Uses of Class
org.snpeff.interval.Gene
-
Packages that use Gene Package Description org.snpeff.geneSets org.snpeff.interval org.snpeff.snpEffect org.snpeff.snpEffect.factory org.snpeff.snpEffect.testCases.unity org.snpeff.stats org.snpeff.svg org.snpeff.vcf -
-
Uses of Gene in org.snpeff.geneSets
Methods in org.snpeff.geneSets with parameters of type Gene Modifier and Type Method Description void
GeneStats. add(Gene gene)
void
GeneStats. add(Gene gene, boolean useGeneId)
Add a gene, update statistics -
Uses of Gene in org.snpeff.interval
Methods in org.snpeff.interval that return Gene Modifier and Type Method Description Gene
Gene. circularClone()
In a circular genome, a gene can have negative coordinates or crosses over chromosome end.Gene
Gene. cloneShallow()
Gene
Genes. get(java.lang.String geneId)
Obtain a gene intervalGene
Genes. getGeneByName(java.lang.String geneName)
Obtain a gene by GeneName WARNING: The first match is returned.Methods in org.snpeff.interval that return types with arguments of type Gene Modifier and Type Method Description java.util.List<Gene>
Genome. getGenesSorted()
Create a sorted list of genes (sorted by gene Id)java.util.List<Gene>
Genome. getGenesSortedPos()
Create a sorted list of genes (sorted by genomic position)java.util.Iterator<Gene>
Genes. iterator()
java.util.Collection<Gene>
Genes. sorted()
java.util.Collection<Gene>
Genes. values()
Methods in org.snpeff.interval with parameters of type Gene Modifier and Type Method Description void
Genes. add(Gene gene)
Add a gene interval to this collectionstatic Intergenic
Intergenic. createIntergenic(Gene geneLeft, Gene geneRight)
Creates an intergenic marker based on the "space" between two genesConstructors in org.snpeff.interval with parameters of type Gene Constructor Description Transcript(Gene gene, int start, int end, boolean strandMinus, java.lang.String id)
-
Uses of Gene in org.snpeff.snpEffect
Methods in org.snpeff.snpEffect that return Gene Modifier and Type Method Description Gene
SnpEffectPredictor. getGene(java.lang.String geneId)
Obtain a gene by geneIdGene
VariantEffect. getGene()
Gene
VariantEffectFusion. getGene()
Gene
VariantEffectStructural. getGene()
Gene
VariantEffectFusion. getGeneLeft()
Gene
VariantEffectFusion. getGeneRight()
Gene
SnpEffectPredictor. queryClosestGene(Marker inputInterval)
Find closest gene to this marker In case more than one 'closest' gene is found (e.g.Methods in org.snpeff.snpEffect that return types with arguments of type Gene Modifier and Type Method Description java.util.List<Gene>
VariantEffect. getGenes()
java.util.List<Gene>
VariantEffectStructural. getGenes()
Methods in org.snpeff.snpEffect with parameters of type Gene Modifier and Type Method Description void
SnpEffectPredictor. add(Gene gene)
Add a gene interval -
Uses of Gene in org.snpeff.snpEffect.factory
Methods in org.snpeff.snpEffect.factory that return Gene Modifier and Type Method Description protected Gene
SnpEffPredictorFactoryGff. addGene(GffMarker gffMarker)
Create and add a gene based on GffMarkerprotected Gene
SnpEffPredictorFactory. findGene(java.lang.String id)
protected Gene
SnpEffPredictorFactory. findGene(java.lang.String geneId, java.lang.String id)
protected Gene
SnpEffPredictorFactoryGff. findOrCreateGene(GffMarker gffMarker)
Find or create a gene based on GffMarkerMethods in org.snpeff.snpEffect.factory with parameters of type Gene Modifier and Type Method Description protected void
SnpEffPredictorFactory. add(Gene gene)
Add a Gene -
Uses of Gene in org.snpeff.snpEffect.testCases.unity
Fields in org.snpeff.snpEffect.testCases.unity declared as Gene Modifier and Type Field Description protected Gene
TestCasesBase. gene
Methods in org.snpeff.snpEffect.testCases.unity with parameters of type Gene Modifier and Type Method Description protected void
TestCasesStructuralInv. checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns, Gene[] genesToAdd)
protected void
TestCasesBase. initSnpEffPredictor(Gene[] genesToAdd)
Create a predictor For the default parameters the first predictor created has only one transcript: 1:880-1001, strand: +, id:transcript_0, Protein Exons: 1:880-1001 'exon_0_0', rank: 1, frame: ., sequence: taaccccatatgattagtacggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgatgaccgatttatttgattccccacatttatttcatcggga CDS : taaccccatatgattagtacggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgatgaccgatttatttgattccccacatttatttcatcgggac Protein : *PHMISTVEEKHLTPIEQDLFRNTLYR*PIYLIPHIYFIG? -
Uses of Gene in org.snpeff.stats
Methods in org.snpeff.stats with parameters of type Gene Modifier and Type Method Description double
ObservedOverExpected. expected(Gene g)
Expected number of sequences (average between plus and minus strand)int
ObservedOverExpected. observed(Gene g)
Observed sequence (average between plus and minus strand)double
ObservedOverExpected. oe(Gene g)
Observed over expected ratiovoid
GeneCountByTypeTable. sample(Gene gene, Transcript tr, java.lang.String type, VariantEffect variantEffect)
Sample thistuple to update statistics -
Uses of Gene in org.snpeff.svg
Constructors in org.snpeff.svg with parameters of type Gene Constructor Description SvgGene(Gene gene, Svg svg)
-
Uses of Gene in org.snpeff.vcf
Constructors in org.snpeff.vcf with parameters of type Gene Constructor Description VcfLof(Gene gene, double percentAffected)
VcfNmd(Gene gene, double percentAffected)
-