Uses of Class
com.compomics.util.experiment.personalization.ExperimentObject
-
Uses of ExperimentObject in com.compomics.util.db.object.objects
Subclasses of ExperimentObject in com.compomics.util.db.object.objects Modifier and Type Class Description class
BlobObject
Class used to store entire objects in the database as a blob. -
Uses of ExperimentObject in com.compomics.util.experiment
Subclasses of ExperimentObject in com.compomics.util.experiment Modifier and Type Class Description class
ProjectParameters
This class contains project specific parameters. -
Uses of ExperimentObject in com.compomics.util.experiment.biology.aminoacids
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.aminoacids Modifier and Type Class Description class
AminoAcid
Class representing amino acids. -
Uses of ExperimentObject in com.compomics.util.experiment.biology.aminoacids.impl
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.aminoacids.impl Modifier and Type Class 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). -
Uses of ExperimentObject in com.compomics.util.experiment.biology.aminoacids.sequence
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.aminoacids.sequence Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.biology.atoms
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.atoms Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.biology.atoms.impl
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.atoms.impl Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.biology.enzymes
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.enzymes Modifier and Type Class Description class
Enzyme
This class models an enzyme. -
Uses of ExperimentObject in com.compomics.util.experiment.biology.genes
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.genes Modifier and Type Class Description class
GeneMaps
The gene maps for a given project. -
Uses of ExperimentObject in com.compomics.util.experiment.biology.ions
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.ions Modifier and Type Class Description class
Ion
This class models an ion.class
NeutralLoss
This class represents a neutral loss. -
Uses of ExperimentObject in com.compomics.util.experiment.biology.ions.impl
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.ions.impl Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.biology.modifications
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.modifications Modifier and Type Class Description class
Modification
This class models a peptide or protein modification. -
Uses of ExperimentObject in com.compomics.util.experiment.biology.proteins
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.proteins Modifier and Type Class Description class
Peptide
This class represents a peptide.class
Protein
This class models a protein. -
Uses of ExperimentObject in com.compomics.util.experiment.biology.variants
Subclasses of ExperimentObject in com.compomics.util.experiment.biology.variants Modifier and Type Class Description class
AaSubstitutionMatrix
Matrix of amino acid substitutions. -
Uses of ExperimentObject in com.compomics.util.experiment.identification
Subclasses of ExperimentObject in com.compomics.util.experiment.identification Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.identification.amino_acid_tags
Subclasses of ExperimentObject in com.compomics.util.experiment.identification.amino_acid_tags Modifier and Type Class Description class
MassGap
An undefined mass gap.class
Tag
This class represents a sequence mass tag. -
Uses of ExperimentObject in com.compomics.util.experiment.identification.features
Subclasses of ExperimentObject in com.compomics.util.experiment.identification.features Modifier and Type Class Description class
IdentificationFeaturesCache
This class caches the identification features calculated by the IdentificationFeaturesGenerator for later reuse. -
Uses of ExperimentObject in com.compomics.util.experiment.identification.filtering
Subclasses of ExperimentObject in com.compomics.util.experiment.identification.filtering Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.identification.matches
Subclasses of ExperimentObject in com.compomics.util.experiment.identification.matches Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.identification.peptide_shaker
Subclasses of ExperimentObject in com.compomics.util.experiment.identification.peptide_shaker Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.identification.protein_inference.fm_index
Subclasses of ExperimentObject in com.compomics.util.experiment.identification.protein_inference.fm_index Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.identification.spectrum_annotation
Subclasses of ExperimentObject in com.compomics.util.experiment.identification.spectrum_annotation Modifier and Type Class Description class
AnnotationParameters
This class contains the spectrum annotation parameters.class
NeutralLossesMap
This class contains the informations relative to the accounting of neutral losses -
Uses of ExperimentObject in com.compomics.util.experiment.identification.spectrum_assumptions
Subclasses of ExperimentObject in com.compomics.util.experiment.identification.spectrum_assumptions Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.io.biology.protein
Subclasses of ExperimentObject in com.compomics.util.experiment.io.biology.protein Modifier and Type Class Description class
FastaParameters
The parameters used to parse a FASTA file.class
Header
This class represents the header for a Protein instance. -
Uses of ExperimentObject in com.compomics.util.experiment.io.identification
Subclasses of ExperimentObject in com.compomics.util.experiment.io.identification Modifier and Type Class Description class
MzIdentMLIdfileSearchParametersConverter
Reads basic search parameters from mzIdentML result files. -
Uses of ExperimentObject in com.compomics.util.experiment.io.identification.idfilereaders
Subclasses of ExperimentObject in com.compomics.util.experiment.io.identification.idfilereaders Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.io.mass_spectrometry.mgf
Subclasses of ExperimentObject in com.compomics.util.experiment.io.mass_spectrometry.mgf Modifier and Type Class Description class
MgfIndex
This class contains the indexes of an mgf file after indexing mapped with the title of the spectrum. -
Uses of ExperimentObject in com.compomics.util.experiment.mass_spectrometry.spectra
Subclasses of ExperimentObject in com.compomics.util.experiment.mass_spectrometry.spectra Modifier and Type Class Description class
Peak
This class represents a peak.class
Precursor
This class models a precursor.class
Spectrum
This class models a spectrum. -
Uses of ExperimentObject in com.compomics.util.experiment.quantification
Subclasses of ExperimentObject in com.compomics.util.experiment.quantification Modifier and Type Class Description class
Quantification
An abstract quantification class. -
Uses of ExperimentObject in com.compomics.util.experiment.quantification.reporterion
Subclasses of ExperimentObject in com.compomics.util.experiment.quantification.reporterion Modifier and Type Class Description class
ReporterIonQuantification
This class contains quantification parameters.class
ReporterMethodFactory
This factory imports reporter methods details from an XMl file. -
Uses of ExperimentObject in com.compomics.util.experiment.refinement_parameters
Subclasses of ExperimentObject in com.compomics.util.experiment.refinement_parameters Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.experiment.units
Subclasses of ExperimentObject in com.compomics.util.experiment.units Modifier and Type Class Description class
UnitOfMeasurement
The unit to use for a measure. -
Uses of ExperimentObject in com.compomics.util.general
Subclasses of ExperimentObject in com.compomics.util.general Modifier and Type Class Description class
BoxedObject<K>
Convenience class allowing the boxing of an object. -
Uses of ExperimentObject in com.compomics.util.gui.filtering
Subclasses of ExperimentObject in com.compomics.util.gui.filtering Modifier and Type Class Description class
FilterParameters
This class groups the display filter preferences. -
Uses of ExperimentObject in com.compomics.util.io.export
Subclasses of ExperimentObject in com.compomics.util.io.export Modifier and Type Class Description class
ExportScheme
This class allows creating a standard output scheme. -
Uses of ExperimentObject in com.compomics.util.io.file
Subclasses of ExperimentObject in com.compomics.util.io.file Modifier and Type Class Description class
LastSelectedFolder
Convenience class keeping class of the last selected folders. -
Uses of ExperimentObject in com.compomics.util.io.json
Subclasses of ExperimentObject in com.compomics.util.io.json Modifier and Type Class Description class
JsonMarshaller
This class converts non specific objects to the JSON format and vice versa. -
Uses of ExperimentObject in com.compomics.util.io.json.marshallers
Subclasses of ExperimentObject in com.compomics.util.io.json.marshallers Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.math.statistics.distributions
Subclasses of ExperimentObject in com.compomics.util.math.statistics.distributions Modifier and Type Class Description class
NonSymmetricalNormalDistribution
This class represents a non symmetrical normal distribution.class
NormalDistribution
This class represents a normal distribution. -
Uses of ExperimentObject in com.compomics.util.parameters
Subclasses of ExperimentObject in com.compomics.util.parameters Modifier and Type Class Description class
UtilitiesUserParameters
Utilities user parameters can be used to store user parameters. -
Uses of ExperimentObject in com.compomics.util.parameters.identification
Subclasses of ExperimentObject in com.compomics.util.parameters.identification Modifier and Type Class Description class
IdentificationParameters
Generic class grouping the parameters used for protein identification. -
Uses of ExperimentObject in com.compomics.util.parameters.identification.advanced
Subclasses of ExperimentObject in com.compomics.util.parameters.identification.advanced Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.parameters.identification.search
Subclasses of ExperimentObject in com.compomics.util.parameters.identification.search Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.parameters.identification.tool_specific
Subclasses of ExperimentObject in com.compomics.util.parameters.identification.tool_specific Modifier and Type Class 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. -
Uses of ExperimentObject in com.compomics.util.parameters.quantification.spectrum_counting
Subclasses of ExperimentObject in com.compomics.util.parameters.quantification.spectrum_counting Modifier and Type Class Description class
SpectrumCountingParameters
This class contains the spectrum counting parameters. -
Uses of ExperimentObject in com.compomics.util.pride
Subclasses of ExperimentObject in com.compomics.util.pride Modifier and Type Class Description class
CvTerm
A simple CvTerm object.class
PtmToPrideMap
Map linking user modification names to Unimod CV terms. -
Uses of ExperimentObject in com.compomics.util.pride.prideobjects
Subclasses of ExperimentObject in com.compomics.util.pride.prideobjects Modifier and Type Class 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.