com.compomics.angrypeptide |
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com.compomics.angrypeptide.bijection |
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com.compomics.angrypeptide.fun |
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com.compomics.angrypeptide.gui |
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com.compomics.software |
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com.compomics.software.dialogs |
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com.compomics.util |
This package contains general util classes.
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com.compomics.util.db |
This package contains database related classes.
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com.compomics.util.db.components |
This package contains database related components.
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com.compomics.util.db.interfaces |
This package contains database related interfaces.
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com.compomics.util.denovo |
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com.compomics.util.enumeration |
This package contains enumeration used by utilties.
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com.compomics.util.examples |
This package contains examples of how the utilities library can
can be used by other projects.
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com.compomics.util.experiment |
This package contains MSExperiment main class and all sub-classes useful for the modeling of an experiment.
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com.compomics.util.experiment.annotation.gene |
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com.compomics.util.experiment.annotation.go |
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com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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com.compomics.util.experiment.biology.aminoacids |
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com.compomics.util.experiment.biology.atoms |
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com.compomics.util.experiment.biology.ions |
This package contains experiment classes related to ions.
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com.compomics.util.experiment.filters.massspectrometry |
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com.compomics.util.experiment.filters.massspectrometry.spectrumfilters |
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com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation |
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.experiment.identification.advocates |
This package contains experiment classes related to modeling identifications.
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com.compomics.util.experiment.identification.identifications |
This package contains experiment classes related to MS/MS identifications.
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com.compomics.util.experiment.identification.matches |
This package contains experiment classes releated to matches.
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com.compomics.util.experiment.identification.protein_inference.proteintree |
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com.compomics.util.experiment.identification.ptm |
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com.compomics.util.experiment.identification.scoring |
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com.compomics.util.experiment.io |
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com.compomics.util.experiment.io.identifications |
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com.compomics.util.experiment.io.identifications.idfilereaders |
This package contains experiment classes related to reading search engine files.
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com.compomics.util.experiment.io.massspectrometry |
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com.compomics.util.experiment.massspectrometry |
This package contains experiment classes related to spectra.
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com.compomics.util.experiment.personalization |
This package contains experiment customization classes.
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com.compomics.util.experiment.quantification |
This package contains experiment classes related to quantification.
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com.compomics.util.experiment.quantification.matches |
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com.compomics.util.experiment.quantification.reporterion |
This package contains experiment classes related to reporter ions.
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com.compomics.util.experiment.quantification.spectrumcounting |
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com.compomics.util.experiment.refinementparameters |
This package contains experiment classes related to specific parametrization of experiment objects.
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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.
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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.
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com.compomics.util.gui.error_handlers |
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com.compomics.util.gui.events |
This package contains GUI event classes.
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com.compomics.util.gui.export_graphics |
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com.compomics.util.gui.filehandling |
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com.compomics.util.gui.gene_mapping |
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com.compomics.util.gui.interfaces |
This package contains GUI related interfaces.
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com.compomics.util.gui.isotopic_calculator |
This package contains the GUI class for the Isotopic Distribution calculator.
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com.compomics.util.gui.protein |
This package contains the GUI class related to protein sequence formatting.
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com.compomics.util.gui.ptm |
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com.compomics.util.gui.renderers |
This package contains GUI renderer classes.
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com.compomics.util.gui.spectrum |
This package contains GUI classes related to Spectrum and Chromatogram visualization.
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com.compomics.util.gui.tablemodels |
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com.compomics.util.gui.utils |
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com.compomics.util.gui.waiting |
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com.compomics.util.gui.waiting.waitinghandlers |
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com.compomics.util.interfaces |
This package defines interfaces for the more specific
implementations in the util package.
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com.compomics.util.io |
This package contains classes related to input/output.
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com.compomics.util.io.filefilters |
This package contains classes related to file filters.
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com.compomics.util.junit |
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com.compomics.util.math |
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com.compomics.util.messages |
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com.compomics.util.nucleotide |
The classes in this package concern useful Objects and their
operations for modelling and handling nucleotides.
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com.compomics.util.pdbfinder |
The classes in this package concern support for mapping between
UniProt accession numbers and PDB structures.
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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.
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com.compomics.util.pdbfinder.pdb |
The classes in this package are related to paring the PDB files.
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com.compomics.util.preferences |
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com.compomics.util.preferences.gui |
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com.compomics.util.pride |
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com.compomics.util.pride.prideobjects |
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com.compomics.util.pride.validation |
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com.compomics.util.protein |
The classes in this package concern useful Objects and their
operations for modelling and handling proteins.
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com.compomics.util.sun |
This package contains classes related to Java's Swing library.
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