Class ModificationLocalizationMapper
java.lang.Object
com.compomics.util.experiment.identification.modification.mapping.ModificationLocalizationMapper
public class ModificationLocalizationMapper extends Object
Function attempting to map modification localization based on their type.
- Author:
- Marc Vaudel, Harald Barsnes
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Field Summary
Fields Modifier and Type Field Description static double
MASS_PER_AA
The mass added per amino acid as part of the reference mass when converting Dalton tolerances to ppm. -
Constructor Summary
Constructors Constructor Description ModificationLocalizationMapper()
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Method Summary
Modifier and Type Method Description static void
modificationLocalization(Peptide peptide, HashMap<Integer,ArrayList<String>> expectedNames, HashMap<ModificationMatch,ArrayList<String>> modNames, IdentificationParameters identificationParameters, IdfileReader idfileReader, ModificationProvider modificationProvider)
Makes an initial modification mapping based on the search engine results and the compatibility to the searched modifications.
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Field Details
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MASS_PER_AA
public static final double MASS_PER_AAThe mass added per amino acid as part of the reference mass when converting Dalton tolerances to ppm.- See Also:
- Constant Field Values
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Constructor Details
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ModificationLocalizationMapper
public ModificationLocalizationMapper()
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Method Details
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modificationLocalization
public static void modificationLocalization(Peptide peptide, HashMap<Integer,ArrayList<String>> expectedNames, HashMap<ModificationMatch,ArrayList<String>> modNames, IdentificationParameters identificationParameters, IdfileReader idfileReader, ModificationProvider modificationProvider)Makes an initial modification mapping based on the search engine results and the compatibility to the searched modifications.- Parameters:
peptide
- The peptide where the modification was found.expectedNames
- The expected modifications at each site.modNames
- The possible names for every modification match.identificationParameters
- The identification parameters.idfileReader
- The identification file reader.modificationProvider
- The modification provider to use.
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