Package org.snpeff.interval
Enum BioType
- java.lang.Object
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- java.lang.Enum<BioType>
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- org.snpeff.interval.BioType
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Comparable<BioType>
public enum BioType extends java.lang.Enum<BioType>
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
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Enum Constant Summary
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static BioType
coding(boolean isCoding)
Basic bioTypes for coding / non-coding genesboolean
isProteinCoding()
static BioType
parse(java.lang.String str)
Parse a BioTypestatic BioType
valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.static BioType[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
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Enum Constant Detail
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prime3_overlapping_ncrna
public static final BioType prime3_overlapping_ncrna
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antisense
public static final BioType antisense
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IG_C_gene
public static final BioType IG_C_gene
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IG_C_pseudogene
public static final BioType IG_C_pseudogene
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IG_D_gene
public static final BioType IG_D_gene
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IG_J_gene
public static final BioType IG_J_gene
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IG_J_pseudogene
public static final BioType IG_J_pseudogene
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IG_V_gene
public static final BioType IG_V_gene
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IG_V_pseudogene
public static final BioType IG_V_pseudogene
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lincRNA
public static final BioType lincRNA
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macro_lncRNA
public static final BioType macro_lncRNA
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miRNA
public static final BioType miRNA
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misc_RNA
public static final BioType misc_RNA
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Mt_rRNA
public static final BioType Mt_rRNA
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Mt_tRNA
public static final BioType Mt_tRNA
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non_coding
public static final BioType non_coding
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nonsense_mediated_decay
public static final BioType nonsense_mediated_decay
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non_stop_decay
public static final BioType non_stop_decay
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polymorphic_pseudogene
public static final BioType polymorphic_pseudogene
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processed_pseudogene
public static final BioType processed_pseudogene
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processed_transcript
public static final BioType processed_transcript
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protein_coding
public static final BioType protein_coding
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pseudogene
public static final BioType pseudogene
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retained_intron
public static final BioType retained_intron
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ribozyme
public static final BioType ribozyme
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rRNA
public static final BioType rRNA
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scaRNA
public static final BioType scaRNA
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scRNA
public static final BioType scRNA
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sense_intronic
public static final BioType sense_intronic
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sense_overlapping
public static final BioType sense_overlapping
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snoRNA
public static final BioType snoRNA
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snRNA
public static final BioType snRNA
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sRNA
public static final BioType sRNA
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TEC
public static final BioType TEC
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transcribed_processed_pseudogene
public static final BioType transcribed_processed_pseudogene
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transcribed_unitary_pseudogene
public static final BioType transcribed_unitary_pseudogene
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transcribed_unprocessed_pseudogene
public static final BioType transcribed_unprocessed_pseudogene
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translated_unprocessed_pseudogene
public static final BioType translated_unprocessed_pseudogene
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TR_C_gene
public static final BioType TR_C_gene
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TR_D_gene
public static final BioType TR_D_gene
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TR_J_gene
public static final BioType TR_J_gene
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TR_J_pseudogene
public static final BioType TR_J_pseudogene
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TR_V_gene
public static final BioType TR_V_gene
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TR_V_pseudogene
public static final BioType TR_V_pseudogene
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unitary_pseudogene
public static final BioType unitary_pseudogene
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unprocessed_pseudogene
public static final BioType unprocessed_pseudogene
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vaultRNA
public static final BioType vaultRNA
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Method Detail
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values
public static BioType[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:for (BioType c : BioType.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
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valueOf
public static BioType valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (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:
java.lang.IllegalArgumentException
- if this enum type has no constant with the specified namejava.lang.NullPointerException
- if the argument is null
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coding
public static BioType coding(boolean isCoding)
Basic bioTypes for coding / non-coding genes
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parse
public static BioType parse(java.lang.String str)
Parse a BioType
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isProteinCoding
public boolean isProteinCoding()
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