com.compomics.util.experiment.identification.search_parameters_cli

Class AbstractIdentificationParametersCli

java.lang.Object

com.compomics.util.experiment.identification.search_parameters_cli.AbstractIdentificationParametersCli

All Implemented Interfaces:

java.util.concurrent.Callable

public abstract class AbstractIdentificationParametersCli
extends java.lang.Object
implements java.util.concurrent.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

Methods

Modifier and Type	Method and Description
java.lang.Object	call() Calling this method will run the configured SearchCLI process.
protected abstract void	createOptionsCLI(org.apache.commons.cli.Options options) Provides the options left to the user.
protected abstract java.io.File	getEnzymeFile() Returns the enzyme file needed to initiate the factory.
static java.lang.String	getHeader() IdentificationParametersCLI header message when printing the usage.
protected abstract java.io.File	getModificationsFile() Returns the modification file needed to initiate the factory.
protected abstract java.lang.String	getOptionsAsString() Returns the options left to the user as a string.
protected abstract java.io.File	getUserModificationsFile() Returns the user modification file needed to initiate the factory.
void	initiate(java.lang.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(java.lang.String[] args)

Initiates the IdentificationParametersCli.

Parameters:

args - the command line arguments

call

public java.lang.Object call()

Calling this method will run the configured SearchCLI process.

Specified by:

call in interface java.util.concurrent.Callable

printModifications

public void printModifications()

Prints the available modifications on the screen.

getModificationsFile

protected abstract java.io.File getModificationsFile()

Returns the modification file needed to initiate the factory.

Returns:

the modification file needed to initiate the factory

getUserModificationsFile

protected abstract java.io.File getUserModificationsFile()

Returns the user modification file needed to initiate the factory.

Returns:

the user modification file needed to initiate the factory

getEnzymeFile

protected abstract java.io.File getEnzymeFile()

Returns the enzyme file needed to initiate the factory.

Returns:

the enzyme file needed to initiate the factory

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 java.lang.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 java.lang.String getHeader()

IdentificationParametersCLI header message when printing the usage.

Returns:

the header message as a string