Package | Description |
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com.compomics.util.experiment |
Gene factory classes.
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
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com.compomics.util.experiment.identification.identification_parameters |
Parameters settings for the spectrum identification algorithms.
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com.compomics.util.experiment.identification.identification_parameters.tool_specific |
Parameters settings for the search algorithms.
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com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
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com.compomics.util.experiment.identification.protein_inference.proteintree |
Protein sequence database indexing classes.
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com.compomics.util.gui.parameters.identification_parameters |
GUI classes for parameters, settings and preferences used for identification.
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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 |
ShotgunProtocol.getEnzyme()
Returns the enzyme used for digestion.
|
Modifier and Type | Method and Description |
---|---|
void |
ShotgunProtocol.setEnzyme(Enzyme enzyme)
Sets the enzyme used for digestion.
|
Modifier and Type | Method and Description |
---|---|
Enzyme |
EnzymeFactory.getEnzyme(String enzymeName)
Returns the enzyme corresponding to the given name.
|
static Enzyme |
EnzymeFactory.getUtilitiesEnzyme(String prideEnzymeName)
Tries to map the enzyme name given in the PRIDE file a utilities/OMSSA
enzyme.
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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.
|
static CvTerm |
EnzymeFactory.getEnzymeCvTerm(Enzyme enzyme)
Tries to convert the given enzyme to a CvTerm for use in mzIdentML etc.
|
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,
double pepMaxLength)
Returns the number of observable amino acids in the sequence.
|
boolean |
Protein.isEnzymaticPeptide(String peptideSequence,
Enzyme enzyme,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns true of the peptide is non-enzymatic, i.e., has one or more end
points that cannot be caused by the enzyme alone.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PeptideAssumptionFilter.validatePeptide(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
Enzyme enzyme)
Validates the peptide based on the peptide length, the share of X's in
the sequence and the allowed number of missed cleavages.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
static String |
MyriMatchParameters.enzymeMapping(Enzyme enzyme)
Tries to map the utilities enzyme to the enzymes supported by MyriMatch.
|
Modifier and Type | Method and Description |
---|---|
boolean |
ProteinMatch.hasEnzymaticPeptide(String accession,
Enzyme enzyme,
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.
|
Modifier and Type | Method and Description |
---|---|
Enzyme |
EnzymeSelectionDialog.getEnzyme()
Returns the selected enzyme.
|
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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