computational omics utilities 5.0.4 API

Packages 
Package Description
com.compomics.cli.enzymes
Command line for the handling of enzymes.
com.compomics.cli.fasta
Command line for the handling of fasta files.
com.compomics.cli.identification_parameters
Command line for the handling of identification parameters.
com.compomics.cli.modifications
Command line for the handling of modifications.
com.compomics.cli.peptide_mapper
Command line for PeptideMapper.
com.compomics.scripts_marc  
com.compomics.software
Convenience classes for command line usage of compomics-utilities tools.
com.compomics.software.autoupdater
Classes related to auto updating compomics-utilities tools.
com.compomics.software.cli
Convenience classes for the handling of command lines.
com.compomics.software.dialogs
Dialogs for starting compomics-utilities tools and setting their Java options.
com.compomics.software.log
Classes related to software log.
com.compomics.software.settings
Settings for compomics-utilities tools.
com.compomics.software.settings.gui
GUI settings for compomics-utilities tools.
com.compomics.util
General utilities classes.
com.compomics.util.db
Database related classes.
com.compomics.util.db.components
Database related components.
com.compomics.util.db.interfaces
Database related interfaces.
com.compomics.util.db.object
This package contains the classes relative to the object database.
com.compomics.util.db.object.objects
This package contains classes of objects that can be stored in the database.
com.compomics.util.enumeration
Enumeration used by compomics-utilities.
com.compomics.util.examples
Examples of how the compomics-utilities library can can be used by other projects.
com.compomics.util.exceptions
Classes for the handling of exceptions.
com.compomics.util.exceptions.exception_handlers
Implementations of the ExceptionHandler interface.
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.genes.ensembl
Classes for the handling of Ensembl data.
com.compomics.util.experiment.biology.genes.go
Classes for the handling of GO terms.
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.taxonomy
Classes related to species and taxonomy.
com.compomics.util.experiment.biology.taxonomy.mappings
Classes related to species mapping.
com.compomics.util.experiment.biology.variants
Experiment classes related to variants.
com.compomics.util.experiment.biology.variants.amino_acids
Type of implemented variants.
com.compomics.util.experiment.filtering
Filtering classes.
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.filtering.items
Items used by the filters to filter on.
com.compomics.util.experiment.identification.identification_parameters
Parameters settings for the spectrum identification algorithms.
com.compomics.util.experiment.identification.matches
Experiment classes related to matches.
com.compomics.util.experiment.identification.matches_iterators
Identification match iterators.
com.compomics.util.experiment.identification.modification
Modification mapping and localization.
com.compomics.util.experiment.identification.modification.mapping
Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.modification.scores
PTM scores.
com.compomics.util.experiment.identification.peptide_fragmentation
Peptide fragment intensities.
com.compomics.util.experiment.identification.peptide_fragmentation.models
Predictors for peptide fragment intensities.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration
This package contains the classes needed to configure the ms2pip features.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
This package contains features implemented for ms2pip.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic
This package contains generic features implemented for ms2pip.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation
This package contains the classes needed to generate ms2pip features.
com.compomics.util.experiment.identification.peptide_inference
Classes related to peptide inference.
com.compomics.util.experiment.identification.peptide_shaker
Experiment classes used in PeptideShaker calculations.
com.compomics.util.experiment.identification.protein_inference
Classes related to protein inference.
com.compomics.util.experiment.identification.protein_inference.fm_index
Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.identification.protein_sequences
Protein sequence handling related classes.
com.compomics.util.experiment.identification.protein_sequences.digestion
This package contains classes used to digest protein sequences into peptides.
com.compomics.util.experiment.identification.protein_sequences.digestion.iterators
This package contains implementations of the SequenceIterator interface.
com.compomics.util.experiment.identification.psm_scoring
Main PSM scoring class.
com.compomics.util.experiment.identification.psm_scoring.psm_scores
Main PTM scoring classes.
com.compomics.util.experiment.identification.spectrum_annotation
Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators
This package contains implementations of the SimpleAnnotator allowing the annotation of specific sets of ions.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
com.compomics.util.experiment.identification.spectrum_assumptions
Implementations of the SpectrumIdentificationAssumption.
com.compomics.util.experiment.identification.utils
This package contains utilities classes to handle identification objects.
com.compomics.util.experiment.identification.validation
Experiment classes related to identification matches validation.
com.compomics.util.experiment.io.biology.protein
Experiment IO classes for biological resources.
com.compomics.util.experiment.io.biology.protein.converters
Fasta file converters.
com.compomics.util.experiment.io.biology.protein.iterators
Fasta file iterators.
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.identification.writers
Writer for identification results.
com.compomics.util.experiment.io.mass_spectrometry
Classes for the handling of mass spectrometry files.
com.compomics.util.experiment.io.mass_spectrometry.apl
Classes for the handling of Andromeda peak list (apl) files.
com.compomics.util.experiment.io.mass_spectrometry.cms
Classes for the handling of Compomics mass spectrometry (cms) files.
com.compomics.util.experiment.io.mass_spectrometry.mgf
Classes for the handling of mgf files.
com.compomics.util.experiment.io.mass_spectrometry.ms2
Classes for the handling of ms2 files.
com.compomics.util.experiment.io.mass_spectrometry.mzml
Classes for the handling of mzml files.
com.compomics.util.experiment.io.parameters
Experiment IO classes relative to the handling of parameters.
com.compomics.util.experiment.io.temp  
com.compomics.util.experiment.mass_spectrometry
Experiment classes related to mass spectrometry.
com.compomics.util.experiment.mass_spectrometry.indexes
Classes related to the indexing of spectra.
com.compomics.util.experiment.mass_spectrometry.proteowizard
Package containing the classes used to interact with ProteoWizard.
com.compomics.util.experiment.mass_spectrometry.spectra
Experiment classes related to spectra.
com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser
Package containing the classes used to interact with ThermoRawFileParser.
com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui
Package containing the GUI classes used to interact with ThermoRawFileParser.
com.compomics.util.experiment.mass_spectrometry.utils
Utility classes for mass spectrometry.
com.compomics.util.experiment.normalization
Classes related to quantification values normalization.
com.compomics.util.experiment.patient
Experiment classes related to patent information.
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.quantification.spectrumcounting
Experiment classes related to spectrum counting.
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.general.servlet
Servlet representation of the classes from the general utilities package (com.compomics.util.general)
com.compomics.util.gui
Basic GUI classes.
com.compomics.util.gui.atoms
Atoms GUI dialogs.
com.compomics.util.gui.enzymes
Dialogs for enzymes.
com.compomics.util.gui.error_handlers
Help handlers.
com.compomics.util.gui.error_handlers.notification
Notification dialogs.
com.compomics.util.gui.events
GUI event classes.
com.compomics.util.gui.export.graphics
Exporting of graphics.
com.compomics.util.gui.export.report
Report editor GUI.
com.compomics.util.gui.file_handling
GUI related file filters.
com.compomics.util.gui.filtering
GUI filters.
com.compomics.util.gui.genes
Dialogs for the handling of genes.
com.compomics.util.gui.interfaces
GUI related interfaces.
com.compomics.util.gui.isotopic_calculator
GUI class for the Isotopic Distribution calculator.
com.compomics.util.gui.modification
PTM GUI dialogs.
com.compomics.util.gui.parameters
GUI classes for parameters, settings and preferences.
com.compomics.util.gui.parameters.identification
GUI classes for parameters, settings and preferences used for identification.
com.compomics.util.gui.parameters.identification.advanced
Dialogs for advanced identification parameters.
com.compomics.util.gui.parameters.identification.algorithm
Search algorithm settings dialogs.
com.compomics.util.gui.parameters.identification.pride
Dialogs for pride reprocessing parameters.
com.compomics.util.gui.parameters.identification.search
Dialogs for search parameters.
com.compomics.util.gui.parameters.proteowizard
Package containing the GUI classes used to interact with ProteoWizard.
com.compomics.util.gui.parameters.tools
GUI classes for parameters, settings and preferences used in tools.
com.compomics.util.gui.protein
GUI class related to protein sequence formatting.
com.compomics.util.gui.renderers
GUI renderer classes.
com.compomics.util.gui.spectrum
Spectrum and Chromatogram visualization GUI classes.
com.compomics.util.gui.tablemodels
Self updating table model classes.
com.compomics.util.gui.utils
GUI utilities classes.
com.compomics.util.gui.utils.user_choice
GUI utils allowing the user to choose something.
com.compomics.util.gui.utils.user_choice.list_choosers
Implementations of the ListChooser.
com.compomics.util.gui.variants.aa_substitutions
GUI classes relative to amino acid substitution.
com.compomics.util.gui.waiting.waitinghandlers
Waiting handler classes.
com.compomics.util.interfaces
Interfaces for the more specific implementations in the util package.
com.compomics.util.io
Classes related to input/output.
com.compomics.util.io.compression
Classes related to file compression.
com.compomics.util.io.compression.SectionGzWriter
Package for writing gzfiles with multiple sections.
com.compomics.util.io.export
Classes related to exporting reports.
com.compomics.util.io.export.styles
Export styles.
com.compomics.util.io.export.writers
Export writer.
com.compomics.util.io.export.xml
Convenience classes for xml exports.
com.compomics.util.io.file
Classes related to the handling of files.
com.compomics.util.io.file.filefilters
Classes related to file filters.
com.compomics.util.io.flat
Export of flat files.
com.compomics.util.io.flat.readers  
com.compomics.util.io.ftp
Classes related to the handling of FTP.
com.compomics.util.io.json
Classes related to the handling of json files.
com.compomics.util.io.json.adapter
JSON adapter classes.
com.compomics.util.io.json.marshallers
JSON marshaller classes.
com.compomics.util.junit
Custom classpath related test class.
com.compomics.util.math
Basic match functions.
com.compomics.util.math.clustering
Basic clustering functions.
com.compomics.util.math.clustering.settings
Settings for the clustering.
com.compomics.util.math.matrix
Double matrix classes.
com.compomics.util.math.roc
ROC curve calculation.
com.compomics.util.math.statistics
Math classes related to statistics.
com.compomics.util.math.statistics.distributions
Math classes related to distributions.
com.compomics.util.math.statistics.linear_regression
Classes to perform linear regressions.
com.compomics.util.math.statistics.linear_regression.filters
Implementation of algorithms performing linear regression.
com.compomics.util.math.statistics.linear_regression.regressions
Filters to apply prior to a linear regression.
com.compomics.util.memory
Memory management.
com.compomics.util.messages
Classes related to sending messages to the user.
com.compomics.util.nucleotide
Useful objects for modeling and handling nucleotides.
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.peptide_shaker
PeptideShaker parameters.
com.compomics.util.parameters.quantification.spectrum_counting
Spectrum counting parameters.
com.compomics.util.parameters.searchgui
SearchGUI parameters.
com.compomics.util.parameters.tools
Tool parameters.
com.compomics.util.pdbfinder
Classes for mapping between UniProt accession numbers and PDB structures.
com.compomics.util.pdbfinder.das.readers
Classes for aligning and annotating PDB files when mapped to UniProt accession numbers.
com.compomics.util.pdbfinder.pdb
Classes for parsing PDB files.
com.compomics.util.pride
Objects related to mapping to PRIDE.
com.compomics.util.pride.prideobjects
Objects related to mapping experiment annotation to PRIDE.
com.compomics.util.pride.prideobjects.webservice
Classes for validating PRIDE web service queries.
com.compomics.util.pride.prideobjects.webservice.file
Classes for validating PRIDE web service file types.
com.compomics.util.pride.prideobjects.webservice.query
Classes for validating PRIDE web service filters.
com.compomics.util.pride.validation
Classes for validating PRIDE XML files.
com.compomics.util.protein
Classes concerning useful Objects and their operations for modeling and handling proteins.
com.compomics.util.sun
Classes related to Java's Swing library.
com.compomics.util.threading
Classes related to maps.
com.compomics.util.waiting
Waiting handler interfaces.