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 |
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 |
ElementaryElement
This class can be used to retrieve elementary elements like a neutron.
|
Modifier and Type | Class and Description |
---|---|
class |
Carbon
Carbon.
|
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 |
Nitrogen
The nitrogen atom.
|
class |
Oxygen
The oxygen atom.
|
class |
Phosphorus
The phosphorus atom.
|
class |
Selenium
Selenium.
|
class |
Sodium
The sodium atom.
|
class |
Sulfur
The sulfur 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 |
PeptideAssumptionFilter
This class filters peptide assumptions based on various properties.
|
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 |
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 |
MassIndexMap
The mass index map.
|
Modifier and Type | Class and Description |
---|---|
class |
AnnotationParameters
This class contains the spectrum annotation parameters.
|
Modifier and Type | Class and Description |
---|---|
class |
PeptideAssumption
This object will 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.
|
Modifier and Type | Class and Description |
---|---|
class |
MzIdentMLIdfileSearchParametersConverter
Reads search parameters from a mzIdentML result files.
|
Modifier and Type | Class and Description |
---|---|
class |
AndromedaIdfileReader
This IdfileReader reads identifications from an Andromeda result file.
|
class |
DirecTagIdfileReader
An identification file reader for Direct tag results.
|
class |
MascotIdfileReader
This IdfileReader reads identifications from a Mascot results file.
|
class |
MsAmandaIdfileReader
This IdfileReader reads identifications from an MS Amanda csv result file.
|
class |
MzIdentMLIdfileReader
This IdfileReader reads identifications from an mzIdentML result file.
|
class |
NovorIdfileReader
This IdfileReader reads identifications from a Novor csv result file.
|
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 |
SpectrumIndex
This map stores the fragment ions indexed by mass.
|
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 |
ExperimentObject
This abstract class provides customization facilities.
|
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 |
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 |
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 |
SearchParameters
This class groups the parameters used for identification.
|
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.
|
Modifier and Type | Class and Description |
---|---|
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 |
ReferenceGroup
An object for storing ReferenceGroup details.
|
class |
Sample
An object for storing Sample details.
|
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