Uses of Package
com.compomics.util.experiment.personalization

Packages that use com.compomics.util.experiment.personalization

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.identification.validation.percolator
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.personalization	Experiment customization classes.
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.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.db.object.objects

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.aminoacids

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.aminoacids.impl

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.aminoacids.sequence

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.atoms

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.atoms.impl

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.enzymes

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.genes

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.ions

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.ions.impl

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.modifications

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.proteins

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.biology.variants

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.identification

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.identification.amino_acid_tags

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.identification.features

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.identification.filtering

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.identification.matches

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.identification.peptide_shaker

Class	Description
ExperimentObject	This abstract class provides customization facilities.
UrParameter	This interface is used to reference refinement parameters.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.identification.protein_inference.fm_index

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.identification.spectrum_annotation

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.identification.spectrum_assumptions

Class	Description
ExperimentObject	This abstract class provides customization facilities.
UrParameter	This interface is used to reference refinement parameters.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.identification.validation.percolator

Class	Description
UrParameter	This interface is used to reference refinement parameters.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.io.biology.protein

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.io.identification

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.io.identification.idfilereaders

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.io.mass_spectrometry.mgf

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.mass_spectrometry.spectra

Class	Description
ExperimentObject	This abstract class provides customization facilities.
UrParameter	This interface is used to reference refinement parameters.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.personalization

Class	Description
UrParameter	This interface is used to reference refinement parameters.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.quantification

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.quantification.reporterion

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.refinement_parameters

Class	Description
ExperimentObject	This abstract class provides customization facilities.
UrParameter	This interface is used to reference refinement parameters.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.experiment.units

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.general

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.gui.filtering

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.io.export

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.io.file

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.io.json

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.io.json.marshallers

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.math.statistics.distributions

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.parameters

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.parameters.identification

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.parameters.identification.advanced

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.parameters.identification.search

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.parameters.identification.tool_specific

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.parameters.quantification.spectrum_counting

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.pride

Class	Description
ExperimentObject	This abstract class provides customization facilities.

Classes in com.compomics.util.experiment.personalization used by com.compomics.util.pride.prideobjects

Class	Description
ExperimentObject	This abstract class provides customization facilities.