Uses of Class
org.snpeff.snpEffect.Config
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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)
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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)
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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)
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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 filevoid
SnpEffectPredictor. save(Config config)
Save predictor to a binary file (specified by the configuration)void
VcfAnnotator. setConfig(Config config)
Set configurationvoid
VcfAnnotatorChain. setConfig(Config config)
Constructors in org.snpeff.snpEffect with parameters of type Config Constructor Description LossOfFunction(Config config, java.util.Collection<VariantEffect> variantEffects)
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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)
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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)
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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()
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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
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Uses of Config in org.snpeff.spliceSites
Constructors in org.snpeff.spliceSites with parameters of type Config Constructor Description SpliceTypes(Config config)
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