computational omics utilities 5.1.16 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.paths	Command line for the handling of paths.
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.peptide_mapping	Classes used to map modifications to acceptor sites in peptides.
com.compomics.util.experiment.identification.modification.peptide_mapping.performance	Classes used to benchmark the modification mapping.
com.compomics.util.experiment.identification.modification.scores	PTM scores.
com.compomics.util.experiment.identification.modification.search_engine_mapping	Mapping between search engine and Utilities modifications.
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.identification.validation.percolator
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	Experiment IO classes relative to the handling of temporary files.
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.features	Classes related to exporting Reporter features.
com.compomics.util.io.export.features.peptideshaker	Package containing classes listing the possible export features for PeptideShaker.
com.compomics.util.io.export.features.reporter	Package containing classes listing the possible export features for Reporter.
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.