eu.isas.peptideshaker.cmd

Class IdentificationParametersCLI

java.lang.Object

com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli

eu.isas.peptideshaker.cmd.IdentificationParametersCLI

All Implemented Interfaces:

Callable

public class IdentificationParametersCLI
extends com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli

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

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
protected void	createOptionsCLI(org.apache.commons.cli.Options options)
String	getJarFilePath() Returns the path to the jar file.
protected String	getOptionsAsString()
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 Detail

IdentificationParametersCLI

public IdentificationParametersCLI(String[] args)

Construct a new SearchParametersCLI 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 Detail

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)

Specified by:

createOptionsCLI in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli

getOptionsAsString

protected String getOptionsAsString()

Specified by:

getOptionsAsString in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli

getJarFilePath

public String getJarFilePath()

Returns the path to the jar file.

Specified by:

getJarFilePath in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli

Returns:

the path to the jar file