computational omics utilities 3.14.13 API

Packages 
Package Description
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.denovo  
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.annotation.gene  
com.compomics.util.experiment.annotation.go  
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.
com.compomics.util.experiment.identification.protein_inference.proteintree  
com.compomics.util.experiment.identification.ptm  
com.compomics.util.experiment.identification.scoring  
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.error_handlers  
com.compomics.util.gui.events
This package contains GUI event classes.
com.compomics.util.gui.export_graphics  
com.compomics.util.gui.filehandling  
com.compomics.util.gui.gene_mapping  
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.ptm  
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.tablemodels  
com.compomics.util.gui.utils  
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.junit  
com.compomics.util.math  
com.compomics.util.messages  
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.preferences.gui  
com.compomics.util.pride  
com.compomics.util.pride.prideobjects  
com.compomics.util.pride.validation  
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.
com.compomics.util.waiting  

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