public class ModificationNameMapper extends Object
Modifier and Type | Field and Description |
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static double |
MOD_MASS_TOLERANCE
The mass tolerance to be used to match modifications from search engines
and expected modifications.
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Constructor and Description |
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ModificationNameMapper() |
Modifier and Type | Method and Description |
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static HashMap<Integer,HashSet<String>> |
getPossibleModificationNames(Peptide peptide,
ModificationMatch modificationMatch,
IdfileReader idfileReader,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible modification names.
|
static HashMap<Integer,HashSet<String>> |
getPossibleModificationNamesAndromeda(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible Andromeda modification names.
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static HashMap<Integer,HashSet<String>> |
getPossibleModificationNamesByMass(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible modifications names by mass.
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static HashMap<Integer,HashSet<String>> |
getPossibleModificationNamesByName(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible modifications by name.
|
static HashMap<Integer,HashSet<String>> |
getPossibleModificationNamesOmssa(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible OMSSA modification names.
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public static final double MOD_MASS_TOLERANCE
public static HashMap<Integer,HashSet<String>> getPossibleModificationNames(Peptide peptide, ModificationMatch modificationMatch, IdfileReader idfileReader, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
peptide
- the peptidemodificationMatch
- the modification matchidfileReader
- the ID file readersearchParameters
- the search parameterssequenceMatchingParameters
- the sequence matching parameterssequenceProvider
- the sequence providermodificationProvider
- the modification providerpublic static HashMap<Integer,HashSet<String>> getPossibleModificationNamesByMass(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
peptide
- the peptidemodificationMatch
- the modification matchsearchParameters
- the search parameterssequenceMatchingParameters
- the sequence matching parameterssequenceProvider
- the sequence providermodificationProvider
- the modification providerpublic static HashMap<Integer,HashSet<String>> getPossibleModificationNamesByName(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
peptide
- the peptidemodificationMatch
- the modification matchsearchParameters
- the search parameterssequenceMatchingParameters
- the sequence matching parameterssequenceProvider
- the sequence providermodificationProvider
- the modification providerpublic static HashMap<Integer,HashSet<String>> getPossibleModificationNamesOmssa(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
peptide
- the peptidemodificationMatch
- the modification matchsearchParameters
- the search parameterssequenceMatchingParameters
- the sequence matching parameterssequenceProvider
- the sequence providermodificationProvider
- the modification providerpublic static HashMap<Integer,HashSet<String>> getPossibleModificationNamesAndromeda(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
peptide
- the peptidemodificationMatch
- the modification matchsearchParameters
- the search parameterssequenceMatchingParameters
- the sequence matching parameterssequenceProvider
- the sequence providermodificationProvider
- the modification providerCopyright © 2021. All rights reserved.