Uses of Class org.snpeff.interval.SpliceSite (SnpEff 5.1 API)

Packages that use SpliceSite
Package Description

org.snpeff.interval

Uses of SpliceSite in org.snpeff.interval

Subclasses of SpliceSite in org.snpeff.interval
Modifier and Type	Class	Description
`class`	`SpliceSiteAcceptor`	Interval for a splice site acceptor Note: Splice sites donnor are defined as the last 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicing
`class`	`SpliceSiteBranch`	A (putative) branch site.
`class`	`SpliceSiteBranchU12`	A (putative) U12 branch site.
`class`	`SpliceSiteDonor`	Interval for a splice site donnor Note: Splice sites donnor are defined as the first 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicing
`class`	`SpliceSiteRegion`	Interval for a splice site acceptor From Sequence Ontology: A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.

Methods in org.snpeff.interval that return types with arguments of type SpliceSite
Modifier and Type	Method	Description
`java.util.ArrayList<SpliceSite>`	Exon.`getSpliceSites()`
`java.util.ArrayList<SpliceSite>`	Intron.`getSpliceSites()`
`java.util.List<SpliceSite>`	Transcript.`spliceSites()`

Methods in org.snpeff.interval with parameters of type SpliceSite
Modifier and Type	Method	Description
`void`	Exon.`add(SpliceSite ss)`	Add a splice site to the collection
`void`	Intron.`add(SpliceSite ss)`	Add a splice site to the collection
`void`	Transcript.`add(SpliceSite spliceSite)`	Add a SpliceSite