Uses of Class
org.snpeff.snpEffect.Config
Packages that use Config
Package
Description
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Uses of Config in org.snpeff
Fields in org.snpeff declared as ConfigMethods in org.snpeff that return ConfigMethods in org.snpeff with parameters of type Config -
Uses of Config in org.snpeff.binseq
Methods in org.snpeff.binseq with parameters of type Config -
Uses of Config in org.snpeff.interval
Constructors in org.snpeff.interval with parameters of type Config -
Uses of Config in org.snpeff.nextProt
Constructors in org.snpeff.nextProt with parameters of type ConfigModifierConstructorDescriptionNextProtDb(String xmlDirName, Config config) NextProtMarkerFactory(Config config) -
Uses of Config in org.snpeff.outputFormatter
Methods in org.snpeff.outputFormatter with parameters of type Config -
Uses of Config in org.snpeff.pdb
Methods in org.snpeff.pdb with parameters of type ConfigModifier and TypeMethodDescriptionvoidProteinInteractions.initialize(Config config) Initialize class (deferred initialization) Note: This is not done at construction because we don't have a 'Config' object ready (loaded) at the timevoid -
Uses of Config in org.snpeff.snpEffect
Methods in org.snpeff.snpEffect that return ConfigMethods in org.snpeff.snpEffect with parameters of type ConfigModifier and TypeMethodDescriptionstatic SnpEffectPredictorLoad predictor from a binary filevoidSave predictor to a binary file (specified by the configuration)voidSet configurationvoidConstructors in org.snpeff.snpEffect with parameters of type ConfigModifierConstructorDescriptionLossOfFunction(Config config, Collection<VariantEffect> variantEffects) -
Uses of Config in org.snpeff.snpEffect.commandLine
Constructors in org.snpeff.snpEffect.commandLine with parameters of type ConfigModifierConstructorDescriptionSnpEffCmdCds(Config config) SnpEffCmdClosest(Config config) SnpEffCmdProtein(Config config, String proteinFile) -
Uses of Config in org.snpeff.snpEffect.factory
Constructors in org.snpeff.snpEffect.factory with parameters of type ConfigModifierConstructorDescriptionSnpEffPredictorFactory(Config config, int inOffset) SnpEffPredictorFactoryEmbl(Config config) SnpEffPredictorFactoryEmbl(Config config, String emblFileName) SnpEffPredictorFactoryFeatures(Config config) SnpEffPredictorFactoryGenBank(Config config) SnpEffPredictorFactoryGenBank(Config config, String fileName) SnpEffPredictorFactoryGff(Config config) SnpEffPredictorFactoryGff2(Config config) SnpEffPredictorFactoryGff3(Config config) SnpEffPredictorFactoryGtf22(Config config) SnpEffPredictorFactoryRand(Config config, Random random, int maxGeneLen, int maxTranscripts, int maxExons) SnpEffPredictorFactoryRefSeq(Config config) -
Uses of Config in org.snpeff.spliceSites
Constructors in org.snpeff.spliceSites with parameters of type Config