Class ModificationMassMapper
java.lang.Object
com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
public class ModificationMassMapper extends Object
Function inferring the mass of a modification based on the search engine
used.
- Author:
- Marc Vaudel, Harald Barsnes
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Constructor Summary
Constructors Constructor Description ModificationMassMapper()
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Method Summary
Modifier and Type Method Description static double
getMass(String searchEngineModificationName, IdfileReader idfileReader, SearchParameters searchParameters, ModificationProvider modificationProvider)
Returns the mass indicated by the identification algorithm for the given modification.static double
getMassAndromeda(String searchEngineModificationName, ModificationProvider modificationProvider, SearchParameters searchParameters)
Returns the mass indicated by the Andromeda for the given modification.static double
getMassByMass(String searchEngineModificationName)
Returns the mass indicated by the identification algorithm for the given modification.static double
getMassByName(String searchEngineModificationName, ModificationProvider modificationProvider)
Returns the mass indicated by the identification algorithm for the given modification.static double
getMassOmssa(String searchEngineModificationName, ModificationProvider modificationProvider, SearchParameters searchParameters)
Returns the mass indicated by the OMSSA for the given modification.
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Constructor Details
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ModificationMassMapper
public ModificationMassMapper()
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Method Details
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getMass
public static double getMass(String searchEngineModificationName, IdfileReader idfileReader, SearchParameters searchParameters, ModificationProvider modificationProvider)Returns the mass indicated by the identification algorithm for the given modification.- Parameters:
searchEngineModificationName
- The name according to the identification file reader.idfileReader
- The identification file reader.searchParameters
- The search parameters.modificationProvider
- The modification provider to use.- Returns:
- The mass of the modification.
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getMassByMass
Returns the mass indicated by the identification algorithm for the given modification.- Parameters:
searchEngineModificationName
- The name according to the identification file reader.- Returns:
- The mass of the modification.
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getMassByName
public static double getMassByName(String searchEngineModificationName, ModificationProvider modificationProvider)Returns the mass indicated by the identification algorithm for the given modification.- Parameters:
searchEngineModificationName
- The name according to the identification file reader.modificationProvider
- The modification provider to use.- Returns:
- The mass of the modification.
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getMassOmssa
public static double getMassOmssa(String searchEngineModificationName, ModificationProvider modificationProvider, SearchParameters searchParameters)Returns the mass indicated by the OMSSA for the given modification.- Parameters:
searchEngineModificationName
- The name according to the identification file reader.modificationProvider
- The modification provider to use.searchParameters
- The search parameters.- Returns:
- The mass of the modification.
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getMassAndromeda
public static double getMassAndromeda(String searchEngineModificationName, ModificationProvider modificationProvider, SearchParameters searchParameters)Returns the mass indicated by the Andromeda for the given modification.- Parameters:
searchEngineModificationName
- The name according to the identification file reader.modificationProvider
- The modification provider to use.searchParameters
- The search parameters.- Returns:
- The mass of the modification.
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