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 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 TranscriptModifierConstructorDescriptionprotected
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) -
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 TypeMethodDescriptionvoid
DistanceResult.setTr1
(Transcript tr) void
DistanceResult.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 TypeMethodDescriptionint
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 String
HgvsProtein.pos
(Transcript tr, int codonNum) Protein positionprotected 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 TranscriptModifier and TypeMethodDescriptionprotected Transcript
SnpEffPredictorFactoryGff.findOrCreateTranscript
(GffMarker gffMarker) Create and add a transcript based on GffMarkerprotected Transcript
SnpEffPredictorFactory.findTranscript
(String id) protected Transcript
SnpEffPredictorFactory.findTranscript
(String trId, String id) Methods in org.snpeff.snpEffect.factory with parameters of type TranscriptModifier and TypeMethodDescriptionprotected void
SnpEffPredictorFactory.add
(Transcript tr) Add a transcriptprotected Exon
SnpEffPredictorFactoryGff.addExon
(Transcript tr, GffMarker gffMarker, 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) -
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 TypeMethodDescriptiondouble
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, String type, VariantEffect variantEffect) Sample this invalid input: '<'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)