Package com.compomics.util.experiment.identification

package com.compomics.util.experiment.identification

Experiment classes related to identifications.

Related Packages

Package	Description
com.compomics.util.experiment	Gene factory classes.
com.compomics.util.experiment.identification.amino_acid_tags	Amino Acid Tag classes.
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.identification_parameters	Parameters settings for the spectrum identification algorithms.
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	Modification mapping and localization.
com.compomics.util.experiment.identification.peptide_fragmentation	Peptide fragment intensities.
com.compomics.util.experiment.identification.peptide_inference	Classes related to peptide inference.
com.compomics.util.experiment.identification.peptide_shaker	Experiment classes used in PeptideShaker calculations.
com.compomics.util.experiment.identification.protein_inference	Classes related to protein inference.
com.compomics.util.experiment.identification.protein_sequences	Protein sequence handling related classes.
com.compomics.util.experiment.identification.psm_scoring	Main PSM scoring class.
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.identification.utils	This package contains utilities classes to handle identification objects.
com.compomics.util.experiment.identification.validation	Experiment classes related to identification matches validation.

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.
Identification	This class interacts with the back-end database to manage identification objects.
IdentificationKeys	Placeholder for the keys of the objects in the identification.
IdentificationMatch	This is an abstract class for an identification match.
IdentificationMatch.MatchType	The type of match.
IdentificationMethod	This class will contain all methods used to obtain identifications.
SpectrumIdentificationAssumption	Spectrum identification assumption made by an identification algorithm.
TagFactory	Convenience class for sequence tag generation.