Package com.compomics.util.experiment.biology

This package contains experiement classes related to biological entities.

See: Description

Class Summary

Class	Description
AminoAcid	Class representing amino acids.
AminoAcidPattern	An amino acid pattern is a sequence of amino acids.
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.
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.
MutationFactory	This class holds the all possible one-letter peptide sequence mutations.
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.

Enum Summary

Enum	Description
AminoAcidPattern.MatchingType	The different types of amino acid matching.
Ion.IonType	An enumerator of the supported ion types.

Package com.compomics.util.experiment.biology Description

This package contains experiement classes related to biological entities.