com.compomics.util.experiment.identification.parameters_cli

Class AbstractIdentificationParametersCli

java.lang.Object

com.compomics.util.experiment.identification.parameters_cli.AbstractIdentificationParametersCli

All Implemented Interfaces:

Callable

public abstract class AbstractIdentificationParametersCli
extends Object
implements Callable

This class serves as a base for the implementation of IdentificationParametersCLI in specific tools. To make an IdentificationParametersCLI extend this class and call initiate in the constructor of your class.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
AbstractIdentificationParametersCli()

Method Summary

Modifier and Type	Method and Description
Object	call()
protected abstract void	createOptionsCLI(org.apache.commons.cli.Options options) Provides the options left to the user.
protected abstract File	getEnzymeFile() Returns the enzyme file needed to initiate the factory.
static String	getHeader() IdentificationParametersCLI header message when printing the usage.
protected abstract String	getJarFilePath() Returns the path to the jar file.
protected abstract String	getOptionsAsString() Returns the options left to the user as a string.
void	initiate(String[] args) Initiates the IdentificationParametersCli.
void	printModifications() Prints the available modifications on the screen.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractIdentificationParametersCli

public AbstractIdentificationParametersCli()

Method Detail

initiate

public void initiate(String[] args)

Initiates the IdentificationParametersCli.

Parameters:

args - the command line arguments

call

public Object call()

Specified by:

call in interface Callable

printModifications

public void printModifications()

Prints the available modifications on the screen.

getEnzymeFile

protected abstract File getEnzymeFile()

Returns the enzyme file needed to initiate the factory.

Returns:

the enzyme file needed to initiate the factory

getJarFilePath

protected abstract String getJarFilePath()

Returns the path to the jar file.

Returns:

the path to the jar file

createOptionsCLI

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

Provides the options left to the user.

Parameters:

options - the options object where the options will be added

getOptionsAsString

protected abstract String getOptionsAsString()

Returns the options left to the user as a string.

Returns:

the options left to the user as a string

getHeader

public static String getHeader()

IdentificationParametersCLI header message when printing the usage.

Returns:

the header message as a string