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

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

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.biology.aminoacids
com.compomics.util.experiment.biology.atoms
com.compomics.util.experiment.biology.ions	This package contains experiment classes related to ions.
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.matches	This package contains experiment classes releated to matches.
com.compomics.util.experiment.identification.protein_inference.proteintree
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.spectrum_annotators
com.compomics.util.experiment.identification.tags
com.compomics.util.experiment.quantification.reporterion	This package contains experiment classes related to reporter ions.
com.compomics.util.gui	This package contains basic GUI classes.
com.compomics.util.gui.ptm
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

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

Class and Description
Sample This class models a proteomic sample.

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

Class and Description
AminoAcid Class representing amino acids.
AminoAcidPattern An amino acid pattern is a sequence of amino acids.
AminoAcidPattern.MatchingType The different types of amino acid matching.
Atom This interface contains information about atoms.
ElementaryElement This class can be used to retrieve elementary elements like a neutron.
Enzyme This class models an enzyme.
EnzymeFactory This factory will provide the implemented enzymes.
GlyconFactory This factory will provide theoretic glycons.
Ion This class models an ion.
Ion.IonType An enumerator of the supported ion types.
IonFactory This factory generates the expected ions from a peptide.
Mutation This class represents a mutation of one amino acid to another from the 20-letter amino acid alphabet.
NeutralLoss This class represents a neutral loss.
Peptide This class models a peptide.
Protein This class models a protein.
PTM This class models a post-translational modification.
PTMFactory This factory will load PTM from an XML file and provide them on demand as standard class.
Sample This class models a proteomic sample.

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology.aminoacids

Class and Description
AminoAcid Class representing amino acids.

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology.atoms

Class and Description
Atom This interface contains information about atoms.

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology.ions

Class and Description
Ion This class models an ion.
NeutralLoss This class represents a neutral loss.

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

Class and Description
AminoAcidPattern.MatchingType The different types of amino acid matching.
Enzyme This class models an enzyme.
Ion This class models an ion.
Ion.IonType An enumerator of the supported ion types.
IonFactory This factory generates the expected ions from a peptide.
NeutralLoss This class represents a neutral loss.
Peptide This class models a peptide.
Protein This class models a protein.

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

Class and Description
Enzyme This class models an enzyme.

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

Class and Description
AminoAcidPattern.MatchingType The different types of amino acid matching.
Enzyme This class models an enzyme.
Ion This class models an ion.
Peptide This class models a peptide.

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

Class and Description
AminoAcidPattern An amino acid pattern is a sequence of amino acids.
AminoAcidPattern.MatchingType The different types of amino acid matching.
Enzyme This class models an enzyme.
Peptide This class models a peptide.

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

Class and Description
Ion.IonType An enumerator of the supported ion types.
Peptide This class models a peptide.

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

Class and Description
Ion.IonType An enumerator of the supported ion types.
Peptide This class models a peptide.

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

Class and Description
Ion.IonType An enumerator of the supported ion types.
Peptide This class models a peptide.
PTM This class models a post-translational modification.

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

Class and Description
AminoAcidPattern.MatchingType The different types of amino acid matching.
Ion.IonType An enumerator of the supported ion types.
Peptide This class models a peptide.
PTM This class models a post-translational modification.

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

Class and Description
AminoAcidPattern.MatchingType The different types of amino acid matching.
Ion This class models an ion.
Ion.IonType An enumerator of the supported ion types.
Peptide This class models a peptide.

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

Class and Description
AminoAcidPattern An amino acid pattern is a sequence of amino acids.
AminoAcidPattern.MatchingType The different types of amino acid matching.
Peptide This class models a peptide.
PTM This class models a post-translational modification.

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.quantification.reporterion

Class and Description
Sample This class models a proteomic sample.

Classes in com.compomics.util.experiment.biology used by com.compomics.util.gui

Class and Description
AminoAcidPattern An amino acid pattern is a sequence of amino acids.

Classes in com.compomics.util.experiment.biology used by com.compomics.util.gui.ptm

Class and Description
PTM This class models a post-translational modification.

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

Class and Description
Enzyme This class models an enzyme.

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

Class and Description
Ion This class models an ion.
Ion.IonType An enumerator of the supported ion types.
NeutralLoss This class represents a neutral loss.
Peptide This class models a peptide.

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

Class and Description
AminoAcidPattern.MatchingType The different types of amino acid matching.
Ion.IonType An enumerator of the supported ion types.
NeutralLoss This class represents a neutral loss.
Peptide This class models a peptide.
PTM This class models a post-translational modification.