Uses of Class
org.snpeff.snpEffect.SnpEffectPredictor

Packages that use SnpEffectPredictor

Package	Description
org.snpeff.coverage
org.snpeff.snpEffect
org.snpeff.snpEffect.factory
org.snpeff.snpEffect.testCases.integration
org.snpeff.snpEffect.testCases.unity
org.snpeff.stats
org.snpeff.svg

Uses of SnpEffectPredictor in org.snpeff.coverage

Constructors in org.snpeff.coverage with parameters of type SnpEffectPredictor

Constructor	Description
CountReads(java.lang.String fileName, SnpEffectPredictor snpEffectPredictor)
CountReadsOnMarkers(SnpEffectPredictor snpEffectPredictor)

Uses of SnpEffectPredictor in org.snpeff.snpEffect

Methods in org.snpeff.snpEffect that return SnpEffectPredictor

Modifier and Type	Method	Description
SnpEffectPredictor	Config.getSnpEffectPredictor()
static SnpEffectPredictor	SnpEffectPredictor.load(Config config)	Load predictor from a binary file
SnpEffectPredictor	Config.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 SnpEffectPredictor

Modifier and Type	Method	Description
void	Config.setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)

Uses of SnpEffectPredictor in org.snpeff.snpEffect.factory

Methods in org.snpeff.snpEffect.factory that return SnpEffectPredictor

Modifier and Type	Method	Description
abstract SnpEffectPredictor	SnpEffPredictorFactory.create()
SnpEffectPredictor	SnpEffPredictorFactoryFeatures.create()
SnpEffectPredictor	SnpEffPredictorFactoryGenesFile.create()
SnpEffectPredictor	SnpEffPredictorFactoryGff.create()
SnpEffectPredictor	SnpEffPredictorFactoryKnownGene.create()
SnpEffectPredictor	SnpEffPredictorFactoryRand.create()
SnpEffectPredictor	SnpEffPredictorFactoryRefSeq.create()

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

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

Modifier and Type	Field	Description
protected SnpEffectPredictor	TestCasesHgvsBase.snpEffectPredictor

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

Modifier and Type	Method	Description
SnpEffectPredictor	TestCasesIntegrationBase.build(java.lang.String genome)	Build a genome, return SnpEffectPredictor
SnpEffectPredictor	TestCasesIntegrationBase.buildAndCompare(java.lang.String genome, java.lang.String refSeqFile, java.lang.String fastaFile, java.lang.String resultFile, boolean hideProtein)	Build a genome from a RefSeq file and compare results to 'expected' results
SnpEffectPredictor	TestCasesIntegrationBase.buildEmbl(java.lang.String genome, java.lang.String emblFile)	Build a genome from a embl file and compare results to 'expected' results
SnpEffectPredictor	TestCasesIntegrationBase.buildGeneBank(java.lang.String genome, java.lang.String genBankFile)
SnpEffectPredictor	TestCasesIntegrationBase.buildGeneBank(java.lang.String genome, java.lang.String genBankFile, boolean circularCorrectlargeGap)	Build a genome from a genbank file and compare results to 'expected' results
SnpEffectPredictor	TestCasesIntegrationBase.buildGff3AndCompare(java.lang.String genome, java.lang.String gff3File, java.lang.String resultFile, boolean readSeqs, boolean createRandSequences)	Build a genome from a GFF3 file and compare results to 'expected' results
SnpEffectPredictor	TestCasesIntegrationBase.loadSnpEffectPredictor(java.lang.String genome, boolean build)	Load predictor and create interval forest

Constructors in org.snpeff.snpEffect.testCases.integration with parameters of type SnpEffectPredictor

Constructor	Description
CompareEffects(SnpEffectPredictor snpEffectPredictor, long randSeed, boolean verbose)

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

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

Modifier and Type	Field	Description
protected SnpEffectPredictor	TestCasesBase.snpEffectPredictor
SnpEffectPredictor	TestGenome.snpEffectPredictor

Methods in org.snpeff.snpEffect.testCases.unity that return SnpEffectPredictor

Modifier and Type	Method	Description
SnpEffectPredictor	TestGenome.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 SnpEffectPredictor

Modifier and Type	Method	Description
void	ReadsOnMarkersModel.setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)

Constructors in org.snpeff.stats with parameters of type SnpEffectPredictor

Constructor	Description
ReadsOnMarkersModel(SnpEffectPredictor snpEffectPredictor)

Uses of SnpEffectPredictor in org.snpeff.svg

Constructors in org.snpeff.svg with parameters of type SnpEffectPredictor

Constructor	Description
SvgTranslocation(Transcript tr1, Transcript tr2, VariantBnd varBnd, SnpEffectPredictor snpEffPredictor)