Uses of Class
org.snpeff.interval.Transcript
Packages that use Transcript
Package
Description
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Uses of Transcript in org.snpeff.interval
Methods in org.snpeff.interval that return TranscriptModifier and TypeMethodDescriptionCreate a new transcript after applying changes in variantGene.canonical()Get canonical transcript Canonical transcripts are defined as the longest CDS of amongst the protein coding transcripts.Transcript.cloneShallow()Genes.findTranscript(String trId) Find a transcript by IDMethods in org.snpeff.interval with parameters of type TranscriptModifier and TypeMethodDescriptionstatic List<ProteinInteractionLocus>ProteinInteractionLocus.factory(Transcript tr, int aaPos, Transcript trInteract, String id) Create interaction.Constructors in org.snpeff.interval with parameters of type TranscriptModifierConstructorDescriptionCds(Transcript parent, int start, int end, boolean strandMinus, String id) CircularCorrection(Transcript tr, int chrLen) Downstream(Transcript parent, int start, int end, boolean strandMinus, String id) Exon(Transcript parent, int start, int end, boolean strandMinus, String id, int rank) Intron(Transcript parent, int start, int end, boolean strandMinus, String id, Exon exonBefore, Exon exonAfter) IntronConserved(Transcript parent, int start, int end, boolean strandMinus, String id) NextProt(Transcript transcript, int start, int end, String id) NextProt(Transcript transcript, int start, int end, String id, String name) ProteinInteractionLocus(Transcript parent, int start, int end, String id) ProteinProteinInteractionLocus(Transcript parent, int start, int end, Transcript trInteract, String id) ProteinStructuralInteractionLocus(Transcript parent, int start, int end, String id) Upstream(Transcript parent, int start, int end, boolean strandMinus, String id) -
Uses of Transcript in org.snpeff.interval.codonChange
Methods in org.snpeff.interval.codonChange with parameters of type TranscriptModifier and TypeMethodDescriptionstatic CodonChangeCodonChange.factory(Variant variant, Transcript transcript, VariantEffects variantEffects) Create a specific codon change for a variantConstructors in org.snpeff.interval.codonChange with parameters of type TranscriptModifierConstructorDescriptionprotectedCodonChange(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) -
Uses of Transcript in org.snpeff.nextProt
Methods in org.snpeff.nextProt with parameters of type TranscriptModifier and TypeMethodDescriptionNextProtMarkerFactory.nextProt(Transcript tr, String accession, String name, int aaStart, int aaEnd) Create a single NextProt markerNextProtMarkerFactory.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 that return TranscriptMethods in org.snpeff.pdb with parameters of type TranscriptModifier and TypeMethodDescriptionvoidDistanceResult.setTr1(Transcript tr) voidDistanceResult.setTr2(Transcript tr) Constructors in org.snpeff.pdb with parameters of type TranscriptModifierConstructorDescriptionDistanceResult(String proteinId, org.biojava.nbio.structure.AminoAcid aa1, org.biojava.nbio.structure.AminoAcid aa2, Transcript tr1, Transcript tr2, double distance) -
Uses of Transcript in org.snpeff.snpEffect
Fields in org.snpeff.snpEffect declared as TranscriptMethods in org.snpeff.snpEffect that return TranscriptModifier and TypeMethodDescriptionSnpEffectPredictor.getTranscript(String trId) VariantEffect.getTranscript()VariantEffectFusion.getTrLeft()VariantEffectFusion.getTrRight()Methods in org.snpeff.snpEffect with parameters of type TranscriptModifier and TypeMethodDescriptionintLossOfFunction.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 StringHgvsProtein.pos(Transcript tr, int codonNum) Protein positionprotected StringHgvsProtein.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 TranscriptModifier and TypeMethodDescriptionprotected TranscriptSnpEffPredictorFactoryGff.findOrCreateTranscript(GffMarker gffMarker) Create and add a transcript based on GffMarkerprotected TranscriptSnpEffPredictorFactory.findTranscript(String id) protected TranscriptSnpEffPredictorFactory.findTranscript(String trId, String id) Methods in org.snpeff.snpEffect.factory with parameters of type TranscriptModifier and TypeMethodDescriptionprotected voidSnpEffPredictorFactory.add(Transcript tr) Add a transcriptprotected ExonSnpEffPredictorFactoryGff.addExon(Transcript tr, GffMarker gffMarker, String exonId) Create a new exonprotected voidSnpEffPredictorFactory.exonsFromCds(Transcript tr) Create exons from CDS info WARNING: We might end up with redundant exons if some exons existed before this processprotected voidSnpEffPredictorFactory.replaceTranscript(Transcript trOld, Transcript trNew) -
Uses of Transcript in org.snpeff.spliceSites
Methods in org.snpeff.spliceSites that return types with arguments of type TranscriptModifier and TypeMethodDescriptionTranscriptSet.getByChromo(String chrName) TranscriptSet.iterator()Methods in org.snpeff.spliceSites with parameters of type TranscriptModifier and TypeMethodDescriptionSpliceTypes.addBestU12Score(Transcript tr, String chrSeq, 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 TranscriptModifier and TypeMethodDescriptiondoubleObservedOverExpected.expected(Transcript t) Expected number of sequences (average between plus and minus strand)intObservedOverExpected.observed(Transcript t) Observed sequence (average between plus and minus strand)doubleObservedOverExpected.oe(Transcript t) Observed over expected ratiovoidGeneCountByTypeTable.sample(Gene gene, Transcript tr, String type, VariantEffect variantEffect) Sample this <gene, marker, type, variant> tuple to update statisticsConstructors in org.snpeff.stats with parameters of type TranscriptModifierConstructorDescriptionTranslocationReport(VariantBnd var, VcfEffect veff, Transcript tr1, Transcript tr2) -
Uses of Transcript in org.snpeff.svg
Constructors in org.snpeff.svg with parameters of type TranscriptModifierConstructorDescriptionSvgNextProt(Transcript tr, Svg svg, Markers nextprotMarkers) SvgTranscript(Transcript tr, Svg svg) SvgTranslocation(Transcript tr1, Transcript tr2, VariantBnd varBnd, SnpEffectPredictor snpEffPredictor)
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