Uses of Package
com.compomics.util.experiment.mass_spectrometry.spectra

Packages that use com.compomics.util.experiment.mass_spectrometry.spectra

Package	Description
com.compomics.util.experiment.identification.modification	Modification mapping and localization.
com.compomics.util.experiment.identification.modification.scores	PTM scores.
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.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
com.compomics.util.experiment.io.mass_spectrometry	Classes for the handling of mass spectrometry files.
com.compomics.util.experiment.io.mass_spectrometry.apl	Classes for the handling of Andromeda peak list (apl) files.
com.compomics.util.experiment.io.mass_spectrometry.cms	Classes for the handling of Compomics mass spectrometry (cms) files.
com.compomics.util.experiment.io.mass_spectrometry.mgf	Classes for the handling of mgf files.
com.compomics.util.experiment.io.mass_spectrometry.ms2	Classes for the handling of ms2 files.
com.compomics.util.experiment.io.mass_spectrometry.mzml	Classes for the handling of mzml files.
com.compomics.util.experiment.mass_spectrometry	Experiment classes related to mass spectrometry.
com.compomics.util.experiment.mass_spectrometry.indexes	Classes related to the indexing of spectra.
com.compomics.util.experiment.mass_spectrometry.spectra	Experiment classes related to spectra.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.identification.modification

Class	Description
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.identification.modification.scores

Class	Description
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.identification.psm_scoring

Class	Description
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.identification.psm_scoring.psm_scores

Class	Description
Precursor	This class models a precursor.
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.identification.spectrum_annotation

Class	Description
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

Class	Description
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.io.mass_spectrometry

Class	Description
Precursor	This class models a precursor.
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.io.mass_spectrometry.apl

Class	Description
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.io.mass_spectrometry.cms

Class	Description
Precursor	This class models a precursor.
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.io.mass_spectrometry.mgf

Class	Description
Precursor	This class models a precursor.
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.io.mass_spectrometry.ms2

Class	Description
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.io.mass_spectrometry.mzml

Class	Description
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.mass_spectrometry

Class	Description
Precursor	This class models a precursor.
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.mass_spectrometry.indexes

Class	Description
Precursor	This class models a precursor.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.experiment.mass_spectrometry.spectra

Class	Description
Peak	This class represents a peak.
Precursor	This class models a precursor.
PrecursorParameter	Parameter for storing additional non-mandatory precursor information.
Spectrum	This class models a spectrum.

Classes in com.compomics.util.experiment.mass_spectrometry.spectra used by com.compomics.util.gui.spectrum

Class	Description
Spectrum	This class models a spectrum.