Uses of Class
com.compomics.util.parameters.identification.advanced.GeneParameters
Package | Description |
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com.compomics.util.experiment.biology.genes |
Classes related to genes.
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com.compomics.util.gui.parameters.identification.advanced |
Dialogs for advanced identification parameters.
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com.compomics.util.parameters.identification |
Identification parameters.
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com.compomics.util.parameters.identification.advanced |
Advanced Identification parameters.
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Uses of GeneParameters in com.compomics.util.experiment.biology.genes
Methods in com.compomics.util.experiment.biology.genes with parameters of type GeneParameters Modifier and Type Method Description GeneMaps
ProteinGeneDetailsProvider. getGeneMaps(GeneParameters genePreferences, FastaSummary fastaSummary, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, WaitingHandler waitingHandler)
Returns the gene maps for the given proteins. -
Uses of GeneParameters in com.compomics.util.gui.parameters.identification.advanced
Methods in com.compomics.util.gui.parameters.identification.advanced that return GeneParameters Modifier and Type Method Description GeneParameters
BackgroundSpeciesDialog. getGeneParameters()
Returns the gene preferences.GeneParameters
GeneParametersDialog. getGeneParameters()
Returns the gene preferences.Constructors in com.compomics.util.gui.parameters.identification.advanced with parameters of type GeneParameters Constructor Description BackgroundSpeciesDialog(JDialog owner, Frame parentFrame, GeneParameters genePreferences, FastaSummary fastaSummary)
Creates a new GenePreferencesDialog with a dialog as owner.BackgroundSpeciesDialog(JFrame parentFrame, GeneParameters genePreferences, FastaSummary fastaSummary)
Creates a new GenePreferencesDialog with a frame as owner.GeneParametersDialog(JDialog owner, Frame parentFrame, GeneParameters genePreferences, SearchParameters searchParameters, boolean editable)
Creates a new GenePreferencesDialog with a dialog as owner.GeneParametersDialog(JFrame parentFrame, GeneParameters genePreferences, SearchParameters searchParameters, boolean editable)
Creates a new GenePreferencesDialog with a frame as owner. -
Uses of GeneParameters in com.compomics.util.parameters.identification
Methods in com.compomics.util.parameters.identification that return GeneParameters Modifier and Type Method Description GeneParameters
IdentificationParameters. getGeneParameters()
Returns the gene parameters.Methods in com.compomics.util.parameters.identification with parameters of type GeneParameters Modifier and Type Method Description void
IdentificationParameters. setGeneParameters(GeneParameters geneParameters)
Sets the gene parameters.Constructors in com.compomics.util.parameters.identification with parameters of type GeneParameters 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 GeneParameters in com.compomics.util.parameters.identification.advanced
Methods in com.compomics.util.parameters.identification.advanced with parameters of type GeneParameters Modifier and Type Method Description boolean
GeneParameters. equals(GeneParameters genePreferences)
Compares these preferences to other preferences.Constructors in com.compomics.util.parameters.identification.advanced with parameters of type GeneParameters Constructor Description GeneParameters(GeneParameters genePreferences)
Creates new gene preferences based on a GenePreferences object.