Enum Class BioType

java.lang.Object
java.lang.Enum<BioType>
org.snpeff.interval.BioType
All Implemented Interfaces:
Serializable, Comparable<BioType>, Constable

public enum BioType extends 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
  • Enum Constant Details

    • prime3_overlapping_ncrna

      public static final BioType prime3_overlapping_ncrna
    • antisense

      public static final BioType antisense
    • IG_C_gene

      public static final BioType IG_C_gene
    • IG_C_pseudogene

      public static final BioType IG_C_pseudogene
    • IG_D_gene

      public static final BioType IG_D_gene
    • IG_J_gene

      public static final BioType IG_J_gene
    • IG_J_pseudogene

      public static final BioType IG_J_pseudogene
    • IG_V_gene

      public static final BioType IG_V_gene
    • IG_V_pseudogene

      public static final BioType IG_V_pseudogene
    • lincRNA

      public static final BioType lincRNA
    • macro_lncRNA

      public static final BioType macro_lncRNA
    • miRNA

      public static final BioType miRNA
    • misc_RNA

      public static final BioType misc_RNA
    • Mt_rRNA

      public static final BioType Mt_rRNA
    • Mt_tRNA

      public static final BioType Mt_tRNA
    • non_coding

      public static final BioType non_coding
    • nonsense_mediated_decay

      public static final BioType nonsense_mediated_decay
    • non_stop_decay

      public static final BioType non_stop_decay
    • polymorphic_pseudogene

      public static final BioType polymorphic_pseudogene
    • processed_pseudogene

      public static final BioType processed_pseudogene
    • processed_transcript

      public static final BioType processed_transcript
    • protein_coding

      public static final BioType protein_coding
    • pseudogene

      public static final BioType pseudogene
    • retained_intron

      public static final BioType retained_intron
    • ribozyme

      public static final BioType ribozyme
    • rRNA

      public static final BioType rRNA
    • scaRNA

      public static final BioType scaRNA
    • scRNA

      public static final BioType scRNA
    • sense_intronic

      public static final BioType sense_intronic
    • sense_overlapping

      public static final BioType sense_overlapping
    • snoRNA

      public static final BioType snoRNA
    • snRNA

      public static final BioType snRNA
    • sRNA

      public static final BioType sRNA
    • TEC

      public static final BioType TEC
    • transcribed_processed_pseudogene

      public static final BioType transcribed_processed_pseudogene
    • transcribed_unitary_pseudogene

      public static final BioType transcribed_unitary_pseudogene
    • transcribed_unprocessed_pseudogene

      public static final BioType transcribed_unprocessed_pseudogene
    • translated_unprocessed_pseudogene

      public static final BioType translated_unprocessed_pseudogene
    • TR_C_gene

      public static final BioType TR_C_gene
    • TR_D_gene

      public static final BioType TR_D_gene
    • TR_J_gene

      public static final BioType TR_J_gene
    • TR_J_pseudogene

      public static final BioType TR_J_pseudogene
    • TR_V_gene

      public static final BioType TR_V_gene
    • TR_V_pseudogene

      public static final BioType TR_V_pseudogene
    • unitary_pseudogene

      public static final BioType unitary_pseudogene
    • unprocessed_pseudogene

      public static final BioType unprocessed_pseudogene
    • vaultRNA

      public static final BioType vaultRNA
  • Method Details

    • values

      public static BioType[] 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
    • valueOf

      public static BioType valueOf(String name)
      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 name
      NullPointerException - if the argument is null
    • coding

      public static BioType coding(boolean isCoding)
      Basic bioTypes for coding / non-coding genes
    • parse

      public static BioType parse(String str)
      Parse a BioType
    • isProteinCoding

      public boolean isProteinCoding()