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

Packages that use FastaParameters

Package	Description
com.compomics.cli.fasta	Command line for the handling of fasta files.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.
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.gui.parameters.identification.search	Dialogs for search parameters.
com.compomics.util.gui.protein	GUI class related to protein sequence formatting.
com.compomics.util.parameters.identification	Identification parameters.

Uses of FastaParameters in com.compomics.cli.fasta

Methods in com.compomics.cli.fasta that return FastaParameters

Modifier and Type	Method	Description
FastaParameters	FastaParametersInputBean.getFastaParameters()	Returns the FASTA parameters as parsed from the command line.

Uses of FastaParameters in com.compomics.util.experiment.identification.protein_inference.fm_index

Constructors in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type FastaParameters

Modifier	Constructor	Description
	FMIndex(File fastaFile, FastaParameters fastaParameters, WaitingHandler waitingHandler, boolean displayProgress, PeptideVariantsParameters peptideVariantsPreferences, SearchParameters searchParameters)	Constructor.
	FMIndex(File fastaFile, FastaParameters fastaParameters, WaitingHandler waitingHandler, boolean displayProgress, IdentificationParameters identificationParameters)	Constructor.

Uses of FastaParameters in com.compomics.util.experiment.identification.utils

Methods in com.compomics.util.experiment.identification.utils with parameters of type FastaParameters

Modifier and Type	Method	Description
static boolean	ProteinUtils.isDecoy(String accession, FastaParameters fastaParameters)	Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given FASTA parameters.

Uses of FastaParameters in com.compomics.util.experiment.io.biology.protein

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

Modifier and Type	Method	Description
static FastaParameters	FastaParameters.inferParameters(String fastaFilePath, WaitingHandler waitingHandler)	Infers the parameters used to parse the file.

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

Modifier and Type	Method	Description
boolean	FastaParameters.equals(FastaParameters fastaParameters)
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.
boolean	FastaParameters.isSameAs(FastaParameters fastaParameters)	Returns a boolean indicating whether the parsing parameters are the same as the given parameters.

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

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

Modifier and Type	Method	Description
static FastaParameters	DecoyConverter.getDecoyParameters(FastaParameters targetParameters)	Returns the FASTA parameters of the target-decoy database based on the parameters of the target database.

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

Modifier and Type	Method	Description
static void	DecoyConverter.appendDecoySequences(File fastaIn, File fastaOut, FastaParameters fastaParameters, WaitingHandler waitingHandler)	Appends decoy sequences to the provided FASTA file.
static FastaParameters	DecoyConverter.getDecoyParameters(FastaParameters targetParameters)	Returns the FASTA parameters of the target-decoy database based on the parameters of the target database.

Uses of FastaParameters in com.compomics.util.gui.parameters.identification.search

Methods in com.compomics.util.gui.parameters.identification.search that return FastaParameters

Modifier and Type	Method	Description
FastaParameters	SequenceDbDetailsDialog.getFastaParameters()	Returns the FASTA parameters.

Constructors in com.compomics.util.gui.parameters.identification.search with parameters of type FastaParameters

Modifier	Constructor	Description
	SequenceDbDetailsDialog(Dialog owner, Frame parent, String selectedFastaFile, FastaParameters fastaParameters, LastSelectedFolder lastSelectedFolder, boolean dbEditable, Image normalImange, Image waitingImage)	Creates a new SequenceDbDetailsDialog with a dialog as owner.
	SequenceDbDetailsDialog(Frame parent, String selectedFastaFile, FastaParameters fastaParameters, LastSelectedFolder lastSelectedFolder, boolean dbEditable, Image normalImange, Image waitingImage)	Creates a new SequenceDbDetailsDialog.

Uses of FastaParameters in com.compomics.util.gui.protein

Methods in com.compomics.util.gui.protein that return FastaParameters

Modifier and Type	Method	Description
FastaParameters	FastaParametersDialog.getFastaSettings()	Returns the FASTA settings as set by the user.

Constructors in com.compomics.util.gui.protein with parameters of type FastaParameters

Modifier	Constructor	Description
	FastaParametersDialog(Dialog owner, Frame parentFrame, FastaParameters fastaSettings, boolean editable)	Creates a new FractionSettingsDialog with a dialog as owner.
	FastaParametersDialog(Frame parentFrame, FastaParameters fastaSettings, boolean editable)	Creates a new FractionSettingsDialog with a frame as owner.

Uses of FastaParameters in com.compomics.util.parameters.identification

Methods in com.compomics.util.parameters.identification that return FastaParameters

Modifier and Type	Method	Description
FastaParameters	IdentificationParameters.getFastaParameters()	Returns the FASTA processing parameters.

Methods in com.compomics.util.parameters.identification with parameters of type FastaParameters

Modifier and Type	Method	Description
void	IdentificationParameters.setFastaParameters(FastaParameters fastaParameters)	Sets the ASTA processing parameters.

Constructors in com.compomics.util.parameters.identification with parameters of type FastaParameters

Modifier	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.