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

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

Package	Description
com.compomics.util.experiment.identification	Experiment classes related to identifications.
com.compomics.util.experiment.identification.features	Classes for the generation of identification features.
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.experiment.identification.matches_iterators	Identification match iterators.
com.compomics.util.experiment.identification.modification.scores	PTM scores.
com.compomics.util.experiment.identification.peptide_inference	Classes related to peptide inference.
com.compomics.util.experiment.identification.protein_inference	Classes related to protein inference.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_assumptions	Implementations of the SpectrumIdentificationAssumption.
com.compomics.util.experiment.quantification.spectrumcounting	Experiment classes related to spectrum counting.
com.compomics.util.gui.modification	PTM GUI dialogs.
com.compomics.util.gui.parameters.identification	GUI classes for parameters, settings and preferences used for identification.
com.compomics.util.parameters.identification.tool_specific	Parameters settings for the search algorithms.

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

Class	Description
Advocate	The advocate of a hit can be a search engine, a sequencing algorithm, a rescoring algorithm, etc.
Advocate.AdvocateType	The different types of advocates.
IdentificationKeys	Placeholder for the keys of the objects in the identification.
IdentificationMatch.MatchType	The type of match.

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

Class	Description
Identification	This class interacts with the back-end database to manage identification objects.

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

Class	Description
Identification	This class interacts with the back-end database to manage identification objects.

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

Class	Description
IdentificationMatch	This is an abstract class for an identification match.
IdentificationMatch.MatchType	The type of match.

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

Class	Description
Identification	This class interacts with the back-end database to manage identification objects.

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

Class	Description
SpectrumIdentificationAssumption	Spectrum identification assumption made by an identification algorithm.

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

Class	Description
Identification	This class interacts with the back-end database to manage identification objects.

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

Class	Description
Identification	This class interacts with the back-end database to manage identification objects.

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

Class	Description
SpectrumIdentificationAssumption	Spectrum identification assumption made by an identification algorithm.

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

Class	Description
SpectrumIdentificationAssumption	Spectrum identification assumption made by an identification algorithm.

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.quantification.spectrumcounting

Class	Description
Identification	This class interacts with the back-end database to manage identification objects.

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

Class	Description
Identification	This class interacts with the back-end database to manage identification objects.

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

Class	Description
Advocate	The advocate of a hit can be a search engine, a sequencing algorithm, a rescoring algorithm, etc.

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

Class	Description
Advocate	The advocate of a hit can be a search engine, a sequencing algorithm, a rescoring algorithm, etc.