Package com.compomics.cli.identification_parameters

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

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
ANDROMEDA_DECOY_MODE
ANDROMEDA_EMP_CORRECTION
ANDROMEDA_EQUAL_IL
ANDROMEDA_FRAG_METHOD
ANDROMEDA_FRAGMENT_ALL
ANDROMEDA_HIGHER_CHARGE
ANDROMEDA_INCL_AMMONIA
ANDROMEDA_INCL_WATER
ANDROMEDA_MAX_COMBINATIONS
ANDROMEDA_MAX_MODS
ANDROMEDA_MAX_PEP_LENGTH
ANDROMEDA_MAX_PEPTIDE_MASS
ANDROMEDA_MAX_PSMS
ANDROMEDA_MIN_PEP_LENGTH
ANDROMEDA_NEUTRAL_LOSSES
ANDROMEDA_TOP_PEAKS
ANDROMEDA_TOP_PEAKS_WINDOW
ANNOTATION_HIGH_RESOLUTION
ANNOTATION_LEVEL
ANNOTATION_LEVEL_TYPE
ANNOTATION_MZ_TOLERANCE
COMET_BATCH_SIZE
COMET_CLEAR_MZ_RANGE_LOWER
COMET_CLEAR_MZ_RANGE_UPPER
COMET_ENZYME_TYPE
COMET_FRAGMENT_BIN_OFFSET
COMET_ISOTOPE_CORRECTION
COMET_MAX_FRAGMENT_CHARGE
COMET_MAX_PEP_LENGTH
COMET_MAX_PREC_MASS
COMET_MIN_PEAK_INTENSITY
COMET_MIN_PEAKS
COMET_MIN_PEP_LENGTH
COMET_MIN_PREC_MASS
COMET_NUM_MATCHES
COMET_OUTPUT
COMET_PTMS
COMET_REMOVE_METH
COMET_REMOVE_PRECURSOR
COMET_REMOVE_PRECURSOR_TOLERANCE
COMET_REQ_PTMS
COMET_THEORETICAL_FRAGMENT_IONS
DESCRIPTION
DIGESTION
DIRECTAG_ADJUST_PRECURSOR_MASS
DIRECTAG_COMPLEMENT_MZ_TOLERANCE
DIRECTAG_COMPLEMENT_SCORE_WEIGHT
DIRECTAG_DEISOTOPING_MODE
DIRECTAG_DUPLICATE_SPECTRA
DIRECTAG_INTENSITY_SCORE_WEIGHT
DIRECTAG_ISOTOPE_MZ_TOLERANCE
DIRECTAG_MAX_DYNAMIC_MODS
DIRECTAG_MAX_PEAK_COUNT
DIRECTAG_MAX_PRECURSOR_ADJUSTMENT
DIRECTAG_MAX_TAG_COUNT
DIRECTAG_MIN_PRECURSOR_ADJUSTMENT
DIRECTAG_MZ_FIDELITY_SCORE_WEIGHT
DIRECTAG_NUM_CHARGE_STATES
DIRECTAG_NUM_INTENSITY_CLASSES
DIRECTAG_OUTPUT_SUFFIX
DIRECTAG_PRECURSOR_ADJUSTMENT_STEP
DIRECTAG_TAG_LENGTH
DIRECTAG_TIC_CUTOFF_PERCENTAGE
DIRECTAG_USE_CHARGE_STATE_FROM_MS
ENZYME
ENZYMES
EXCLUDE_UNKNOWN_PTMs
FASTA_DECOY_FILE_TAG
FASTA_DECOY_SUFFIX
FASTA_DECOY_TAG
FASTA_TARGET_DECOY
FI
FIXED_MODS
FRAG_PPM
FRAG_TOL
IDENTIFICATION_PARAMETERS
IMPORT_MC_MAX
IMPORT_MC_MIN
IMPORT_PEPTIDE_LENGTH_MAX
IMPORT_PEPTIDE_LENGTH_MIN
IMPORT_PRECURSOR_MZ
IMPORT_PRECURSOR_MZ_PPM
MAX_CHARGE
MAX_ISOTOPE
MC
META_MORPHEUS_DECONVOLUTION_INT_RATIO
META_MORPHEUS_DECONVOLUTION_MASS_TOL
META_MORPHEUS_DECONVOLUTION_MASS_TOL_TYPE
META_MORPHEUS_DECOY_TYPE
META_MORPHEUS_DISSOCIATION_TYPE
META_MORPHEUS_DO_PREC_DECONVOLUTION
META_MORPHEUS_FRAGMENTATION_TERMINUS
META_MORPHEUS_GPTM
META_MORPHEUS_GPTM_CATEGORIES
META_MORPHEUS_INITIATOR_METHIONINE_BEHAVIOR
META_MORPHEUS_MASS_DIFF_ACCEPTOR_TYPE
META_MORPHEUS_MAX_FRAGMENTATION_SIZE
META_MORPHEUS_MAX_HETROZYGOUS_VARIANTS
META_MORPHEUS_MAX_MOD_ISOFORMS
META_MORPHEUS_MAX_MODS_FOR_PEPTIDE
META_MORPHEUS_MAX_PEP_LENGTH
META_MORPHEUS_MIN_ALLOWED_INT_RATIO_TO_BASE_PEAK
META_MORPHEUS_MIN_ALLOWED_INTERNAL_FRAGMENT_LENGTH
META_MORPHEUS_MIN_PEP_LENGTH
META_MORPHEUS_MIN_VARIANT_DEPTH
META_MORPHEUS_MOD_PEPTIDES_ARE_DIFFERENT
META_MORPHEUS_NO_ONE_HIT_WONDERS
META_MORPHEUS_NORMALIZE_PEAKS_ACROSS_ALL_WINDOWS
META_MORPHEUS_NUM_PARTITIONS
META_MORPHEUS_NUM_PEAKS_PER_WINDOWS
META_MORPHEUS_NUM_WINDOWS
META_MORPHEUS_SCORE_CUTOFF
META_MORPHEUS_SEARCH_TARGET
META_MORPHEUS_SEARCH_TYPE
META_MORPHEUS_TRIM_MS1_PEAKS
META_MORPHEUS_TRIM_MSMS_PEAKS
META_MORPHEUS_USE_DELTA_SCORE
META_MORPHEUS_USE_PROVIDED_PRECURSOR
META_MORPHEUS_WINDOW_WITH_THOMPSON
META_MORPHEUS_WRITE_MZID
META_MORPHEUS_WRITE_PEPXML
MIN_CHARGE
MIN_ISOTOPE
MODS
MS_AMANDA_COMBINE_CHARGE_STATES
MS_AMANDA_CONSIDERED_CHARGE_STATES_FOR_PRECURSOR
MS_AMANDA_DECOY
MS_AMANDA_DECOY_RANKING
MS_AMANDA_EXCLUDE_FIRST_PRECURSOR
MS_AMANDA_GENERATE_PIN_FILE
MS_AMANDA_INSTRUMENT
MS_AMANDA_KEEP_Y1_ION
MS_AMANDA_LOADED_PROTEINS
MS_AMANDA_LOADED_SPECTRA
MS_AMANDA_MAX_ALLOWED_CHARGE_STATE
MS_AMANDA_MAX_MOD
MS_AMANDA_MAX_MOD_SITES
MS_AMANDA_MAX_MULTIPLE_PRECURORS
MS_AMANDA_MAX_NEUTRAL_LOSSES
MS_AMANDA_MAX_NEUTRAL_LOSSES_MODIFICATIONS
MS_AMANDA_MAX_PEAK_DEPTH
MS_AMANDA_MAX_PEPTIDE_LENGTH
MS_AMANDA_MAX_RANK
MS_AMANDA_MAX_VAR_MOD
MS_AMANDA_MIN_PEAK_DEPTH
MS_AMANDA_MIN_PEPTIDE_LENGTH
MS_AMANDA_MONOISOTOPIC
MS_AMANDA_OUTPUT_FORMAT
MS_AMANDA_PERFORM_DEISOTOPING
MS_AMANDA_REMOVE_AMMONIA_LOSSES
MS_AMANDA_REMOVE_WATER_LOSSES
MS_AMANDA_RUN_PERCOLATOR
MS_AMANDA_SECOND_SEARCH
MSGF_ADDITIONAL
MSGF_DECOY
MSGF_FRAGMENTATION
MSGF_INSTRUMENT
MSGF_MAX_PEP_LENGTH
MSGF_MIN_PEP_LENGTH
MSGF_NUM_MATCHES
MSGF_PROTOCOL
MSGF_PTMS
MSGF_TASKS
MSGF_TERMINI
MYRIMATCH_CLASS_MULTIPLIER
MYRIMATCH_FRAGMENTATION
MYRIMATCH_INTENSTITY_CLASSES
MYRIMATCH_MAX_PEAK_COUNT
MYRIMATCH_MAX_PEP_LENGTH
MYRIMATCH_MAX_PREC_MASS
MYRIMATCH_MIN_PEP_LENGTH
MYRIMATCH_MIN_PREC_MASS
MYRIMATCH_NUM_BATCHES
MYRIMATCH_NUM_MATCHES
MYRIMATCH_OUTPUT_FORMAT
MYRIMATCH_PTMS
MYRIMATCH_SMART_PLUS_THREE
MYRIMATCH_TERMINI
MYRIMATCH_TIC_CUTOFF
MYRIMATCH_XCORR
NOVOR_FRAGMENTATION
NOVOR_MASS_ANALYZER
OMSSA_CONSECUTIVE_ION_PROBABILITY
OMSSA_CORRELATION_CORRECTION
OMSSA_DOUBLE_WINDOW_PEAKS
OMSSA_DOUBLE_WINDOW_WIDTH
OMSSA_ESTIMATE_CHARGE
OMSSA_FORMAT
OMSSA_FORWARD_IONS
OMSSA_HIGH_INTENSITY
OMSSA_HITLIST_LENGTH
OMSSA_HITLIST_LENGTH_CHARGE
OMSSA_INTENSITY_INCREMENT
OMSSA_ITERATIVE_REPLACE_EVALUE
OMSSA_ITERATIVE_SEQUENCE_EVALUE
OMSSA_ITERATIVE_SPECTRUM_EVALUE
OMSSA_LOW_INTENSITY
OMSSA_MAX_EVALUE
OMSSA_MAX_FRACTION
OMSSA_MAX_FRAG_CHARGE
OMSSA_MAX_FRAG_SERIES
OMSSA_MAX_LADDERS
OMSSA_MAX_PEP_LENGTH
OMSSA_METHIONINE
OMSSA_MIN_ANNOTATED_INTENSE_PEAKS
OMSSA_MIN_ANNOTATED_PEAKS
OMSSA_MIN_PEAKS
OMSSA_MIN_PEP_LENGTH
OMSSA_NEUTRON
OMSSA_PLUS_ONE
OMSSA_POSITIVE_IONS
OMSSA_PREC_PER_SPECTRUM
OMSSA_REMOVE_PREC
OMSSA_REWIND_IONS
OMSSA_SCALE_PREC
OMSSA_SEQUENCES_IN_MEMORY
OMSSA_SINGLE_WINDOW_PEAKS
OMSSA_SINGLE_WINDOW_WIDTH
OUT
PEPNOVO_CORRECT_PREC_MASS
PEPNOVO_DISCARD_SPECTRA
PEPNOVO_ESTIMATE_CHARGE
PEPNOVO_FRAGMENTATION_MODEL
PEPNOVO_GENERATE_BLAST
PEPNOVO_HITLIST_LENGTH
PEPTIDE_FDR
PNOVO_ACTIVATION_TYPE
PNOVO_LOWER_PRECURSOR_MASS
PNOVO_NUMBER_OF_PEPTIDES
PNOVO_UPPER_PRECURSOR_MASS
PREC_PPM
PREC_TOL
PROTEIN_FDR
PROTEIN_FRACTION_MW_CONFIDENCE
PROTEIN_INFERENCE_MODIFICATIONS
PSM_FDR
PTM_ALIGNMENT
PTM_SCORE
PTM_SEQUENCE_MATCHING_TYPE
PTM_THRESHOLD
RI
SAGE_BATCH_SIZE
SAGE_BUCKET_SIZE
SAGE_CHIMERA
SAGE_DECOY_TAG
SAGE_DEISOTOPE
SAGE_GENERATE_DECOYS
SAGE_LFQ
SAGE_LFQ_COMBINE_CHARGE_STATES
SAGE_LFQ_INTEGRATION
SAGE_LFQ_PEAK_SCORING
SAGE_LFQ_PPM_TOLERANCE
SAGE_LFQ_SPECTRAL_ANGLE
SAGE_MAX_FRAG_MZ
SAGE_MAX_FRAGMENT_CHARGE
SAGE_MAX_PEAKS
SAGE_MAX_PEP_LENGTH
SAGE_MAX_PEP_MASS
SAGE_MAX_VAR_MODS
SAGE_MIN_FRAG_MZ
SAGE_MIN_ION_INDEX
SAGE_MIN_MATCHED_PEAKS
SAGE_MIN_PEAKS
SAGE_MIN_PEP_LENGTH
SAGE_MIN_PEP_MASS
SAGE_NUM_PSMS
SAGE_PREDICT_RT
SAGE_TMT
SAGE_TMT_LEVEL
SAGE_TMT_SN
SAGE_WIDE_WINDOW
SCORE_NEUTRAL_LOSSES
SEQUENCE_MATCHING_ENZYMATIC_TAGS
SEQUENCE_MATCHING_MAX_PTMS_PER_TAG
SEQUENCE_MATCHING_MIN_AMINO_ACID_SCORE
SEQUENCE_MATCHING_MIN_TAG_LENGTH
SEQUENCE_MATCHING_TYPE
SEQUENCE_MATCHING_X
SIMPLIFY_GOUPS
SIMPLIFY_GOUPS_CONFIDENCE
SIMPLIFY_GOUPS_CONFIDENCE_THRESHOLD
SIMPLIFY_GOUPS_ENZYMATICITY
SIMPLIFY_GOUPS_EVIDENCE
SIMPLIFY_GOUPS_VARIANT
SPECIFICITY
TIDE_CLIP_N_TERM
TIDE_COMPUTE_P
TIDE_COMPUTE_SP
TIDE_CONCAT
TIDE_DECOY_FORMAT
TIDE_DECOY_SEED
TIDE_DIGESTION_TYPE
TIDE_EXPORT_MZID
TIDE_EXPORT_PEPXML
TIDE_EXPORT_PIN
TIDE_EXPORT_SQT
TIDE_EXPORT_TEXT
TIDE_KEEP_TERM_AA
TIDE_MAX_PEP_LENGTH
TIDE_MAX_PREC_MASS
TIDE_MAX_PSMS
TIDE_MAX_PTMS
TIDE_MAX_SPECTRUM_MZ
TIDE_MIN_PEP_LENGTH
TIDE_MIN_PREC_MASS
TIDE_MIN_SPECTRUM_MZ
TIDE_MIN_SPECTRUM_PEAKS
TIDE_MONOISOTOPIC
TIDE_MZ_BIN_OFFSET
TIDE_MZ_BIN_WIDTH
TIDE_OUTPUT_FOLDER
TIDE_PRINT_PEPTIDES
TIDE_PROGRESS_INDICATOR
TIDE_PTMS_PER_TYPE
TIDE_REMOVE_PREC
TIDE_REMOVE_PREC_TOL
TIDE_REMOVE_TEMP
TIDE_STORE_SPECTRA
TIDE_USE_FLANKING
TIDE_USE_NEUTRAL_LOSSES
TIDE_VERBOSITY
UPDATE_GENE_MAPPING
USAGE
USAGE_2
USAGE_3
USE_GENE_MAPPING
VARIABLE_MODS
XTANDEM_DYNAMIC_RANGE
XTANDEM_EVALUE
XTANDEM_MIN_FRAG_MZ
XTANDEM_MIN_PEAKS
XTANDEM_MIN_PREC_MASS
XTANDEM_NOISE_SUPPRESSION
XTANDEM_NPEAKS
XTANDEM_OUTPUT_HISTOGRAMS
XTANDEM_OUTPUT_PROTEINS
XTANDEM_OUTPUT_RESULTS
XTANDEM_OUTPUT_SEQUENCES
XTANDEM_OUTPUT_SPECTRA
XTANDEM_PARENT_MONOISOTOPIC_MASS_ISOTOPE_ERROR
XTANDEM_PTM_COMPLEXITY
XTANDEM_QUICK_ACETYL
XTANDEM_QUICK_PYRO
XTANDEM_REFINE
XTANDEM_REFINE_EVALUE
XTANDEM_REFINE_POINT_MUTATIONS
XTANDEM_REFINE_POTENTIAL_MOD_FULL_REFINEMENT
XTANDEM_REFINE_SEMI
XTANDEM_REFINE_SNAPS
XTANDEM_REFINE_SPECTRUM_SYNTHESIS
XTANDEM_REFINE_UNANTICIPATED_CLEAVAGE
XTANDEM_SKYLINE
XTANDEM_STP_BIAS

Field Summary

Fields

Modifier and Type	Field	Description
final String	description	Explanation for the CLI parameter.
final boolean	hasArgument	Boolean indicating whether this command line option needs an argument.
final String	id	Short Id for the CLI parameter.
final 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.

Methods inherited from class java.lang.Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

DESCRIPTION

public static final IdentificationParametersCLIParams DESCRIPTION

USAGE

public static final IdentificationParametersCLIParams USAGE

USAGE_2

public static final IdentificationParametersCLIParams USAGE_2

USAGE_3

public static final IdentificationParametersCLIParams USAGE_3

MODS

public static final IdentificationParametersCLIParams MODS

ENZYMES

public static final IdentificationParametersCLIParams ENZYMES

IDENTIFICATION_PARAMETERS

public static final IdentificationParametersCLIParams IDENTIFICATION_PARAMETERS

OUT

public static final IdentificationParametersCLIParams OUT

PREC_PPM

public static final IdentificationParametersCLIParams PREC_PPM

FRAG_PPM

public static final IdentificationParametersCLIParams FRAG_PPM

PREC_TOL

public static final IdentificationParametersCLIParams PREC_TOL

FRAG_TOL

public static final IdentificationParametersCLIParams FRAG_TOL

DIGESTION

public static final IdentificationParametersCLIParams DIGESTION

ENZYME

public static final IdentificationParametersCLIParams ENZYME

MC

public static final IdentificationParametersCLIParams MC

SPECIFICITY

public static final IdentificationParametersCLIParams SPECIFICITY

FIXED_MODS

public static final IdentificationParametersCLIParams FIXED_MODS

VARIABLE_MODS

public static final IdentificationParametersCLIParams VARIABLE_MODS

MIN_CHARGE

public static final IdentificationParametersCLIParams MIN_CHARGE

MAX_CHARGE

public static final IdentificationParametersCLIParams MAX_CHARGE

FI

public static final IdentificationParametersCLIParams FI

RI

public static final IdentificationParametersCLIParams RI

MIN_ISOTOPE

public static final IdentificationParametersCLIParams MIN_ISOTOPE

MAX_ISOTOPE

public static final IdentificationParametersCLIParams MAX_ISOTOPE

XTANDEM_DYNAMIC_RANGE

public static final IdentificationParametersCLIParams XTANDEM_DYNAMIC_RANGE

XTANDEM_NPEAKS

public static final IdentificationParametersCLIParams XTANDEM_NPEAKS

XTANDEM_MIN_FRAG_MZ

public static final IdentificationParametersCLIParams XTANDEM_MIN_FRAG_MZ

XTANDEM_MIN_PEAKS

public static final IdentificationParametersCLIParams XTANDEM_MIN_PEAKS

XTANDEM_NOISE_SUPPRESSION

public static final IdentificationParametersCLIParams XTANDEM_NOISE_SUPPRESSION

XTANDEM_MIN_PREC_MASS

public static final IdentificationParametersCLIParams XTANDEM_MIN_PREC_MASS

XTANDEM_PARENT_MONOISOTOPIC_MASS_ISOTOPE_ERROR

public static final IdentificationParametersCLIParams XTANDEM_PARENT_MONOISOTOPIC_MASS_ISOTOPE_ERROR

XTANDEM_QUICK_ACETYL

public static final IdentificationParametersCLIParams XTANDEM_QUICK_ACETYL

XTANDEM_QUICK_PYRO

public static final IdentificationParametersCLIParams XTANDEM_QUICK_PYRO

XTANDEM_STP_BIAS

public static final IdentificationParametersCLIParams XTANDEM_STP_BIAS

XTANDEM_PTM_COMPLEXITY

public static final IdentificationParametersCLIParams XTANDEM_PTM_COMPLEXITY

XTANDEM_REFINE

public static final IdentificationParametersCLIParams XTANDEM_REFINE

XTANDEM_REFINE_EVALUE

public static final IdentificationParametersCLIParams XTANDEM_REFINE_EVALUE

XTANDEM_REFINE_UNANTICIPATED_CLEAVAGE

public static final IdentificationParametersCLIParams XTANDEM_REFINE_UNANTICIPATED_CLEAVAGE

XTANDEM_REFINE_SEMI

public static final IdentificationParametersCLIParams XTANDEM_REFINE_SEMI

XTANDEM_REFINE_POTENTIAL_MOD_FULL_REFINEMENT

public static final IdentificationParametersCLIParams XTANDEM_REFINE_POTENTIAL_MOD_FULL_REFINEMENT

XTANDEM_REFINE_POINT_MUTATIONS

public static final IdentificationParametersCLIParams XTANDEM_REFINE_POINT_MUTATIONS

XTANDEM_REFINE_SNAPS

public static final IdentificationParametersCLIParams XTANDEM_REFINE_SNAPS

XTANDEM_REFINE_SPECTRUM_SYNTHESIS

public static final IdentificationParametersCLIParams XTANDEM_REFINE_SPECTRUM_SYNTHESIS

XTANDEM_EVALUE

public static final IdentificationParametersCLIParams XTANDEM_EVALUE

XTANDEM_OUTPUT_RESULTS

public static final IdentificationParametersCLIParams XTANDEM_OUTPUT_RESULTS

XTANDEM_OUTPUT_PROTEINS

public static final IdentificationParametersCLIParams XTANDEM_OUTPUT_PROTEINS

XTANDEM_OUTPUT_SEQUENCES

public static final IdentificationParametersCLIParams XTANDEM_OUTPUT_SEQUENCES

XTANDEM_OUTPUT_SPECTRA

public static final IdentificationParametersCLIParams XTANDEM_OUTPUT_SPECTRA

XTANDEM_OUTPUT_HISTOGRAMS

public static final IdentificationParametersCLIParams XTANDEM_OUTPUT_HISTOGRAMS

XTANDEM_SKYLINE

public static final IdentificationParametersCLIParams XTANDEM_SKYLINE

MSGF_DECOY

public static final IdentificationParametersCLIParams MSGF_DECOY

MSGF_INSTRUMENT

public static final IdentificationParametersCLIParams MSGF_INSTRUMENT

MSGF_FRAGMENTATION

public static final IdentificationParametersCLIParams MSGF_FRAGMENTATION

MSGF_PROTOCOL

public static final IdentificationParametersCLIParams MSGF_PROTOCOL

MSGF_TERMINI

public static final IdentificationParametersCLIParams MSGF_TERMINI

MSGF_MIN_PEP_LENGTH

public static final IdentificationParametersCLIParams MSGF_MIN_PEP_LENGTH

MSGF_MAX_PEP_LENGTH

public static final IdentificationParametersCLIParams MSGF_MAX_PEP_LENGTH

MSGF_PTMS

public static final IdentificationParametersCLIParams MSGF_PTMS

MSGF_NUM_MATCHES

public static final IdentificationParametersCLIParams MSGF_NUM_MATCHES

MSGF_ADDITIONAL

public static final IdentificationParametersCLIParams MSGF_ADDITIONAL

MSGF_TASKS

public static final IdentificationParametersCLIParams MSGF_TASKS

MS_AMANDA_DECOY

public static final IdentificationParametersCLIParams MS_AMANDA_DECOY

MS_AMANDA_DECOY_RANKING

public static final IdentificationParametersCLIParams MS_AMANDA_DECOY_RANKING

MS_AMANDA_INSTRUMENT

public static final IdentificationParametersCLIParams MS_AMANDA_INSTRUMENT

MS_AMANDA_MAX_RANK

public static final IdentificationParametersCLIParams MS_AMANDA_MAX_RANK

MS_AMANDA_MONOISOTOPIC

public static final IdentificationParametersCLIParams MS_AMANDA_MONOISOTOPIC

MS_AMANDA_PERFORM_DEISOTOPING

public static final IdentificationParametersCLIParams MS_AMANDA_PERFORM_DEISOTOPING

MS_AMANDA_MAX_MOD

public static final IdentificationParametersCLIParams MS_AMANDA_MAX_MOD

MS_AMANDA_MAX_VAR_MOD

public static final IdentificationParametersCLIParams MS_AMANDA_MAX_VAR_MOD

MS_AMANDA_MAX_MOD_SITES

public static final IdentificationParametersCLIParams MS_AMANDA_MAX_MOD_SITES

MS_AMANDA_MAX_NEUTRAL_LOSSES

public static final IdentificationParametersCLIParams MS_AMANDA_MAX_NEUTRAL_LOSSES

MS_AMANDA_MAX_NEUTRAL_LOSSES_MODIFICATIONS

public static final IdentificationParametersCLIParams MS_AMANDA_MAX_NEUTRAL_LOSSES_MODIFICATIONS

MS_AMANDA_MIN_PEPTIDE_LENGTH

public static final IdentificationParametersCLIParams MS_AMANDA_MIN_PEPTIDE_LENGTH

MS_AMANDA_MAX_PEPTIDE_LENGTH

public static final IdentificationParametersCLIParams MS_AMANDA_MAX_PEPTIDE_LENGTH

MS_AMANDA_LOADED_PROTEINS

public static final IdentificationParametersCLIParams MS_AMANDA_LOADED_PROTEINS

MS_AMANDA_LOADED_SPECTRA

public static final IdentificationParametersCLIParams MS_AMANDA_LOADED_SPECTRA

MS_AMANDA_OUTPUT_FORMAT

public static final IdentificationParametersCLIParams MS_AMANDA_OUTPUT_FORMAT

MS_AMANDA_MAX_ALLOWED_CHARGE_STATE

public static final IdentificationParametersCLIParams MS_AMANDA_MAX_ALLOWED_CHARGE_STATE

MS_AMANDA_MIN_PEAK_DEPTH

public static final IdentificationParametersCLIParams MS_AMANDA_MIN_PEAK_DEPTH

MS_AMANDA_MAX_PEAK_DEPTH

public static final IdentificationParametersCLIParams MS_AMANDA_MAX_PEAK_DEPTH

MS_AMANDA_SECOND_SEARCH

public static final IdentificationParametersCLIParams MS_AMANDA_SECOND_SEARCH

MS_AMANDA_KEEP_Y1_ION

public static final IdentificationParametersCLIParams MS_AMANDA_KEEP_Y1_ION

MS_AMANDA_REMOVE_WATER_LOSSES

public static final IdentificationParametersCLIParams MS_AMANDA_REMOVE_WATER_LOSSES

MS_AMANDA_REMOVE_AMMONIA_LOSSES

public static final IdentificationParametersCLIParams MS_AMANDA_REMOVE_AMMONIA_LOSSES

MS_AMANDA_EXCLUDE_FIRST_PRECURSOR

public static final IdentificationParametersCLIParams MS_AMANDA_EXCLUDE_FIRST_PRECURSOR

MS_AMANDA_MAX_MULTIPLE_PRECURORS

public static final IdentificationParametersCLIParams MS_AMANDA_MAX_MULTIPLE_PRECURORS

MS_AMANDA_CONSIDERED_CHARGE_STATES_FOR_PRECURSOR

public static final IdentificationParametersCLIParams MS_AMANDA_CONSIDERED_CHARGE_STATES_FOR_PRECURSOR

MS_AMANDA_COMBINE_CHARGE_STATES

public static final IdentificationParametersCLIParams MS_AMANDA_COMBINE_CHARGE_STATES

MS_AMANDA_RUN_PERCOLATOR

public static final IdentificationParametersCLIParams MS_AMANDA_RUN_PERCOLATOR

MS_AMANDA_GENERATE_PIN_FILE

public static final IdentificationParametersCLIParams MS_AMANDA_GENERATE_PIN_FILE

MYRIMATCH_MIN_PEP_LENGTH

public static final IdentificationParametersCLIParams MYRIMATCH_MIN_PEP_LENGTH

MYRIMATCH_MAX_PEP_LENGTH

public static final IdentificationParametersCLIParams MYRIMATCH_MAX_PEP_LENGTH

MYRIMATCH_MIN_PREC_MASS

public static final IdentificationParametersCLIParams MYRIMATCH_MIN_PREC_MASS

MYRIMATCH_MAX_PREC_MASS

public static final IdentificationParametersCLIParams MYRIMATCH_MAX_PREC_MASS

MYRIMATCH_NUM_MATCHES

public static final IdentificationParametersCLIParams MYRIMATCH_NUM_MATCHES

MYRIMATCH_PTMS

public static final IdentificationParametersCLIParams MYRIMATCH_PTMS

MYRIMATCH_FRAGMENTATION

public static final IdentificationParametersCLIParams MYRIMATCH_FRAGMENTATION

MYRIMATCH_TERMINI

public static final IdentificationParametersCLIParams MYRIMATCH_TERMINI

MYRIMATCH_SMART_PLUS_THREE

public static final IdentificationParametersCLIParams MYRIMATCH_SMART_PLUS_THREE

MYRIMATCH_XCORR

public static final IdentificationParametersCLIParams MYRIMATCH_XCORR

MYRIMATCH_TIC_CUTOFF

public static final IdentificationParametersCLIParams MYRIMATCH_TIC_CUTOFF

MYRIMATCH_INTENSTITY_CLASSES

public static final IdentificationParametersCLIParams MYRIMATCH_INTENSTITY_CLASSES

MYRIMATCH_CLASS_MULTIPLIER

public static final IdentificationParametersCLIParams MYRIMATCH_CLASS_MULTIPLIER

MYRIMATCH_NUM_BATCHES

public static final IdentificationParametersCLIParams MYRIMATCH_NUM_BATCHES

MYRIMATCH_MAX_PEAK_COUNT

public static final IdentificationParametersCLIParams MYRIMATCH_MAX_PEAK_COUNT

MYRIMATCH_OUTPUT_FORMAT

public static final IdentificationParametersCLIParams MYRIMATCH_OUTPUT_FORMAT

OMSSA_LOW_INTENSITY

public static final IdentificationParametersCLIParams OMSSA_LOW_INTENSITY

OMSSA_HIGH_INTENSITY

public static final IdentificationParametersCLIParams OMSSA_HIGH_INTENSITY

OMSSA_INTENSITY_INCREMENT

public static final IdentificationParametersCLIParams OMSSA_INTENSITY_INCREMENT

OMSSA_MIN_PEAKS

public static final IdentificationParametersCLIParams OMSSA_MIN_PEAKS

OMSSA_REMOVE_PREC

public static final IdentificationParametersCLIParams OMSSA_REMOVE_PREC

OMSSA_ESTIMATE_CHARGE

public static final IdentificationParametersCLIParams OMSSA_ESTIMATE_CHARGE

OMSSA_PLUS_ONE

public static final IdentificationParametersCLIParams OMSSA_PLUS_ONE

OMSSA_MAX_FRACTION

public static final IdentificationParametersCLIParams OMSSA_MAX_FRACTION

OMSSA_PREC_PER_SPECTRUM

public static final IdentificationParametersCLIParams OMSSA_PREC_PER_SPECTRUM

OMSSA_SCALE_PREC

public static final IdentificationParametersCLIParams OMSSA_SCALE_PREC

OMSSA_SEQUENCES_IN_MEMORY

public static final IdentificationParametersCLIParams OMSSA_SEQUENCES_IN_MEMORY

OMSSA_METHIONINE

public static final IdentificationParametersCLIParams OMSSA_METHIONINE

OMSSA_NEUTRON

public static final IdentificationParametersCLIParams OMSSA_NEUTRON

OMSSA_SINGLE_WINDOW_WIDTH

public static final IdentificationParametersCLIParams OMSSA_SINGLE_WINDOW_WIDTH

OMSSA_DOUBLE_WINDOW_WIDTH

public static final IdentificationParametersCLIParams OMSSA_DOUBLE_WINDOW_WIDTH

OMSSA_SINGLE_WINDOW_PEAKS

public static final IdentificationParametersCLIParams OMSSA_SINGLE_WINDOW_PEAKS

OMSSA_DOUBLE_WINDOW_PEAKS

public static final IdentificationParametersCLIParams OMSSA_DOUBLE_WINDOW_PEAKS

OMSSA_MIN_ANNOTATED_INTENSE_PEAKS

public static final IdentificationParametersCLIParams OMSSA_MIN_ANNOTATED_INTENSE_PEAKS

OMSSA_MIN_ANNOTATED_PEAKS

public static final IdentificationParametersCLIParams OMSSA_MIN_ANNOTATED_PEAKS

OMSSA_MAX_LADDERS

public static final IdentificationParametersCLIParams OMSSA_MAX_LADDERS

OMSSA_MAX_FRAG_CHARGE

public static final IdentificationParametersCLIParams OMSSA_MAX_FRAG_CHARGE

OMSSA_POSITIVE_IONS

public static final IdentificationParametersCLIParams OMSSA_POSITIVE_IONS

OMSSA_FORWARD_IONS

public static final IdentificationParametersCLIParams OMSSA_FORWARD_IONS

OMSSA_REWIND_IONS

public static final IdentificationParametersCLIParams OMSSA_REWIND_IONS

OMSSA_MAX_FRAG_SERIES

public static final IdentificationParametersCLIParams OMSSA_MAX_FRAG_SERIES

OMSSA_CORRELATION_CORRECTION

public static final IdentificationParametersCLIParams OMSSA_CORRELATION_CORRECTION

OMSSA_CONSECUTIVE_ION_PROBABILITY

public static final IdentificationParametersCLIParams OMSSA_CONSECUTIVE_ION_PROBABILITY

OMSSA_HITLIST_LENGTH_CHARGE

public static final IdentificationParametersCLIParams OMSSA_HITLIST_LENGTH_CHARGE

OMSSA_ITERATIVE_SEQUENCE_EVALUE

public static final IdentificationParametersCLIParams OMSSA_ITERATIVE_SEQUENCE_EVALUE

OMSSA_ITERATIVE_SPECTRUM_EVALUE

public static final IdentificationParametersCLIParams OMSSA_ITERATIVE_SPECTRUM_EVALUE

OMSSA_ITERATIVE_REPLACE_EVALUE

public static final IdentificationParametersCLIParams OMSSA_ITERATIVE_REPLACE_EVALUE

OMSSA_MIN_PEP_LENGTH

public static final IdentificationParametersCLIParams OMSSA_MIN_PEP_LENGTH

OMSSA_MAX_PEP_LENGTH

public static final IdentificationParametersCLIParams OMSSA_MAX_PEP_LENGTH

OMSSA_MAX_EVALUE

public static final IdentificationParametersCLIParams OMSSA_MAX_EVALUE

OMSSA_HITLIST_LENGTH

public static final IdentificationParametersCLIParams OMSSA_HITLIST_LENGTH

OMSSA_FORMAT

public static final IdentificationParametersCLIParams OMSSA_FORMAT

COMET_MIN_PEAKS

public static final IdentificationParametersCLIParams COMET_MIN_PEAKS

COMET_MIN_PEAK_INTENSITY

public static final IdentificationParametersCLIParams COMET_MIN_PEAK_INTENSITY

COMET_REMOVE_PRECURSOR

public static final IdentificationParametersCLIParams COMET_REMOVE_PRECURSOR

COMET_REMOVE_PRECURSOR_TOLERANCE

public static final IdentificationParametersCLIParams COMET_REMOVE_PRECURSOR_TOLERANCE

COMET_CLEAR_MZ_RANGE_LOWER

public static final IdentificationParametersCLIParams COMET_CLEAR_MZ_RANGE_LOWER

COMET_CLEAR_MZ_RANGE_UPPER

public static final IdentificationParametersCLIParams COMET_CLEAR_MZ_RANGE_UPPER

COMET_ENZYME_TYPE

public static final IdentificationParametersCLIParams COMET_ENZYME_TYPE

COMET_ISOTOPE_CORRECTION

public static final IdentificationParametersCLIParams COMET_ISOTOPE_CORRECTION

COMET_MIN_PREC_MASS

public static final IdentificationParametersCLIParams COMET_MIN_PREC_MASS

COMET_MAX_PREC_MASS

public static final IdentificationParametersCLIParams COMET_MAX_PREC_MASS

COMET_MIN_PEP_LENGTH

public static final IdentificationParametersCLIParams COMET_MIN_PEP_LENGTH

COMET_MAX_PEP_LENGTH

public static final IdentificationParametersCLIParams COMET_MAX_PEP_LENGTH

COMET_MAX_FRAGMENT_CHARGE

public static final IdentificationParametersCLIParams COMET_MAX_FRAGMENT_CHARGE

COMET_REMOVE_METH

public static final IdentificationParametersCLIParams COMET_REMOVE_METH

COMET_BATCH_SIZE

public static final IdentificationParametersCLIParams COMET_BATCH_SIZE

COMET_PTMS

public static final IdentificationParametersCLIParams COMET_PTMS

COMET_REQ_PTMS

public static final IdentificationParametersCLIParams COMET_REQ_PTMS

COMET_THEORETICAL_FRAGMENT_IONS

public static final IdentificationParametersCLIParams COMET_THEORETICAL_FRAGMENT_IONS

COMET_FRAGMENT_BIN_OFFSET

public static final IdentificationParametersCLIParams COMET_FRAGMENT_BIN_OFFSET

COMET_NUM_MATCHES

public static final IdentificationParametersCLIParams COMET_NUM_MATCHES

COMET_OUTPUT

public static final IdentificationParametersCLIParams COMET_OUTPUT

TIDE_MIN_PEP_LENGTH

public static final IdentificationParametersCLIParams TIDE_MIN_PEP_LENGTH

TIDE_MAX_PEP_LENGTH

public static final IdentificationParametersCLIParams TIDE_MAX_PEP_LENGTH

TIDE_MIN_PREC_MASS

public static final IdentificationParametersCLIParams TIDE_MIN_PREC_MASS

TIDE_MAX_PREC_MASS

public static final IdentificationParametersCLIParams TIDE_MAX_PREC_MASS

TIDE_MONOISOTOPIC

public static final IdentificationParametersCLIParams TIDE_MONOISOTOPIC

TIDE_CLIP_N_TERM

public static final IdentificationParametersCLIParams TIDE_CLIP_N_TERM

TIDE_MAX_PTMS

public static final IdentificationParametersCLIParams TIDE_MAX_PTMS

TIDE_PTMS_PER_TYPE

public static final IdentificationParametersCLIParams TIDE_PTMS_PER_TYPE

TIDE_DIGESTION_TYPE

public static final IdentificationParametersCLIParams TIDE_DIGESTION_TYPE

TIDE_PRINT_PEPTIDES

public static final IdentificationParametersCLIParams TIDE_PRINT_PEPTIDES

TIDE_DECOY_FORMAT

public static final IdentificationParametersCLIParams TIDE_DECOY_FORMAT

TIDE_KEEP_TERM_AA

public static final IdentificationParametersCLIParams TIDE_KEEP_TERM_AA

TIDE_DECOY_SEED

public static final IdentificationParametersCLIParams TIDE_DECOY_SEED

TIDE_REMOVE_TEMP

public static final IdentificationParametersCLIParams TIDE_REMOVE_TEMP

TIDE_COMPUTE_P

public static final IdentificationParametersCLIParams TIDE_COMPUTE_P

TIDE_COMPUTE_SP

public static final IdentificationParametersCLIParams TIDE_COMPUTE_SP

TIDE_MIN_SPECTRUM_MZ

public static final IdentificationParametersCLIParams TIDE_MIN_SPECTRUM_MZ

TIDE_MAX_SPECTRUM_MZ

public static final IdentificationParametersCLIParams TIDE_MAX_SPECTRUM_MZ

TIDE_MIN_SPECTRUM_PEAKS

public static final IdentificationParametersCLIParams TIDE_MIN_SPECTRUM_PEAKS

TIDE_REMOVE_PREC

public static final IdentificationParametersCLIParams TIDE_REMOVE_PREC

TIDE_REMOVE_PREC_TOL

public static final IdentificationParametersCLIParams TIDE_REMOVE_PREC_TOL

TIDE_USE_FLANKING

public static final IdentificationParametersCLIParams TIDE_USE_FLANKING

TIDE_USE_NEUTRAL_LOSSES

public static final IdentificationParametersCLIParams TIDE_USE_NEUTRAL_LOSSES

TIDE_MZ_BIN_WIDTH

public static final IdentificationParametersCLIParams TIDE_MZ_BIN_WIDTH

TIDE_MZ_BIN_OFFSET

public static final IdentificationParametersCLIParams TIDE_MZ_BIN_OFFSET

TIDE_MAX_PSMS

public static final IdentificationParametersCLIParams TIDE_MAX_PSMS

TIDE_EXPORT_TEXT

public static final IdentificationParametersCLIParams TIDE_EXPORT_TEXT

TIDE_EXPORT_SQT

public static final IdentificationParametersCLIParams TIDE_EXPORT_SQT

TIDE_EXPORT_PEPXML

public static final IdentificationParametersCLIParams TIDE_EXPORT_PEPXML

TIDE_EXPORT_MZID

public static final IdentificationParametersCLIParams TIDE_EXPORT_MZID

TIDE_EXPORT_PIN

public static final IdentificationParametersCLIParams TIDE_EXPORT_PIN

TIDE_OUTPUT_FOLDER

public static final IdentificationParametersCLIParams TIDE_OUTPUT_FOLDER

TIDE_VERBOSITY

public static final IdentificationParametersCLIParams TIDE_VERBOSITY

TIDE_PROGRESS_INDICATOR

public static final IdentificationParametersCLIParams TIDE_PROGRESS_INDICATOR

TIDE_CONCAT

public static final IdentificationParametersCLIParams TIDE_CONCAT

TIDE_STORE_SPECTRA

public static final IdentificationParametersCLIParams TIDE_STORE_SPECTRA

ANDROMEDA_MAX_PEPTIDE_MASS

public static final IdentificationParametersCLIParams ANDROMEDA_MAX_PEPTIDE_MASS

ANDROMEDA_MAX_COMBINATIONS

public static final IdentificationParametersCLIParams ANDROMEDA_MAX_COMBINATIONS

ANDROMEDA_TOP_PEAKS

public static final IdentificationParametersCLIParams ANDROMEDA_TOP_PEAKS

ANDROMEDA_TOP_PEAKS_WINDOW

public static final IdentificationParametersCLIParams ANDROMEDA_TOP_PEAKS_WINDOW

ANDROMEDA_INCL_WATER

public static final IdentificationParametersCLIParams ANDROMEDA_INCL_WATER

ANDROMEDA_INCL_AMMONIA

public static final IdentificationParametersCLIParams ANDROMEDA_INCL_AMMONIA

ANDROMEDA_NEUTRAL_LOSSES

public static final IdentificationParametersCLIParams ANDROMEDA_NEUTRAL_LOSSES

ANDROMEDA_FRAGMENT_ALL

public static final IdentificationParametersCLIParams ANDROMEDA_FRAGMENT_ALL

ANDROMEDA_EMP_CORRECTION

public static final IdentificationParametersCLIParams ANDROMEDA_EMP_CORRECTION

ANDROMEDA_HIGHER_CHARGE

public static final IdentificationParametersCLIParams ANDROMEDA_HIGHER_CHARGE

ANDROMEDA_FRAG_METHOD

public static final IdentificationParametersCLIParams ANDROMEDA_FRAG_METHOD

ANDROMEDA_MAX_MODS

public static final IdentificationParametersCLIParams ANDROMEDA_MAX_MODS

ANDROMEDA_MIN_PEP_LENGTH

public static final IdentificationParametersCLIParams ANDROMEDA_MIN_PEP_LENGTH

ANDROMEDA_MAX_PEP_LENGTH

public static final IdentificationParametersCLIParams ANDROMEDA_MAX_PEP_LENGTH

ANDROMEDA_EQUAL_IL

public static final IdentificationParametersCLIParams ANDROMEDA_EQUAL_IL

ANDROMEDA_MAX_PSMS

public static final IdentificationParametersCLIParams ANDROMEDA_MAX_PSMS

ANDROMEDA_DECOY_MODE

public static final IdentificationParametersCLIParams ANDROMEDA_DECOY_MODE

META_MORPHEUS_MIN_PEP_LENGTH

public static final IdentificationParametersCLIParams META_MORPHEUS_MIN_PEP_LENGTH

META_MORPHEUS_MAX_PEP_LENGTH

public static final IdentificationParametersCLIParams META_MORPHEUS_MAX_PEP_LENGTH

META_MORPHEUS_SEARCH_TYPE

public static final IdentificationParametersCLIParams META_MORPHEUS_SEARCH_TYPE

META_MORPHEUS_NUM_PARTITIONS

public static final IdentificationParametersCLIParams META_MORPHEUS_NUM_PARTITIONS

META_MORPHEUS_DISSOCIATION_TYPE

public static final IdentificationParametersCLIParams META_MORPHEUS_DISSOCIATION_TYPE

META_MORPHEUS_MAX_MODS_FOR_PEPTIDE

public static final IdentificationParametersCLIParams META_MORPHEUS_MAX_MODS_FOR_PEPTIDE

META_MORPHEUS_INITIATOR_METHIONINE_BEHAVIOR

public static final IdentificationParametersCLIParams META_MORPHEUS_INITIATOR_METHIONINE_BEHAVIOR

META_MORPHEUS_SCORE_CUTOFF

public static final IdentificationParametersCLIParams META_MORPHEUS_SCORE_CUTOFF

META_MORPHEUS_USE_DELTA_SCORE

public static final IdentificationParametersCLIParams META_MORPHEUS_USE_DELTA_SCORE

META_MORPHEUS_FRAGMENTATION_TERMINUS

public static final IdentificationParametersCLIParams META_MORPHEUS_FRAGMENTATION_TERMINUS

META_MORPHEUS_MAX_FRAGMENTATION_SIZE

public static final IdentificationParametersCLIParams META_MORPHEUS_MAX_FRAGMENTATION_SIZE

META_MORPHEUS_MIN_ALLOWED_INTERNAL_FRAGMENT_LENGTH

public static final IdentificationParametersCLIParams META_MORPHEUS_MIN_ALLOWED_INTERNAL_FRAGMENT_LENGTH

META_MORPHEUS_MASS_DIFF_ACCEPTOR_TYPE

public static final IdentificationParametersCLIParams META_MORPHEUS_MASS_DIFF_ACCEPTOR_TYPE

META_MORPHEUS_WRITE_MZID

public static final IdentificationParametersCLIParams META_MORPHEUS_WRITE_MZID

META_MORPHEUS_WRITE_PEPXML

public static final IdentificationParametersCLIParams META_MORPHEUS_WRITE_PEPXML

META_MORPHEUS_USE_PROVIDED_PRECURSOR

public static final IdentificationParametersCLIParams META_MORPHEUS_USE_PROVIDED_PRECURSOR

META_MORPHEUS_DO_PREC_DECONVOLUTION

public static final IdentificationParametersCLIParams META_MORPHEUS_DO_PREC_DECONVOLUTION

META_MORPHEUS_DECONVOLUTION_INT_RATIO

public static final IdentificationParametersCLIParams META_MORPHEUS_DECONVOLUTION_INT_RATIO

META_MORPHEUS_DECONVOLUTION_MASS_TOL

public static final IdentificationParametersCLIParams META_MORPHEUS_DECONVOLUTION_MASS_TOL

META_MORPHEUS_DECONVOLUTION_MASS_TOL_TYPE

public static final IdentificationParametersCLIParams META_MORPHEUS_DECONVOLUTION_MASS_TOL_TYPE

META_MORPHEUS_TRIM_MS1_PEAKS

public static final IdentificationParametersCLIParams META_MORPHEUS_TRIM_MS1_PEAKS

META_MORPHEUS_TRIM_MSMS_PEAKS

public static final IdentificationParametersCLIParams META_MORPHEUS_TRIM_MSMS_PEAKS

META_MORPHEUS_NUM_PEAKS_PER_WINDOWS

public static final IdentificationParametersCLIParams META_MORPHEUS_NUM_PEAKS_PER_WINDOWS

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

public static final IdentificationParametersCLIParams META_MORPHEUS_WINDOW_WITH_THOMPSON

META_MORPHEUS_NUM_WINDOWS

public static final IdentificationParametersCLIParams META_MORPHEUS_NUM_WINDOWS

META_MORPHEUS_NORMALIZE_PEAKS_ACROSS_ALL_WINDOWS

public static final IdentificationParametersCLIParams META_MORPHEUS_NORMALIZE_PEAKS_ACROSS_ALL_WINDOWS

META_MORPHEUS_MOD_PEPTIDES_ARE_DIFFERENT

public static final IdentificationParametersCLIParams META_MORPHEUS_MOD_PEPTIDES_ARE_DIFFERENT

META_MORPHEUS_NO_ONE_HIT_WONDERS

public static final IdentificationParametersCLIParams META_MORPHEUS_NO_ONE_HIT_WONDERS

META_MORPHEUS_SEARCH_TARGET

public static final IdentificationParametersCLIParams META_MORPHEUS_SEARCH_TARGET

META_MORPHEUS_DECOY_TYPE

public static final IdentificationParametersCLIParams META_MORPHEUS_DECOY_TYPE

META_MORPHEUS_MAX_MOD_ISOFORMS

public static final IdentificationParametersCLIParams META_MORPHEUS_MAX_MOD_ISOFORMS

META_MORPHEUS_MIN_VARIANT_DEPTH

public static final IdentificationParametersCLIParams META_MORPHEUS_MIN_VARIANT_DEPTH

META_MORPHEUS_MAX_HETROZYGOUS_VARIANTS

public static final IdentificationParametersCLIParams META_MORPHEUS_MAX_HETROZYGOUS_VARIANTS

META_MORPHEUS_GPTM

public static final IdentificationParametersCLIParams META_MORPHEUS_GPTM

META_MORPHEUS_GPTM_CATEGORIES

public static final IdentificationParametersCLIParams META_MORPHEUS_GPTM_CATEGORIES

SAGE_BUCKET_SIZE

public static final IdentificationParametersCLIParams SAGE_BUCKET_SIZE

SAGE_MIN_PEP_LENGTH

public static final IdentificationParametersCLIParams SAGE_MIN_PEP_LENGTH

SAGE_MAX_PEP_LENGTH

public static final IdentificationParametersCLIParams SAGE_MAX_PEP_LENGTH

SAGE_MIN_FRAG_MZ

public static final IdentificationParametersCLIParams SAGE_MIN_FRAG_MZ

SAGE_MAX_FRAG_MZ

public static final IdentificationParametersCLIParams SAGE_MAX_FRAG_MZ

SAGE_MIN_PEP_MASS

public static final IdentificationParametersCLIParams SAGE_MIN_PEP_MASS

SAGE_MAX_PEP_MASS

public static final IdentificationParametersCLIParams SAGE_MAX_PEP_MASS

SAGE_MIN_ION_INDEX

public static final IdentificationParametersCLIParams SAGE_MIN_ION_INDEX

SAGE_MAX_VAR_MODS

public static final IdentificationParametersCLIParams SAGE_MAX_VAR_MODS

SAGE_DECOY_TAG

public static final IdentificationParametersCLIParams SAGE_DECOY_TAG

SAGE_GENERATE_DECOYS

public static final IdentificationParametersCLIParams SAGE_GENERATE_DECOYS

SAGE_TMT

public static final IdentificationParametersCLIParams SAGE_TMT

SAGE_TMT_LEVEL

public static final IdentificationParametersCLIParams SAGE_TMT_LEVEL

SAGE_TMT_SN

public static final IdentificationParametersCLIParams SAGE_TMT_SN

SAGE_LFQ

public static final IdentificationParametersCLIParams SAGE_LFQ

SAGE_LFQ_PEAK_SCORING

public static final IdentificationParametersCLIParams SAGE_LFQ_PEAK_SCORING

SAGE_LFQ_INTEGRATION

public static final IdentificationParametersCLIParams SAGE_LFQ_INTEGRATION

SAGE_LFQ_SPECTRAL_ANGLE

public static final IdentificationParametersCLIParams SAGE_LFQ_SPECTRAL_ANGLE

SAGE_LFQ_PPM_TOLERANCE

public static final IdentificationParametersCLIParams SAGE_LFQ_PPM_TOLERANCE

SAGE_LFQ_COMBINE_CHARGE_STATES

public static final IdentificationParametersCLIParams SAGE_LFQ_COMBINE_CHARGE_STATES

SAGE_DEISOTOPE

public static final IdentificationParametersCLIParams SAGE_DEISOTOPE

SAGE_CHIMERA

public static final IdentificationParametersCLIParams SAGE_CHIMERA

SAGE_WIDE_WINDOW

public static final IdentificationParametersCLIParams SAGE_WIDE_WINDOW

SAGE_PREDICT_RT

public static final IdentificationParametersCLIParams SAGE_PREDICT_RT

SAGE_MIN_PEAKS

public static final IdentificationParametersCLIParams SAGE_MIN_PEAKS

SAGE_MAX_PEAKS

public static final IdentificationParametersCLIParams SAGE_MAX_PEAKS

SAGE_MIN_MATCHED_PEAKS

public static final IdentificationParametersCLIParams SAGE_MIN_MATCHED_PEAKS

SAGE_MAX_FRAGMENT_CHARGE

public static final IdentificationParametersCLIParams SAGE_MAX_FRAGMENT_CHARGE

SAGE_NUM_PSMS

public static final IdentificationParametersCLIParams SAGE_NUM_PSMS

SAGE_BATCH_SIZE

public static final IdentificationParametersCLIParams SAGE_BATCH_SIZE

DIRECTAG_TAG_LENGTH

public static final IdentificationParametersCLIParams DIRECTAG_TAG_LENGTH

DIRECTAG_MAX_DYNAMIC_MODS

public static final IdentificationParametersCLIParams DIRECTAG_MAX_DYNAMIC_MODS

DIRECTAG_NUM_CHARGE_STATES

public static final IdentificationParametersCLIParams DIRECTAG_NUM_CHARGE_STATES

DIRECTAG_DUPLICATE_SPECTRA

public static final IdentificationParametersCLIParams DIRECTAG_DUPLICATE_SPECTRA

DIRECTAG_ISOTOPE_MZ_TOLERANCE

public static final IdentificationParametersCLIParams DIRECTAG_ISOTOPE_MZ_TOLERANCE

DIRECTAG_DEISOTOPING_MODE

public static final IdentificationParametersCLIParams DIRECTAG_DEISOTOPING_MODE

DIRECTAG_NUM_INTENSITY_CLASSES

public static final IdentificationParametersCLIParams DIRECTAG_NUM_INTENSITY_CLASSES

DIRECTAG_OUTPUT_SUFFIX

public static final IdentificationParametersCLIParams DIRECTAG_OUTPUT_SUFFIX

DIRECTAG_MAX_PEAK_COUNT

public static final IdentificationParametersCLIParams DIRECTAG_MAX_PEAK_COUNT

DIRECTAG_MAX_TAG_COUNT

public static final IdentificationParametersCLIParams DIRECTAG_MAX_TAG_COUNT

DIRECTAG_TIC_CUTOFF_PERCENTAGE

public static final IdentificationParametersCLIParams DIRECTAG_TIC_CUTOFF_PERCENTAGE

DIRECTAG_COMPLEMENT_MZ_TOLERANCE

public static final IdentificationParametersCLIParams DIRECTAG_COMPLEMENT_MZ_TOLERANCE

DIRECTAG_PRECURSOR_ADJUSTMENT_STEP

public static final IdentificationParametersCLIParams DIRECTAG_PRECURSOR_ADJUSTMENT_STEP

DIRECTAG_MIN_PRECURSOR_ADJUSTMENT

public static final IdentificationParametersCLIParams DIRECTAG_MIN_PRECURSOR_ADJUSTMENT

DIRECTAG_MAX_PRECURSOR_ADJUSTMENT

public static final IdentificationParametersCLIParams DIRECTAG_MAX_PRECURSOR_ADJUSTMENT

DIRECTAG_INTENSITY_SCORE_WEIGHT

public static final IdentificationParametersCLIParams DIRECTAG_INTENSITY_SCORE_WEIGHT

DIRECTAG_MZ_FIDELITY_SCORE_WEIGHT

public static final IdentificationParametersCLIParams DIRECTAG_MZ_FIDELITY_SCORE_WEIGHT

DIRECTAG_COMPLEMENT_SCORE_WEIGHT

public static final IdentificationParametersCLIParams DIRECTAG_COMPLEMENT_SCORE_WEIGHT

DIRECTAG_ADJUST_PRECURSOR_MASS

public static final IdentificationParametersCLIParams DIRECTAG_ADJUST_PRECURSOR_MASS

DIRECTAG_USE_CHARGE_STATE_FROM_MS

public static final IdentificationParametersCLIParams DIRECTAG_USE_CHARGE_STATE_FROM_MS

PEPNOVO_HITLIST_LENGTH

public static final IdentificationParametersCLIParams PEPNOVO_HITLIST_LENGTH

PEPNOVO_ESTIMATE_CHARGE

public static final IdentificationParametersCLIParams PEPNOVO_ESTIMATE_CHARGE

PEPNOVO_CORRECT_PREC_MASS

public static final IdentificationParametersCLIParams PEPNOVO_CORRECT_PREC_MASS

PEPNOVO_DISCARD_SPECTRA

public static final IdentificationParametersCLIParams PEPNOVO_DISCARD_SPECTRA

PEPNOVO_FRAGMENTATION_MODEL

public static final IdentificationParametersCLIParams PEPNOVO_FRAGMENTATION_MODEL

PEPNOVO_GENERATE_BLAST

public static final IdentificationParametersCLIParams PEPNOVO_GENERATE_BLAST

PNOVO_NUMBER_OF_PEPTIDES

public static final IdentificationParametersCLIParams PNOVO_NUMBER_OF_PEPTIDES

PNOVO_LOWER_PRECURSOR_MASS

public static final IdentificationParametersCLIParams PNOVO_LOWER_PRECURSOR_MASS

PNOVO_UPPER_PRECURSOR_MASS

public static final IdentificationParametersCLIParams PNOVO_UPPER_PRECURSOR_MASS

PNOVO_ACTIVATION_TYPE

public static final IdentificationParametersCLIParams PNOVO_ACTIVATION_TYPE

NOVOR_FRAGMENTATION

public static final IdentificationParametersCLIParams NOVOR_FRAGMENTATION

NOVOR_MASS_ANALYZER

public static final IdentificationParametersCLIParams NOVOR_MASS_ANALYZER

USE_GENE_MAPPING

public static final IdentificationParametersCLIParams USE_GENE_MAPPING

UPDATE_GENE_MAPPING

public static final IdentificationParametersCLIParams UPDATE_GENE_MAPPING

ANNOTATION_LEVEL

public static final IdentificationParametersCLIParams ANNOTATION_LEVEL

ANNOTATION_LEVEL_TYPE

public static final IdentificationParametersCLIParams ANNOTATION_LEVEL_TYPE

ANNOTATION_MZ_TOLERANCE

public static final IdentificationParametersCLIParams ANNOTATION_MZ_TOLERANCE

ANNOTATION_HIGH_RESOLUTION

public static final IdentificationParametersCLIParams ANNOTATION_HIGH_RESOLUTION

SEQUENCE_MATCHING_TYPE

public static final IdentificationParametersCLIParams SEQUENCE_MATCHING_TYPE

SEQUENCE_MATCHING_X

public static final IdentificationParametersCLIParams SEQUENCE_MATCHING_X

SEQUENCE_MATCHING_ENZYMATIC_TAGS

public static final IdentificationParametersCLIParams SEQUENCE_MATCHING_ENZYMATIC_TAGS

SEQUENCE_MATCHING_MAX_PTMS_PER_TAG

public static final IdentificationParametersCLIParams SEQUENCE_MATCHING_MAX_PTMS_PER_TAG

SEQUENCE_MATCHING_MIN_AMINO_ACID_SCORE

public static final IdentificationParametersCLIParams SEQUENCE_MATCHING_MIN_AMINO_ACID_SCORE

SEQUENCE_MATCHING_MIN_TAG_LENGTH

public static final IdentificationParametersCLIParams SEQUENCE_MATCHING_MIN_TAG_LENGTH

IMPORT_PEPTIDE_LENGTH_MIN

public static final IdentificationParametersCLIParams IMPORT_PEPTIDE_LENGTH_MIN

IMPORT_PEPTIDE_LENGTH_MAX

public static final IdentificationParametersCLIParams IMPORT_PEPTIDE_LENGTH_MAX

IMPORT_MC_MIN

public static final IdentificationParametersCLIParams IMPORT_MC_MIN

IMPORT_MC_MAX

public static final IdentificationParametersCLIParams IMPORT_MC_MAX

IMPORT_PRECURSOR_MZ

public static final IdentificationParametersCLIParams IMPORT_PRECURSOR_MZ

IMPORT_PRECURSOR_MZ_PPM

public static final IdentificationParametersCLIParams IMPORT_PRECURSOR_MZ_PPM

EXCLUDE_UNKNOWN_PTMs

public static final IdentificationParametersCLIParams EXCLUDE_UNKNOWN_PTMs

PTM_SCORE

public static final IdentificationParametersCLIParams PTM_SCORE

PTM_THRESHOLD

public static final IdentificationParametersCLIParams PTM_THRESHOLD

SCORE_NEUTRAL_LOSSES

public static final IdentificationParametersCLIParams SCORE_NEUTRAL_LOSSES

PTM_SEQUENCE_MATCHING_TYPE

public static final IdentificationParametersCLIParams PTM_SEQUENCE_MATCHING_TYPE

PTM_ALIGNMENT

public static final IdentificationParametersCLIParams PTM_ALIGNMENT

SIMPLIFY_GOUPS

public static final IdentificationParametersCLIParams SIMPLIFY_GOUPS

SIMPLIFY_GOUPS_EVIDENCE

public static final IdentificationParametersCLIParams SIMPLIFY_GOUPS_EVIDENCE

SIMPLIFY_GOUPS_CONFIDENCE

public static final IdentificationParametersCLIParams SIMPLIFY_GOUPS_CONFIDENCE

SIMPLIFY_GOUPS_CONFIDENCE_THRESHOLD

public static final IdentificationParametersCLIParams SIMPLIFY_GOUPS_CONFIDENCE_THRESHOLD

SIMPLIFY_GOUPS_ENZYMATICITY

public static final IdentificationParametersCLIParams SIMPLIFY_GOUPS_ENZYMATICITY

SIMPLIFY_GOUPS_VARIANT

public static final IdentificationParametersCLIParams SIMPLIFY_GOUPS_VARIANT

PROTEIN_INFERENCE_MODIFICATIONS

public static final IdentificationParametersCLIParams PROTEIN_INFERENCE_MODIFICATIONS

PSM_FDR

public static final IdentificationParametersCLIParams PSM_FDR

PEPTIDE_FDR

public static final IdentificationParametersCLIParams PEPTIDE_FDR

PROTEIN_FDR

public static final IdentificationParametersCLIParams PROTEIN_FDR

PROTEIN_FRACTION_MW_CONFIDENCE

public static final IdentificationParametersCLIParams PROTEIN_FRACTION_MW_CONFIDENCE

FASTA_TARGET_DECOY

public static final IdentificationParametersCLIParams FASTA_TARGET_DECOY

FASTA_DECOY_TAG

public static final IdentificationParametersCLIParams FASTA_DECOY_TAG

FASTA_DECOY_SUFFIX

public static final IdentificationParametersCLIParams FASTA_DECOY_SUFFIX

FASTA_DECOY_FILE_TAG

public static final IdentificationParametersCLIParams FASTA_DECOY_FILE_TAG

Field Details

id

public final String id

Short Id for the CLI parameter.

description

public final String description

Explanation for the CLI parameter.

mandatory

public final boolean mandatory

Boolean indicating whether the parameter is mandatory.

hasArgument

public final boolean hasArgument

Boolean indicating whether this command line option needs an argument.

Method Details

values

public static IdentificationParametersCLIParams[] 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

valueOf

public static IdentificationParametersCLIParams 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

getParametersOptionsAsString

public static String getParametersOptionsAsString()

Returns the options as a string.

Returns:

the options as a string