Modifier and Type | Class and Description |
---|---|
class |
BlobObject
Class used to store entire objects in the database as a blob.
|
Modifier and Type | Class and Description |
---|---|
class |
ProjectParameters
This class contains project specific parameters.
|
Modifier and Type | Class and Description |
---|---|
class |
AminoAcid
Class representing amino acids.
|
Modifier and Type | Class and Description |
---|---|
class |
Alanine
Alanine.
|
class |
Arginine
Arginine.
|
class |
Asparagine
Asparagine.
|
class |
AsparticAcid
Aspartic Acid.
|
class |
B
Asn or Asp: Asx (Mascot).
|
class |
Cysteine
Cysteine.
|
class |
GlutamicAcid
Glutamic Acid.
|
class |
Glutamine
Glutamine.
|
class |
Glycine
Glycine.
|
class |
Histidine
Histidine.
|
class |
Isoleucine
Isoleucine.
|
class |
J
Isoleucine or Leucine.
|
class |
Leucine
Leucine.
|
class |
Lysine
Lysine.
|
class |
Methionine
Methionine.
|
class |
Phenylalanine
Phenylalanine.
|
class |
Proline
Proline.
|
class |
Pyrrolysine
Pyrrolysine.
|
class |
Selenocysteine
SeC (U) (Mascot)-
|
class |
Serine
Serine.
|
class |
Threonine
Threonine.
|
class |
Tryptophan
Tryptophan.
|
class |
Tyrosine
Tyrosine.
|
class |
Valine
Valine.
|
class |
X
Unknown amino acid (Mascot).
|
class |
Z
Glu or Gln: Glx (Mascot).
|
Modifier and Type | Class and Description |
---|---|
class |
AminoAcidPattern
An amino acid pattern is a sequence of amino acids.
|
class |
AminoAcidSequence
This class represents a series of amino acids with associated modifications.
|
Modifier and Type | Class and Description |
---|---|
class |
Atom
This interface contains information about atoms.
|
class |
AtomChain
A chain of atoms.
|
class |
AtomImpl
Class for a specific atom.
|
class |
ElementaryElement
This class can be used to retrieve elementary elements like a neutron.
|
Modifier and Type | Class and Description |
---|---|
class |
Calcium
The calcium atom.
|
class |
Carbon
Carbon.
|
class |
Copper
The copper atom.
|
class |
Fluorine
The fluorine atom.
|
class |
Helium
The helium atom.
|
class |
Hydrogen
The hydrogen atom.
|
class |
Iodine
Iodine.
|
class |
Iron
The iron atom.
|
class |
Lithium
The Lithium atom.
|
class |
Magnesium
The magnesium atom.
|
class |
Nitrogen
The nitrogen atom.
|
class |
Oxygen
The oxygen atom.
|
class |
Phosphorus
The phosphorus atom.
|
class |
Potassium
The potassium atom.
|
class |
Selenium
Selenium.
|
class |
Sodium
The sodium atom.
|
class |
Sulfur
The sulfur atom.
|
class |
Zinc
The zinc atom.
|
Modifier and Type | Class and Description |
---|---|
class |
Enzyme
This class models an enzyme.
|
Modifier and Type | Class and Description |
---|---|
class |
GeneMaps
The gene maps for a given project.
|
Modifier and Type | Class and Description |
---|---|
class |
Ion
This class models an ion.
|
class |
NeutralLoss
This class represents a neutral loss.
|
Modifier and Type | Class and Description |
---|---|
class |
ElementaryIon
This class represents an elementary ion.
|
class |
Glycan
This class represents a glycan.
|
class |
ImmoniumIon
Represents an immonium ion.
|
class |
PeptideFragmentIon
This class models a peptide fragment ion.
|
class |
PrecursorIon
A precursor ion.
|
class |
RelatedIon
Represents a related ion, i.e., an ion that is related to a given amino acid,
and is its own factory.
|
class |
ReporterIon
This class models a reporter ion and is its own factory.
|
class |
TagFragmentIon
A fragment ion obtained from a tag.
|
Modifier and Type | Class and Description |
---|---|
class |
Modification
This class models a peptide or protein modification.
|
Modifier and Type | Class and Description |
---|---|
class |
Peptide
This class represents a peptide.
|
class |
Protein
This class models a protein.
|
Modifier and Type | Class and Description |
---|---|
class |
AaSubstitutionMatrix
Matrix of amino acid substitutions.
|
Modifier and Type | Class and Description |
---|---|
class |
Advocate
The advocate of a hit can be a search engine, a sequencing algorithm, a
rescoring algorithm, etc.
|
class |
Identification
This class interacts with the back-end database to manage identification
objects.
|
class |
IdentificationKeys
Placeholder for the keys of the objects in the identification.
|
class |
IdentificationMatch
This is an abstract class for an identification match.
|
class |
IdentificationMethod
This class will contain all methods used to obtain identifications.
|
class |
SpectrumIdentificationAssumption
Spectrum identification assumption made by an identification algorithm.
|
Modifier and Type | Class and Description |
---|---|
class |
MassGap
An undefined mass gap.
|
class |
Tag
This class represents a sequence mass tag.
|
Modifier and Type | Class and Description |
---|---|
class |
IdentificationFeaturesCache
This class caches the identification features calculated by the
IdentificationFeaturesGenerator for later reuse.
|
Modifier and Type | Class and Description |
---|---|
class |
AssumptionFilter
Peptide Assumption filter.
|
class |
MatchFilter
Abstract representing a filter.
|
class |
PeptideAssumptionFilter
This class filters peptide assumptions based on various properties.
|
class |
PeptideFilter
Peptide filter.
|
class |
ProteinFilter
Protein filter.
|
class |
PsmFilter
PSM filter.
|
Modifier and Type | Class and Description |
---|---|
class |
IonMatch
This class represents the assignment of a peak to a theoretical ion.
|
class |
ModificationMatch
This class models the match between theoretic PTM and identification results.
|
class |
PeptideMatch
This class models a peptide match.
|
class |
PeptideVariantMatches
This class represents a set of variants found on a peptide.
|
class |
ProteinMatch
This class models a protein match.
|
class |
SpectrumMatch
This class models a spectrum match.
|
Modifier and Type | Class and Description |
---|---|
class |
Metrics
This class contains metrics gathered during the creation of a PeptideShaker project.
|
class |
ModificationScoring
This class contains stores the modification localization scores.
|
class |
PSModificationScores
This class contains the scores for the locations of the possible
modifications.
|
class |
PSParameter
PeptideShaker compomics utilities experiment customizable parameter.
|
Modifier and Type | Class and Description |
---|---|
class |
CacheElement
The cache element.
|
class |
FMIndex
The FM index.
|
class |
MassIndexMap
The mass index map.
|
class |
MatrixContent
Element for the matrix necessary in pattern search of the FMIndex.
|
class |
SNPElement |
class |
TagElement
The tag element.
|
Modifier and Type | Class and Description |
---|---|
class |
AnnotationParameters
This class contains the spectrum annotation parameters.
|
class |
NeutralLossesMap
This class contains the informations relative to the accounting of neutral
losses
|
Modifier and Type | Class and Description |
---|---|
class |
PeptideAssumption
This object models the assumption made by an advocate.
|
class |
TagAssumption
This class represent a tag assumption made by an identification algorithm
based on a sequence tag.
|
Modifier and Type | Class and Description |
---|---|
class |
FastaParameters
The parameters used to parse a FASTA file.
|
class |
Header
This class represents the header for a Protein instance.
|
Modifier and Type | Class and Description |
---|---|
class |
MzIdentMLIdfileSearchParametersConverter
Reads basic search parameters from mzIdentML result files.
|
Modifier and Type | Class and Description |
---|---|
class |
PepNovoIdfileReader
This class can be used to parse PepNovo identification files.
|
class |
PNovoIdfileReader
This class can be used to parse pNovo identification files.
|
class |
TideIdfileReader
This IdfileReader reads identifications from an Tide tsv results file.
|
class |
XTandemIdfileReader
This IdfileReader reads identifications from an X! Tandem xml result file.
|
Modifier and Type | Class and Description |
---|---|
class |
MgfIndex
This class contains the indexes of an mgf file after indexing mapped with the
title of the spectrum.
|
Modifier and Type | Class and Description |
---|---|
class |
Peak
This class represents a peak.
|
class |
Precursor
This class models a precursor.
|
class |
Spectrum
This class models a spectrum.
|
Modifier and Type | Class and Description |
---|---|
class |
Quantification
An abstract quantification class.
|
Modifier and Type | Class and Description |
---|---|
class |
ReporterIonQuantification
This class contains quantification parameters.
|
class |
ReporterMethodFactory
This factory imports reporter methods details from an XMl file.
|
Modifier and Type | Class and Description |
---|---|
class |
PepnovoAssumptionDetails
This class contains pepnovo assumption details which are not contained in the
tag assumption class which will be saved as additional parameter.
|
Modifier and Type | Class and Description |
---|---|
class |
UnitOfMeasurement
The unit to use for a measure.
|
Modifier and Type | Class and Description |
---|---|
class |
BoxedObject<K>
Convenience class allowing the boxing of an object.
|
Modifier and Type | Class and Description |
---|---|
class |
FilterParameters
This class groups the display filter preferences.
|
Modifier and Type | Class and Description |
---|---|
class |
ExportScheme
This class allows creating a standard output scheme.
|
Modifier and Type | Class and Description |
---|---|
class |
LastSelectedFolder
Convenience class keeping class of the last selected folders.
|
Modifier and Type | Class and Description |
---|---|
class |
JsonMarshaller
This class converts non-specific objects to the JSON format and vice versa.
|
Modifier and Type | Class and Description |
---|---|
class |
IdentificationParametersMarshaller
This class is a convenience class to have a DefaultJsonConverter with the
identification parameters interfaces.
|
class |
PrideMarshaller
A json marshaller for use with the PRIDE webservice.
|
class |
PTMFactoryMarshaller
This class is a convenience class to have a DefaultJsonConverter with the
search parameter interfaces.
|
Modifier and Type | Class and Description |
---|---|
class |
NonSymmetricalNormalDistribution
This class represents a non symmetrical normal distribution.
|
class |
NormalDistribution
This class represents a normal distribution.
|
Modifier and Type | Class and Description |
---|---|
class |
UtilitiesUserParameters
Utilities user parameters can be used to store user parameters.
|
Modifier and Type | Class and Description |
---|---|
class |
IdentificationParameters
Generic class grouping the parameters used for protein identification.
|
Modifier and Type | Class and Description |
---|---|
class |
FractionParameters
Settings for the handling of fractions.
|
class |
GeneParameters
Contains methods for downloading gene and GO mappings.
|
class |
IdMatchValidationParameters
Generic class grouping the identification matches validation preferences.
|
class |
ModificationLocalizationParameters
This class contains the modification localization preferences.
|
class |
PeptideVariantsParameters
Preferences for the allowed variants in peptide sequences.
|
class |
ProteinInferenceParameters
Generic class grouping the protein inference preferences.
|
class |
PsmScoringParameters
Generic class for peptide spectrum match scoring.
|
class |
SequenceMatchingParameters
The sequence matching options.
|
class |
ValidationQcParameters
This class lists the criteria used for quality control of the validated
matches.
|
Modifier and Type | Class and Description |
---|---|
class |
DigestionParameters
This class groups the parameters for the digestion of proteins.
|
class |
ModificationParameters
This class stores the information about the modification parameters (usage,
colors, names).
|
class |
SearchParameters
This class groups the parameters used for identification.
|
Modifier and Type | Class and Description |
---|---|
class |
AndromedaParameters
The Andromeda specific parameters.
|
class |
CometParameters
The Comet specific parameters.
|
class |
DirecTagParameters
The DirecTag specific parameters.
|
class |
MetaMorpheusParameters
The MetaMorpheus specific parameters.
|
class |
MsAmandaParameters
The MS Amanda specific parameters.
|
class |
MsgfParameters
The MS-GF+ specific parameters.
|
class |
MyriMatchParameters
The MyriMatch specific parameters.
|
class |
NovorParameters
Novor specific parameters.
|
class |
OmssaParameters
The OMSSA specific parameters.
|
class |
PepnovoParameters
PepNovo specific parameters.
|
class |
PNovoParameters
pNovo specific parameters.
|
class |
TideParameters
The Tide specific parameters.
|
class |
XtandemParameters
The X!Tandem specific parameters.
|
Modifier and Type | Class and Description |
---|---|
class |
SpectrumCountingParameters
This class contains the spectrum counting parameters.
|
Modifier and Type | Class and Description |
---|---|
class |
CvTerm
A simple CvTerm object.
|
class |
PtmToPrideMap
Map linking user modification names to Unimod CV terms.
|
Modifier and Type | Class and Description |
---|---|
class |
Contact
An object for storing Contact details.
|
class |
ContactGroup
An object for storing ContactGroup details.
|
class |
Instrument
An object for storing Instrument details.
|
class |
Protocol
An object for storing Protocol details.
|
class |
Reference
A simple publication reference object.
|
class |
ReferenceGroup
An object for storing ReferenceGroup details.
|
class |
Sample
An object for storing Sample details.
|
Copyright © 2021. All rights reserved.