com.compomics.util.experiment.identification
Enum SearchParametersCLIParams

java.lang.Object
  extended by java.lang.Enum<SearchParametersCLIParams>
      extended by com.compomics.util.experiment.identification.SearchParametersCLIParams
All Implemented Interfaces:
Serializable, Comparable<SearchParametersCLIParams>

public enum SearchParametersCLIParams
extends Enum<SearchParametersCLIParams>

Enum class specifying the SearchParameter command line option parameters for SearchCLI and DeNovoCLI.

Author:
Marc Vaudel, Harald Barsnes

Enum Constant Summary
CORRECT_PRECURSOR_MASS
           
DB
           
DISCARD_SPECTRA
           
ENZYME
           
ESTIMATE_CHARGE
           
ESTIMATE_CHARGE_DE_NOVO
           
FI
           
FIX_DUPLICATE_TITLES
           
FIXED_MODS
           
FRAG_TOL
           
FRAGMENTATION_MODEL
           
GENERATE_BLAST
           
HITLIST_LENGTH
           
HITLIST_LENGTH_DE_NOVO
           
MAX_CHARGE
           
MAX_EVALUE
           
MAX_PEP_LENGTH
           
MC
           
MGF_MAX_SPECTRA
           
MGF_SPLITTING_LIMIT
           
MIN_CHARGE
           
MIN_PEP_LENGTH
           
OMSSA
           
OMSSA_FORMAT
           
OMSSA_LOCATION
           
OUTPUT_FOLDER
           
PEP_NOVO_LOCATION
           
PPM
           
PREC_TOL
           
REMOVE_PREC
           
RI
           
SCALE_PREC
           
SEARCH_PARAMETERS
           
SPECTRUM_FILES
           
VARIABLE_MODS
           
XTANDEM
           
XTANDEM_LOCATION
           
 
Field Summary
 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
static SearchParametersCLIParams valueOf(String name)
          Returns the enum constant of this type with the specified name.
static SearchParametersCLIParams[] 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

SPECTRUM_FILES

public static final SearchParametersCLIParams SPECTRUM_FILES

OUTPUT_FOLDER

public static final SearchParametersCLIParams OUTPUT_FOLDER

SEARCH_PARAMETERS

public static final SearchParametersCLIParams SEARCH_PARAMETERS

PPM

public static final SearchParametersCLIParams PPM

PREC_TOL

public static final SearchParametersCLIParams PREC_TOL

FRAG_TOL

public static final SearchParametersCLIParams FRAG_TOL

ENZYME

public static final SearchParametersCLIParams ENZYME

FIXED_MODS

public static final SearchParametersCLIParams FIXED_MODS

VARIABLE_MODS

public static final SearchParametersCLIParams VARIABLE_MODS

MC

public static final SearchParametersCLIParams MC

MIN_CHARGE

public static final SearchParametersCLIParams MIN_CHARGE

MAX_CHARGE

public static final SearchParametersCLIParams MAX_CHARGE

MAX_EVALUE

public static final SearchParametersCLIParams MAX_EVALUE

FI

public static final SearchParametersCLIParams FI

RI

public static final SearchParametersCLIParams RI

DB

public static final SearchParametersCLIParams DB

HITLIST_LENGTH

public static final SearchParametersCLIParams HITLIST_LENGTH

MIN_PEP_LENGTH

public static final SearchParametersCLIParams MIN_PEP_LENGTH

MAX_PEP_LENGTH

public static final SearchParametersCLIParams MAX_PEP_LENGTH

REMOVE_PREC

public static final SearchParametersCLIParams REMOVE_PREC

SCALE_PREC

public static final SearchParametersCLIParams SCALE_PREC

ESTIMATE_CHARGE

public static final SearchParametersCLIParams ESTIMATE_CHARGE

OMSSA

public static final SearchParametersCLIParams OMSSA

XTANDEM

public static final SearchParametersCLIParams XTANDEM

OMSSA_FORMAT

public static final SearchParametersCLIParams OMSSA_FORMAT

OMSSA_LOCATION

public static final SearchParametersCLIParams OMSSA_LOCATION

XTANDEM_LOCATION

public static final SearchParametersCLIParams XTANDEM_LOCATION

MGF_SPLITTING_LIMIT

public static final SearchParametersCLIParams MGF_SPLITTING_LIMIT

MGF_MAX_SPECTRA

public static final SearchParametersCLIParams MGF_MAX_SPECTRA

FIX_DUPLICATE_TITLES

public static final SearchParametersCLIParams FIX_DUPLICATE_TITLES

HITLIST_LENGTH_DE_NOVO

public static final SearchParametersCLIParams HITLIST_LENGTH_DE_NOVO

ESTIMATE_CHARGE_DE_NOVO

public static final SearchParametersCLIParams ESTIMATE_CHARGE_DE_NOVO

CORRECT_PRECURSOR_MASS

public static final SearchParametersCLIParams CORRECT_PRECURSOR_MASS

DISCARD_SPECTRA

public static final SearchParametersCLIParams DISCARD_SPECTRA

FRAGMENTATION_MODEL

public static final SearchParametersCLIParams FRAGMENTATION_MODEL

GENERATE_BLAST

public static final SearchParametersCLIParams GENERATE_BLAST

PEP_NOVO_LOCATION

public static final SearchParametersCLIParams PEP_NOVO_LOCATION
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 SearchParametersCLIParams[] 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 (SearchParametersCLIParams c : SearchParametersCLIParams.values())
    System.out.println(c);

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

valueOf

public static SearchParametersCLIParams 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


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