Package org.snpeff.interval
Enum Class BioType
- All Implemented Interfaces:
Serializable
,Comparable<BioType>
,Constable
BioTypes: Gene or transcript bioType annotation
References: http://www.ensembl.org/info/genome/genebuild/biotypes.html
Biotypes classifies genes and transcripts into groups including: protein coding, pseudogene
, processed pseudogene, miRNA, rRNA, scRNA, snoRNA, snRNA. The biotypes can be grouped into
protein coding, pseudogene, long noncoding and short noncoding. Examples of biotypes in each
group are as follows:
Protein coding: IGC gene, IGD gene, IG gene, IGJ gene, IGLV gene, IGM gene, IGV gene
, IGZ gene, nonsense mediated decay, nontranslating CDS, non stop decay
, polymorphic pseudogene, TRC gene, TRD gene, TRJ gene.
Pseudogene: disrupted domain, IGC pseudogene, IGJ pseudogene, IG pseudogene, IGV pseudogene
, processed pseudogene, transcribed processed pseudogene, transcribed unitary pseudogene
, transcribed unprocessed pseudogene, translated processed pseudogene
, TRJ pseudogene, unprocessed pseudogene
Long noncoding: 3prime overlapping ncrna, ambiguous orf, antisense, antisense RNA, lincRNA
, ncrna host, processed transcript, sense intronic, sense overlapping
Short noncoding: miRNA, miRNA_pseudogene, miscRNA, miscRNA pseudogene, Mt rRNA, Mt tRNA, rRNA
, scRNA, snlRNA, snoRNA, snRNA, tRNA, tRNA_pseudogene
- Author:
- pcingola
-
Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>
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Enum Constant Summary
Enum ConstantsEnum ConstantDescription -
Method Summary
Modifier and TypeMethodDescriptionstatic BioType
coding
(boolean isCoding) Basic bioTypes for coding / non-coding genesboolean
static BioType
Parse a BioTypestatic BioType
Returns the enum constant of this class with the specified name.static BioType[]
values()
Returns an array containing the constants of this enum class, in the order they are declared.
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Enum Constant Details
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prime3_overlapping_ncrna
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antisense
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IG_C_gene
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IG_C_pseudogene
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IG_D_gene
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IG_J_gene
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IG_J_pseudogene
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IG_V_gene
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IG_V_pseudogene
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lincRNA
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macro_lncRNA
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miRNA
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misc_RNA
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Mt_rRNA
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Mt_tRNA
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non_coding
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nonsense_mediated_decay
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non_stop_decay
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polymorphic_pseudogene
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processed_pseudogene
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processed_transcript
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protein_coding
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pseudogene
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retained_intron
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ribozyme
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rRNA
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scaRNA
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scRNA
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sense_intronic
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sense_overlapping
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snoRNA
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snRNA
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sRNA
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TEC
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transcribed_processed_pseudogene
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transcribed_unitary_pseudogene
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transcribed_unprocessed_pseudogene
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translated_unprocessed_pseudogene
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TR_C_gene
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TR_D_gene
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TR_J_gene
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TR_J_pseudogene
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TR_V_gene
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TR_V_pseudogene
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unitary_pseudogene
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unprocessed_pseudogene
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vaultRNA
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Method Details
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values
Returns an array containing the constants of this enum class, in the order they are declared.- Returns:
- an array containing the constants of this enum class, in the order they are declared
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valueOf
Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)- Parameters:
name
- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException
- if this enum class has no constant with the specified nameNullPointerException
- if the argument is null
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coding
Basic bioTypes for coding / non-coding genes -
parse
Parse a BioType -
isProteinCoding
public boolean isProteinCoding()
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