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.
|