Package | Description |
---|---|
com.compomics.cli.enzymes |
Command line for the handling of enzymes.
|
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.
|
com.compomics.util.experiment.identification.utils |
This package contains utilities classes to handle identification objects.
|
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.
|
Modifier and Type | Method and Description |
---|---|
Enzyme |
EnzymesCLIInputBean.getEnzymeToAdd()
Returns the enzyme to add.
|
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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Enzyme |
EnzymeFactory.getUtilitiesEnzyme(String cvTermAccession)
Returns the enzyme associated to the given cvTerm.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Enzyme> |
EnzymeFactory.getEnzymes()
Get the imported enzymes.
|
Modifier and Type | Method and Description |
---|---|
void |
EnzymeFactory.addEnzyme(Enzyme enzyme)
Adds an enzyme in the factory.
|
boolean |
Enzyme.equals(Enzyme otherEnzyme)
Returns true of the two enzymes are identical.
|
Modifier and Type | Method and Description |
---|---|
int |
Peptide.getNMissedCleavages(Enzyme enzyme)
Returns the number of missed cleavages using the specified enzyme.
|
Constructor and Description |
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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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
Enzyme |
EnzymeParametersDialog.getEnzyme()
Returns the selected enzyme.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Enzyme> |
DigestionParameters.getEnzymes()
Returns the enzymes used for digestion in a list.
|
Modifier and Type | Method and Description |
---|---|
void |
DigestionParameters.addEnzyme(Enzyme enzyme)
Adds an enzyme.
|
Modifier and Type | Method and Description |
---|---|
void |
DigestionParameters.setEnzymes(ArrayList<Enzyme> enzymes)
Sets the enzymes used for digestion.
|
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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