Uses of Class
com.compomics.util.parameters.identification.search.SearchParameters

Packages that use SearchParameters

Package	Description
com.compomics.util.experiment.biology.modifications
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.modification.mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.modification.search_engine_mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.
com.compomics.util.experiment.io.identification	Experiment identification classes.
com.compomics.util.experiment.io.identification.idfilereaders	Experiment classes related to reading search engine files.
com.compomics.util.experiment.io.mass_spectrometry	Classes for the handling of mass spectrometry files.
com.compomics.util.experiment.io.parameters	Experiment IO classes relative to the handling of parameters.
com.compomics.util.gui.parameters.identification.advanced	Dialogs for advanced identification parameters.
com.compomics.util.gui.parameters.identification.search	Dialogs for search parameters.
com.compomics.util.parameters.identification	Identification parameters.
com.compomics.util.parameters.identification.search	Identification parameters relative to the search.
com.compomics.util.pride	Objects related to mapping to PRIDE.

Uses of SearchParameters in com.compomics.util.experiment.biology.modifications

Methods in com.compomics.util.experiment.biology.modifications with parameters of type SearchParameters

Modifier and Type	Method	Description
ArrayList<String>	ModificationFactory.getExpectedVariableModifications(SearchParameters searchParameters)	Returns the expected variable modifications given the search parameters.
ArrayList<String>	ModificationFactory.getSameMassNotFixedModifications(double modificationMass, SearchParameters searchParameters)	Returns a list containing all not fixed modifications with the same mass.
ArrayList<String>	ModificationFactory.loadBackedUpModifications(SearchParameters searchParameters, boolean overwrite)	Verifies that the modifications backed-up in the search parameters are loaded and alerts the user in case conflicts are found.

Uses of SearchParameters in com.compomics.util.experiment.identification.filtering

Methods in com.compomics.util.experiment.identification.filtering with parameters of type SearchParameters

Modifier and Type	Method	Description
void	PeptideAssumptionFilter.setFilterFromSearchParameters(SearchParameters searchParameters)	Updates the filter based on the search parameters.
boolean	PeptideAssumptionFilter.validatePrecursor(PeptideAssumption assumption, String spectrumFile, String spectrumTitle, SpectrumProvider spectrumProvider, SearchParameters searchParameters)	Validates the mass deviation of a peptide assumption.

Uses of SearchParameters in com.compomics.util.experiment.identification.modification.mapping

Methods in com.compomics.util.experiment.identification.modification.mapping with parameters of type SearchParameters

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.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.

Uses of SearchParameters 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 SearchParameters

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.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.

Uses of SearchParameters in com.compomics.util.experiment.identification.protein_inference.fm_index

Constructors in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type SearchParameters

Modifier	Constructor	Description
	FMIndex(File fastaFile, FastaParameters fastaParameters, WaitingHandler waitingHandler, boolean displayProgress, PeptideVariantsParameters peptideVariantsPreferences, SearchParameters searchParameters)	Constructor.

Uses of SearchParameters in com.compomics.util.experiment.identification.spectrum_annotation

Methods in com.compomics.util.experiment.identification.spectrum_annotation with parameters of type SearchParameters

Modifier and Type	Method	Description
void	AnnotationParameters.setParametersFromSearchParameters(SearchParameters searchParameters)	Updates the annotation parameters based on search parameters.

Constructors in com.compomics.util.experiment.identification.spectrum_annotation with parameters of type SearchParameters

Modifier	Constructor	Description
	AnnotationParameters(SearchParameters searchParameters)	Constructor setting preferences from search parameters.

Uses of SearchParameters in com.compomics.util.experiment.identification.utils

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

Modifier and Type	Method	Description
static HashMap<Integer,HashSet<String>>	ModificationUtils.getExpectedModifications(double modMass, ModificationParameters modificationParameters, Peptide peptide, double massTolerance, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters, SearchParameters searchParameters)	Returns the expected modifications for a given modification mass indexed by site.

Uses of SearchParameters in com.compomics.util.experiment.io.identification

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

Modifier and Type	Method	Description
ArrayList<SpectrumMatch>	IdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)	Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum.
ArrayList<SpectrumMatch>	IdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)	Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum.It is very important to close the file reader after creation.

Constructors in com.compomics.util.experiment.io.identification with parameters of type SearchParameters

Modifier	Constructor	Description
	MzIdentMLIdfileSearchParametersConverter(File mzIdentMLFile, SearchParameters searchParameters, String species, WaitingHandler waitingHandler)	Constructor.

Uses of SearchParameters in com.compomics.util.experiment.io.identification.idfilereaders

Methods in com.compomics.util.experiment.io.identification.idfilereaders with parameters of type SearchParameters

Modifier and Type	Method	Description
ArrayList<SpectrumMatch>	AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	SageIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	SageIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)

Uses of SearchParameters in com.compomics.util.experiment.io.mass_spectrometry

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

Modifier and Type	Method	Description
static void	MsFileExporter.writeAplFile(SpectrumProvider spectrumProvider, boolean includeAllSpectrumLevels, String fileNameWithoutExtension, File destinationFile, SearchParameters searchParameters, WaitingHandler waitingHandler)	Writes the spectra of a file in the Andromeda peak list (apl) format.
static void	MsFileExporter.writeMsFile(SpectrumProvider spectrumProvider, boolean includeAllSpectrumLevels, String fileNameWithoutExtension, File destinationFile, MsFileExporter.Format format, SearchParameters searchParameters, WaitingHandler waitingHandler)	Writes the spectra of a file in the given format.

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

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

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

Uses of SearchParameters in com.compomics.util.gui.parameters.identification.advanced

Constructors in com.compomics.util.gui.parameters.identification.advanced with parameters of type SearchParameters

Modifier	Constructor	Description
	GeneParametersDialog(JDialog owner, Frame parentFrame, GeneParameters genePreferences, SearchParameters searchParameters, boolean editable)	Creates a new GeneParametersDialog with a dialog as owner.
	GeneParametersDialog(JFrame parentFrame, GeneParameters genePreferences, SearchParameters searchParameters, boolean editable)	Creates a new GeneParametersDialog with a frame as owner.

Uses of SearchParameters in com.compomics.util.gui.parameters.identification.search

Methods in com.compomics.util.gui.parameters.identification.search that return SearchParameters

Modifier and Type	Method	Description
SearchParameters	SearchParametersDialog.getSearchParameters()	Returns a SearchParameters instance based on the user input in the GUI.

Constructors in com.compomics.util.gui.parameters.identification.search with parameters of type SearchParameters

Modifier	Constructor	Description
	SearchParametersDialog(Dialog owner, Frame parentFrame, SearchParameters searchParameters, Image normalIcon, Image waitingIcon, boolean setVisible, boolean modal, LastSelectedFolder lastSelectedFolder, String settingsName, boolean editable)	Creates a new SearchSettingsDialog with a dialog as owner.
	SearchParametersDialog(Frame parentFrame, SearchParameters searchParameters, Image normalIcon, Image waitingIcon, boolean setVisible, boolean modal, LastSelectedFolder lastSelectedFolder, String settingsName, boolean editable)	Creates a new SearchSettingsDialog with a frame as owner.

Uses of SearchParameters in com.compomics.util.parameters.identification

Methods in com.compomics.util.parameters.identification that return SearchParameters

Modifier and Type	Method	Description
SearchParameters	IdentificationParameters.getSearchParameters()	Returns the parameters used for the spectrum matching.

Methods in com.compomics.util.parameters.identification with parameters of type SearchParameters

Modifier and Type	Method	Description
void	IdentificationParameters.setParametersFromSearch(SearchParameters searchParameters)	Sets identification parameters based on given search parameters.
void	IdentificationParameters.setSearchParameters(SearchParameters searchParameters)	Sets the parameters used for the spectrum matching.

Constructors in com.compomics.util.parameters.identification with parameters of type SearchParameters

Modifier	Constructor	Description
	IdentificationParameters(SearchParameters searchParameters)	Creates default identification parameters from the given search parameters.
	IdentificationParameters(String name, String description, SearchParameters searchParameters, AnnotationParameters annotationParameters, SequenceMatchingParameters sequenceMatchingParameters, PeptideVariantsParameters peptideVariantsParameters, GeneParameters geneParameters, PsmScoringParameters psmScoringParameters, PeptideAssumptionFilter peptideAssumptionFilter, ModificationLocalizationParameters ModificationLocalizationParameters, ProteinInferenceParameters proteinInferenceParameters, IdMatchValidationParameters idValidationParameters, FractionParameters fractionParameters, FastaParameters fastaParameters)	Constructor.

Uses of SearchParameters in com.compomics.util.parameters.identification.search

Methods in com.compomics.util.parameters.identification.search that return SearchParameters

Modifier and Type	Method	Description
static SearchParameters	SearchParameters.getIdentificationParameters(File searchParametersFile)	Loads the identification parameters from a file.

Methods in com.compomics.util.parameters.identification.search with parameters of type SearchParameters

Modifier and Type	Method	Description
boolean	SearchParameters.equals(SearchParameters otherSearchParameters)	Returns true if the search parameter objects have identical settings.
static void	SearchParameters.saveIdentificationParameters(SearchParameters searchParameters, File searchParametersFile)	Saves the identification parameters to a serialized file.
void	SearchParameters.setDefaultAdvancedSettings(SearchParameters searchParameters)	Set the advanced settings to the values in the given search parameters object or to the default values if the advanced settings are not set for a given advocate.

Constructors in com.compomics.util.parameters.identification.search with parameters of type SearchParameters

Modifier	Constructor	Description
	SearchParameters(SearchParameters searchParameters)	Constructor.

Uses of SearchParameters in com.compomics.util.pride

Methods in com.compomics.util.pride with parameters of type SearchParameters

Modifier and Type	Method	Description
static PtmToPrideMap	PtmToPrideMap.loadPtmToPrideMap(SearchParameters searchParameters)	Deprecated. the CV term is now part of the PTM object