Uses of Class
com.compomics.util.parameters.identification.search.DigestionParameters
Package | Description |
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com.compomics.util.experiment.biology.proteins |
Classes related to proteins.
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com.compomics.util.experiment.identification.features |
Classes for the generation of identification features.
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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.protein_sequences.digestion |
This package contains classes used to digest protein sequences into peptides.
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com.compomics.util.parameters.identification.search |
Identification parameters relative to the search.
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com.compomics.util.parameters.identification.tool_specific |
Parameters settings for the search algorithms.
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Uses of DigestionParameters in com.compomics.util.experiment.biology.proteins
Methods in com.compomics.util.experiment.biology.proteins with parameters of type DigestionParameters Modifier and Type Method Description int
Peptide. getNMissedCleavages(DigestionParameters digestionPreferences)
Returns the number of missed cleavages using the digestion preferences. -
Uses of DigestionParameters in com.compomics.util.experiment.identification.features
Methods in com.compomics.util.experiment.identification.features with parameters of type DigestionParameters Modifier and Type Method Description long[]
IdentificationFeaturesGenerator. getNonEnzymatic(long proteinMatchKey, DigestionParameters digestionPreferences)
Returns a list of non-enzymatic peptides for a given protein match. -
Uses of DigestionParameters in com.compomics.util.experiment.identification.filtering
Methods in com.compomics.util.experiment.identification.filtering with parameters of type DigestionParameters Modifier and Type Method 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. -
Uses of DigestionParameters in com.compomics.util.experiment.identification.protein_sequences.digestion
Methods in com.compomics.util.experiment.identification.protein_sequences.digestion with parameters of type DigestionParameters Modifier and Type Method Description SequenceIterator
IteratorFactory. getSequenceIterator(String sequence, DigestionParameters digestionPreferences, double massMin, double massMax)
Returns a sequence iterator for the given protein sequence and digestion preferences. -
Uses of DigestionParameters in com.compomics.util.parameters.identification.search
Methods in com.compomics.util.parameters.identification.search that return DigestionParameters Modifier and Type Method 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.Methods in com.compomics.util.parameters.identification.search with parameters of type DigestionParameters Modifier and Type Method 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. -
Uses of DigestionParameters in com.compomics.util.parameters.identification.tool_specific
Methods in com.compomics.util.parameters.identification.tool_specific with parameters of type DigestionParameters Modifier and Type Method Description static String
MyriMatchParameters. enzymeMapping(DigestionParameters digestionPreferences)
Tries to map the utilities enzyme in the digestion preferences to the enzymes supported by MyriMatch.