Uses of Class
com.compomics.util.experiment.personalization.ExperimentObject

Packages that use ExperimentObject

Package	Description
com.compomics.util.db.object.objects	This package contains classes of objects that can be stored in the database.
com.compomics.util.experiment	Gene factory classes.
com.compomics.util.experiment.biology.aminoacids	The amino acid classes.
com.compomics.util.experiment.biology.aminoacids.impl	The amino acid implementations.
com.compomics.util.experiment.biology.aminoacids.sequence	Classes related to the handling of protein sequences.
com.compomics.util.experiment.biology.atoms	The atom classes.
com.compomics.util.experiment.biology.atoms.impl	Atoms implementations.
com.compomics.util.experiment.biology.enzymes	Classes related to enzymes.
com.compomics.util.experiment.biology.genes	Classes related to genes.
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
com.compomics.util.experiment.biology.ions.impl	Ion implementations.
com.compomics.util.experiment.biology.modifications
com.compomics.util.experiment.biology.proteins	Classes related to proteins.
com.compomics.util.experiment.biology.variants	Experiment classes related to variants.
com.compomics.util.experiment.identification	Experiment classes related to identifications.
com.compomics.util.experiment.identification.amino_acid_tags	Amino Acid Tag classes.
com.compomics.util.experiment.identification.features	Classes for the generation of identification features.
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.experiment.identification.peptide_shaker	Experiment classes used in PeptideShaker calculations.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_assumptions	Implementations of the SpectrumIdentificationAssumption.
com.compomics.util.experiment.io.biology.protein	Experiment IO classes for biological resources.
com.compomics.util.experiment.io.identification	Experiment identification classes.
com.compomics.util.experiment.io.identification.idfilereaders	Experiment classes related to reading search engine files.
com.compomics.util.experiment.io.mass_spectrometry.mgf	Classes for the handling of mgf files.
com.compomics.util.experiment.mass_spectrometry.spectra	Experiment classes related to spectra.
com.compomics.util.experiment.quantification	Experiment classes related to quantification.
com.compomics.util.experiment.quantification.reporterion	Experiment classes related to reporter ions.
com.compomics.util.experiment.refinement_parameters	Experiment classes related to specific parametrization of experiment objects.
com.compomics.util.experiment.units	Unit related classes.
com.compomics.util.general	General, top-level tasks that are used throughout the other packages in the util section.
com.compomics.util.gui.filtering	GUI filters.
com.compomics.util.io.export	Classes related to exporting reports.
com.compomics.util.io.file	Classes related to the handling of files.
com.compomics.util.io.json	Classes related to the handling of json files.
com.compomics.util.io.json.marshallers	JSON marshaller classes.
com.compomics.util.math.statistics.distributions	Math classes related to distributions.
com.compomics.util.parameters	Utilities parameters.
com.compomics.util.parameters.identification	Identification parameters.
com.compomics.util.parameters.identification.advanced	Advanced Identification parameters.
com.compomics.util.parameters.identification.search	Identification parameters relative to the search.
com.compomics.util.parameters.identification.tool_specific	Parameters settings for the search algorithms.
com.compomics.util.parameters.quantification.spectrum_counting	Spectrum counting parameters.
com.compomics.util.pride	Objects related to mapping to PRIDE.
com.compomics.util.pride.prideobjects	Objects related to mapping experiment annotation to PRIDE.

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	Chlorine	The Chlorine atom.
class	Cobalt	The Cobalt atom.
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	Manganese	The Manganese atom.
class	Nickel	The Nickel 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	SageParameters	The Sage 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.