Uses of Class
org.snpeff.snpEffect.SnpEffectPredictor
Packages that use SnpEffectPredictor
Package
Description
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Uses of SnpEffectPredictor in org.snpeff.coverage
Constructors in org.snpeff.coverage with parameters of type SnpEffectPredictorModifierConstructorDescriptionCountReads
(String fileName, SnpEffectPredictor snpEffectPredictor) CountReadsOnMarkers
(SnpEffectPredictor snpEffectPredictor) -
Uses of SnpEffectPredictor in org.snpeff.snpEffect
Methods in org.snpeff.snpEffect that return SnpEffectPredictorModifier and TypeMethodDescriptionConfig.getSnpEffectPredictor()
static SnpEffectPredictor
Load predictor from a binary fileConfig.loadSnpEffectPredictor()
Load a snpEff predictor WARNING: 'genome' object get replaced upon loading a snpEffectPredictor (this is a dangerous side effect)Methods in org.snpeff.snpEffect with parameters of type SnpEffectPredictorModifier and TypeMethodDescriptionvoid
Config.setSnpEffectPredictor
(SnpEffectPredictor snpEffectPredictor) -
Uses of SnpEffectPredictor in org.snpeff.snpEffect.factory
Methods in org.snpeff.snpEffect.factory that return SnpEffectPredictorModifier and TypeMethodDescriptionabstract SnpEffectPredictor
SnpEffPredictorFactory.create()
SnpEffPredictorFactoryFeatures.create()
SnpEffPredictorFactoryGenesFile.create()
SnpEffPredictorFactoryGff.create()
SnpEffPredictorFactoryKnownGene.create()
SnpEffPredictorFactoryRand.create()
SnpEffPredictorFactoryRefSeq.create()
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Uses of SnpEffectPredictor in org.snpeff.snpEffect.testCases.integration
Fields in org.snpeff.snpEffect.testCases.integration declared as SnpEffectPredictorModifier and TypeFieldDescriptionprotected SnpEffectPredictor
TestCasesHgvsBase.snpEffectPredictor
Methods in org.snpeff.snpEffect.testCases.integration that return SnpEffectPredictorModifier and TypeMethodDescriptionBuild a genome, return SnpEffectPredictorTestCasesIntegrationBase.buildAndCompare
(String genome, String refSeqFile, String fastaFile, String resultFile, boolean hideProtein) Build a genome from a RefSeq file and compare results to 'expected' resultsBuild a genome from a embl file and compare results to 'expected' resultsTestCasesIntegrationBase.buildGeneBank
(String genome, String genBankFile) TestCasesIntegrationBase.buildGeneBank
(String genome, String genBankFile, boolean circularCorrectlargeGap) Build a genome from a genbank file and compare results to 'expected' resultsTestCasesIntegrationBase.buildGff3AndCompare
(String genome, String gff3File, String resultFile, boolean readSeqs, boolean createRandSequences) Build a genome from a GFF3 file and compare results to 'expected' resultsTestCasesIntegrationBase.loadSnpEffectPredictor
(String genome, boolean build) Load predictor and create interval forestConstructors in org.snpeff.snpEffect.testCases.integration with parameters of type SnpEffectPredictorModifierConstructorDescriptionCompareEffects
(SnpEffectPredictor snpEffectPredictor, long randSeed, boolean verbose) -
Uses of SnpEffectPredictor in org.snpeff.snpEffect.testCases.unity
Fields in org.snpeff.snpEffect.testCases.unity declared as SnpEffectPredictorModifier and TypeFieldDescriptionprotected SnpEffectPredictor
TestCasesBase.snpEffectPredictor
TestGenome.snpEffectPredictor
Methods in org.snpeff.snpEffect.testCases.unity that return SnpEffectPredictorModifier and TypeMethodDescriptionTestGenome.createSnpEffectPredictor()
Create a snpEff predictor and build the forest -
Uses of SnpEffectPredictor in org.snpeff.stats
Methods in org.snpeff.stats with parameters of type SnpEffectPredictorModifier and TypeMethodDescriptionvoid
ReadsOnMarkersModel.setSnpEffectPredictor
(SnpEffectPredictor snpEffectPredictor) Constructors in org.snpeff.stats with parameters of type SnpEffectPredictor -
Uses of SnpEffectPredictor in org.snpeff.svg
Constructors in org.snpeff.svg with parameters of type SnpEffectPredictorModifierConstructorDescriptionSvgTranslocation
(Transcript tr1, Transcript tr2, VariantBnd varBnd, SnpEffectPredictor snpEffPredictor)