Enum IdentificationParametersCLIParams
java.lang.Object
java.lang.Enum<IdentificationParametersCLIParams>
com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
- All Implemented Interfaces:
Serializable
,Comparable<IdentificationParametersCLIParams>
,java.lang.constant.Constable
public enum IdentificationParametersCLIParams extends Enum<IdentificationParametersCLIParams>
Enum class specifying the SearchParameter command line option parameters to
create a SearchParameters object
- Author:
- Marc Vaudel, Harald Barsnes
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Nested Class Summary
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Enum Constant Summary
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Field Summary
Fields Modifier and Type Field Description String
description
Explanation for the CLI parameter.boolean
hasArgument
Boolean indicating whether this command line option needs an argument.String
id
Short Id for the CLI parameter.boolean
mandatory
Boolean indicating whether the parameter is mandatory. -
Method Summary
Modifier and Type Method 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
getParametersOptionsAsString()
Returns the options as a string.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.
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Enum Constant Details
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DESCRIPTION
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USAGE
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USAGE_2
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USAGE_3
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MODS
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ENZYMES
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IDENTIFICATION_PARAMETERS
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OUT
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PREC_PPM
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FRAG_PPM
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PREC_TOL
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FRAG_TOL
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DIGESTION
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ENZYME
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MC
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SPECIFICITY
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FIXED_MODS
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VARIABLE_MODS
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MIN_CHARGE
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MAX_CHARGE
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FI
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RI
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MIN_ISOTOPE
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MAX_ISOTOPE
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XTANDEM_DYNAMIC_RANGE
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XTANDEM_NPEAKS
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XTANDEM_MIN_FRAG_MZ
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XTANDEM_MIN_PEAKS
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XTANDEM_NOISE_SUPPRESSION
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XTANDEM_MIN_PREC_MASS
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XTANDEM_PARENT_MONOISOTOPIC_MASS_ISOTOPE_ERROR
public static final IdentificationParametersCLIParams XTANDEM_PARENT_MONOISOTOPIC_MASS_ISOTOPE_ERROR -
XTANDEM_QUICK_ACETYL
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XTANDEM_QUICK_PYRO
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XTANDEM_STP_BIAS
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XTANDEM_PTM_COMPLEXITY
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XTANDEM_REFINE
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XTANDEM_REFINE_EVALUE
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XTANDEM_REFINE_UNANTICIPATED_CLEAVAGE
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XTANDEM_REFINE_SEMI
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XTANDEM_REFINE_POTENTIAL_MOD_FULL_REFINEMENT
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XTANDEM_REFINE_POINT_MUTATIONS
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XTANDEM_REFINE_SNAPS
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XTANDEM_REFINE_SPECTRUM_SYNTHESIS
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XTANDEM_EVALUE
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XTANDEM_OUTPUT_RESULTS
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XTANDEM_OUTPUT_PROTEINS
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XTANDEM_OUTPUT_SEQUENCES
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XTANDEM_OUTPUT_SPECTRA
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XTANDEM_OUTPUT_HISTOGRAMS
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XTANDEM_SKYLINE
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MSGF_DECOY
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MSGF_INSTRUMENT
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MSGF_FRAGMENTATION
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MSGF_PROTOCOL
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MSGF_TERMINI
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MSGF_MIN_PEP_LENGTH
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MSGF_MAX_PEP_LENGTH
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MSGF_PTMS
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MSGF_NUM_MATCHES
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MSGF_ADDITIONAL
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MSGF_TASKS
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MS_AMANDA_DECOY
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MS_AMANDA_DECOY_RANKING
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MS_AMANDA_INSTRUMENT
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MS_AMANDA_MAX_RANK
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MS_AMANDA_MONOISOTOPIC
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MS_AMANDA_PERFORM_DEISOTOPING
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MS_AMANDA_MAX_MOD
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MS_AMANDA_MAX_VAR_MOD
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MS_AMANDA_MAX_MOD_SITES
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MS_AMANDA_MAX_NEUTRAL_LOSSES
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MS_AMANDA_MAX_NEUTRAL_LOSSES_MODIFICATIONS
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MS_AMANDA_MIN_PEPTIDE_LENGTH
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MS_AMANDA_MAX_PEPTIDE_LENGTH
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MS_AMANDA_LOADED_PROTEINS
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MS_AMANDA_LOADED_SPECTRA
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MS_AMANDA_OUTPUT_FORMAT
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MYRIMATCH_MIN_PEP_LENGTH
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MYRIMATCH_MAX_PEP_LENGTH
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MYRIMATCH_MIN_PREC_MASS
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MYRIMATCH_MAX_PREC_MASS
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MYRIMATCH_NUM_MATCHES
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MYRIMATCH_PTMS
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MYRIMATCH_FRAGMENTATION
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MYRIMATCH_TERMINI
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MYRIMATCH_SMART_PLUS_THREE
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MYRIMATCH_XCORR
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MYRIMATCH_TIC_CUTOFF
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MYRIMATCH_INTENSTITY_CLASSES
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MYRIMATCH_CLASS_MULTIPLIER
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MYRIMATCH_NUM_BATCHES
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MYRIMATCH_MAX_PEAK_COUNT
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MYRIMATCH_OUTPUT_FORMAT
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OMSSA_LOW_INTENSITY
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OMSSA_HIGH_INTENSITY
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OMSSA_INTENSITY_INCREMENT
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OMSSA_MIN_PEAKS
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OMSSA_REMOVE_PREC
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OMSSA_ESTIMATE_CHARGE
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OMSSA_PLUS_ONE
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OMSSA_MAX_FRACTION
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OMSSA_PREC_PER_SPECTRUM
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OMSSA_SCALE_PREC
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OMSSA_SEQUENCES_IN_MEMORY
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OMSSA_METHIONINE
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OMSSA_NEUTRON
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OMSSA_SINGLE_WINDOW_WIDTH
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OMSSA_DOUBLE_WINDOW_WIDTH
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OMSSA_SINGLE_WINDOW_PEAKS
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OMSSA_DOUBLE_WINDOW_PEAKS
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OMSSA_MIN_ANNOTATED_INTENSE_PEAKS
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OMSSA_MIN_ANNOTATED_PEAKS
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OMSSA_MAX_LADDERS
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OMSSA_MAX_FRAG_CHARGE
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OMSSA_POSITIVE_IONS
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OMSSA_FORWARD_IONS
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OMSSA_REWIND_IONS
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OMSSA_MAX_FRAG_SERIES
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OMSSA_CORRELATION_CORRECTION
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OMSSA_CONSECUTIVE_ION_PROBABILITY
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OMSSA_HITLIST_LENGTH_CHARGE
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OMSSA_ITERATIVE_SEQUENCE_EVALUE
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OMSSA_ITERATIVE_SPECTRUM_EVALUE
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OMSSA_ITERATIVE_REPLACE_EVALUE
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OMSSA_MIN_PEP_LENGTH
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OMSSA_MAX_PEP_LENGTH
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OMSSA_MAX_EVALUE
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OMSSA_HITLIST_LENGTH
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OMSSA_FORMAT
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COMET_MIN_PEAKS
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COMET_MIN_PEAK_INTENSITY
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COMET_REMOVE_PRECURSOR
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COMET_REMOVE_PRECURSOR_TOLERANCE
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COMET_CLEAR_MZ_RANGE_LOWER
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COMET_CLEAR_MZ_RANGE_UPPER
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COMET_ENZYME_TYPE
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COMET_ISOTOPE_CORRECTION
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COMET_MIN_PREC_MASS
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COMET_MAX_PREC_MASS
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COMET_MIN_PEP_LENGTH
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COMET_MAX_PEP_LENGTH
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COMET_MAX_FRAGMENT_CHARGE
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COMET_REMOVE_METH
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COMET_BATCH_SIZE
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COMET_PTMS
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COMET_REQ_PTMS
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COMET_THEORETICAL_FRAGMENT_IONS
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COMET_FRAGMENT_BIN_OFFSET
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COMET_NUM_MATCHES
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COMET_OUTPUT
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TIDE_MIN_PEP_LENGTH
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TIDE_MAX_PEP_LENGTH
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TIDE_MIN_PREC_MASS
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TIDE_MAX_PREC_MASS
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TIDE_MONOISOTOPIC
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TIDE_CLIP_N_TERM
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TIDE_PTMS
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TIDE_PTMS_PER_TYPE
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TIDE_DIGESTION_TYPE
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TIDE_PRINT_PEPTIDES
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TIDE_DECOY_FORMAT
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TIDE_KEEP_TERM_AA
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TIDE_DECOY_SEED
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TIDE_REMOVE_TEMP
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TIDE_COMPUTE_P
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TIDE_COMPUTE_SP
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TIDE_MIN_SPECTRUM_MZ
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TIDE_MAX_SPECTRUM_MZ
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TIDE_MIN_SPECTRUM_PEAKS
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TIDE_SPECTRUM_CHARGES
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TIDE_REMOVE_PREC
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TIDE_REMOVE_PREC_TOL
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TIDE_USE_FLANKING
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TIDE_USE_NEUTRAL_LOSSES
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TIDE_MZ_BIN_WIDTH
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TIDE_MZ_BIN_OFFSET
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TIDE_MAX_PSMS
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TIDE_EXPORT_TEXT
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TIDE_EXPORT_SQT
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TIDE_EXPORT_PEPXML
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TIDE_EXPORT_MZID
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TIDE_EXPORT_PIN
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TIDE_OUTPUT_FOLDER
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TIDE_VERBOSITY
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TIDE_PROGRESS_INDICATOR
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TIDE_CONCAT
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TIDE_STORE_SPECTRA
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ANDROMEDA_MAX_PEPTIDE_MASS
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ANDROMEDA_MAX_COMBINATIONS
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ANDROMEDA_TOP_PEAKS
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ANDROMEDA_TOP_PEAKS_WINDOW
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ANDROMEDA_INCL_WATER
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ANDROMEDA_INCL_AMMONIA
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ANDROMEDA_NEUTRAL_LOSSES
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ANDROMEDA_FRAGMENT_ALL
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ANDROMEDA_EMP_CORRECTION
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ANDROMEDA_HIGHER_CHARGE
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ANDROMEDA_FRAG_METHOD
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ANDROMEDA_MAX_MODS
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ANDROMEDA_MIN_PEP_LENGTH
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ANDROMEDA_MAX_PEP_LENGTH
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ANDROMEDA_EQUAL_IL
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ANDROMEDA_MAX_PSMS
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ANDROMEDA_DECOY_MODE
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META_MORPHEUS_MIN_PEP_LENGTH
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META_MORPHEUS_MAX_PEP_LENGTH
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META_MORPHEUS_SEARCH_TYPE
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META_MORPHEUS_NUM_PARTITIONS
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META_MORPHEUS_DISSOCIATION_TYPE
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META_MORPHEUS_MAX_MODS_FOR_PEPTIDE
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META_MORPHEUS_INITIATOR_METHIONINE_BEHAVIOR
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META_MORPHEUS_SCORE_CUTOFF
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META_MORPHEUS_USE_DELTA_SCORE
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META_MORPHEUS_FRAGMENTATION_TERMINUS
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META_MORPHEUS_MAX_FRAGMENTATION_SIZE
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META_MORPHEUS_MASS_DIFF_ACCEPTOR_TYPE
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META_MORPHEUS_WRITE_MZID
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META_MORPHEUS_WRITE_PEPXML
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META_MORPHEUS_USE_PROVIDED_PRECURSOR
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META_MORPHEUS_DO_PREC_DECONVOLUTION
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META_MORPHEUS_DECONVOLUTION_INT_RATIO
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META_MORPHEUS_DECONVOLUTION_MASS_TOL
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META_MORPHEUS_DECONVOLUTION_MASS_TOL_TYPE
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META_MORPHEUS_TRIM_MS1_PEAKS
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META_MORPHEUS_TRIM_MSMS_PEAKS
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META_MORPHEUS_NUM_PEAKS_PER_WINDOWS
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META_MORPHEUS_MIN_ALLOWED_INT_RATIO_TO_BASE_PEAK
public static final IdentificationParametersCLIParams META_MORPHEUS_MIN_ALLOWED_INT_RATIO_TO_BASE_PEAK -
META_MORPHEUS_WINDOW_WITH_THOMPSON
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META_MORPHEUS_NUM_WINDOWS
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META_MORPHEUS_NORMALIZE_PEAKS_ACROSS_ALL_WINDOWS
public static final IdentificationParametersCLIParams META_MORPHEUS_NORMALIZE_PEAKS_ACROSS_ALL_WINDOWS -
META_MORPHEUS_MOD_PEPTIDES_ARE_DIFFERENT
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META_MORPHEUS_NO_ONE_HIT_WONDERS
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META_MORPHEUS_SEARCH_TARGET
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META_MORPHEUS_DECOY_TYPE
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META_MORPHEUS_MAX_MOD_ISOFORMS
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META_MORPHEUS_MIN_VARIANT_DEPTH
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META_MORPHEUS_MAX_HETROZYGOUS_VARIANTS
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META_MORPHEUS_GPTM
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META_MORPHEUS_GPTM_CATEGORIES
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DIRECTAG_TAG_LENGTH
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DIRECTAG_MAX_DYNAMIC_MODS
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DIRECTAG_NUM_CHARGE_STATES
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DIRECTAG_DUPLICATE_SPECTRA
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DIRECTAG_ISOTOPE_MZ_TOLERANCE
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DIRECTAG_DEISOTOPING_MODE
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DIRECTAG_NUM_INTENSITY_CLASSES
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DIRECTAG_OUTPUT_SUFFIX
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DIRECTAG_MAX_PEAK_COUNT
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DIRECTAG_MAX_TAG_COUNT
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DIRECTAG_TIC_CUTOFF_PERCENTAGE
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DIRECTAG_COMPLEMENT_MZ_TOLERANCE
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DIRECTAG_PRECURSOR_ADJUSTMENT_STEP
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DIRECTAG_MIN_PRECURSOR_ADJUSTMENT
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DIRECTAG_MAX_PRECURSOR_ADJUSTMENT
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DIRECTAG_INTENSITY_SCORE_WEIGHT
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DIRECTAG_MZ_FIDELITY_SCORE_WEIGHT
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DIRECTAG_COMPLEMENT_SCORE_WEIGHT
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DIRECTAG_ADJUST_PRECURSOR_MASS
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DIRECTAG_USE_CHARGE_STATE_FROM_MS
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PEPNOVO_HITLIST_LENGTH
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PEPNOVO_ESTIMATE_CHARGE
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PEPNOVO_CORRECT_PREC_MASS
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PEPNOVO_DISCARD_SPECTRA
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PEPNOVO_FRAGMENTATION_MODEL
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PEPNOVO_GENERATE_BLAST
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PNOVO_NUMBER_OF_PEPTIDES
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PNOVO_LOWER_PRECURSOR_MASS
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PNOVO_UPPER_PRECURSOR_MASS
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PNOVO_ACTIVATION_TYPE
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NOVOR_FRAGMENTATION
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NOVOR_MASS_ANALYZER
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USE_GENE_MAPPING
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UPDATE_GENE_MAPPING
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ANNOTATION_LEVEL
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ANNOTATION_LEVEL_TYPE
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ANNOTATION_MZ_TOLERANCE
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ANNOTATION_HIGH_RESOLUTION
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SEQUENCE_MATCHING_TYPE
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SEQUENCE_MATCHING_X
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SEQUENCE_MATCHING_ENZYMATIC_TAGS
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SEQUENCE_MATCHING_MAX_PTMS_PER_TAG
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SEQUENCE_MATCHING_MIN_AMINO_ACID_SCORE
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SEQUENCE_MATCHING_MIN_TAG_LENGTH
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IMPORT_PEPTIDE_LENGTH_MIN
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IMPORT_PEPTIDE_LENGTH_MAX
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IMPORT_MC_MIN
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IMPORT_MC_MAX
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IMPORT_PRECURSOR_MZ
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IMPORT_PRECURSOR_MZ_PPM
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EXCLUDE_UNKNOWN_PTMs
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PTM_SCORE
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PTM_THRESHOLD
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SCORE_NEUTRAL_LOSSES
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PTM_SEQUENCE_MATCHING_TYPE
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PTM_ALIGNMENT
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SIMPLIFY_GOUPS
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SIMPLIFY_GOUPS_EVIDENCE
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SIMPLIFY_GOUPS_CONFIDENCE
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SIMPLIFY_GOUPS_CONFIDENCE_THRESHOLD
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SIMPLIFY_GOUPS_ENZYMATICITY
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SIMPLIFY_GOUPS_VARIANT
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PROTEIN_INFERENCE_MODIFICATIONS
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PSM_FDR
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PEPTIDE_FDR
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PROTEIN_FDR
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PROTEIN_FRACTION_MW_CONFIDENCE
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FASTA_TARGET_DECOY
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FASTA_DECOY_TAG
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FASTA_DECOY_SUFFIX
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FASTA_DECOY_FILE_TAG
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Field Details
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id
Short Id for the CLI parameter. -
description
Explanation for the CLI parameter. -
mandatory
public final boolean mandatoryBoolean indicating whether the parameter is mandatory. -
hasArgument
public final boolean hasArgumentBoolean indicating whether this command line option needs an argument.
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Method Details
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values
Returns an array containing the constants of this enum type, in the order they are declared.- Returns:
- an array containing the constants of this enum type, in the order they are declared
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valueOf
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 nameNullPointerException
- if the argument is null
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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
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getOptionsAsString
Returns the options as a string.- Returns:
- the options as a string
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getParametersOptionsAsString
Returns the options as a string.- Returns:
- the options as a string
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