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

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

Package	Description
com.compomics.util.experiment	Gene factory classes.
com.compomics.util.experiment.identification	Experiment classes related to identifications.
com.compomics.util.experiment.identification.identification_parameters	Parameters settings for the spectrum identification algorithms.
com.compomics.util.experiment.identification.identification_parameters.tool_specific	Parameters settings for the search algorithms.
com.compomics.util.experiment.identification.identifications	Experiment classes related to MS//MS identifications.
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.ptm.ptmscores	PTM scores.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_assumptions	Implementations of the SpectrumIdentificationAssumption.

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

Class and Description
Identification This class contains identification results.

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

Class and 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.
IdentificationDB This class uses a database to manage identification matches.
IdentificationMatch This is an abstract class for an identification match.
IdentificationMatch.MatchType The type of match.
SpectrumIdentificationAssumption Spectrum identification assumption made by an identification algorithm.

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

Class and 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.experiment.identification.identification_parameters.tool_specific

Class and 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.experiment.identification.identifications

Class and Description
Identification This class contains identification results.

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

Class and Description
IdentificationMatch This is an abstract class for an identification match.
IdentificationMatch.MatchType The type of match.
SpectrumIdentificationAssumption Spectrum identification assumption made by an identification algorithm.

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

Class and Description
Identification This class contains identification results.

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

Class and 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_annotation

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