com.compomics.util.experiment.identification.parameters_cli

Enum IdentificationParametersCLIParams

java.lang.Object

java.lang.Enum<IdentificationParametersCLIParams>

com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersCLIParams

All Implemented Interfaces:

Serializable, Comparable<IdentificationParametersCLIParams>

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

Enum Constant Summary

Enum Constants

Enum Constant and Description
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_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_PREC_MASS
COMET_MIN_PEAK_INTENSITY
COMET_MIN_PEAKS
COMET_MIN_PREC_MASS
COMET_NUM_MATCHES
COMET_PTMS
COMET_REMOVE_METH
COMET_REMOVE_PRECURSOR
COMET_REMOVE_PRECURSOR_TOLERANCE
COMET_REQ_PTMS
COMET_THEORETICAL_FRAGMENT_IONS
DB
DB_PI
DESCRIPTION
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_PRECUSOR_ADJUSTMENT
DIRECTAG_MAX_TAG_COUNT
DIRECTAG_MIN_PRECUSOR_ADJUSTMENT
DIRECTAG_MZ_FIDELITY_SCORE_WEIGHT
DIRECTAG_NUM_CHARGE_STATES
DIRECTAG_NUM_INTENSITY_CLASSES
DIRECTAG_OUTPUT_SUFFIX
DIRECTAG_PRECUSOR_ADJUSTMENT_STEP
DIRECTAG_TAG_LENGTH
DIRECTAG_TIC_CUTOFF_PERCENTAGE
DIRECTAG_USE_CHARGE_STATE_FROM_MS
ENZYME
EXCLUDE_UNKNOWN_PTMs
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
MERGE_SUBGROUPS
MIN_CHARGE
MIN_ISOTOPE
MODS
MS_AMANDA_DECOY
MS_AMANDA_INSTRUMENT
MS_AMANDA_LOW_MEM_MODE
MS_AMANDA_MAX_RANK
MS_AMANDA_MONOISOTOPIC
MSGF_ADDITIONAL
MSGF_DECOY
MSGF_FRAGMENTATION
MSGF_INSTRUMENT
MSGF_MAX_PEP_LENGTH
MSGF_MIN_PEP_LENGTH
MSGF_NUM_MATCHES
MSGF_PROTOCOL
MSGF_PTMS
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_FRAGMENTATION_MODEL
PEPNOVO_GENERATE_BLAST
PEPNOVO_HITLIST_LENGTH
PEPTIDE_FDR
PEPTNOVO_ESTIMATE_CHARGE
PNOVO_ACTIVATION_TYPE
PNOVO_LOWER_PRECURSOR_MASS
PNOVO_NUMBER_OF_PEPTIDES
PNOVO_UPPER_PRECURSOR_MASS
PREC_PPM
PREC_TOL
PREC_TOL_DA
PROTEIN_FDR
PROTEIN_FRACTION_MW_CONFIDENCE
PSM_FDR
PTM_SCORE
PTM_SEQUENCE_MATCHING_TYPE
PTM_THRESHOLD
RI
SCORE_NEUTRAL_LOSSES
SEPARATE_PEPTIDES
SEPARATE_PSMs
SEQUENCE_MATCHING_TYPE
SEQUENCE_MATCHING_X
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_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
TIDE_PTMS_PER_TYPE
TIDE_REMOVE_PREC
TIDE_REMOVE_PREC_TOL
TIDE_REMOVE_TEMP
TIDE_SPECTRUM_CHARGES
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_PROTEINS
XTANDEM_OUTPUT_RESULTS
XTANDEM_OUTPUT_SEQUENCES
XTANDEM_OUTPUT_SPECTRA
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 and 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 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.

Methods inherited from class java.lang.Enum

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

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

IDENTIFICATION_PARAMETERS

public static final IdentificationParametersCLIParams IDENTIFICATION_PARAMETERS

OUT

public static final IdentificationParametersCLIParams OUT

DB

public static final IdentificationParametersCLIParams DB

PREC_PPM

public static final IdentificationParametersCLIParams PREC_PPM

FRAG_PPM

public static final IdentificationParametersCLIParams FRAG_PPM

PREC_TOL

public static final IdentificationParametersCLIParams PREC_TOL

PREC_TOL_DA

public static final IdentificationParametersCLIParams PREC_TOL_DA

FRAG_TOL

public static final IdentificationParametersCLIParams FRAG_TOL

ENZYME

public static final IdentificationParametersCLIParams ENZYME

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

MC

public static final IdentificationParametersCLIParams MC

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

OMSSA_SEQUENCES_IN_MEMORY

public static final IdentificationParametersCLIParams OMSSA_SEQUENCES_IN_MEMORY

OMSSA_NEUTRON

public static final IdentificationParametersCLIParams OMSSA_NEUTRON

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_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_MIN_PEAKS

public static final IdentificationParametersCLIParams OMSSA_MIN_PEAKS

OMSSA_METHIONINE

public static final IdentificationParametersCLIParams OMSSA_METHIONINE

OMSSA_MAX_LADDERS

public static final IdentificationParametersCLIParams OMSSA_MAX_LADDERS

OMSSA_MAX_FRAG_CHARGE

public static final IdentificationParametersCLIParams OMSSA_MAX_FRAG_CHARGE

OMSSA_MAX_FRACTION

public static final IdentificationParametersCLIParams OMSSA_MAX_FRACTION

OMSSA_PLUS_ONE

public static final IdentificationParametersCLIParams OMSSA_PLUS_ONE

OMSSA_POSITIVE_IONS

public static final IdentificationParametersCLIParams OMSSA_POSITIVE_IONS

OMSSA_PREC_PER_SPECTRUM

public static final IdentificationParametersCLIParams OMSSA_PREC_PER_SPECTRUM

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_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_REMOVE_PREC

public static final IdentificationParametersCLIParams OMSSA_REMOVE_PREC

OMSSA_SCALE_PREC

public static final IdentificationParametersCLIParams OMSSA_SCALE_PREC

OMSSA_ESTIMATE_CHARGE

public static final IdentificationParametersCLIParams OMSSA_ESTIMATE_CHARGE

OMSSA_MAX_EVALUE

public static final IdentificationParametersCLIParams OMSSA_MAX_EVALUE

OMSSA_HITLIST_LENGTH

public static final IdentificationParametersCLIParams OMSSA_HITLIST_LENGTH

OMSSA_HITLIST_LENGTH_CHARGE

public static final IdentificationParametersCLIParams OMSSA_HITLIST_LENGTH_CHARGE

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_FORMAT

public static final IdentificationParametersCLIParams OMSSA_FORMAT

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_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_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_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_MIN_PEP_LENGTH

public static final IdentificationParametersCLIParams MSGF_MIN_PEP_LENGTH

MSGF_MAX_PEP_LENGTH

public static final IdentificationParametersCLIParams MSGF_MAX_PEP_LENGTH

MSGF_NUM_MATCHES

public static final IdentificationParametersCLIParams MSGF_NUM_MATCHES

MSGF_ADDITIONAL

public static final IdentificationParametersCLIParams MSGF_ADDITIONAL

MSGF_TERMINI

public static final IdentificationParametersCLIParams MSGF_TERMINI

MSGF_PTMS

public static final IdentificationParametersCLIParams MSGF_PTMS

MS_AMANDA_DECOY

public static final IdentificationParametersCLIParams MS_AMANDA_DECOY

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_LOW_MEM_MODE

public static final IdentificationParametersCLIParams MS_AMANDA_LOW_MEM_MODE

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

COMET_NUM_MATCHES

public static final IdentificationParametersCLIParams COMET_NUM_MATCHES

COMET_PTMS

public static final IdentificationParametersCLIParams COMET_PTMS

COMET_REQ_PTMS

public static final IdentificationParametersCLIParams COMET_REQ_PTMS

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_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_THEORETICAL_FRAGMENT_IONS

public static final IdentificationParametersCLIParams COMET_THEORETICAL_FRAGMENT_IONS

COMET_FRAGMENT_BIN_OFFSET

public static final IdentificationParametersCLIParams COMET_FRAGMENT_BIN_OFFSET

TIDE_PTMS

public static final IdentificationParametersCLIParams TIDE_PTMS

TIDE_PTMS_PER_TYPE

public static final IdentificationParametersCLIParams TIDE_PTMS_PER_TYPE

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_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_OUTPUT_FOLDER

public static final IdentificationParametersCLIParams TIDE_OUTPUT_FOLDER

TIDE_PRINT_PEPTIDES

public static final IdentificationParametersCLIParams TIDE_PRINT_PEPTIDES

TIDE_VERBOSITY

public static final IdentificationParametersCLIParams TIDE_VERBOSITY

TIDE_MONOISOTOPIC

public static final IdentificationParametersCLIParams TIDE_MONOISOTOPIC

TIDE_CLIP_N_TERM

public static final IdentificationParametersCLIParams TIDE_CLIP_N_TERM

TIDE_DIGESTION_TYPE

public static final IdentificationParametersCLIParams TIDE_DIGESTION_TYPE

TIDE_COMPUTE_SP

public static final IdentificationParametersCLIParams TIDE_COMPUTE_SP

TIDE_MAX_PSMS

public static final IdentificationParametersCLIParams TIDE_MAX_PSMS

TIDE_COMPUTE_P

public static final IdentificationParametersCLIParams TIDE_COMPUTE_P

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_SPECTRUM_CHARGES

public static final IdentificationParametersCLIParams TIDE_SPECTRUM_CHARGES

TIDE_REMOVE_PREC

public static final IdentificationParametersCLIParams TIDE_REMOVE_PREC

TIDE_REMOVE_PREC_TOL

public static final IdentificationParametersCLIParams TIDE_REMOVE_PREC_TOL

TIDE_PROGRESS_INDICATOR

public static final IdentificationParametersCLIParams TIDE_PROGRESS_INDICATOR

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_CONCAT

public static final IdentificationParametersCLIParams TIDE_CONCAT

TIDE_STORE_SPECTRA

public static final IdentificationParametersCLIParams TIDE_STORE_SPECTRA

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_REMOVE_TEMP

public static final IdentificationParametersCLIParams TIDE_REMOVE_TEMP

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

PEPNOVO_HITLIST_LENGTH

public static final IdentificationParametersCLIParams PEPNOVO_HITLIST_LENGTH

PEPTNOVO_ESTIMATE_CHARGE

public static final IdentificationParametersCLIParams PEPTNOVO_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

DIRECTAG_TIC_CUTOFF_PERCENTAGE

public static final IdentificationParametersCLIParams DIRECTAG_TIC_CUTOFF_PERCENTAGE

DIRECTAG_MAX_PEAK_COUNT

public static final IdentificationParametersCLIParams DIRECTAG_MAX_PEAK_COUNT

DIRECTAG_NUM_INTENSITY_CLASSES

public static final IdentificationParametersCLIParams DIRECTAG_NUM_INTENSITY_CLASSES

DIRECTAG_ADJUST_PRECURSOR_MASS

public static final IdentificationParametersCLIParams DIRECTAG_ADJUST_PRECURSOR_MASS

DIRECTAG_MIN_PRECUSOR_ADJUSTMENT

public static final IdentificationParametersCLIParams DIRECTAG_MIN_PRECUSOR_ADJUSTMENT

DIRECTAG_MAX_PRECUSOR_ADJUSTMENT

public static final IdentificationParametersCLIParams DIRECTAG_MAX_PRECUSOR_ADJUSTMENT

DIRECTAG_PRECUSOR_ADJUSTMENT_STEP

public static final IdentificationParametersCLIParams DIRECTAG_PRECUSOR_ADJUSTMENT_STEP

DIRECTAG_NUM_CHARGE_STATES

public static final IdentificationParametersCLIParams DIRECTAG_NUM_CHARGE_STATES

DIRECTAG_OUTPUT_SUFFIX

public static final IdentificationParametersCLIParams DIRECTAG_OUTPUT_SUFFIX

DIRECTAG_USE_CHARGE_STATE_FROM_MS

public static final IdentificationParametersCLIParams DIRECTAG_USE_CHARGE_STATE_FROM_MS

DIRECTAG_DUPLICATE_SPECTRA

public static final IdentificationParametersCLIParams DIRECTAG_DUPLICATE_SPECTRA

DIRECTAG_DEISOTOPING_MODE

public static final IdentificationParametersCLIParams DIRECTAG_DEISOTOPING_MODE

DIRECTAG_ISOTOPE_MZ_TOLERANCE

public static final IdentificationParametersCLIParams DIRECTAG_ISOTOPE_MZ_TOLERANCE

DIRECTAG_COMPLEMENT_MZ_TOLERANCE

public static final IdentificationParametersCLIParams DIRECTAG_COMPLEMENT_MZ_TOLERANCE

DIRECTAG_TAG_LENGTH

public static final IdentificationParametersCLIParams DIRECTAG_TAG_LENGTH

DIRECTAG_MAX_DYNAMIC_MODS

public static final IdentificationParametersCLIParams DIRECTAG_MAX_DYNAMIC_MODS

DIRECTAG_MAX_TAG_COUNT

public static final IdentificationParametersCLIParams DIRECTAG_MAX_TAG_COUNT

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

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_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

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

DB_PI

public static final IdentificationParametersCLIParams DB_PI

PSM_FDR

public static final IdentificationParametersCLIParams PSM_FDR

PEPTIDE_FDR

public static final IdentificationParametersCLIParams PEPTIDE_FDR

PROTEIN_FDR

public static final IdentificationParametersCLIParams PROTEIN_FDR

SEPARATE_PSMs

public static final IdentificationParametersCLIParams SEPARATE_PSMs

SEPARATE_PEPTIDES

public static final IdentificationParametersCLIParams SEPARATE_PEPTIDES

MERGE_SUBGROUPS

public static final IdentificationParametersCLIParams MERGE_SUBGROUPS

PROTEIN_FRACTION_MW_CONFIDENCE

public static final IdentificationParametersCLIParams PROTEIN_FRACTION_MW_CONFIDENCE

Field Detail

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 Detail

values

public static IdentificationParametersCLIParams[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (IdentificationParametersCLIParams c : IdentificationParametersCLIParams.values())
    System.out.println(c);

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