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

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

Package	Description
com.compomics.util.experiment	Gene factory classes.
com.compomics.util.experiment.biology	Experiment classes related to biological entities.
com.compomics.util.experiment.biology.aminoacids	The amino acid classes.
com.compomics.util.experiment.biology.atoms	The atom classes.
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
com.compomics.util.experiment.biology.mutations	Experiment classes related to mutations.
com.compomics.util.experiment.identification	Experiment classes related to identifications.
com.compomics.util.experiment.identification.amino_acid_tags	Amino Acid Tag classes.
com.compomics.util.experiment.identification.amino_acid_tags.matchers	Tag matching classes.
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.identification_parameters.tool_specific	Parameters settings for the search algorithms.
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.experiment.identification.protein_inference.proteintree	Protein sequence database indexing classes.
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.psm_scoring.psm_scores	Main PTM scoring classes.
com.compomics.util.experiment.identification.ptm	Additional PSM scoring classes.
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_annotation.spectrum_annotators	Spectrum annotation.
com.compomics.util.experiment.identification.spectrum_assumptions	Implementations of the SpectrumIdentificationAssumption.
com.compomics.util.experiment.quantification.reporterion	Experiment classes related to reporter ions.
com.compomics.util.gui	Basic GUI classes.
com.compomics.util.gui.atoms	Atoms GUI dialogs.
com.compomics.util.gui.parameters.identification_parameters	GUI classes for parameters, settings and preferences used for identification.
com.compomics.util.gui.ptm	PTM GUI dialogs.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

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

Class and Description
Enzyme This class models an enzyme.
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.
AminoAcidSequence This class represents a series of amino acids with associated modifications.
Atom This interface contains information about atoms.
AtomChain A chain of atoms.
AtomImpl Class for a specific atom.
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.
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
AminoAcid Class representing amino acids.
AtomChain A chain of atoms.
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.biology.mutations

Class and Description
AminoAcid Class representing amino acids.

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

Class and Description
Peptide This class models a peptide.

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

Class and Description
AminoAcid Class representing amino acids.
AminoAcidPattern An amino acid pattern is a sequence of amino acids.
AminoAcidSequence This class represents a series of amino acids with associated modifications.
PTM This class models a post-translational modification.

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

Class and Description
AminoAcid Class representing amino acids.
Peptide This class models a peptide.

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

Class and Description
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.identification_parameters

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

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

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
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
AminoAcidSequence This class represents a series of amino acids with associated modifications.
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.protein_sequences

Class and Description
Protein This class models a protein.

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

Class and Description
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
Peptide This class models a peptide.

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

Class and Description
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
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_annotation

Class and Description
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.

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

Class and Description
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.spectrum_assumptions

Class and Description
Peptide This class models a peptide.

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.atoms

Class and Description
Atom This interface contains information about atoms.
AtomChain A chain of atoms.

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

Class and Description
Enzyme This class models an enzyme.
NeutralLoss This class represents a neutral loss.

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.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.