Uses of Class
com.compomics.util.experiment.biology.enzymes.Enzyme

Packages that use Enzyme

Package	Description
com.compomics.cli.enzymes	Command line for the handling of enzymes.
com.compomics.util.experiment.biology.enzymes	Classes related to enzymes.
com.compomics.util.experiment.biology.proteins	Classes related to proteins.
com.compomics.util.experiment.identification.protein_sequences.digestion.iterators	This package contains implementations of the SequenceIterator interface.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.
com.compomics.util.gui.parameters.identification.pride	Dialogs for pride reprocessing parameters.
com.compomics.util.parameters.identification.search	Identification parameters relative to the search.
com.compomics.util.protein	Classes concerning useful Objects and their operations for modeling and handling proteins.

Uses of Enzyme in com.compomics.cli.enzymes

Methods in com.compomics.cli.enzymes that return Enzyme

Modifier and Type	Method	Description
Enzyme	EnzymesCLIInputBean.getEnzymeToAdd()	Returns the enzyme to add.

Uses of Enzyme in com.compomics.util.experiment.biology.enzymes

Methods in com.compomics.util.experiment.biology.enzymes that return Enzyme

Modifier and Type	Method	Description
Enzyme	EnzymeFactory.getEnzyme(String enzymeName)	Returns the enzyme corresponding to the given name.
Enzyme	EnzymeFactory.getUtilitiesEnzyme(String cvTermAccession)	Returns the enzyme associated to the given cvTerm.

Methods in com.compomics.util.experiment.biology.enzymes that return types with arguments of type Enzyme

Modifier and Type	Method	Description
ArrayList<Enzyme>	EnzymeFactory.getEnzymes()	Get the imported enzymes.

Methods in com.compomics.util.experiment.biology.enzymes with parameters of type Enzyme

Modifier and Type	Method	Description
void	EnzymeFactory.addEnzyme(Enzyme enzyme)	Adds an enzyme in the factory.
boolean	Enzyme.equals(Enzyme otherEnzyme)	Returns true of the two enzymes are identical.

Uses of Enzyme in com.compomics.util.experiment.biology.proteins

Methods in com.compomics.util.experiment.biology.proteins with parameters of type Enzyme

Modifier and Type	Method	Description
int	Peptide.getNMissedCleavages(Enzyme enzyme)	Returns the number of missed cleavages using the specified enzyme.

Uses of Enzyme in com.compomics.util.experiment.identification.protein_sequences.digestion.iterators

Constructors in com.compomics.util.experiment.identification.protein_sequences.digestion.iterators with parameters of type Enzyme

Modifier	Constructor	Description
	SpecificSingleEnzymeCombinationIterator(ProteinIteratorUtils proteinIteratorUtils, String proteinSequence, Enzyme enzyme, int nMissedCleavages, double massMin, double massMax)	Constructor.
	SpecificSingleEnzymeIterator(ProteinIteratorUtils proteinIteratorUtils, String proteinSequence, Enzyme enzyme, int nMissedCleavages, double massMin, double massMax)	Constructor.

Uses of Enzyme in com.compomics.util.experiment.identification.utils

Methods in com.compomics.util.experiment.identification.utils with parameters of type Enzyme

Modifier and Type	Method	Description
static int	PeptideUtils.getNEnzymaticTermini(int peptideStart, int peptideEnd, String proteinSequence, Enzyme enzyme)	Returns the number of enzymatic termini for the given peptide coordinates and enzyme on this protein.
static boolean	PeptideUtils.isCtermEnzymatic(int peptideStart, int peptideEnd, String proteinSequence, Enzyme enzyme)	Returns whether the N-terminus of the given peptide is enzymatic at the given coordinates and enzyme on this protein.
static boolean	PeptideUtils.isNtermEnzymatic(int peptideStart, int peptideEnd, String proteinSequence, Enzyme enzyme)	Returns whether the N-terminus of the given peptide is enzymatic at the given coordinates and enzyme on this protein.

Method parameters in com.compomics.util.experiment.identification.utils with type arguments of type Enzyme

Modifier and Type	Method	Description
static int	ProteinUtils.getNCleavageSites(String sequence, ArrayList<Enzyme> enzymes)	Returns the number of cleavage sites.
static int[]	ProteinUtils.getObservableAminoAcids(String sequence, ArrayList<Enzyme> enzymes, double pepMaxLength)	Returns the observable amino acids in the sequence when using the given enzymes with the given maximal peptide length.
static int	ProteinUtils.getObservableLength(String sequence, ArrayList<Enzyme> enzymes, double pepMaxLength)	Returns the number of observable amino acids in the sequence.
static boolean	PeptideUtils.isEnzymatic(Peptide peptide, SequenceProvider sequenceProvider, ArrayList<Enzyme> enzymes)	Returns a boolean indicating whether the peptide is enzymatic in at least one protein using one of the given enzymes.
static boolean	PeptideUtils.isEnzymatic(Peptide peptide, String proteinAccession, String proteinSequence, ArrayList<Enzyme> enzymes)	Returns a boolean indicating whether the peptide is enzymatic using one of the given enzymes.

Uses of Enzyme in com.compomics.util.gui.parameters.identification.pride

Methods in com.compomics.util.gui.parameters.identification.pride that return Enzyme

Modifier and Type	Method	Description
Enzyme	EnzymeParametersDialog.getEnzyme()	Returns the selected enzyme.

Uses of Enzyme in com.compomics.util.parameters.identification.search

Methods in com.compomics.util.parameters.identification.search that return types with arguments of type Enzyme

Modifier and Type	Method	Description
ArrayList<Enzyme>	DigestionParameters.getEnzymes()	Returns the enzymes used for digestion in a list.

Methods in com.compomics.util.parameters.identification.search with parameters of type Enzyme

Modifier and Type	Method	Description
void	DigestionParameters.addEnzyme(Enzyme enzyme)	Adds an enzyme.

Method parameters in com.compomics.util.parameters.identification.search with type arguments of type Enzyme

Modifier and Type	Method	Description
void	DigestionParameters.setEnzymes(ArrayList<Enzyme> enzymes)	Sets the enzymes used for digestion.

Uses of Enzyme in com.compomics.util.protein

Constructors in com.compomics.util.protein with parameters of type Enzyme

Modifier	Constructor	Description
	Enzyme(Enzyme enzyme, int maxMissedCleavages)	Creates a new Enzyme from a com.compomics.util.experiment.biology.Enzyme enzyme and the maximum number of missed cleavages.