Package | Description |
---|---|
com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
|
com.compomics.util.experiment.identification.identification_parameters |
Parameters settings for the spectrum identification algorithms.
|
com.compomics.util.experiment.identification.identification_parameters.tool_specific |
Parameters settings for the search algorithms.
|
com.compomics.util.experiment.identification.protein_sequences.digestion |
This package contains classes used to digest protein sequences into peptides.
|
com.compomics.util.preferences |
Utilities preferences classes.
|
Modifier and Type | Method and Description |
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Integer |
Peptide.getNMissedCleavages(DigestionPreferences digestionPreferences)
Returns the number of missed cleavages using the digestion preferences.
|
Modifier and Type | Method and Description |
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boolean |
PeptideAssumptionFilter.validatePeptide(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
DigestionPreferences 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 |
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DigestionPreferences |
SearchParameters.getDigestionPreferences()
Returns the digestion preferences.
|
Modifier and Type | Method and Description |
---|---|
void |
SearchParameters.setDigestionPreferences(DigestionPreferences digestionPreferences)
Sets the digestion preferences.
|
Modifier and Type | Method and Description |
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static String |
MyriMatchParameters.enzymeMapping(DigestionPreferences digestionPreferences)
Tries to map the utilities enzyme in the digestion preferences to the
enzymes supported by MyriMatch.
|
Modifier and Type | Method and Description |
---|---|
SequenceIterator |
IteratorFactory.getSequenceIterator(String sequence,
DigestionPreferences digestionPreferences,
double massMin,
double massMax)
Returns a sequence iterator for the given protein sequence and digestion
preferences.
|
Modifier and Type | Method and Description |
---|---|
static DigestionPreferences |
DigestionPreferences.clone(DigestionPreferences digestionPreferences)
Clones the given preferences.
|
static DigestionPreferences |
DigestionPreferences.getDefaultPreferences()
Returns default digestion preferences.
|
Modifier and Type | Method and Description |
---|---|
static DigestionPreferences |
DigestionPreferences.clone(DigestionPreferences digestionPreferences)
Clones the given preferences.
|
boolean |
DigestionPreferences.isSameAs(DigestionPreferences otherDigestionPreferences)
Returns a boolean indicating whether these digestion preferences are the
same as the given other preferences.
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