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.experiment.identification.matches This package contains experiment classes releated to matches. 
com.compomics.util.experiment.identification.protein_inference.proteintree   
com.compomics.util.gui.searchsettings   
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.
 Enzyme EnzymeFactory.getUtilitiesEnzyme(String prideEnzymeName)
          Tries to map the enzyme name given in the PRIDE file a utilities/OMSSA enzyme.
 

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.
 boolean Enzyme.equals(Enzyme otherEnzyme)
          Returns true of the two enzymes are identical.
 int Protein.getNCleavageSites(Enzyme enzyme)
          Returns the number of cleavage sites.
 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.getObservableLength(Enzyme enzyme, int pepMaxLength)
          Returns the number of observable amino acids in the sequence.
 boolean Protein.isEnzymaticPeptide(String peptideSequence, Enzyme enzyme, ProteinMatch.MatchingType matchingType, Double massTolerance)
          Returns true of the peptide is non-enzymatic, i.e., has one or more end points that cannot be caused by the enzyme alone.
 

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.experiment.identification.matches
 

Methods in com.compomics.util.experiment.identification.matches with parameters of type Enzyme
 boolean ProteinMatch.hasEnzymaticPeptide(String accession, Enzyme enzyme, ProteinMatch.MatchingType matchingType, Double massTolerance)
          Indicates whether the protein group has an enzymatic peptide when considering the given accession as main accession.
 

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

Methods in com.compomics.util.experiment.identification.protein_inference.proteintree with parameters of type Enzyme
 void ProteinTree.initiateTree(int initialTagSize, int maxNodeSize, int maxPeptideSize, Enzyme enzyme, WaitingHandler waitingHandler, boolean printExpectedImportTime)
          Initiates the tree.
 

Uses of Enzyme in com.compomics.util.gui.searchsettings
 

Methods in com.compomics.util.gui.searchsettings that return Enzyme
 Enzyme EnzymeSelectionDialog.getEnzyme()
          Returns the selected enzyme.
 

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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