Class ModificationNameMapper
java.lang.Object
com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
public class ModificationNameMapper extends Object
Functions mapping search engine modifications to utilities by name.
- Author:
- Marc Vaudel, Harald Barsnes
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Field Summary
Fields Modifier and Type Field Description static double
MOD_MASS_TOLERANCE
The mass tolerance to be used to match modifications from search engines and expected modifications. -
Constructor Summary
Constructors Constructor Description ModificationNameMapper()
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Method Summary
Modifier and Type Method Description 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.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.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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Field Details
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MOD_MASS_TOLERANCE
public static final double MOD_MASS_TOLERANCEThe mass tolerance to be used to match modifications from search engines and expected modifications. 0.01 by default, the mass resolution in X!Tandem result files.- See Also:
- Constant Field Values
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Constructor Details
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ModificationNameMapper
public ModificationNameMapper()
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Method Details
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getPossibleModificationNames
public 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.- Parameters:
peptide
- the peptidemodificationMatch
- the modification matchidfileReader
- the ID file readersearchParameters
- the search parameterssequenceMatchingParameters
- the sequence matching parameterssequenceProvider
- the sequence providermodificationProvider
- the modification provider- Returns:
- the possible modification names
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getPossibleModificationNamesByMass
public 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.- Parameters:
peptide
- the peptidemodificationMatch
- the modification matchsearchParameters
- the search parameterssequenceMatchingParameters
- the sequence matching parameterssequenceProvider
- the sequence providermodificationProvider
- the modification provider- Returns:
- the possible modifications names by mass
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getPossibleModificationNamesByName
public static HashMap<Integer,HashSet<String>> getPossibleModificationNamesByName(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)Returns the possible modifications by name.- Parameters:
peptide
- the peptidemodificationMatch
- the modification matchsearchParameters
- the search parameterssequenceMatchingParameters
- the sequence matching parameterssequenceProvider
- the sequence providermodificationProvider
- the modification provider- Returns:
- the possible modifications by name
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getPossibleModificationNamesOmssa
public static HashMap<Integer,HashSet<String>> getPossibleModificationNamesOmssa(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)Returns the possible OMSSA modification names.- Parameters:
peptide
- the peptidemodificationMatch
- the modification matchsearchParameters
- the search parameterssequenceMatchingParameters
- the sequence matching parameterssequenceProvider
- the sequence providermodificationProvider
- the modification provider- Returns:
- the possible OMSSA modification names
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getPossibleModificationNamesAndromeda
public static HashMap<Integer,HashSet<String>> getPossibleModificationNamesAndromeda(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)Returns the possible Andromeda modification names.- Parameters:
peptide
- the peptidemodificationMatch
- the modification matchsearchParameters
- the search parameterssequenceMatchingParameters
- the sequence matching parameterssequenceProvider
- the sequence providermodificationProvider
- the modification provider- Returns:
- the possible Andromeda modification names
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