Uses of Interface
com.compomics.util.experiment.biology.modifications.ModificationProvider
Package | Description |
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com.compomics.util.experiment.biology.modifications | |
com.compomics.util.experiment.identification.modification.mapping |
Mapping between search engine and Utilities modifications.
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com.compomics.util.experiment.identification.peptide_inference |
Classes related to peptide inference.
|
com.compomics.util.experiment.identification.peptide_shaker |
Experiment classes used in PeptideShaker calculations.
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com.compomics.util.experiment.io.identification.writers |
Writer for identification results.
|
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Uses of ModificationProvider in com.compomics.util.experiment.biology.modifications
Classes in com.compomics.util.experiment.biology.modifications that implement ModificationProvider Modifier and Type Class Description class
ModificationFactory
This factory will load Modification from an XML file and provide them on demand as standard class. -
Uses of ModificationProvider in com.compomics.util.experiment.identification.modification.mapping
Methods in com.compomics.util.experiment.identification.modification.mapping with parameters of type ModificationProvider Modifier and Type Method Description static double
ModificationMassMapper. getMass(String searchEngineModificationName, IdfileReader idfileReader, SearchParameters searchParameters, ModificationProvider modificationProvider)
Returns the mass indicated by the identification algorithm for the given modification.static double
ModificationMassMapper. getMassAndromeda(String searchEngineModificationName, ModificationProvider modificationProvider, SearchParameters searchParameters)
Returns the mass indicated by the Andromeda for the given modification.static double
ModificationMassMapper. getMassByName(String searchEngineModificationName, ModificationProvider modificationProvider)
Returns the mass indicated by the identification algorithm for the given modification.static double
ModificationMassMapper. getMassOmssa(String searchEngineModificationName, ModificationProvider modificationProvider, SearchParameters searchParameters)
Returns the mass indicated by the OMSSA for the given modification.static HashMap<Integer,HashSet<String>>
ModificationNameMapper. 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>>
ModificationNameMapper. getPossibleModificationNamesAndromeda(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
Returns the possible Andromeda modification names.static HashMap<Integer,HashSet<String>>
ModificationNameMapper. 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>>
ModificationNameMapper. getPossibleModificationNamesByName(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
Returns the possible modifications by name.static HashMap<Integer,HashSet<String>>
ModificationNameMapper. getPossibleModificationNamesOmssa(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
Returns the possible OMSSA modification names.static void
ModificationLocalizationMapper. 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. -
Uses of ModificationProvider in com.compomics.util.experiment.identification.peptide_inference
Methods in com.compomics.util.experiment.identification.peptide_inference with parameters of type ModificationProvider Modifier and Type Method Description void
PeptideInference. peptideInference(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider, WaitingHandler waitingHandler)
Infers the PTM localization and its confidence for the best match of every spectrum. -
Uses of ModificationProvider in com.compomics.util.experiment.identification.peptide_shaker
Methods in com.compomics.util.experiment.identification.peptide_shaker with parameters of type ModificationProvider Modifier and Type Method Description void
PSModificationScores. changeRepresentativeSite(String modName, String originalModName, int originalRepresentativeSite, int newRepresentativeSite, int nMod, ModificationProvider modificationProvider)
Changes the representative site for a given ambiguously localized modification in all maps. -
Uses of ModificationProvider in com.compomics.util.experiment.io.identification.writers
Constructors in com.compomics.util.experiment.io.identification.writers with parameters of type ModificationProvider Constructor Description SimpleMzIdentMLExporter(String softwareName, String softwareVersion, String softwareUrl, File tempFolder, File destinationFile, ArrayList<File> spectrumFiles, File searchEngineFile, HashMap<String,ArrayList<String>> searchEngines, File fastaFile, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider, ModificationProvider modificationProvider, FastaSummary fastaSummary, String contactFirstName, String contactLastName, String contactAddress, String contactEmail, String contactOrganizationName, String contactOrganizationAddress, String contactOrganizationEmail, boolean peptideInference)
Constructor.