Uses of Class
com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters

Packages that use PeptideVariantsParameters

Package	Description
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.gui.parameters.identification.advanced	Dialogs for advanced identification parameters.
com.compomics.util.parameters.identification	Identification parameters.
com.compomics.util.parameters.identification.advanced	Advanced Identification parameters.

Uses of PeptideVariantsParameters 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 PeptideVariantsParameters

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

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

Methods in com.compomics.util.gui.parameters.identification.advanced that return PeptideVariantsParameters

Modifier and Type	Method	Description
PeptideVariantsParameters	PeptideVariantsParametersDialog.getPeptideVariantsPreferences()	Returns the peptide variants settings as set by the user.

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

Modifier	Constructor	Description
	PeptideVariantsParametersDialog(Dialog owner, Frame parentFrame, PeptideVariantsParameters peptideVariantPreferences, boolean editable)	Creates a new FractionSettingsDialog with a dialog as owner.
	PeptideVariantsParametersDialog(Frame parentFrame, PeptideVariantsParameters peptideVariantPreferences, boolean editable)	Creates a new FractionSettingsDialog with a frame as owner.

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

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

Modifier and Type	Method	Description
PeptideVariantsParameters	IdentificationParameters.getPeptideVariantsParameters()	Returns the peptide variant parameters.

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

Modifier and Type	Method	Description
void	IdentificationParameters.setPeptideVariantsParameters(PeptideVariantsParameters peptideVariantsParameters)	Sets the peptide variant parameters.

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

Modifier	Constructor	Description
	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 PeptideVariantsParameters in com.compomics.util.parameters.identification.advanced

Methods in com.compomics.util.parameters.identification.advanced that return PeptideVariantsParameters

Modifier and Type	Method	Description
static PeptideVariantsParameters	PeptideVariantsParameters.getNoVariantParameters()	Returns the parameters corresponding to no variants allowed.

Methods in com.compomics.util.parameters.identification.advanced with parameters of type PeptideVariantsParameters

Modifier and Type	Method	Description
boolean	PeptideVariantsParameters.isSameAs(PeptideVariantsParameters peptideVariantsParameters)	Indicates whether another peptide variant parameters is the same as this one.