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Packages that use Enzyme | |
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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 |
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Methods in com.compomics.util.experiment.biology that return Enzyme | |
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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 | |
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ArrayList<Enzyme> |
EnzymeFactory.getEnzymes()
Get the imported enzymes. |
Methods in com.compomics.util.experiment.biology with parameters of type Enzyme | |
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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 |
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Methods in com.compomics.util.experiment.identification that return Enzyme | |
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Enzyme |
SearchParameters.getEnzyme()
Returns the enzyme used for digestion. |
Methods in com.compomics.util.experiment.identification with parameters of type Enzyme | |
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void |
SearchParameters.setEnzyme(Enzyme enzyme)
Sets the enzyme used for digestion. |
Uses of Enzyme in com.compomics.util.experiment.identification.matches |
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Methods in com.compomics.util.experiment.identification.matches with parameters of type Enzyme | |
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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 |
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Methods in com.compomics.util.experiment.identification.protein_inference.proteintree with parameters of type Enzyme | |
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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 |
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Methods in com.compomics.util.gui.searchsettings that return Enzyme | |
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Enzyme |
EnzymeSelectionDialog.getEnzyme()
Returns the selected enzyme. |
Uses of Enzyme in com.compomics.util.protein |
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Constructors in com.compomics.util.protein with parameters of type Enzyme | |
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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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