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 |
---|---|
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 USAGE
public static final IdentificationParametersCLIParams USAGE_2
public static final IdentificationParametersCLIParams USAGE_3
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 MS_AMANDA_LOW_MEM_MODE
public static final IdentificationParametersCLIParams MYRIMATCH_MIN_PEP_LENGTH
public static final IdentificationParametersCLIParams MYRIMATCH_MAX_PEP_LENGTH
public static final IdentificationParametersCLIParams MYRIMATCH_MIN_PREC_MASS
public static final IdentificationParametersCLIParams MYRIMATCH_MAX_PREC_MASS
public static final IdentificationParametersCLIParams MYRIMATCH_ISOTOPE_LOW
public static final IdentificationParametersCLIParams MYRIMATCH_ISOTOPE_HIGH
public static final IdentificationParametersCLIParams MYRIMATCH_NUM_MATCHES
public static final IdentificationParametersCLIParams MYRIMATCH_PTMS
public static final IdentificationParametersCLIParams MYRIMATCH_FRAGMENTATION
public static final IdentificationParametersCLIParams MYRIMATCH_TERMINI
public static final IdentificationParametersCLIParams MYRIMATCH_SMART_PLUS_THREE
public static final IdentificationParametersCLIParams MYRIMATCH_XCORR
public static final IdentificationParametersCLIParams MYRIMATCH_TIC_CUTOFF
public static final IdentificationParametersCLIParams MYRIMATCH_INTENSTITY_CLASSES
public static final IdentificationParametersCLIParams MYRIMATCH_CLASS_MULTIPLIER
public static final IdentificationParametersCLIParams MYRIMATCH_NUM_BATCHES
public static final IdentificationParametersCLIParams MYRIMATCH_MAX_PEAK_COUNT
public static final IdentificationParametersCLIParams MYRIMATCH_OUTPUT_FORMAT
public static final IdentificationParametersCLIParams COMET_NUM_MATCHES
public static final IdentificationParametersCLIParams COMET_PTMS
public static final IdentificationParametersCLIParams COMET_REQ_PTMS
public static final IdentificationParametersCLIParams COMET_MIN_PEAKS
public static final IdentificationParametersCLIParams COMET_MIN_PEAK_INTENSITY
public static final IdentificationParametersCLIParams COMET_REMOVE_PRECURSOR
public static final IdentificationParametersCLIParams COMET_REMOVE_PRECURSOR_TOLERANCE
public static final IdentificationParametersCLIParams COMET_CLEAR_MZ_RANGE_LOWER
public static final IdentificationParametersCLIParams COMET_CLEAR_MZ_RANGE_UPPER
public static final IdentificationParametersCLIParams COMET_ENZYME_TYPE
public static final IdentificationParametersCLIParams COMET_ISOTOPE_CORRECTION
public static final IdentificationParametersCLIParams COMET_MIN_PREC_MASS
public static final IdentificationParametersCLIParams COMET_MAX_PREC_MASS
public static final IdentificationParametersCLIParams COMET_MAX_FRAGMENT_CHARGE
public static final IdentificationParametersCLIParams COMET_REMOVE_METH
public static final IdentificationParametersCLIParams COMET_BATCH_SIZE
public static final IdentificationParametersCLIParams COMET_THEORETICAL_FRAGMENT_IONS
public static final IdentificationParametersCLIParams COMET_FRAGMENT_BIN_OFFSET
public static final IdentificationParametersCLIParams COMET_USE_SPARSE_MATRIX
public static final IdentificationParametersCLIParams TIDE_PTMS
public static final IdentificationParametersCLIParams TIDE_PTMS_PER_TYPE
public static final IdentificationParametersCLIParams TIDE_MIN_PEP_LENGTH
public static final IdentificationParametersCLIParams TIDE_MAX_PEP_LENGTH
public static final IdentificationParametersCLIParams TIDE_MIN_PREC_MASS
public static final IdentificationParametersCLIParams TIDE_MAX_PREC_MASS
public static final IdentificationParametersCLIParams TIDE_DECOY_FORMAT
public static final IdentificationParametersCLIParams TIDE_KEEP_TERM_AA
public static final IdentificationParametersCLIParams TIDE_DECOY_SEED
public static final IdentificationParametersCLIParams TIDE_OUTPUT_FOLDER
public static final IdentificationParametersCLIParams TIDE_PRINT_PEPTIDES
public static final IdentificationParametersCLIParams TIDE_VERBOSITY
public static final IdentificationParametersCLIParams TIDE_MONOISOTOPIC
public static final IdentificationParametersCLIParams TIDE_CLIP_N_TERM
public static final IdentificationParametersCLIParams TIDE_DIGESTION_TYPE
public static final IdentificationParametersCLIParams TIDE_COMPUTE_SP
public static final IdentificationParametersCLIParams TIDE_MAX_PSMS
public static final IdentificationParametersCLIParams TIDE_COMPUTE_P
public static final IdentificationParametersCLIParams TIDE_MIN_SPECTRUM_MZ
public static final IdentificationParametersCLIParams TIDE_MAX_SPECTRUM_MZ
public static final IdentificationParametersCLIParams TIDE_MIN_SPECTRUM_PEAKS
public static final IdentificationParametersCLIParams TIDE_SPECTRUM_CHARGES
public static final IdentificationParametersCLIParams TIDE_REMOVE_PREC
public static final IdentificationParametersCLIParams TIDE_REMOVE_PREC_TOL
public static final IdentificationParametersCLIParams TIDE_PROGRESS_INDICATOR
public static final IdentificationParametersCLIParams TIDE_USE_FLANKING
public static final IdentificationParametersCLIParams TIDE_USE_NEUTRAL_LOSSES
public static final IdentificationParametersCLIParams TIDE_MZ_BIN_WIDTH
public static final IdentificationParametersCLIParams TIDE_MZ_BIN_OFFSET
public static final IdentificationParametersCLIParams TIDE_CONCAT
public static final IdentificationParametersCLIParams TIDE_STORE_SPECTRA
public static final IdentificationParametersCLIParams TIDE_EXPORT_TEXT
public static final IdentificationParametersCLIParams TIDE_EXPORT_SQT
public static final IdentificationParametersCLIParams TIDE_EXPORT_PEPXML
public static final IdentificationParametersCLIParams TIDE_EXPORT_MZID
public static final IdentificationParametersCLIParams TIDE_EXPORT_PIN
public static final IdentificationParametersCLIParams TIDE_REMOVE_TEMP
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 static final IdentificationParametersCLIParams PNOVO_NUMBER_OF_PEPTIDES
public static final IdentificationParametersCLIParams PNOVO_LOWER_PRECURSOR_MASS
public static final IdentificationParametersCLIParams PNOVO_UPPER_PRECURSOR_MASS
public static final IdentificationParametersCLIParams PNOVO_ACTIVATION_TYPE
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 © 2015. All rights reserved.