Uses of Class
com.compomics.util.experiment.io.biology.protein.FastaSummary

Packages that use FastaSummary

Package	Description
com.compomics.util.experiment.biology.genes	Classes related to genes.
com.compomics.util.experiment.io.biology.protein	Experiment IO classes for biological resources.
com.compomics.util.experiment.io.biology.protein.converters	Fasta file converters.
com.compomics.util.experiment.io.identification.writers	Writer for identification results.
com.compomics.util.gui.parameters.identification.advanced	Dialogs for advanced identification parameters.
com.compomics.util.parameters.identification.advanced	Advanced Identification parameters.

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

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

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 FastaSummary in com.compomics.util.experiment.io.biology.protein

Methods in com.compomics.util.experiment.io.biology.protein that return FastaSummary

Modifier and Type	Method	Description
static FastaSummary	FastaSummary.getSummary(String fastaFile, FastaParameters fastaParameters, boolean alwaysCreateNew, WaitingHandler waitingHandler)	Gathers summary data on the FASTA file content.
static FastaSummary	FastaSummary.getSummary(String fastaFile, FastaParameters fastaParameters, WaitingHandler waitingHandler)	Gathers summary data on the FASTA file content.

Methods in com.compomics.util.experiment.io.biology.protein with parameters of type FastaSummary

Modifier and Type	Method	Description
static void	FastaSummary.saveSummary(String fastaFile, FastaSummary fastaSummary)	Saves the summary in the user folder.

Uses of FastaSummary in com.compomics.util.experiment.io.biology.protein.converters

Methods in com.compomics.util.experiment.io.biology.protein.converters that return FastaSummary

Modifier and Type	Method	Description
static FastaSummary	DecoyConverter.getDecoySummary(File newFastaFile, FastaSummary targetSummary)	Returns the FASTA summary of the target-decoy database based on the summary of the target database.

Methods in com.compomics.util.experiment.io.biology.protein.converters with parameters of type FastaSummary

Modifier and Type	Method	Description
static FastaSummary	DecoyConverter.getDecoySummary(File newFastaFile, FastaSummary targetSummary)	Returns the FASTA summary of the target-decoy database based on the summary of the target database.

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

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

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 FastaSummary in com.compomics.util.gui.parameters.identification.advanced

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

Modifier	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.

Uses of FastaSummary in com.compomics.util.parameters.identification.advanced

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

Modifier and Type	Method	Description
void	GeneParameters.setBackgroundSpeciesFromFastaSummary(FastaSummary fastaSummary)	Set the background species to the most common species in the FASTA file.