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

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

Package	Description
com.compomics.util.experiment	This package contains MSExperiment main class and all sub-classes useful for the modeling of an experiment.
com.compomics.util.experiment.biology	This package contains experiement classes related to biological entities.
com.compomics.util.experiment.identification	This package contains experiment classes related to identifications.
com.compomics.util.experiment.identification.identification_parameters
com.compomics.util.experiment.identification.identifications	This package contains experiment classes related to MS/MS identifications.
com.compomics.util.experiment.identification.matches	This package contains experiment classes releated to matches.
com.compomics.util.experiment.identification.psm_scoring
com.compomics.util.experiment.identification.psm_scoring.psm_scores
com.compomics.util.experiment.identification.ptm
com.compomics.util.experiment.identification.ptm.ptmscores
com.compomics.util.experiment.identification.search_parameters_cli
com.compomics.util.experiment.identification.spectrum_annotators
com.compomics.util.experiment.io.identifications
com.compomics.util.experiment.io.identifications.idfilereaders	This package contains experiment classes related to reading search engine files.
com.compomics.util.gui.searchsettings
com.compomics.util.gui.spectrum	This package contains GUI classes related to Spectrum and Chromatogram visualization.
com.compomics.util.preferences
com.compomics.util.pride

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.biology

Class and Description
SearchParameters This class groups the parameters used for identification.

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.
FastaIndex This class contains the index of a FASTA file.
IdentificationAlgorithmParameter Interface for the algorithm specific parameters.
IdentificationMatch This is an abstract class for an identification match.
IdentificationMatch.MatchType The type of match.
NeutralLossesMap This class contains the informations relative to the accounting of neutral losses
SearchParameters This class groups the parameters used for identification.
SearchParameters.MassAccuracyType Possible mass accuracy types.
SearchParameters.PrecursorAccuracyType Deprecated. use MassAccuracyType
SequenceFactory Factory retrieving the information of the loaded FASTA file.
SequenceFactory.HeaderIterator Convenience iterator iterating the headers of a FASTA file without using the cache.
SequenceFactory.ProteinIterator Convenience iterator iterating all proteins in a FASTA file without using index or cache.
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.
IdentificationAlgorithmParameter Interface for the algorithm specific parameters.

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.
PeptideAssumption This object will models the assumption made by an advocate.
SpectrumIdentificationAssumption Spectrum identification assumption made by an identification algorithm.
TagAssumption This class represent a tag assumption made by an identification algorithm based on a sequence tag.

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

Class and Description
NeutralLossesMap This class contains the informations relative to the accounting of neutral losses
SearchParameters This class groups the parameters used for identification.

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

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

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

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

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

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

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

Class and Description
SearchParameters This class groups the parameters used for identification.

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

Class and Description
NeutralLossesMap This class contains the informations relative to the accounting of neutral losses
SpectrumAnnotator The spectrum annotator annotates peaks in a spectrum.

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

Class and Description
SearchParameters This class groups the parameters used for identification.

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.io.identifications.idfilereaders

Class and Description
SearchParameters This class groups the parameters used for identification.

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

Class and Description
SearchParameters This class groups the parameters used for identification.

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

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

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

Class and Description
NeutralLossesMap This class contains the informations relative to the accounting of neutral losses
PeptideAssumption This object will models the assumption made by an advocate.
SearchParameters This class groups the parameters used for identification.
SpectrumIdentificationAssumption Spectrum identification assumption made by an identification algorithm.

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

Class and Description
SearchParameters This class groups the parameters used for identification.