Enum BioType

  • 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
    • Enum Constant Detail

      • 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 Detail

      • 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
      • 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 name
        java.lang.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​(java.lang.String str)
        Parse a BioType
      • isProteinCoding

        public boolean isProteinCoding()