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

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

Package	Description
com.compomics.util.experiment.biology.aminoacids.sequence	Classes related to the handling of protein sequences.
com.compomics.util.experiment.biology.proteins	Classes related to proteins.
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.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.modification.mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.modification.search_engine_mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.protein_inference	Classes related to protein inference.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
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.simple_annotators	This package contains implementations of the SimpleAnnotator allowing the annotation of specific sets of ions.
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.identification.utils	This package contains utilities classes to handle identification objects.
com.compomics.util.experiment.io.identification	Experiment identification classes.
com.compomics.util.experiment.io.identification.idfilereaders	Experiment classes related to reading search engine files.
com.compomics.util.gui.genes	Dialogs for the handling of genes.
com.compomics.util.gui.modification	PTM GUI dialogs.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

Classes in com.compomics.util.experiment.identification.matches used by com.compomics.util.experiment.biology.aminoacids.sequence

Class	Description
ModificationMatch	This class models the match between theoretic PTM and identification results.

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

Class	Description
ModificationMatch	This class models the match between theoretic PTM and identification results.
PeptideVariantMatches	This class represents a set of variants found on a peptide.

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

Class	Description
IonMatch	This class represents the assignment of a peak to a theoretical ion.
PeptideMatch	This class models a peptide match.
ProteinMatch	This class models a protein match.
SpectrumMatch	This class models a spectrum match.

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

Class	Description
ModificationMatch	This class models the match between theoretic PTM and identification results.

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

Class	Description
IonMatch.MzErrorType	Enum of the supported error types.
ModificationMatch	This class models the match between theoretic PTM and identification results.

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

Class	Description
PeptideMatch	This class models a peptide match.
ProteinMatch	This class models a protein match.
SpectrumMatch	This class models a spectrum match.

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

Class	Description
IonMatch	This class represents the assignment of a peak to a theoretical ion.

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

Class	Description
ModificationMatch	This class models the match between theoretic PTM and identification results.

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

Class	Description
ModificationMatch	This class models the match between theoretic PTM and identification results.

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

Class	Description
ModificationMatch	This class models the match between theoretic PTM and identification results.
PeptideVariantMatches	This class represents a set of variants found on a peptide.
SpectrumMatch	This class models a spectrum match.

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

Class	Description
ModificationMatch	This class models the match between theoretic PTM and identification results.

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

Class	Description
IonMatch	This class represents the assignment of a peak to a theoretical ion.

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

Class	Description
IonMatch	This class represents the assignment of a peak to a theoretical ion.

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

Class	Description
IonMatch	This class represents the assignment of a peak to a theoretical ion.

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

Class	Description
IonMatch	This class represents the assignment of a peak to a theoretical ion.

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

Class	Description
ModificationMatch	This class models the match between theoretic PTM and identification results.

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

Class	Description
SpectrumMatch	This class models a spectrum match.

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

Class	Description
SpectrumMatch	This class models a spectrum match.

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

Class	Description
ProteinMatch	This class models a protein match.

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

Class	Description
PeptideMatch	This class models a peptide match.

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

Class	Description
IonMatch	This class represents the assignment of a peak to a theoretical ion.