Package com.compomics.cli.identification_parameters

Class IdentificationParametersCLI

java.lang.Object

com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli

com.compomics.cli.identification_parameters.IdentificationParametersCLI

All Implemented Interfaces:

Callable

public class IdentificationParametersCLI
extends AbstractIdentificationParametersCli

The IdentificationParametersCLI allows creating search parameters files using command line arguments.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor	Description
IdentificationParametersCLI(String[] args)	Construct a new IdentificationParametersCLI runnable from a list of arguments.

Method Summary

Modifier and Type	Method	Description
protected void	createOptionsCLI(org.apache.commons.cli.Options options)	Provides the options left to the user.
protected String	getOptionsAsString()	Returns the options left to the user as a string.
static void	main(String[] args)	Starts the launcher by calling the launch method.

Methods inherited from class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli

call, getHeader, initiate, printEnzymes, printModifications

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

IdentificationParametersCLI

public IdentificationParametersCLI(String[] args)

Construct a new IdentificationParametersCLI runnable from a list of arguments. When initialization is successful, calling "run" will write the created parameters file.

Parameters:

args - the command line arguments

Method Details

main

public static void main(String[] args)

Starts the launcher by calling the launch method. Use this as the main class in the jar file.

Parameters:

args - the command line arguments

createOptionsCLI

protected void createOptionsCLI(org.apache.commons.cli.Options options)

Description copied from class: AbstractIdentificationParametersCli

Provides the options left to the user.

Specified by:

createOptionsCLI in class AbstractIdentificationParametersCli

Parameters:

options - the options object where the options will be added

getOptionsAsString

protected String getOptionsAsString()

Description copied from class: AbstractIdentificationParametersCli

Returns the options left to the user as a string.

Specified by:

getOptionsAsString in class AbstractIdentificationParametersCli

Returns:

the options left to the user as a string