Package | Description |
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com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.experiment.identification.protein_inference.proteintree | |
com.compomics.util.protein |
The classes in this package concern useful Objects and their
operations for modelling and handling proteins.
|
Modifier and Type | Method and Description |
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Enzyme |
EnzymeFactory.getEnzyme(String enzymeName)
Returns the enzyme corresponding to the given name.
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Modifier and Type | Method and Description |
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ArrayList<Enzyme> |
EnzymeFactory.getEnzymes()
Get the imported enzymes.
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Modifier and Type | Method and Description |
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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 |
Peptide.getNMissedCleavages(Enzyme enzyme)
Returns the number of missed cleavages using the specified enzyme.
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static int |
Peptide.getNMissedCleavages(String sequence,
Enzyme enzyme)
Returns the number of missed cleavages using the specified enzyme for the
given sequence.
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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.
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boolean |
Protein.isEnzymaticPeptide(String peptideSequence,
Enzyme enzyme)
Returns true of the peptide is non-enzymatic, i.e., has one or more end
points that cannot be caused by the enzyme alone.
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Modifier and Type | Method and Description |
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Enzyme |
SearchParameters.getEnzyme()
Returns the enzyme used for digestion.
|
Modifier and Type | Method and Description |
---|---|
void |
SearchParameters.setEnzyme(Enzyme enzyme)
Sets the enzyme used for digestion.
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Modifier and Type | Method and Description |
---|---|
void |
ProteinTree.initiateTree(int initialTagSize,
int maxNodeSize,
Enzyme enzyme,
WaitingHandler waitingHandler)
Initiates the tree.
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Constructor and Description |
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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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