Package | Description |
---|---|
com.compomics.util.experiment.biology.proteins |
Classes related to proteins.
|
com.compomics.util.experiment.identification.features |
Classes for the generation of identification features.
|
com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
|
com.compomics.util.experiment.identification.protein_sequences.digestion |
This package contains classes used to digest protein sequences into peptides.
|
com.compomics.util.parameters.identification.search |
Identification parameters relative to the search.
|
com.compomics.util.parameters.identification.tool_specific |
Parameters settings for the search algorithms.
|
Modifier and Type | Method and Description |
---|---|
int |
Peptide.getNMissedCleavages(DigestionParameters digestionPreferences)
Returns the number of missed cleavages using the digestion preferences.
|
Modifier and Type | Method and Description |
---|---|
long[] |
IdentificationFeaturesGenerator.getNonEnzymatic(long proteinMatchKey,
DigestionParameters digestionPreferences)
Returns a list of non-enzymatic peptides for a given protein match.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PeptideAssumptionFilter.validatePeptide(Peptide peptide,
SequenceMatchingParameters sequenceMatchingPreferences,
DigestionParameters digestionPreferences)
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 |
---|---|
SequenceIterator |
IteratorFactory.getSequenceIterator(String sequence,
DigestionParameters digestionPreferences,
double massMin,
double massMax)
Returns a sequence iterator for the given protein sequence and digestion
preferences.
|
Modifier and Type | Method and Description |
---|---|
static DigestionParameters |
DigestionParameters.clone(DigestionParameters digestionParameters)
Clones the given parameters.
|
static DigestionParameters |
DigestionParameters.getDefaultParameters()
Returns default digestion parameters.
|
DigestionParameters |
SearchParameters.getDigestionParameters()
Returns the digestion preferences.
|
Modifier and Type | Method and Description |
---|---|
static DigestionParameters |
DigestionParameters.clone(DigestionParameters digestionParameters)
Clones the given parameters.
|
boolean |
DigestionParameters.isSameAs(DigestionParameters otherDigestionParameters)
Returns a boolean indicating whether these digestion parameters are the
same as the given other parameters.
|
void |
SearchParameters.setDigestionParameters(DigestionParameters digestionParameters)
Sets the digestion preferences.
|
Modifier and Type | Method and Description |
---|---|
static String |
MyriMatchParameters.enzymeMapping(DigestionParameters digestionPreferences)
Tries to map the utilities enzyme in the digestion preferences to the
enzymes supported by MyriMatch.
|
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