computational omics utilities 3.45.14 API

Packages 
Package Description
com.compomics.software
Helper classes for command line usage of compomics-utilities tools.
com.compomics.software.autoupdater
Classes related to auto updating compomics-utilities tools.
com.compomics.software.dialogs
Dialogs for starting compomics-utilities tools and setting their Java options.
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.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.annotation.gene
MSExperiment main class and all sub-classes useful for the modeling of an experiment.
com.compomics.util.experiment.annotation.go
GO factory classes.
com.compomics.util.experiment.biology
Experiment classes related to biological entities.
com.compomics.util.experiment.biology.aminoacids
The amino acid classes.
com.compomics.util.experiment.biology.atoms
The atom classes.
com.compomics.util.experiment.biology.ions
Experiment classes related to ions.
com.compomics.util.experiment.identification
Experiment classes related to identifications.
com.compomics.util.experiment.identification.identification_parameters
Parameters settings for the search algorithms.
com.compomics.util.experiment.identification.identifications
Experiment classes related to MS//MS identifications.
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.protein_inference.proteintree
Peptide to protein mapping classes.
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.ptm
Additional PSM scoring classes.
com.compomics.util.experiment.identification.ptm.ptmscores
PTM scores.
com.compomics.util.experiment.identification.search_parameters_cli
Identification search parameters.
com.compomics.util.experiment.identification.spectrum_annotators
Spectrum annotation.
com.compomics.util.experiment.identification.tags
Tag classes.
com.compomics.util.experiment.identification.tags.matchers
Tag matching classes.
com.compomics.util.experiment.identification.tags.tagcomponents
Tag component classes.
com.compomics.util.experiment.io
Experiment IO classes.
com.compomics.util.experiment.io.identifications
Experiment identification classes.
com.compomics.util.experiment.io.identifications.idfilereaders
Experiment classes related to reading search engine files.
com.compomics.util.experiment.io.massspectrometry
Reading and indexing of mgf files.
com.compomics.util.experiment.io.massspectrometry.export  
com.compomics.util.experiment.massspectrometry
Experiment classes related to spectra.
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.refinementparameters
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.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.filehandling
File handling.
com.compomics.util.gui.gene_mapping
Species selection dialog.
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.protein
GUI class related to protein sequence formatting.
com.compomics.util.gui.ptm
PTM GUI dialogs.
com.compomics.util.gui.renderers
GUI renderer classes.
com.compomics.util.gui.searchsettings
Search settings dialog.
com.compomics.util.gui.searchsettings.algorithm_settings
Search algorithm settings dialogs.
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.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.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.filefilters
Classes related to file filters.
com.compomics.util.junit
Custom classpath related test class.
com.compomics.util.math
Basic match functions.
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.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.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.preferences
Utilities preferences classes.
com.compomics.util.preferences.gui
Utilities preferences GUI classes.
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.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.waiting
Waiting handler interfaces.

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