| com.compomics.software |
Helper classes for command line usage of compomics-utilities tools.
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| com.compomics.software.autoupdater |
Classes related to auto updating compomics-utilities tools.
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| com.compomics.software.dialogs |
Dialogs for starting compomics-utilities tools and setting their Java options.
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| com.compomics.software.settings |
Settings for compomics-utilities tools.
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| com.compomics.software.settings.gui |
GUI settings for compomics-utilities tools.
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| com.compomics.util |
General utilities classes.
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| com.compomics.util.db |
Database related classes.
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| com.compomics.util.db.components |
Database related components.
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| com.compomics.util.db.interfaces |
Database related interfaces.
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| com.compomics.util.enumeration |
Enumeration used by compomics-utilities.
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| com.compomics.util.examples |
Examples of how the compomics-utilities library can
can be used by other projects.
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| com.compomics.util.exceptions |
Classes for the handling of exceptions.
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| com.compomics.util.exceptions.exception_handlers |
Implementations of the ExceptionHandler interface.
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| com.compomics.util.experiment |
Gene factory classes.
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| com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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| com.compomics.util.experiment.biology.aminoacids |
The amino acid classes.
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| com.compomics.util.experiment.biology.atoms |
The atom classes.
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| com.compomics.util.experiment.biology.genes |
Classes related to genes.
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| com.compomics.util.experiment.biology.genes.ensembl |
Classes for the handling of Ensembl data.
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| com.compomics.util.experiment.biology.genes.go |
Classes for the handling of GO terms.
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| com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
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| com.compomics.util.experiment.biology.mutations |
Experiment classes related to mutations.
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| com.compomics.util.experiment.biology.taxonomy |
Classes related to species and taxonomy.
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| com.compomics.util.experiment.biology.taxonomy.mappings |
Classes related to species mapping.
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| com.compomics.util.experiment.filtering |
Filtering classes.
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| com.compomics.util.experiment.identification |
Experiment classes related to identifications.
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| com.compomics.util.experiment.identification.amino_acid_tags |
Amino Acid Tag classes.
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| com.compomics.util.experiment.identification.amino_acid_tags.matchers |
Tag matching classes.
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| com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
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| com.compomics.util.experiment.identification.identification_parameters |
Parameters settings for the spectrum identification algorithms.
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| com.compomics.util.experiment.identification.identification_parameters.tool_specific |
Parameters settings for the search algorithms.
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| com.compomics.util.experiment.identification.identifications |
Experiment classes related to MS//MS identifications.
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| com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
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| com.compomics.util.experiment.identification.matches_iterators |
Identification match iterators.
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| com.compomics.util.experiment.identification.parameters_cli |
Identification search parameters.
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| com.compomics.util.experiment.identification.protein_inference.proteintree |
Protein sequence database indexing classes.
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| com.compomics.util.experiment.identification.protein_sequences |
Protein sequence handling related classes.
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| com.compomics.util.experiment.identification.psm_scoring |
Main PSM scoring class.
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| com.compomics.util.experiment.identification.psm_scoring.psm_scores |
Main PTM scoring classes.
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| com.compomics.util.experiment.identification.ptm |
Additional PSM scoring classes.
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| com.compomics.util.experiment.identification.ptm.ptmscores |
PTM scores.
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| com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
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| com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators |
Spectrum annotation.
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| com.compomics.util.experiment.identification.spectrum_assumptions |
Implementations of the SpectrumIdentificationAssumption.
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| com.compomics.util.experiment.io |
Experiment IO classes.
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| com.compomics.util.experiment.io.identifications |
Experiment identification classes.
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| com.compomics.util.experiment.io.identifications.idfilereaders |
Experiment classes related to reading search engine files.
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| com.compomics.util.experiment.io.massspectrometry |
Reading and indexing of mgf files.
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| com.compomics.util.experiment.io.massspectrometry.export |
Experiment classes related to exporting mass spectrometry files.
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| com.compomics.util.experiment.massspectrometry |
Experiment classes related to spectra.
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| com.compomics.util.experiment.massspectrometry.proteowizard |
Package containing the classes used to interact with ProteoWizard.
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| com.compomics.util.experiment.massspectrometry.proteowizard.gui |
Package containing the GUI classes used to interact with ProteoWizard.
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| com.compomics.util.experiment.normalization |
Classes related to quantification values normalization.
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| com.compomics.util.experiment.patient |
Experiment classes related to patent information.
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| com.compomics.util.experiment.personalization |
Experiment customization classes.
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| com.compomics.util.experiment.quantification |
Experiment classes related to quantification.
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| com.compomics.util.experiment.quantification.reporterion |
Experiment classes related to reporter ions.
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| com.compomics.util.experiment.quantification.spectrumcounting |
Experiment classes related to spectrum counting.
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| com.compomics.util.experiment.refinementparameters |
Experiment classes related to specific parametrization of experiment objects.
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| com.compomics.util.experiment.units |
Unit related classes.
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| com.compomics.util.general |
General, top-level tasks that are used throughout the other packages in the util section.
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| com.compomics.util.general.servlet |
Servlet representation of the
classes from the general utilities package (com.compomics.util.general)
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| com.compomics.util.gui |
Basic GUI classes.
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| com.compomics.util.gui.atoms |
Atoms GUI dialogs.
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| com.compomics.util.gui.error_handlers |
Help handlers.
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| com.compomics.util.gui.error_handlers.notification |
Notification dialogs.
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| com.compomics.util.gui.events |
GUI event classes.
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| com.compomics.util.gui.export.graphics |
Exporting of graphics.
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| com.compomics.util.gui.export.report |
Report editor GUI.
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| com.compomics.util.gui.filehandling |
File handling.
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| com.compomics.util.gui.genes |
Dialogs for the handling of genes.
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| com.compomics.util.gui.interfaces |
GUI related interfaces.
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| com.compomics.util.gui.isotopic_calculator |
GUI class for the Isotopic Distribution calculator.
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| com.compomics.util.gui.parameters |
GUI classes for parameters, settings and preferences.
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| com.compomics.util.gui.parameters.identification_parameters |
GUI classes for parameters, settings and preferences used for identification.
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| com.compomics.util.gui.parameters.identification_parameters.algorithm_settings |
Search algorithm settings dialogs.
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| com.compomics.util.gui.protein |
GUI class related to protein sequence formatting.
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| com.compomics.util.gui.ptm |
PTM GUI dialogs.
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| com.compomics.util.gui.renderers |
GUI renderer classes.
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| com.compomics.util.gui.spectrum |
Spectrum and Chromatogram visualization GUI classes.
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| com.compomics.util.gui.tablemodels |
Self updating table model classes.
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| com.compomics.util.gui.utils |
GUI utilities classes.
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| com.compomics.util.gui.utils.user_choice |
GUI utils allowing the user to choose something.
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| com.compomics.util.gui.utils.user_choice.list_choosers |
Implementations of the ListChooser.
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| com.compomics.util.gui.waiting.waitinghandlers |
Waiting handler classes.
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| com.compomics.util.interfaces |
Interfaces for the more specific implementations in the util package.
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| com.compomics.util.io |
Classes related to input/output.
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| com.compomics.util.io.compression |
Classes related to file compression.
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| com.compomics.util.io.export |
Classes related to exporting reports.
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| com.compomics.util.io.export.styles |
Export styles.
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| com.compomics.util.io.export.writers |
Export writer.
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| com.compomics.util.io.filefilters |
Classes related to file filters.
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| com.compomics.util.io.json |
JSON marshaller.
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| com.compomics.util.io.json.adapter |
JSON adapter classes.
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| com.compomics.util.io.json.marshallers |
JSON marshaller classes.
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| com.compomics.util.junit |
Custom classpath related test class.
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| com.compomics.util.maps |
Classes related to maps.
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| com.compomics.util.math |
Basic match functions.
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| com.compomics.util.math.clustering |
Basic clustering functions.
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| com.compomics.util.math.clustering.settings |
Settings for the clustering.
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| com.compomics.util.math.matrix |
Double matrix classes.
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| com.compomics.util.math.roc |
ROC curve calculation.
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| com.compomics.util.math.statistics |
Math classes related to statistics.
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| com.compomics.util.math.statistics.distributions |
Math classes related to distributions.
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| com.compomics.util.math.statistics.linear_regression |
Classes to perform linear regressions.
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| com.compomics.util.math.statistics.linear_regression.filters |
Implementation of algorithms performing linear regression.
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| com.compomics.util.math.statistics.linear_regression.regressions |
Filters to apply prior to a linear regression.
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| com.compomics.util.memory |
Memory management.
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| com.compomics.util.messages |
Classes related to sending messages to the user.
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| com.compomics.util.nucleotide |
Useful objects for modeling and handling nucleotides.
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| com.compomics.util.pdbfinder |
Classes for mapping between UniProt accession numbers and PDB structures.
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| com.compomics.util.pdbfinder.das.readers |
Classes for aligning and annotating PDB files when mapped to UniProt accession numbers.
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| com.compomics.util.pdbfinder.pdb |
Classes for parsing PDB files.
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| com.compomics.util.preferences |
Utilities preferences classes.
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| com.compomics.util.pride |
Objects related to mapping to PRIDE.
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| com.compomics.util.pride.prideobjects |
Objects related to mapping experiment annotation to PRIDE.
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| com.compomics.util.pride.prideobjects.webservice |
Classes for validating PRIDE web service queries.
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| com.compomics.util.pride.prideobjects.webservice.file |
Classes for validating PRIDE web service file types.
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| com.compomics.util.pride.prideobjects.webservice.query |
Classes for validating PRIDE web service filters.
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| com.compomics.util.pride.validation |
Classes for validating PRIDE XML files.
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| com.compomics.util.protein |
Classes concerning useful Objects and their operations for modeling and handling proteins.
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| com.compomics.util.protein_sequences_manager |
Classes used for the management of FASTA files.
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| com.compomics.util.protein_sequences_manager.enums |
Enums used for the management of FASTA files.
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| com.compomics.util.protein_sequences_manager.gui |
GUI classes used for the management of FASTA files.
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| com.compomics.util.protein_sequences_manager.gui.preferences |
Classes used for the preferences for the management of FASTA files.
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| com.compomics.util.protein_sequences_manager.gui.sequences_import |
GUI classes for importing of FASTA files.
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| com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy |
Classes related to FASTA taxonomy.
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| com.compomics.util.sun |
Classes related to Java's Swing library.
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| com.compomics.util.waiting |
Waiting handler interfaces.
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