StirredOptions (PeptideShaker 2.2.2 API)

java.lang.Object
- java.lang.Enum<StirredOptions>
- - eu.isas.peptideshaker.cmd.StirredOptions

All Implemented Interfaces:

Serializable, Comparable<StirredOptions>
```
public enum StirredOptions
extends Enum<StirredOptions>
```
Enum class specifying the ModificationsCLI parameters.

Author:

Marc Vaudel, Harald Barsnes

Enum Constant Summary

Enum Constants
Enum Constant and Description
`contactAddress`
`contactEmail`
`contactFirstName`
`contactLastName`
`contactOrganizationAddress`
`contactOrganizationEmail`
`contactOrganizationName`
`fasta`
`identificationParametersFile`
`input`
`log`
`nThreads`
`output`
`spectrum`
`tempFolder`
`timeOutDays`

Field Summary

Fields
Modifier and Type	Field and Description
`String`	`description` Description for the command line argument.
`boolean`	`hasValue` If true this command line argument needs a value.
`String`	`longOpt` Key for the command line argument.
`boolean`	`mandatory` If true the parameter is mandatory.
`String`	`opt` Short key for the command line argument.

Method Summary

All Methods Static Methods Concrete Methods
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 StirredOptions`	`valueOf(String name)` Returns the enum constant of this type with the specified name.
`static StirredOptions[]`	`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
  - input
```
public static final StirredOptions input
```
  - spectrum
```
public static final StirredOptions spectrum
```
  - fasta
```
public static final StirredOptions fasta
```
  - identificationParametersFile
```
public static final StirredOptions identificationParametersFile
```
  - tempFolder
```
public static final StirredOptions tempFolder
```
  - log
```
public static final StirredOptions log
```
  - nThreads
```
public static final StirredOptions nThreads
```
  - timeOutDays
```
public static final StirredOptions timeOutDays
```
  - contactFirstName
```
public static final StirredOptions contactFirstName
```
  - contactLastName
```
public static final StirredOptions contactLastName
```
  - contactAddress
```
public static final StirredOptions contactAddress
```
  - contactEmail
```
public static final StirredOptions contactEmail
```
  - contactOrganizationName
```
public static final StirredOptions contactOrganizationName
```
  - contactOrganizationAddress
```
public static final StirredOptions contactOrganizationAddress
```
  - contactOrganizationEmail
```
public static final StirredOptions contactOrganizationEmail
```
  - output
```
public static final StirredOptions output
```
- Field Detail
  - opt
```
public final String opt
```
    Short key for the command line argument.
  - longOpt
```
public final String longOpt
```
    Key for the command line argument.
  - description
```
public final String description
```
    Description for the command line argument.
  - mandatory
```
public final boolean mandatory
```
    If true the parameter is mandatory.
  - hasValue
```
public final boolean hasValue
```
    If true this command line argument needs a value.
- Method Detail
  - values
```
public static StirredOptions[] 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 (StirredOptions c : StirredOptions.values())
    System.out.println(c);
```
    Returns:
    
    an array containing the constants of this enum type, in the order they are declared
  - valueOf
```
public static StirredOptions 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

Enum StirredOptions

Enum Constant Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Detail

input

spectrum

fasta

identificationParametersFile

tempFolder

log

nThreads

timeOutDays

contactFirstName

contactLastName

contactAddress

contactEmail

contactOrganizationName

contactOrganizationAddress

contactOrganizationEmail

output

Field Detail

opt

longOpt

description

mandatory

hasValue

Method Detail

values

valueOf

createOptionsCLI

getOptionsAsString