# Uses of Class
org.snpeff.interval.Interval

Packages that use Interval
Package
Description
org.snpeff.interval
org.snpeff.interval.tree
org.snpeff.vcf

## Uses of Interval in org.snpeff.interval

Subclasses of Interval in org.snpeff.interval
Modifier and Type
Class
Description
`class`
`Cds`
CDS: The coding region of a gene, also known as the coding sequence or CDS (from Coding DNA Sequence), is that portion of a gene's DNA or RNA, composed of exons, that codes for protein.
`class`
`Chromosome`
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
`class`
`Custom`
This is a custom interval (i.e.
`class`
`Downstream`
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
`class`
`Exon`
Interval for an exon
`class`
`Gene`
Interval for a gene, as well as transcripts
`class`
`GenericMarker`
An interval intended as a mark
`class`
`Genome`
This is just used for the Interval class.
`class`
`GffMarker`
An interval intended as a mark
`class`
`Gtf2Marker`
An interval intended as a mark
`class`
`Intergenic`
Interval for in intergenic region
`class`
`IntergenicConserved`
Interval for a conserved intergenic region
`class`
`IntervalAndSubIntervals<T extends Marker>`
Interval that contains sub intervals.
`class`
`Intron`
Intron
`class`
`IntronConserved`
Interval for a conserved non-coding region in an intron
`class`
`Marker`
An interval intended as a mark (i.e.
`class`
`MarkerParentId`
This is a marker used as a 'fake' parent during data serialization
`class`
`MarkerSeq`
Marker with a DNA sequence
`class`
`MicroRnaBindingSite`
miRna binding site (usually this was predicted by some algorithm)
`class`
`Motif`
Regulatory elements
`class`
`NextProt`
NextProt annotation marker
`class`
`ProteinInteractionLocus`
Protein interaction: An amino acid that is "in contact" with another amino acid.
`class`
`ProteinProteinInteractionLocus`
Protein interaction: An amino acid that is "in contact" with another amino acid within the same protein.
`class`
`ProteinStructuralInteractionLocus`
Protein interaction: An amino acid that is "in contact" with another amino acid.
`class`
`RareAminoAcid`
Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.
`class`
`Regulation`
Regulatory elements
`class`
`SpliceSite`
Interval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes.
`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.
`class`
`Transcript`
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
`class`
`Upstream`
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
`class`
`Utr`
Interval for a UTR (5 prime UTR and 3 prime UTR
`class`
`Utr3prime`
Interval for a UTR (5 prime UTR and 3 prime UTR
`class`
`Utr5prime`
Interval for a UTR (5 prime UTR and 3 prime UTR
`class`
`Variant`
A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
`class`
`VariantBnd`
A 'BND' variant (i.e.
`class`
`VariantNonRef`
A variant respect to non-reference (e.g.
`class`
`VariantWithScore`
A variant that has a numeric score.
Fields in org.snpeff.interval declared as Interval
Modifier and Type
Field
Description
`protected Interval`
Interval.`parent`
Methods in org.snpeff.interval that return Interval
Modifier and Type
Method
Description
`Interval`
Interval.`clone()`
`Interval`
Interval.`findParent(Class clazz)`
Go up (parent) until we find an instance of 'clazz'
`Interval`
Interval.`getParent()`
`Interval`
Markers.`rand()`
Return a random interval within this collection
Methods in org.snpeff.interval with parameters of type Interval
Modifier and Type
Method
Description
`int`
Chromosome.`compareChromoName(Interval interval)`
Compare only chromosome's name
`int`
Interval.`compareTo(Interval i2)`
Compare by start and end
`int`
Marker.`compareTo(Interval i2)`
Compare by start and end
`int`
Variant.`compareTo(Interval i2)`
Compare by start and end
`int`
Marker.`compareToPos(Interval i2)`
Compare genomic coordinates
`boolean`
Interval.`equals(Interval interval)`
`boolean`
Interval.`intersects(Interval interval)`
Return true if this intersects 'interval'
`void`
Interval.`setParent(Interval parent)`
Constructors in org.snpeff.interval with parameters of type Interval
Modifier
Constructor
Description
``
`Interval(Interval parent, int start, int end, boolean strandMinus, String id)`

## Uses of Interval in org.snpeff.interval.tree

Methods in org.snpeff.interval.tree with parameters of type Interval
Modifier and Type
Method
Description
`Markers`
IntervalNode.`query(Interval queryInterval)`
Perform an interval intersection query on the node
`Markers`
IntervalNodeOri.`query(Interval target)`
Perform an interval intersection query on the node
`Markers`
IntervalTree.`query(Interval interval)`
Perform an interval query, returning the intervals that intersect with 'interval'
`Markers`
IntervalTreeArray.`query(Interval marker)`
Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'
`protected void`
IntervalTreeArray.`query(Interval marker, int idx, Markers results)`
Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'
`Markers`
IntervalTreeOri.`query(Interval interval)`
Perform an interval query, returning the intervals that intersect with 'interval'
`Markers`
Itree.`query(Interval interval)`
Perform an interval query, returning the intervals that intersect with 'interval'
`protected void`
IntervalTreeArray.`queryIntersects(Interval marker, int idx, Markers results)`
Query entries intersecting 'marker' at node 'idx'

## Uses of Interval in org.snpeff.vcf

Subclasses of Interval in org.snpeff.vcf
Modifier and Type
Class
Description
`class`
`VariantVcfEntry`
Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.
`class`
`VcfEntry`
A VCF entry is a line in a VCF file A VCF line can have multiple variants, and multiple genotypes The VcfEntry represents the VCF line, NOT the variant itself.