Uses of Package
com.compomics.util.experiment.identification.spectrum_annotation

Packages that use com.compomics.util.experiment.identification.spectrum_annotation

Package	Description
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
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.mass_spectrometry.spectra	Experiment classes related to spectra.
com.compomics.util.gui.modification	PTM GUI dialogs.
com.compomics.util.gui.parameters.identification.advanced	Dialogs for advanced identification parameters.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.
com.compomics.util.parameters.identification	Identification parameters.

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

Class	Description
SpecificAnnotationParameters	The spectrum annotation preferences specific to a spectrum and an identification assumption.

Classes in com.compomics.util.experiment.identification.spectrum_annotation used by com.compomics.util.experiment.identification.matches

Class	Description
IonMatchKeysCache	Cache for the keys of the ions.

Classes in com.compomics.util.experiment.identification.spectrum_annotation used by com.compomics.util.experiment.identification.modification

Class	Description
AnnotationParameters	This class contains the spectrum annotation parameters.
SpecificAnnotationParameters	The spectrum annotation preferences specific to a spectrum and an identification assumption.

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

Class	Description
AnnotationParameters	This class contains the spectrum annotation parameters.
SpecificAnnotationParameters	The spectrum annotation preferences specific to a spectrum and an identification assumption.

Classes in com.compomics.util.experiment.identification.spectrum_annotation used by com.compomics.util.experiment.identification.psm_scoring

Class	Description
SpecificAnnotationParameters	The spectrum annotation preferences specific to a spectrum and an identification assumption.

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

Class	Description
AnnotationParameters	This class contains the spectrum annotation parameters.
SpecificAnnotationParameters	The spectrum annotation preferences specific to a spectrum and an identification assumption.

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

Class	Description
AnnotationParameters	This class contains the spectrum annotation parameters.
AnnotationParameters.IntensityThresholdType	Enum of the types of intensity thresholds available.
IonMatchKeysCache	Cache for the keys of the ions.
NeutralLossesMap	This class contains the informations relative to the accounting of neutral losses
SpecificAnnotationParameters	The spectrum annotation preferences specific to a spectrum and an identification assumption.
SpectrumAnnotator	The spectrum annotator annotates peaks in a spectrum.
SpectrumAnnotator.TiesResolution	Enum of the possibilities for ties resolution when multiple peaks can be annotated.

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

Class	Description
AnnotationParameters	This class contains the spectrum annotation parameters.
NeutralLossesMap	This class contains the informations relative to the accounting of neutral losses
SpecificAnnotationParameters	The spectrum annotation preferences specific to a spectrum and an identification assumption.
SpectrumAnnotator	The spectrum annotator annotates peaks in a spectrum.

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

Class	Description
AnnotationParameters.IntensityThresholdType	Enum of the types of intensity thresholds available.

Classes in com.compomics.util.experiment.identification.spectrum_annotation used by com.compomics.util.gui.modification

Class	Description
AnnotationParameters	This class contains the spectrum annotation parameters.

Classes in com.compomics.util.experiment.identification.spectrum_annotation used by com.compomics.util.gui.parameters.identification.advanced

Class	Description
AnnotationParameters	This class contains the spectrum annotation parameters.

Classes in com.compomics.util.experiment.identification.spectrum_annotation used by com.compomics.util.gui.spectrum

Class	Description
NeutralLossesMap	This class contains the informations relative to the accounting of neutral losses

Classes in com.compomics.util.experiment.identification.spectrum_annotation used by com.compomics.util.parameters.identification

Class	Description
AnnotationParameters	This class contains the spectrum annotation parameters.