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Packages | |
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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.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)
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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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