Uses of Class
org.snpeff.interval.Transcript

Packages that use Transcript

Package	Description
org.snpeff.interval
org.snpeff.interval.codonChange
org.snpeff.nextProt
org.snpeff.pdb
org.snpeff.snpEffect
org.snpeff.snpEffect.factory
org.snpeff.snpEffect.testCases.integration
org.snpeff.snpEffect.testCases.unity
org.snpeff.spliceSites
org.snpeff.stats
org.snpeff.svg

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 variant
Transcript	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 ID

Methods 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)

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 variant

Constructors 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)

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 marker
Markers	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)

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 position
protected 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 GffMarker
protected 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 transcript
protected Exon	SnpEffPredictorFactoryGff.addExon(Transcript tr, GffMarker gffMarker, java.lang.String exonId)	Create a new exon
protected void	SnpEffPredictorFactory.exonsFromCds(Transcript tr)	Create exons from CDS info WARNING: We might end up with redundant exons if some exons existed before this process
protected void	SnpEffPredictorFactory.replaceTranscript(Transcript trOld, Transcript trNew)

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

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 ratio
void	GeneCountByTypeTable.sample(Gene gene, Transcript tr, java.lang.String type, VariantEffect variantEffect)	Sample this tuple to update statistics

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

Constructor	Description
TranslocationReport(VariantBnd var, VcfEffect veff, Transcript tr1, Transcript tr2)

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)