Uses of Interface
com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider

Packages that use ProteinDetailsProvider

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.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.io.identification.writers	Writer for identification results.
com.compomics.util.gui.genes	Dialogs for the handling of genes.

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

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

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

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

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 ProteinDetailsProvider in com.compomics.util.experiment.identification.protein_inference.fm_index

Classes in com.compomics.util.experiment.identification.protein_inference.fm_index that implement ProteinDetailsProvider

Modifier and Type	Class	Description
class	FMIndex	The FM index.

Uses of ProteinDetailsProvider in com.compomics.util.experiment.io.identification.writers

Constructors in com.compomics.util.experiment.io.identification.writers with parameters of type ProteinDetailsProvider

Modifier	Constructor	Description
	SimpleMzIdentMLExporter(String softwareName, String softwareVersion, String softwareUrl, File tempFolder, File destinationFile, ArrayList<File> spectrumFiles, File searchEngineFile, HashMap<String,ArrayList<String>> searchEngines, File fastaFile, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider, ModificationProvider modificationProvider, FastaSummary fastaSummary, String contactFirstName, String contactLastName, String contactAddress, String contactEmail, String contactOrganizationName, String contactOrganizationAddress, String contactOrganizationEmail, boolean peptideInference)	Constructor.

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

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

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