public enum IdentificationParametersCLIParams extends Enum<IdentificationParametersCLIParams>
Modifier and Type | Field and Description |
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String |
description
Explanation for the CLI parameter.
|
String |
id
Short Id for the CLI parameter.
|
boolean |
mandatory
Boolean indicating whether the parameter is mandatory.
|
Modifier and Type | Method and Description |
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static IdentificationParametersCLIParams |
valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static IdentificationParametersCLIParams[] |
values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
public static final IdentificationParametersCLIParams OUTPUT
public static final IdentificationParametersCLIParams DB
public static final IdentificationParametersCLIParams PREC_PPM
public static final IdentificationParametersCLIParams FRAG_PPM
public static final IdentificationParametersCLIParams PREC_TOL
public static final IdentificationParametersCLIParams PREC_TOL_DA
public static final IdentificationParametersCLIParams FRAG_TOL
public static final IdentificationParametersCLIParams ENZYME
public static final IdentificationParametersCLIParams FIXED_MODS
public static final IdentificationParametersCLIParams VARIABLE_MODS
public static final IdentificationParametersCLIParams MIN_CHARGE
public static final IdentificationParametersCLIParams MAX_CHARGE
public static final IdentificationParametersCLIParams MC
public static final IdentificationParametersCLIParams FI
public static final IdentificationParametersCLIParams RI
public static final IdentificationParametersCLIParams MODS
public static final IdentificationParametersCLIParams OMSSA_SEQUENCES_IN_MEMORY
public static final IdentificationParametersCLIParams OMSSA_ISOTOPES
public static final IdentificationParametersCLIParams OMSSA_NEUTRON
public static final IdentificationParametersCLIParams OMSSA_LOW_INTENSITY
public static final IdentificationParametersCLIParams OMSSA_HIGH_INTENSITY
public static final IdentificationParametersCLIParams OMSSA_INTENSITY_INCREMENT
public static final IdentificationParametersCLIParams OMSSA_SINGLE_WINDOW_WIDTH
public static final IdentificationParametersCLIParams OMSSA_DOUBLE_WINDOW_WIDTH
public static final IdentificationParametersCLIParams OMSSA_SINGLE_WINDOW_PEAKS
public static final IdentificationParametersCLIParams OMSSA_DOUBLE_WINDOW_PEAKS
public static final IdentificationParametersCLIParams OMSSA_MIN_ANNOTATED_INTENSE_PEAKS
public static final IdentificationParametersCLIParams OMSSA_MIN_ANNOTATED_PEAKS
public static final IdentificationParametersCLIParams OMSSA_MIN_PEAKS
public static final IdentificationParametersCLIParams OMSSA_METHIONINE
public static final IdentificationParametersCLIParams OMSSA_MAX_LADDERS
public static final IdentificationParametersCLIParams OMSSA_MAX_FRAG_CHARGE
public static final IdentificationParametersCLIParams OMSSA_MAX_FRACTION
public static final IdentificationParametersCLIParams OMSSA_PLUS_ONE
public static final IdentificationParametersCLIParams OMSSA_POSITIVE_IONS
public static final IdentificationParametersCLIParams OMSSA_PREC_PER_SPECTRUM
public static final IdentificationParametersCLIParams OMSSA_FORWARD_IONS
public static final IdentificationParametersCLIParams OMSSA_REWIND_IONS
public static final IdentificationParametersCLIParams OMSSA_MAX_FRAG_SERIES
public static final IdentificationParametersCLIParams OMSSA_CORRELATION_CORRECTION
public static final IdentificationParametersCLIParams OMSSA_CONSECUTIVE_ION_PROBABILITY
public static final IdentificationParametersCLIParams OMSSA_ITERATIVE_SEQUENCE_EVALUE
public static final IdentificationParametersCLIParams OMSSA_ITERATIVE_SPECTRUM_EVALUE
public static final IdentificationParametersCLIParams OMSSA_ITERATIVE_REPLACE_EVALUE
public static final IdentificationParametersCLIParams OMSSA_REMOVE_PREC
public static final IdentificationParametersCLIParams OMSSA_SCALE_PREC
public static final IdentificationParametersCLIParams OMSSA_ESTIMATE_CHARGE
public static final IdentificationParametersCLIParams OMSSA_MAX_EVALUE
public static final IdentificationParametersCLIParams OMSSA_HITLIST_LENGTH
public static final IdentificationParametersCLIParams OMSSA_HITLIST_LENGTH_CHARGE
public static final IdentificationParametersCLIParams OMSSA_MIN_PEP_LENGTH
public static final IdentificationParametersCLIParams OMSSA_MAX_PEP_LENGTH
public static final IdentificationParametersCLIParams OMSSA_FORMAT
public static final IdentificationParametersCLIParams XTANDEM_DYNAMIC_RANGE
public static final IdentificationParametersCLIParams XTANDEM_NPEAKS
public static final IdentificationParametersCLIParams XTANDEM_MIN_FRAG_MZ
public static final IdentificationParametersCLIParams XTANDEM_MIN_PEAKS
public static final IdentificationParametersCLIParams XTANDEM_NOISE_SUPPRESSION
public static final IdentificationParametersCLIParams XTANDEM_MIN_PREC_MASS
public static final IdentificationParametersCLIParams XTANDEM_QUICK_ACETYL
public static final IdentificationParametersCLIParams XTANDEM_QUICK_PYRO
public static final IdentificationParametersCLIParams XTANDEM_STP_BIAS
public static final IdentificationParametersCLIParams XTANDEM_REFINE
public static final IdentificationParametersCLIParams XTANDEM_REFINE_EVALUE
public static final IdentificationParametersCLIParams XTANDEM_REFINE_UNANTICIPATED_CLEAVAGE
public static final IdentificationParametersCLIParams XTANDEM_REFINE_SEMI
public static final IdentificationParametersCLIParams XTANDEM_REFINE_POTENTIAL_MOD_FULL_REFINEMENT
public static final IdentificationParametersCLIParams XTANDEM_REFINE_POINT_MUTATIONS
public static final IdentificationParametersCLIParams XTANDEM_REFINE_SNAPS
public static final IdentificationParametersCLIParams XTANDEM_REFINE_SPECTRUM_SYNTHESIS
public static final IdentificationParametersCLIParams XTANDEM_EVALUE
public static final IdentificationParametersCLIParams XTANDEM_OUTPUT_PROTEINS
public static final IdentificationParametersCLIParams XTANDEM_OUTPUT_SEQUENCES
public static final IdentificationParametersCLIParams XTANDEM_OUTPUT_SPECTRA
public static final IdentificationParametersCLIParams XTANDEM_SKYLINE
public static final IdentificationParametersCLIParams MSGF_DECOY
public static final IdentificationParametersCLIParams MSGF_INSTRUMENT
public static final IdentificationParametersCLIParams MSGF_FRAGMENTATION
public static final IdentificationParametersCLIParams MSGF_PROTOCOL
public static final IdentificationParametersCLIParams MSGF_MIN_PEP_LENGTH
public static final IdentificationParametersCLIParams MSGF_MAX_PEP_LENGTH
public static final IdentificationParametersCLIParams MSGF_NUM_MATCHES
public static final IdentificationParametersCLIParams MSGF_ADDITIONAL
public static final IdentificationParametersCLIParams MSGF_ISOTOPE_LOW
public static final IdentificationParametersCLIParams MSGF_ISOTOPE_HIGH
public static final IdentificationParametersCLIParams MSGF_TERMINI
public static final IdentificationParametersCLIParams MSGF_PTMS
public static final IdentificationParametersCLIParams MS_AMANDA_DECOY
public static final IdentificationParametersCLIParams MS_AMANDA_INSTRUMENT
public static final IdentificationParametersCLIParams MS_AMANDA_MAX_RANK
public static final IdentificationParametersCLIParams MS_AMANDA_MONOISOTOPIC
public static final IdentificationParametersCLIParams PEPNOVO_HITLIST_LENGTH
public static final IdentificationParametersCLIParams PEPTNOVO_ESTIMATE_CHARGE
public static final IdentificationParametersCLIParams PEPNOVO_CORRECT_PREC_MASS
public static final IdentificationParametersCLIParams PEPNOVO_DISCARD_SPECTRA
public static final IdentificationParametersCLIParams PEPNOVO_FRAGMENTATION_MODEL
public static final IdentificationParametersCLIParams PEPNOVO_GENERATE_BLAST
public static final IdentificationParametersCLIParams DIRECTAG_TIC_CUTOFF_PERCENTAGE
public static final IdentificationParametersCLIParams DIRECTAG_MAX_PEAK_COUNT
public static final IdentificationParametersCLIParams DIRECTAG_NUM_INTENSITY_CLASSES
public static final IdentificationParametersCLIParams DIRECTAG_ADJUST_PRECURSOR_MASS
public static final IdentificationParametersCLIParams DIRECTAG_MIN_PRECUSOR_ADJUSTMENT
public static final IdentificationParametersCLIParams DIRECTAG_MAX_PRECUSOR_ADJUSTMENT
public static final IdentificationParametersCLIParams DIRECTAG_PRECUSOR_ADJUSTMENT_STEP
public static final IdentificationParametersCLIParams DIRECTAG_NUM_CHARGE_STATES
public static final IdentificationParametersCLIParams DIRECTAG_OUTPUT_SUFFIX
public static final IdentificationParametersCLIParams DIRECTAG_USE_CHARGE_STATE_FROM_MS
public static final IdentificationParametersCLIParams DIRECTAG_DUPLICATE_SPECTRA
public static final IdentificationParametersCLIParams DIRECTAG_DEISOTOPING_MODE
public static final IdentificationParametersCLIParams DIRECTAG_ISOTOPE_MZ_TOLERANCE
public static final IdentificationParametersCLIParams DIRECTAG_COMPLEMENT_MZ_TOLERANCE
public static final IdentificationParametersCLIParams DIRECTAG_TAG_LENGTH
public static final IdentificationParametersCLIParams DIRECTAG_MAX_DYNAMIC_MODS
public static final IdentificationParametersCLIParams DIRECTAG_MAX_TAG_COUNT
public static final IdentificationParametersCLIParams DIRECTAG_INTENSITY_SCORE_WEIGHT
public static final IdentificationParametersCLIParams DIRECTAG_MZ_FIDELITY_SCORE_WEIGHT
public static final IdentificationParametersCLIParams DIRECTAG_COMPLEMENT_SCORE_WEIGHT
public String id
public String description
public boolean mandatory
public static IdentificationParametersCLIParams[] values()
for (IdentificationParametersCLIParams c : IdentificationParametersCLIParams.values()) System.out.println(c);
public static IdentificationParametersCLIParams valueOf(String name)
name
- the name of the enum constant to be returned.IllegalArgumentException
- if this enum type has no constant
with the specified nameNullPointerException
- if the argument is nullCopyright © 2014. All rights reserved.