eu.isas.peptideshaker.cmd

Enum FollowUpCLIParams

java.lang.Object

java.lang.Enum<FollowUpCLIParams>

eu.isas.peptideshaker.cmd.FollowUpCLIParams

All Implemented Interfaces:

Serializable, Comparable<FollowUpCLIParams>

public enum FollowUpCLIParams
extends Enum<FollowUpCLIParams>

Enum class specifying the Command Line Parameters for follow up analysis.

Author:

Marc Vaudel, Harald Barsnes

Enum Constant Summary

Enum Constants

Enum Constant and Description
ACCESSIONS_FILE
ACCESSIONS_TYPE
DEEPLC_FILE
INCLUSION_LIST_FILE
INCLUSION_LIST_FORMAT
INCLUSION_LIST_PEPTIDE_FILTERS
INCLUSION_LIST_PROTEIN_FILTERS
INCLUSION_LIST_RT_WINDOW
MS2PIP_FILE
MS2PIP_MODELS
PEPNOVO_TRAINING_FDR
PEPNOVO_TRAINING_FNR
PEPNOVO_TRAINING_FOLDER
PEPNOVO_TRAINING_RECALIBRATION
PERCOLATOR_FILE
PERCOLATOR_FRAGMENTATION
PERCOLATOR_RT
PROGENESIS_FILE
PROGENESIS_TARGETED_PTMS
PROGENESIS_TYPE
PROTEOFORMS_FILE
PSDB_FILE
PSM_TYPE
RECALIBRATION_FOLDER
RECALIBRATION_MODE
SEQUENCES_FILE
SEQUENCES_TYPE
SPECTRUM_FOLDER

Field Summary

Fields

Modifier and Type	Field and Description
String	description Explanation for the CLI parameter.
boolean	hasArgument Indicates whether user input is expected.
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 String	getOutputOptionsAsString() Returns the output options as a string.
static FollowUpCLIParams	valueOf(String name) Returns the enum constant of this type with the specified name.
static FollowUpCLIParams[]	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

PSDB_FILE

public static final FollowUpCLIParams PSDB_FILE

RECALIBRATION_FOLDER

public static final FollowUpCLIParams RECALIBRATION_FOLDER

RECALIBRATION_MODE

public static final FollowUpCLIParams RECALIBRATION_MODE

SPECTRUM_FOLDER

public static final FollowUpCLIParams SPECTRUM_FOLDER

PSM_TYPE

public static final FollowUpCLIParams PSM_TYPE

ACCESSIONS_FILE

public static final FollowUpCLIParams ACCESSIONS_FILE

ACCESSIONS_TYPE

public static final FollowUpCLIParams ACCESSIONS_TYPE

SEQUENCES_FILE

public static final FollowUpCLIParams SEQUENCES_FILE

SEQUENCES_TYPE

public static final FollowUpCLIParams SEQUENCES_TYPE

PROGENESIS_FILE

public static final FollowUpCLIParams PROGENESIS_FILE

PROGENESIS_TYPE

public static final FollowUpCLIParams PROGENESIS_TYPE

PROGENESIS_TARGETED_PTMS

public static final FollowUpCLIParams PROGENESIS_TARGETED_PTMS

PEPNOVO_TRAINING_FOLDER

public static final FollowUpCLIParams PEPNOVO_TRAINING_FOLDER

PEPNOVO_TRAINING_RECALIBRATION

public static final FollowUpCLIParams PEPNOVO_TRAINING_RECALIBRATION

PEPNOVO_TRAINING_FDR

public static final FollowUpCLIParams PEPNOVO_TRAINING_FDR

PEPNOVO_TRAINING_FNR

public static final FollowUpCLIParams PEPNOVO_TRAINING_FNR

INCLUSION_LIST_FILE

public static final FollowUpCLIParams INCLUSION_LIST_FILE

INCLUSION_LIST_FORMAT

public static final FollowUpCLIParams INCLUSION_LIST_FORMAT

INCLUSION_LIST_PROTEIN_FILTERS

public static final FollowUpCLIParams INCLUSION_LIST_PROTEIN_FILTERS

INCLUSION_LIST_PEPTIDE_FILTERS

public static final FollowUpCLIParams INCLUSION_LIST_PEPTIDE_FILTERS

INCLUSION_LIST_RT_WINDOW

public static final FollowUpCLIParams INCLUSION_LIST_RT_WINDOW

PROTEOFORMS_FILE

public static final FollowUpCLIParams PROTEOFORMS_FILE

DEEPLC_FILE

public static final FollowUpCLIParams DEEPLC_FILE

MS2PIP_FILE

public static final FollowUpCLIParams MS2PIP_FILE

MS2PIP_MODELS

public static final FollowUpCLIParams MS2PIP_MODELS

PERCOLATOR_RT

public static final FollowUpCLIParams PERCOLATOR_RT

PERCOLATOR_FRAGMENTATION

public static final FollowUpCLIParams PERCOLATOR_FRAGMENTATION

PERCOLATOR_FILE

public static final FollowUpCLIParams PERCOLATOR_FILE

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.

hasArgument

public final boolean hasArgument

Indicates whether user input is expected.

Method Detail

values

public static FollowUpCLIParams[] 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 (FollowUpCLIParams c : FollowUpCLIParams.values())
    System.out.println(c);

Returns:

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

valueOf

public static FollowUpCLIParams 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

getOutputOptionsAsString

public static String getOutputOptionsAsString()

Returns the output options as a string.

Returns:

the output options as a string