Uses of Class
org.snpeff.interval.Interval
Packages that use Interval
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Uses of Interval in org.snpeff.interval
Subclasses of Interval in org.snpeff.intervalModifier and TypeClassDescriptionclass
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
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalidclass
This is a custom interval (i.e.class
Interval for a gene, as well as some other information: exons, utrs, cds, etc.class
Interval for an exonclass
Interval for a gene, as well as transcriptsclass
An interval intended as a markclass
This is just used for the Interval class.class
An interval intended as a markclass
An interval intended as a markclass
Interval for in intergenic regionclass
Interval for a conserved intergenic regionclass
IntervalAndSubIntervals<T extends Marker>
Interval that contains sub intervals.class
Intronclass
Interval for a conserved non-coding region in an intronclass
An interval intended as a markclass
This is a marker used as a 'fake' parent during data serializationclass
Marker with a DNA sequenceclass
miRna binding site (usually this was predicted by some algorithm)class
Regulatory elementsclass
NextProt annotation markerclass
Protein interaction: An amino acid that is "in contact" with another amino acid.class
Protein interaction: An amino acid that is "in contact" with another amino acid within the same protein.class
Protein interaction: An amino acid that is "in contact" with another amino acid.class
Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.class
Regulatory elementsclass
Interval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes.class
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_splicingclass
A (putative) branch site.class
A (putative) U12 branch site.class
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_splicingclass
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
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.class
Interval for a gene, as well as some other information: exons, utrs, cds, etc.class
Interval for a UTR (5 prime UTR and 3 prime UTRclass
Interval for a UTR (5 prime UTR and 3 prime UTRclass
Interval for a UTR (5 prime UTR and 3 prime UTRclass
A variant represents a change in a reference sequenceclass
A 'BND' variant (i.e.class
A variant respect to non-reference (e.g.class
A variant that has a numeric score.Fields in org.snpeff.interval declared as IntervalMethods in org.snpeff.interval that return IntervalModifier and TypeMethodDescriptionInterval.clone()
Interval.findParent
(Class clazz) Go up (parent) until we find an instance of 'clazz'Interval.getParent()
Markers.rand()
Return a random interval within this collectionMethods in org.snpeff.interval with parameters of type IntervalModifier and TypeMethodDescriptionint
Chromosome.compareChromoName
(Interval interval) Compare only chromosome's nameint
Compare by start and endint
Compare by start and endint
Compare by start and endint
Marker.compareToPos
(Interval i2) Compare genomic coordinatesboolean
boolean
Interval.intersects
(Interval interval) Return true if this intersects 'interval'void
Constructors in org.snpeff.interval with parameters of type Interval -
Uses of Interval in org.snpeff.interval.tree
Methods in org.snpeff.interval.tree with parameters of type IntervalModifier and TypeMethodDescriptionPerform an interval intersection query on the nodePerform an interval intersection query on the nodePerform an interval query, returning the intervals that intersect with 'interval'Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'protected void
Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'Perform an interval query, returning the intervals that intersect with '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.vcfModifier and TypeClassDescriptionclass
Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.class
A VCF entry (a line) in a VCF file