Uses of Package
com.compomics.util.experiment.biology.ions

Packages that use com.compomics.util.experiment.biology.ions

Package	Description
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
com.compomics.util.experiment.biology.ions.impl	Ion implementations.
com.compomics.util.experiment.biology.modifications
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.experiment.identification.peptide_fragmentation	Peptide fragment intensities.
com.compomics.util.experiment.identification.peptide_fragmentation.models	Predictors for peptide fragment intensities.
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.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

Classes in com.compomics.util.experiment.biology.ions used by com.compomics.util.experiment.biology.ions

Class	Description
Ion	This class models an ion.
Ion.IonType	An enumerator of the supported ion types.
IonFactory	This factory generates the expected ions from a peptide.
NeutralLoss	This class represents a neutral loss.
NeutralLossCombination	This class represents a combination of multiple neutral losses.

Classes in com.compomics.util.experiment.biology.ions used by com.compomics.util.experiment.biology.ions.impl

Class	Description
Ion	This class models an ion.
NeutralLoss	This class represents a neutral loss.

Classes in com.compomics.util.experiment.biology.ions used by com.compomics.util.experiment.biology.modifications

Class	Description
NeutralLoss	This class represents a neutral loss.

Classes in com.compomics.util.experiment.biology.ions used by com.compomics.util.experiment.identification.matches

Class	Description
Ion	This class models an ion.

Classes in com.compomics.util.experiment.biology.ions used by com.compomics.util.experiment.identification.peptide_fragmentation

Class	Description
Ion	This class models an ion.

Classes in com.compomics.util.experiment.biology.ions used by com.compomics.util.experiment.identification.peptide_fragmentation.models

Class	Description
Ion	This class models an ion.

Classes in com.compomics.util.experiment.biology.ions used by com.compomics.util.experiment.identification.spectrum_annotation

Class	Description
Ion	This class models an ion.
Ion.IonType	An enumerator of the supported ion types.
IonFactory	This factory generates the expected ions from a peptide.
NeutralLoss	This class represents a neutral loss.

Classes in com.compomics.util.experiment.biology.ions used by com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

Class	Description
Ion	This class models an ion.

Classes in com.compomics.util.experiment.biology.ions used by com.compomics.util.gui.spectrum

Class	Description
Ion	This class models an ion.
Ion.IonType	An enumerator of the supported ion types.
NeutralLoss	This class represents a neutral loss.