Uses of Interface
com.compomics.util.experiment.biology.modifications.ModificationProvider

Packages that use ModificationProvider

Package	Description
com.compomics.util.experiment.biology.modifications
com.compomics.util.experiment.identification.modification.mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.modification.scores	PTM scores.
com.compomics.util.experiment.identification.modification.search_engine_mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.peptide_inference	Classes related to peptide inference.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.
com.compomics.util.experiment.io.identification.writers	Writer for identification results.
com.compomics.util.experiment.io.parameters	Experiment IO classes relative to the handling of parameters.

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.modification.scores

Methods in com.compomics.util.experiment.identification.modification.scores with parameters of type ModificationProvider

Modifier and Type	Method	Description
static HashMap<Integer,Double>	PhosphoRS.getSequenceProbabilities(Peptide peptide, ArrayList<Modification> modifications, ModificationParameters modificationParameters, Spectrum spectrum, SequenceProvider sequenceProvider, AnnotationParameters annotationParameters, SpecificAnnotationParameters specificAnnotationSettings, boolean accountNeutralLosses, SequenceMatchingParameters sequenceMatchingParameters, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator spectrumAnnotator, ModificationProvider modificationProvider)	Returns the PhosphoRS sequence probabilities for the modification possible locations.

Uses of ModificationProvider in com.compomics.util.experiment.identification.modification.search_engine_mapping

Methods in com.compomics.util.experiment.identification.modification.search_engine_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 from a search engine modification indexed by site.
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, IdentificationParameters identificationParameters, IdfileReader idfileReader, ModificationProvider modificationProvider, SequenceProvider sequenceProvider)	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.utils

Methods in com.compomics.util.experiment.identification.utils with parameters of type ModificationProvider

Modifier and Type	Method	Description
static int[]	ModificationUtils.getPossibleModificationSites(Peptide peptide, Modification modification, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters, ModificationProvider modificationProvider, boolean avoidOverlap)	Returns an array of the possible modification sites for the given modification on the given peptide.

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

Modifier	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.

Uses of ModificationProvider in com.compomics.util.experiment.io.parameters

Methods in com.compomics.util.experiment.io.parameters with parameters of type ModificationProvider

Modifier and Type	Method	Description
static void	SdrfExport.writeSdrf(File sdrfFile, SearchParameters searchParameters, ArrayList<String> msFileNames, ModificationProvider modificationProvider)	Write an SDFR file.