eu.isas.peptideshaker.cmd

Class PathSettingsCLI

java.lang.Object

eu.isas.peptideshaker.cmd.PathSettingsCLI

public class PathSettingsCLI
extends Object

Allows the user to set the path settings in command line.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
PathSettingsCLI(PathSettingsCLIInputBean pathSettingsCLIInputBean) Constructor.

Method Summary

Modifier and Type	Method and Description
Object	call()
static String[]	extractAndUpdatePathOptions(String[] args) If the arguments contains changes to the paths these arguments will be extracted and the paths updated, before the remaining non-path options are returned for further processing.
static void	main(String[] args) Starts the launcher by calling the launch method.
void	setPathSettings() Sets the path settings according to the pathSettingsCLIInputBean.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

PathSettingsCLI

public PathSettingsCLI(PathSettingsCLIInputBean pathSettingsCLIInputBean)

Constructor.

Parameters:

pathSettingsCLIInputBean - an input bean containing the user parameters

Method Detail

call

public Object call()

setPathSettings

public void setPathSettings()

Sets the path settings according to the pathSettingsCLIInputBean.

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

toString

public String toString()

Overrides:

toString in class Object

extractAndUpdatePathOptions

public static String[] extractAndUpdatePathOptions(String[] args)
                                            throws org.apache.commons.cli.ParseException

If the arguments contains changes to the paths these arguments will be extracted and the paths updated, before the remaining non-path options are returned for further processing.

Parameters:

args - the command line arguments

Returns:

a list of all non-path related arguments

Throws:

org.apache.commons.cli.ParseException - if a ParseException occurs