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