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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Modifier and Type | Method and Description |
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GeneMaps |
ProteinGeneDetailsProvider.getGeneMaps(GeneParameters genePreferences,
FastaSummary fastaSummary,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
WaitingHandler waitingHandler)
Returns the gene maps for the given proteins.
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Modifier and Type | Method and Description |
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static FastaSummary |
FastaSummary.getSummary(String fastaFile,
FastaParameters fastaParameters,
boolean alwaysCreateNew,
WaitingHandler waitingHandler)
Gathers summary data on the FASTA file content.
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static FastaSummary |
FastaSummary.getSummary(String fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler)
Gathers summary data on the FASTA file content.
|
Modifier and Type | Method and Description |
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static void |
FastaSummary.saveSummary(String fastaFile,
FastaSummary fastaSummary)
Saves the summary in the user folder.
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Modifier and Type | Method and Description |
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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.
|
Modifier and Type | Method and Description |
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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.
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Constructor and Description |
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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.
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Constructor and Description |
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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.
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Modifier and Type | Method and Description |
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void |
GeneParameters.setBackgroundSpeciesFromFastaSummary(FastaSummary fastaSummary)
Set the background species to the most common species in the FASTA file.
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