Uses of Class
com.compomics.util.experiment.io.biology.protein.FastaSummary
Package | Description |
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com.compomics.util.experiment.biology.genes |
Classes related to genes.
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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.experiment.io.identification.writers |
Writer for identification results.
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com.compomics.util.gui.parameters.identification.advanced |
Dialogs for advanced identification parameters.
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com.compomics.util.parameters.identification.advanced |
Advanced Identification parameters.
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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 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 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.