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
    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
    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 (a line) in a VCF file