eu.isas.peptideshaker.cmd

Enum PeptideShakerCLIParams

java.lang.Object

java.lang.Enum<PeptideShakerCLIParams>

eu.isas.peptideshaker.cmd.PeptideShakerCLIParams

All Implemented Interfaces:

Serializable, Comparable<PeptideShakerCLIParams>

public enum PeptideShakerCLIParams
extends Enum<PeptideShakerCLIParams>

Enum class specifying the Command Line Parameters for PeptideShaker.

Author:

Marc Vaudel, Harald Barsnes

Enum Constant Summary

Enum Constants

Enum Constant and Description
FASTA_FILE
GUI
IDENTIFICATION_FILES
OUTPUT_MGF
PEPTIDESHAKER_OUTPUT
PROJECT_TYPE
REFERENCE
SPECTRUM_FILES
THREADS
ZIP

Field Summary

Fields

Modifier and Type	Field and Description
String	description Explanation for the CLI parameter.
String	id Short Id for the CLI parameter.
boolean	mandatory Boolean indicating whether the parameter is mandatory.

Method Summary

Modifier and Type	Method and Description
static void	createOptionsCLI(org.apache.commons.cli.Options aOptions) Creates the options for the command line interface based on the possible values.
static String	getOptionsAsString() Returns the options as a string.
static PeptideShakerCLIParams	valueOf(String name) Returns the enum constant of this type with the specified name.
static PeptideShakerCLIParams[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

REFERENCE

public static final PeptideShakerCLIParams REFERENCE

PROJECT_TYPE

public static final PeptideShakerCLIParams PROJECT_TYPE

SPECTRUM_FILES

public static final PeptideShakerCLIParams SPECTRUM_FILES

FASTA_FILE

public static final PeptideShakerCLIParams FASTA_FILE

IDENTIFICATION_FILES

public static final PeptideShakerCLIParams IDENTIFICATION_FILES

PEPTIDESHAKER_OUTPUT

public static final PeptideShakerCLIParams PEPTIDESHAKER_OUTPUT

GUI

public static final PeptideShakerCLIParams GUI

ZIP

public static final PeptideShakerCLIParams ZIP

OUTPUT_MGF

public static final PeptideShakerCLIParams OUTPUT_MGF

THREADS

public static final PeptideShakerCLIParams THREADS

Field Detail

id

public String id

Short Id for the CLI parameter.

description

public String description

Explanation for the CLI parameter.

mandatory

public boolean mandatory

Boolean indicating whether the parameter is mandatory.

Method Detail

values

public static PeptideShakerCLIParams[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (PeptideShakerCLIParams c : PeptideShakerCLIParams.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static PeptideShakerCLIParams valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

createOptionsCLI

public static void createOptionsCLI(org.apache.commons.cli.Options aOptions)

Creates the options for the command line interface based on the possible values.

Parameters:

aOptions - the options object where the options will be added

getOptionsAsString

public static String getOptionsAsString()

Returns the options as a string.

Returns:

the options as a string