BALL::CommandlineParser Class Reference

#include <BALL/FORMAT/commandlineParser.h>

Public Member Functions
	CommandlineParser (String tool_name, String tool_description, String tool_version, String build_date, String category="")
void	setToolManual (const String &manual)
void	registerParameter (String name, String description, ParameterType type, bool mandatory=false, String default_value="", bool hidden=false)
void	registerFlag (String name, String description, bool default_gui_value=false, bool hidden=false)
void	registerAdvancedParameters (Options &options)
void	setParameterAsAdvanced (String name)
void	setParameterRestrictions (String par_name, double min_value, double max_value)
void	setParameterRestrictions (String par_name, list< String > &allowed_values)
void	setOutputFormatSource (String output_parname, String input_parname)
void	setSupportedFormats (String par_name, String supported_formats)
void	parse (int argc, char *argv[])
void	copyAdvancedParametersToOptions (Options &options)
const String &	get (String name)
bool	has (String name)
const list< String > &	getList (String name)
void	printHelp (const std::set< String > &parameter_names=std::set< String >(), bool show_manual=true)
void	printToolInfo ()
const String &	getStartTime ()
const String &	getStartCommand ()

Static Public Attributes
static const String	NOT_FOUND
static const list< String >	EMTPY_LIST

Detailed Description

Class for parsing parameters specified on the command line.
Register the parameters and flags of your tool with registerParameter(), resp. registerFlag() and have the command-line parsed with parse(). After this, you can retrieve the values of all parameters with get().
In addition to this, you can also register a tool-manual text, define restrictions on parameters and register file-formats that are supported for in- or output-files.
If the parameter '-write_par somefilename.xml' is given to the program, an xml-based parameter-file will be automatically written, containing the specification the tool, all its parameters and all parameter values used on the commend-line.
If the parameter '-par somefilename.xml' is used, such a file can be read, so that the parameter-values stored in it will be used. However, if, although this is not necessary, parameters (other than -par) are specified on the command-line, their values will automatically overload those stored in the xml-file.

The parameter '-env' allows to differentiate between command line ('cmdline') behaviour and special adaptions to workflow systems like galaxy or knime.

Definition at line 45 of file commandlineParser.h.

Constructor & Destructor Documentation

BALL::CommandlineParser::CommandlineParser	(	String	tool_name,
		String	tool_description,
		String	tool_version,
		String	build_date,
		String	category = ""
	)

Member Function Documentation

void BALL::CommandlineParser::copyAdvancedParametersToOptions

(

Options &

options

)

Copies names and values of all advanced parameters to the given Options object.

const String& BALL::CommandlineParser::get

(

String

name

)

Returns the value for a given parameter name.
Example: For "-o outfile.sdf", CommandlineParser::get("o") will return "outfile.sdf".

const list<String>& BALL::CommandlineParser::getList

(

String

name

)

Returns a parameter-list for a given parameter name.
Example: For "-i infile1.sdf infile2.sdf", CommandlineParser::getList("i") will return a vector containing 'infile1.sdf' and infile2.sdf'.

const String& BALL::CommandlineParser::getStartCommand

(

)

Get the exact command with which the tool was started on the command-line.

const String& BALL::CommandlineParser::getStartTime

(

)

bool BALL::CommandlineParser::has

(

String

name

)

Find out whether a the parameter or flag has been specified on the command-line.

void BALL::CommandlineParser::parse	(	int	argc,
		char *	argv[]
	)

Parse all parameters found in the command line

void BALL::CommandlineParser::printHelp	(	const std::set< String > &	parameter_names = std::set< String >(),
		bool	show_manual = true
	)

Print information about about all registered parameters.
If 'parameter_names' is specified, only information those parameters is shown.

void BALL::CommandlineParser::printToolInfo

(

)

void BALL::CommandlineParser::registerAdvancedParameters

(

Options &

options

)

void BALL::CommandlineParser::registerFlag	(	String	name,
		String	description,
		bool	default_gui_value = false,
		bool	hidden = false
	)

void BALL::CommandlineParser::registerParameter	(	String	name,
		String	description,
		ParameterType	type,
		bool	mandatory = false,
		String	default_value = "",
		bool	hidden = false
	)

void BALL::CommandlineParser::setOutputFormatSource	(	String	output_parname,
		String	input_parname
	)

In case of output-files, this functions allows to specify the name of an input-parameter, whose format should be used for the given output-parameter.
Note, that this function will only have an effect on the creation of config-files for workflow-systems (Galaxy, Knime, etc.) and not for the command-line interface, where the user will directly specify output-filenames.

void BALL::CommandlineParser::setParameterAsAdvanced

(

String

name

)

void BALL::CommandlineParser::setParameterRestrictions	(	String	par_name,
		double	min_value,
		double	max_value
	)

Register the minimal and maximal allowed value for a numerical parameter.

void BALL::CommandlineParser::setParameterRestrictions	(	String	par_name,
		list< String > &	allowed_values
	)

Register the allowed values for a string-parameter.

void BALL::CommandlineParser::setSupportedFormats	(	String	par_name,
		String	supported_formats
	)

Register the supported formats for input-/output-files.

Parameters

supported_formats

supported file-formats separated by commas

void BALL::CommandlineParser::setToolManual

(

const String &

manual

)

Set the text to be displayed as mini-manual when starting the tool, containing a few sentences describing what the tool should be good for ...

Member Data Documentation

const list<String> BALL::CommandlineParser::EMTPY_LIST

static

Definition at line 54 of file commandlineParser.h.

const String BALL::CommandlineParser::NOT_FOUND

static

Definition at line 53 of file commandlineParser.h.