Uses of Class
com.compomics.util.experiment.biology.genes.GeneMaps

Packages that use GeneMaps

Package	Description
com.compomics.util.experiment.biology.genes	Classes related to genes.
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
com.compomics.util.gui.genes	Dialogs for the handling of genes.

Uses of GeneMaps in com.compomics.util.experiment.biology.genes

Methods in com.compomics.util.experiment.biology.genes that return GeneMaps

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 GeneMaps in com.compomics.util.experiment.identification.filtering

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

Modifier and Type	Method	Description
boolean	AssumptionFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean	MatchFilter.isValidated(long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)	Tests whether a match is validated by this filter.
abstract boolean	MatchFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)	Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.
boolean	PeptideFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean	ProteinFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean	PsmFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)

Uses of GeneMaps in com.compomics.util.gui.genes

Constructors in com.compomics.util.gui.genes with parameters of type GeneMaps

Modifier	Constructor	Description
	GeneDetailsDialog(Frame parent, ProteinMatch proteinMatch, GeneMaps geneMaps, ProteinDetailsProvider proteinDetailsProvider)	Creates a new GeneDetailsDialog.