Uses of Class
com.compomics.util.experiment.biology.genes.GeneMaps
Package | Description |
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com.compomics.util.experiment.biology.genes |
Classes related to genes.
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com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
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com.compomics.util.gui.genes |
Dialogs for the handling of genes.
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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)
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Uses of GeneMaps in com.compomics.util.gui.genes
Constructors in com.compomics.util.gui.genes with parameters of type GeneMaps Constructor Description GeneDetailsDialog(Frame parent, ProteinMatch proteinMatch, GeneMaps geneMaps, ProteinDetailsProvider proteinDetailsProvider)
Creates a new GeneDetailsDialog.