Uses of Interface
org.snpeff.serializer.TxtSerializable

Packages that use TxtSerializable
Package
Description
org.snpeff.interval
 
org.snpeff.serializer
 
org.snpeff.vcf
 

  • Uses of TxtSerializable in org.snpeff.interval

    Classes in org.snpeff.interval that implement TxtSerializable
    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.

  • Uses of TxtSerializable in org.snpeff.serializer

    Methods in org.snpeff.serializer that return TxtSerializable
    Modifier and Type
    Method
    Description
    protected TxtSerializable
    MarkerSerializer.getById(int id)
     

  • Uses of TxtSerializable in org.snpeff.vcf

    Classes in org.snpeff.vcf that implement TxtSerializable
    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