ArgumentParser

Class

ArgumentParser

Stores multiple ArgParseOption objects and parses the command line arguments for these options.

ArgumentParser

Include Headers

seqan/arg_parse.h

Remarks

See the documentation of ToolDoc on how to format text. Where possible, formatting is added automatically for you. You have to use formatting in the following places: (1) usage lines, (2) option help texts, (3) description and additional text sections.

Member Functions

ArgumentParser

Constructor

Functions

addArgument	Adds a ArgParseArgument object to the ArgumentParser.
addDefaultValue	Add to the default values of an option of an ArgumentParser.
addDescription	Appends a description paragraph to the ArgumentParser documentation.
addLine	Adds a line of text to the help output of the ArgumentParser in the block of ArgParseOptions.
addListItem	Appends a list item to the ArgumentParser.
addOption	Adds a ArgParseOption object to the ArgumentParser.
addSection	Begins a new section of ArgParseOption the help output of the ArgumentParser.
addText	Appends a text paragraph to the ArgumentParser.
addTextSection	Adds a text section to the ArgumentParser.
addTextSubSection	Adds a text subsection to the ArgumentParser.
addUsageLine	Adds a line of text to the usage output of the ArgumentParser.
getAppName	Get tool name of ArgumentParser object.
getArgument	Returns a reference to the specified argument.
getArgumentValue	Retrieves the value of an argument given by its position.
getArgumentValueCount	Returns the number of values stored in the specified option.
getArgumentValues	Returns all values of an option given on the command line.
getCategory	Get tool category of ArgumentParser object.
getOption	Returns a reference to the specified option.
getOptionValue	Retrieves the value of an option given either the short or long name.
getOptionValueCount	Returns the number of values stored in the specified option.
getOptionValues	Returns all values of an option given on the command line.
getShortDescription	Gets short description of ArgumentParser.
getVersion	Get version string from ArgumentParser object.
hasDefault	Returns whether an option has a default value or not.
hasOption	Returns whether a certain option is registered in the parser.
hideOption	Hides the ArgParseOption defined by the parameter name (which can be either the short or the long name) from the help screen.
isSet	Returns whether an option was set on the parsed command line.
parse	Parses the command line.
printHelp	Prints the complete help message for the parser to a stream.
printShortHelp	Prints a short help message for the parser to a stream
printVersion	Prints the version information of the parser to a stream.
setAppName	Sets application name of ArgumentParser.
setCategory	Set tool category for ArgumentParser object.
setDate	Sets date string of ArgumentParser.
setDefaultValue	Set default value of an option of an ArgumentParser.
setHelpText	Set help text of argument parser.
setMaxValue	Set largest allowed value for an option or argument of an ArgumentParser.
setMinValue	Set smallest allowed value for an option or argument of an ArgumentParser.
setRequired	Sets whether or not the option defined by the parameter name (which can be either the short or the long name) is mandatory.
setShortDescription	Sets short description of the ArgumentParser object.
setValidValues	Set valid values for an argument or option of an ArgumentParser.
setVersion	Sets version string of ArgumentParser.
writeCTD	Exports the app's interface description to a .ctd file.

Examples

The following gives a simple example of how to use the ArgumentParser.

ArgumentParser parser("alf");
setShortDescription(parser, "Alignment free sequence comparison");
setVersion(parser, "1.0");
setDate(parser, "Jan 2010");

addUsageLine(parser, "[\fIOPTIONS\fP] \fB-i\fP \fIIN\fP \fB-o\fP \fIOUT\fP");

addDescription(parser,
               "ALF can be used to calculate the pairwise similarity of sequences "
               "using alignment-free methods. All methods which are implemented are "
               "based on k-mer counts.");

addOption(parser, ArgParseOption("i", "inputFile", "Name of the multi-FASTA input.",
                                 ArgParseArgument(ArgParseArgument::INPUTFILE, "IN")));
setRequired(parser, "i");

addOption(parser, ArgParseOption("o", "outputFile", "Name of the multi-FASTA input.",
                                 ArgParseArgument(ArgParseArgument::OUTPUTFILE, "OUT")));
setRequired(parser, "o");

addTextSection(parser, "See Also");
addText(parser, "http://www.seqan.de/projects/alf");