Uses of Interface
org.snpeff.serializer.TxtSerializable
Packages that use TxtSerializable
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Uses of TxtSerializable in org.snpeff.interval
Classes in org.snpeff.interval that implement TxtSerializableModifier 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 mark (i.e.class
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 sequence As of version 4.0, variants have no strand, i.e.class
A 'BND' variant (i.e.class
A variant respect to non-reference (e.g.class
A variant that has a numeric score. -
Uses of TxtSerializable in org.snpeff.serializer
Methods in org.snpeff.serializer that return TxtSerializable -
Uses of TxtSerializable in org.snpeff.vcf
Classes in org.snpeff.vcf that implement TxtSerializableModifier and TypeClassDescriptionclass
Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.class
A VCF entry is a line in a VCF file A VCF line can have multiple variants, and multiple genotypes