite of check(). Here, a true is returned if there are no problems.

Reimplemented from loos::OptionsFramework::OptionsPackage.

print() [1/5]

string ToolOptions::print ( ) const

inlinevirtual

Returns a string listing the encapsulated options, suitable for logging.

Reimplemented from loos::OptionsFramework::OptionsPackage.

print() [2/5]

string ToolOptions::print ( ) const

inlinevirtual

Returns a string listing the encapsulated options, suitable for logging.

Reimplemented from loos::OptionsFramework::OptionsPackage.

print() [3/5]

string ToolOptions::print ( ) const

inlinevirtual

Returns a string listing the encapsulated options, suitable for logging.

Reimplemented from loos::OptionsFramework::OptionsPackage.

print() [4/5]

string ToolOptions::print ( ) const

inlinevirtual

Returns a string listing the encapsulated options, suitable for logging.

Reimplemented from loos::OptionsFramework::OptionsPackage.

print() [5/5]

string ToolOptions::print ( ) const

inlinevirtual

Returns a string listing the encapsulated options, suitable for logging.

Reimplemented from loos::OptionsFramework::OptionsPackage.

---

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

• Tools/esp_mesh.cpp
• Tools/lipid_survival.cpp
• Tools/membrane_map.cpp
• Tools/model-select.cpp
• Tools/ocf.cpp
• Tools/rad-gyr.cpp
• Tools/rna_suites.cpp