computational omics utilities 3.8.6 API

Packages
com.compomics.software  
com.compomics.software.dialogs  
com.compomics.util This package contains general util classes.
com.compomics.util.db This package contains database related classes.
com.compomics.util.db.components This package contains database related components.
com.compomics.util.db.interfaces This package contains database related interfaces.
com.compomics.util.enumeration This package contains enumeration used by utilties.
com.compomics.util.examples This package contains examples of how the utilities library can can be used by other projects.
com.compomics.util.experiment This package contains MSExperiment main class and all sub-classes useful for the modeling of an experiment.
com.compomics.util.experiment.biology This package contains experiement classes related to biological entities.
com.compomics.util.experiment.biology.aminoacids  
com.compomics.util.experiment.biology.atoms  
com.compomics.util.experiment.biology.ions This package contains experiment classes related to ions.
com.compomics.util.experiment.filters.massspectrometry  
com.compomics.util.experiment.filters.massspectrometry.spectrumfilters  
com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation  
com.compomics.util.experiment.identification This package contains experiment classes related to identifications.
com.compomics.util.experiment.identification.advocates This package contains experiment classes related to modeling identifications.
com.compomics.util.experiment.identification.identifications This package contains experiment classes related to MS/MS identifications.
com.compomics.util.experiment.identification.matches This package contains experiment classes releated to matches. e.g., pepties, proteins, modifications and spectra.
com.compomics.util.experiment.identification.ptm  
com.compomics.util.experiment.io  
com.compomics.util.experiment.io.identifications  
com.compomics.util.experiment.io.identifications.idfilereaders This package contains experiment classes related to reading search engine files.
com.compomics.util.experiment.io.massspectrometry  
com.compomics.util.experiment.massspectrometry This package contains experiment classes related to spectra.
com.compomics.util.experiment.personalization This package contains experiment customization classes.
com.compomics.util.experiment.quantification This package contains experiment classes related to quantification.
com.compomics.util.experiment.quantification.matches  
com.compomics.util.experiment.quantification.reporterion This package contains experiment classes related to reporter ions.
com.compomics.util.experiment.quantification.spectrumcounting  
com.compomics.util.experiment.refinementparameters This package contains experiment classes related to specific parametrization of experiment objects.
com.compomics.util.general The classes in this package focus mainly on very general, top-level tasks that are used throughout the other packages in the util section.
com.compomics.util.general.servlet This package holds the servlet representation of the classes from the general utilities package (com.compomics.util.general)
com.compomics.util.gui This package contains basic GUI classes.
com.compomics.util.gui.dialogs This package contains GUI dialogs.
com.compomics.util.gui.events This package contains GUI event classes.
com.compomics.util.gui.interfaces This package contains GUI related interfaces.
com.compomics.util.gui.isotopic_calculator This package contains the GUI class for the Isotopic Distribution calculator.
com.compomics.util.gui.protein This package contains the GUI class related to protein sequence formatting.
com.compomics.util.gui.renderers This package contains GUI renderer classes.
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization.
com.compomics.util.gui.waiting  
com.compomics.util.gui.waiting.waitinghandlers  
com.compomics.util.interfaces This package defines interfaces for the more specific implementations in the util package.
com.compomics.util.io This package contains classes related to input/output.
com.compomics.util.io.filefilters This package contains classes related to file filters.
com.compomics.util.math  
com.compomics.util.nucleotide The classes in this package concern useful Objects and their operations for modelling and handling nucleotides.
com.compomics.util.pdbfinder The classes in this package concern support for mapping between UniProt accession numbers and PDB structures.
com.compomics.util.pdbfinder.das.readers The classes in this package concern support for aligning and annotating PDB files when mapped to UniProt accession numbers.
com.compomics.util.pdbfinder.pdb The classes in this package are related to paring the PDB files.
com.compomics.util.preferences  
com.compomics.util.pride  
com.compomics.util.pride.prideobjects  
com.compomics.util.protein The classes in this package concern useful Objects and their operations for modelling and handling proteins.
com.compomics.util.sun This package contains classes related to Java's Swing library.

 



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