Uses of Class
org.snpeff.interval.MarkerSeq

Packages that use MarkerSeq

Package	Description
org.snpeff.binseq
org.snpeff.interval

Uses of MarkerSeq in org.snpeff.binseq

Methods in org.snpeff.binseq that return MarkerSeq

Modifier and Type	Method	Description
MarkerSeq	GenomicSequences.queryMarkerSequence(Marker marker)	Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form database

Methods in org.snpeff.binseq that return types with arguments of type MarkerSeq

Modifier and Type	Method	Description
java.util.Iterator<MarkerSeq>	GenomicSequences.iterator()

Uses of MarkerSeq in org.snpeff.interval

Subclasses of MarkerSeq in org.snpeff.interval

Modifier and Type	Class	Description
class	Exon	Interval for an exon

Methods in org.snpeff.interval that return MarkerSeq

Modifier and Type	Method	Description
MarkerSeq	MarkerSeq.apply(Variant variant)	Apply variant
MarkerSeq	MarkerSeq.cloneShallow()

Methods in org.snpeff.interval with parameters of type MarkerSeq

Modifier and Type	Method	Description
protected void	MarkerSeq.applyDel(Variant variant, MarkerSeq markerSeq)	Apply a change type deletion (update sequence)
protected void	MarkerSeq.applyDup(Variant variant, MarkerSeq markerSeq)	Apply a change type duplication (update sequence)
protected void	MarkerSeq.applyIns(Variant variant, MarkerSeq markerSeq)	Apply a change type insertion (update sequence)
protected void	MarkerSeq.applyMnp(Variant variant, MarkerSeq markerSeq)	Apply a change type MNP (update sequence)
protected void	MarkerSeq.applySnp(Variant variant, MarkerSeq markerSeq)	Apply a change type SNP (update sequence)