Uses of Class
org.snpeff.snpEffect.Config

Packages that use Config

Package	Description
org.snpeff
org.snpeff.binseq
org.snpeff.nextProt
org.snpeff.outputFormatter
org.snpeff.snpEffect
org.snpeff.snpEffect.commandLine
org.snpeff.snpEffect.factory
org.snpeff.snpEffect.testCases.integration
org.snpeff.snpEffect.testCases.unity
org.snpeff.spliceSites

Uses of Config in org.snpeff

Fields in org.snpeff declared as Config

Modifier and Type	Field	Description
protected Config	SnpEff.config

Methods in org.snpeff that return Config

Modifier and Type	Method	Description
Config	SnpEff.getConfig()

Methods in org.snpeff with parameters of type Config

Modifier and Type	Method	Description
void	SnpEff.setConfig(Config config)

Uses of Config in org.snpeff.binseq

Methods in org.snpeff.binseq with parameters of type Config

Modifier and Type	Method	Description
void	GenomicSequences.save(Config config)	Save genomic sequence into separate files (per chromosome)

Uses of Config in org.snpeff.nextProt

Constructors in org.snpeff.nextProt with parameters of type Config

Constructor	Description
NextProtDb(java.lang.String xmlDirName, Config config)
NextProtMarkerFactory(Config config)

Uses of Config in org.snpeff.outputFormatter

Methods in org.snpeff.outputFormatter with parameters of type Config

Modifier and Type	Method	Description
void	OutputFormatter.setConfig(Config config)

Uses of Config in org.snpeff.snpEffect

Methods in org.snpeff.snpEffect that return Config

Modifier and Type	Method	Description
static Config	Config.get()
static Config	Config.reset()

Methods in org.snpeff.snpEffect with parameters of type Config

Modifier and Type	Method	Description
static SnpEffectPredictor	SnpEffectPredictor.load(Config config)	Load predictor from a binary file
void	SnpEffectPredictor.save(Config config)	Save predictor to a binary file (specified by the configuration)
void	VcfAnnotator.setConfig(Config config)	Set configuration
void	VcfAnnotatorChain.setConfig(Config config)

Constructors in org.snpeff.snpEffect with parameters of type Config

Constructor	Description
LossOfFunction(Config config, java.util.Collection<VariantEffect> variantEffects)

Uses of Config in org.snpeff.snpEffect.commandLine

Constructors in org.snpeff.snpEffect.commandLine with parameters of type Config

Constructor	Description
SnpEffCmdCds(Config config)
SnpEffCmdClosest(Config config)
SnpEffCmdProtein(Config config)
SnpEffCmdProtein(Config config, java.lang.String proteinFile)

Uses of Config in org.snpeff.snpEffect.factory

Constructors in org.snpeff.snpEffect.factory with parameters of type Config

Constructor	Description
SnpEffPredictorFactory(Config config, int inOffset)
SnpEffPredictorFactoryEmbl(Config config)
SnpEffPredictorFactoryEmbl(Config config, java.lang.String emblFileName)
SnpEffPredictorFactoryFeatures(Config config)
SnpEffPredictorFactoryGenBank(Config config)
SnpEffPredictorFactoryGenBank(Config config, java.lang.String fileName)
SnpEffPredictorFactoryGenesFile(Config config)
SnpEffPredictorFactoryGff(Config config)
SnpEffPredictorFactoryGff2(Config config)
SnpEffPredictorFactoryGff3(Config config)
SnpEffPredictorFactoryGtf22(Config config)
SnpEffPredictorFactoryKnownGene(Config config)
SnpEffPredictorFactoryRand(Config config, java.util.Random random, int maxGeneLen, int maxTranscripts, int maxExons)
SnpEffPredictorFactoryRefSeq(Config config)

Uses of Config in org.snpeff.snpEffect.testCases.integration

Fields in org.snpeff.snpEffect.testCases.integration declared as Config

Modifier and Type	Field	Description
protected Config	TestCasesHgvsBase.config

Methods in org.snpeff.snpEffect.testCases.integration that return Config

Modifier and Type	Method	Description
Config	CompareEffects.getConfig()

Uses of Config in org.snpeff.snpEffect.testCases.unity

Fields in org.snpeff.snpEffect.testCases.unity declared as Config

Modifier and Type	Field	Description
protected Config	TestCasesBase.config
Config	TestGenome.config

Uses of Config in org.snpeff.spliceSites

Constructors in org.snpeff.spliceSites with parameters of type Config

Constructor	Description
SpliceTypes(Config config)