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

Packages that use Enzyme
com.compomics.util.experiment.biology This package contains experiement classes related to biological entities. 
com.compomics.util.experiment.identification This package contains experiment classes related to identifications. 
com.compomics.util.protein The classes in this package concern useful Objects and their operations for modelling and handling proteins. 
 

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

Methods in com.compomics.util.experiment.biology that return Enzyme
 Enzyme EnzymeFactory.getEnzyme(String enzymeName)
          Returns the enzyme corresponding to the given name.
 

Methods in com.compomics.util.experiment.biology that return types with arguments of type Enzyme
 ArrayList<Enzyme> EnzymeFactory.getEnzymes()
          Get the imported enzymes.
 

Methods in com.compomics.util.experiment.biology with parameters of type Enzyme
 void EnzymeFactory.addEnzyme(Enzyme enzyme)
          Adds an enzyme in the factory.
 int Peptide.getNMissedCleavages(Enzyme enzyme)
          Returns the number of missed cleavages using the specified enzyme.
static int Peptide.getNMissedCleavages(String sequence, Enzyme enzyme)
          Returns the number of missed cleavages using the specified enzyme for the given sequence.
 int Protein.getNPossiblePeptides(Enzyme enzyme)
          Returns the number of possible peptides (not accounting PTMs nor missed cleavages) with the selected enzyme.
 int Protein.getObservableLength(Enzyme enzyme, int pepMaxLength)
          Returns the number of observable amino acids of the sequence.
 

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

Methods in com.compomics.util.experiment.identification that return Enzyme
 Enzyme SearchParameters.getEnzyme()
          Returns the enzyme used for digestion.
 

Methods in com.compomics.util.experiment.identification with parameters of type Enzyme
 void SearchParameters.setEnzyme(Enzyme enzyme)
          Sets the enzyme used for digestion.
 

Uses of Enzyme in com.compomics.util.protein
 

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



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