Package | Description |
---|---|
com.compomics.cli.enzymes |
Command line for the handling of enzymes.
|
com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.identification.identification_parameters |
Parameters settings for the spectrum identification algorithms.
|
com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
|
com.compomics.util.experiment.identification.protein_inference.proteintree |
Protein sequence database indexing classes.
|
com.compomics.util.experiment.identification.protein_sequences.digestion.iterators |
This package contains implementations of the SequenceIterator interface.
|
com.compomics.util.gui.parameters.identification_parameters |
GUI classes for parameters, settings and preferences used for identification.
|
com.compomics.util.preferences |
Utilities preferences classes.
|
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 |
---|---|
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.
|
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.
|
int |
Peptide.getNMissedCleavages(Enzyme enzyme)
Returns the number of missed cleavages using the specified enzyme.
|
boolean |
Protein.isEnzymaticPeptide(String peptideSequence,
Enzyme enzyme,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns true if the peptide is enzymatic, i.e., both termini can be
generated by the enzyme used.
|
Modifier and Type | Method and Description |
---|---|
int |
Protein.getNCleavageSites(ArrayList<Enzyme> enzymes)
Returns the number of cleavage sites.
|
int[] |
Protein.getObservableAminoAcids(ArrayList<Enzyme> enzymes,
double pepMaxLength)
Returns the observable amino acids in the sequence when using the given
enzymes with the given maximal peptide length.
|
int |
Protein.getObservableLength(ArrayList<Enzyme> enzymes,
double pepMaxLength)
Returns the number of observable amino acids in the sequence.
|
boolean |
Protein.isEnzymaticPeptide(String peptideSequence,
ArrayList<Enzyme> enzymes,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns true if the peptide is enzymatic, i.e., both termini can be
generated by one of the enzymes used.
|
Modifier and Type | Method and Description |
---|---|
Enzyme |
SearchParameters.getEnzyme()
Deprecated.
use the PTM Digestion preferences instead.
|
Modifier and Type | Method and Description |
---|---|
boolean |
ProteinMatch.hasEnzymaticPeptide(String accession,
ArrayList<Enzyme> enzymes,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the protein group has an enzymatic peptide when
considering the given accession as main accession.
|
Modifier and Type | Method and Description |
---|---|
void |
ProteinTree.initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean printExpectedImportTime,
boolean displayProgress,
int nThreads)
Initiates the tree.
|
Constructor and 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.
|
Modifier and Type | Method and Description |
---|---|
Enzyme |
EnzymeSelectionDialog.getEnzyme()
Returns the selected enzyme.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Enzyme> |
DigestionPreferences.getEnzymes()
Returns the enzymes used for digestion in a list.
|
Modifier and Type | Method and Description |
---|---|
void |
DigestionPreferences.addEnzyme(Enzyme enzyme)
Adds an enzyme.
|
Modifier and Type | Method and Description |
---|---|
void |
DigestionPreferences.setEnzymes(ArrayList<Enzyme> enzymes)
Sets the enzymes used for digestion.
|
Constructor and 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.
|
Copyright © 2019. All rights reserved.