Uses of Class
com.compomics.util.experiment.identification.identification_parameters.SearchParameters

Packages that use SearchParameters

Package	Description
com.compomics.util.experiment	Gene factory classes.
com.compomics.util.experiment.biology	Experiment classes related to biological entities.
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.identification_parameters	Parameters settings for the spectrum identification algorithms.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.io.identifications	Experiment identification classes.
com.compomics.util.experiment.io.identifications.idfilereaders	Experiment classes related to reading search engine files.
com.compomics.util.gui.parameters.identification_parameters	GUI classes for parameters, settings and preferences used for identification.
com.compomics.util.gui.parameters.identification_parameters.algorithm_settings	Search algorithm settings dialogs.
com.compomics.util.preferences	Utilities preferences classes.
com.compomics.util.pride	Objects related to mapping to PRIDE.

Uses of SearchParameters in com.compomics.util.experiment

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

Modifier and Type	Method and Description
static ShotgunProtocol	ShotgunProtocol.inferProtocolFromSearchSettings(SearchParameters searchParameters) Backward compatibility inferring the protocol from search settings.

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

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

Modifier and Type	Method and Description
ArrayList<String>	PTMFactory.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 and Description
void	PeptideAssumptionFilter.setFilterFromSearchParameters(SearchParameters searchParameters) Updates the filter based on the search parameters.
boolean	PeptideAssumptionFilter.validatePrecursor(PeptideAssumption assumption, String spectrumKey, SpectrumFactory spectrumFactory, SearchParameters searchParameters) Validates the mass deviation of a peptide assumption.

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

Methods in com.compomics.util.experiment.identification.identification_parameters that return SearchParameters

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

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

Modifier and Type	Method and 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 of the advanced settings are not set for a given advocate.

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

Constructor and Description
SearchParameters(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 and Description
void	AnnotationSettings.setPreferencesFromSearchParameters(SearchParameters searchParameters) Updates the annotation parameters based on search parameters.

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

Constructor and Description
AnnotationSettings(SearchParameters searchParameters) Constructor setting preferences from search parameters.

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

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

Modifier and Type	Method and Description
LinkedList<SpectrumMatch>	IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters) Retrieves all the identifications from an identification file as a list of spectrum matches It is very important to close the file reader after creation.
LinkedList<SpectrumMatch>	IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations) Retrieves all the identifications from an identification file as a list of spectrum matches It is very important to close the file reader after creation.
static String	MzIdentMLIdfileSearchParametersConverter.getSearchParameters(File mzIdentMLFile, SearchParameters searchParameters, String species, WaitingHandler waitingHandler) Constructor.

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

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

Modifier and Type	Method and Description
LinkedList<SpectrumMatch>	TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	NovorIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	NovorIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)

Uses of SearchParameters in com.compomics.util.gui.parameters.identification_parameters

Methods in com.compomics.util.gui.parameters.identification_parameters that return SearchParameters

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

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

Constructor and Description
GenePreferencesDialog(JDialog owner, GenePreferences genePreferences, SearchParameters searchParameters, boolean editable) Creates a new GenePreferencesDialog with a dialog as owner.
GenePreferencesDialog(JFrame parent, GenePreferences genePreferences, SearchParameters searchParameters, boolean editable) Creates a new GenePreferencesDialog with a frame as owner.
SearchSettingsDialog(Dialog owner, Frame parentFrame, SearchParameters searchParameters, Image normalIcon, Image waitingIcon, boolean setVisible, boolean modal, ConfigurationFile configurationFile, LastSelectedFolder lastSelectedFolder, String settingsName, boolean editable) Creates a new SearchSettingsDialog with a dialog as owner.
SearchSettingsDialog(Frame parentFrame, SearchParameters searchParameters, Image normalIcon, Image waitingIcon, boolean setVisible, boolean modal, ConfigurationFile configurationFile, LastSelectedFolder lastSelectedFolder, String settingsName, boolean editable) Creates a new SearchSettingsDialog with a frame as owner.
SpectrumMatchingSettingsDialog(Dialog owner, Frame parentFrame, String settingsName, SearchParameters searchParameters, Image normalIcon, Image waitingIcon, ConfigurationFile configurationFile, LastSelectedFolder lastSelectedFolder, boolean editable) Creates a new SpectrumMatchingSettingsDialog with a dialog as owner.
SpectrumMatchingSettingsDialog(Frame parentFrame, String settingsName, SearchParameters searchParameters, Image normalIcon, Image waitingIcon, ConfigurationFile configurationFile, LastSelectedFolder lastSelectedFolder, boolean editable) Creates a new SpectrumMatchingSettingsDialog with a frame as owner.

Uses of SearchParameters in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings

Methods in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings that return SearchParameters

Modifier and Type	Method and Description
SearchParameters	PNovoSettingsDialog.getSearchParametersFromGUI() Returns the search parameters as set in the GUI.
SearchParameters	NovorSettingsDialog.getSearchParametersFromGUI() Returns the search parameters as set in the GUI.
SearchParameters	DirecTagSettingsDialog.getSearchParametersFromGUI() Returns the search parameters as set in the GUI.

Constructors in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings with parameters of type SearchParameters

Constructor and Description
DirecTagSettingsDialog(Dialog owner, Frame parent, SearchParameters searchParameters, boolean editable) Creates a new DirecTagSettingsDialog with a dialog as owner.
DirecTagSettingsDialog(Frame parent, SearchParameters searchParameters, boolean editable) Creates a new DirecTagSettingsDialog with a frame as owner.
NovorSettingsDialog(Dialog owner, Frame parent, SearchParameters searchParameters, boolean editable) Creates a new NovorSettingsDialog with a dialog as owner.
NovorSettingsDialog(Frame parent, SearchParameters searchParameters, boolean editable) Creates a new NovorSettingsDialog with a frame as owner.
PNovoSettingsDialog(Dialog owner, Frame parent, SearchParameters searchParameters, boolean editable) Creates a new PNovoSettingsDialog with a dialog as owner.
PNovoSettingsDialog(Frame parent, SearchParameters searchParameters, boolean editable) Creates a new PNovoSettingsDialog with a frame as owner.

Uses of SearchParameters in com.compomics.util.preferences

Methods in com.compomics.util.preferences that return SearchParameters

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

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

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

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

Constructor and Description
IdentificationParameters(SearchParameters searchParameters) Creates default identification parameters from the given search parameters.
IdentificationParameters(String name, String description, SearchParameters searchParameters, AnnotationSettings annotationSettings, SequenceMatchingPreferences sequenceMatchingPreferences, GenePreferences genePreferences, PsmScoringPreferences psmScoringPreferences, PeptideAssumptionFilter peptideAssumptionFilter, PTMScoringPreferences ptmScoringPreferences, ProteinInferencePreferences proteinInferencePreferences, IdMatchValidationPreferences idValidationPreferences, FractionSettings fractionSettings) Constructor.

Uses of SearchParameters in com.compomics.util.pride

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

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