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.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.