Uses of Class
org.snpeff.interval.Transcript
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Uses of Transcript in org.snpeff.interval
Methods in org.snpeff.interval that return Transcript Modifier and Type Method Description Transcript
Transcript. apply(Variant variant)
Create a new transcript after applying changes in variantTranscript
Gene. canonical()
Get canonical transcript Canonical transcripts are defined as the longest CDS of amongst the protein coding transcripts.Transcript
Transcript. cloneShallow()
Transcript
Genes. findTranscript(java.lang.String trId)
Find a transcript by IDMethods in org.snpeff.interval with parameters of type Transcript Modifier and Type Method Description static java.util.List<ProteinInteractionLocus>
ProteinInteractionLocus. factory(Transcript tr, int aaPos, Transcript trInteract, java.lang.String id)
Create interaction.Constructors in org.snpeff.interval with parameters of type Transcript Constructor Description Cds(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id)
CircularCorrection(Transcript tr)
CircularCorrection(Transcript tr, int chrLen)
Downstream(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id)
Exon(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id, int rank)
Intron(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id, Exon exonBefore, Exon exonAfter)
IntronConserved(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id)
NextProt(Transcript transcript, int start, int end, java.lang.String id)
NextProt(Transcript transcript, int start, int end, java.lang.String id, java.lang.String name)
ProteinInteractionLocus(Transcript parent, int start, int end, java.lang.String id)
ProteinProteinInteractionLocus(Transcript parent, int start, int end, Transcript trInteract, java.lang.String id)
ProteinStructuralInteractionLocus(Transcript parent, int start, int end, java.lang.String id)
Upstream(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id)
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Uses of Transcript in org.snpeff.interval.codonChange
Methods in org.snpeff.interval.codonChange with parameters of type Transcript Modifier and Type Method Description static CodonChange
CodonChange. factory(Variant variant, Transcript transcript, VariantEffects variantEffects)
Create a specific codon change for a variantConstructors in org.snpeff.interval.codonChange with parameters of type Transcript Constructor Description CodonChange(Variant variant, Transcript transcript, VariantEffects variantEffects)
CodonChangeDel(Variant variant, Transcript transcript, VariantEffects variantEffects)
CodonChangeDup(Variant variant, Transcript transcript, VariantEffects variantEffects)
CodonChangeIns(Variant variant, Transcript transcript, VariantEffects changeEffects)
CodonChangeInterval(Variant variant, Transcript transcript, VariantEffects varEffects)
CodonChangeInv(Variant variant, Transcript transcript, VariantEffects variantEffects)
CodonChangeMixed(Variant variant, Transcript transcript, VariantEffects variantEffects)
CodonChangeMnp(Variant variant, Transcript transcript, VariantEffects variantEffects)
CodonChangeSnp(Variant variant, Transcript transcript, VariantEffects variantEffects)
CodonChangeStructural(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Uses of Transcript in org.snpeff.nextProt
Methods in org.snpeff.nextProt with parameters of type Transcript Modifier and Type Method Description Markers
NextProtMarkerFactory. nextProt(Transcript tr, java.lang.String accession, java.lang.String name, int aaStart, int aaEnd)
Create a single NextProt markerMarkers
NextProtMarkerFactory. nextProt(Transcript tr, NextProtXmlAnnotation annotation, Location location)
Create a list of NextProt markers according to this annotation -
Uses of Transcript in org.snpeff.pdb
Methods in org.snpeff.pdb with parameters of type Transcript Modifier and Type Method Description void
DistanceResult. setTr1(Transcript tr)
void
DistanceResult. setTr2(Transcript tr)
Constructors in org.snpeff.pdb with parameters of type Transcript Constructor Description DistanceResult(org.biojava.nbio.structure.AminoAcid aa1, org.biojava.nbio.structure.AminoAcid aa2, Transcript tr1, Transcript tr2, double distance)
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Uses of Transcript in org.snpeff.snpEffect
Fields in org.snpeff.snpEffect declared as Transcript Modifier and Type Field Description protected Transcript
Hgvs. tr
Methods in org.snpeff.snpEffect that return Transcript Modifier and Type Method Description Transcript
SnpEffectPredictor. getTranscript(java.lang.String trId)
Transcript
VariantEffect. getTranscript()
Transcript
VariantEffectFusion. getTrLeft()
Transcript
VariantEffectFusion. getTrRight()
Methods in org.snpeff.snpEffect with parameters of type Transcript Modifier and Type Method Description int
LossOfFunction. lastNmdPos(Transcript tr)
Find the last position where a nonsense mediated decay is supposed to occurr This is 50 bases (MND_BASES_BEFORE_LAST_JUNCTION bases) before the last exon-exon junction.protected java.lang.String
HgvsProtein. pos(Transcript tr, int codonNum)
Protein positionprotected java.lang.String
HgvsProtein. pos(Transcript tr, int start, int end)
Position string given two coordinates -
Uses of Transcript in org.snpeff.snpEffect.factory
Methods in org.snpeff.snpEffect.factory that return Transcript Modifier and Type Method Description protected Transcript
SnpEffPredictorFactoryGff. findOrCreateTranscript(GffMarker gffMarker)
Create and add a transcript based on GffMarkerprotected Transcript
SnpEffPredictorFactory. findTranscript(java.lang.String id)
protected Transcript
SnpEffPredictorFactory. findTranscript(java.lang.String trId, java.lang.String id)
Methods in org.snpeff.snpEffect.factory with parameters of type Transcript Modifier and Type Method Description protected void
SnpEffPredictorFactory. add(Transcript tr)
Add a transcriptprotected Exon
SnpEffPredictorFactoryGff. addExon(Transcript tr, GffMarker gffMarker, java.lang.String exonId)
Create a new exonprotected void
SnpEffPredictorFactory. exonsFromCds(Transcript tr)
Create exons from CDS info WARNING: We might end up with redundant exons if some exons existed before this processprotected void
SnpEffPredictorFactory. replaceTranscript(Transcript trOld, Transcript trNew)
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Uses of Transcript in org.snpeff.snpEffect.testCases.integration
Fields in org.snpeff.snpEffect.testCases.integration declared as Transcript Modifier and Type Field Description protected Transcript
TestCasesHgvsBase. transcript
Methods in org.snpeff.snpEffect.testCases.integration that return Transcript Modifier and Type Method Description Transcript
TestCasesIntegrationBase. applyTranscript(java.lang.String genome, java.lang.String trId, java.lang.String vcfFileName)
Apply a variant to a transcript -
Uses of Transcript in org.snpeff.snpEffect.testCases.unity
Fields in org.snpeff.snpEffect.testCases.unity declared as Transcript Modifier and Type Field Description Transcript
TestGenome. tr
protected Transcript
TestCasesBase. transcript
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Uses of Transcript in org.snpeff.spliceSites
Methods in org.snpeff.spliceSites that return types with arguments of type Transcript Modifier and Type Method Description java.util.List<Transcript>
TranscriptSet. getByChromo(java.lang.String chrName)
java.util.Iterator<Transcript>
TranscriptSet. iterator()
Methods in org.snpeff.spliceSites with parameters of type Transcript Modifier and Type Method Description Tuple<java.lang.Double,java.lang.Integer>
SpliceTypes. addBestU12Score(Transcript tr, java.lang.String chrSeq, java.lang.String donorAcceptor, int intronStart, int intronEnd)
Calculate the best U12 score. -
Uses of Transcript in org.snpeff.stats
Methods in org.snpeff.stats with parameters of type Transcript Modifier and Type Method Description double
ObservedOverExpected. expected(Transcript t)
Expected number of sequences (average between plus and minus strand)int
ObservedOverExpected. observed(Transcript t)
Observed sequence (average between plus and minus strand)double
ObservedOverExpected. oe(Transcript t)
Observed over expected ratiovoid
GeneCountByTypeTable. sample(Gene gene, Transcript tr, java.lang.String type, VariantEffect variantEffect)
Sample thistuple to update statistics Constructors in org.snpeff.stats with parameters of type Transcript Constructor Description TranslocationReport(VariantBnd var, VcfEffect veff, Transcript tr1, Transcript tr2)
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Uses of Transcript in org.snpeff.svg
Constructors in org.snpeff.svg with parameters of type Transcript Constructor Description SvgNextProt(Transcript tr, Svg svg, Markers nextprotMarkers)
SvgTranscript(Transcript tr, Svg svg)
SvgTranslocation(Transcript tr1, Transcript tr2, VariantBnd varBnd, SnpEffectPredictor snpEffPredictor)
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