Uses of Class
com.compomics.util.experiment.io.biology.protein.FastaParameters
Package | Description |
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com.compomics.cli.fasta |
Command line for the handling of fasta files.
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com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
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com.compomics.util.experiment.identification.utils |
This package contains utilities classes to handle identification objects.
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com.compomics.util.experiment.io.biology.protein |
Experiment IO classes for biological resources.
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com.compomics.util.experiment.io.biology.protein.converters |
Fasta file converters.
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com.compomics.util.gui.parameters.identification.search |
Dialogs for search parameters.
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com.compomics.util.gui.protein |
GUI class related to protein sequence formatting.
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com.compomics.util.parameters.identification |
Identification parameters.
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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 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 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 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 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.