Enum EffectType

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<EffectType>

    public enum EffectType
    extends java.lang.Enum<EffectType>
    Effect type: Note that effects are sorted (declared) by impact (highest to lowest putative impact). The idea is to be able to report only one effect per variant/transcript
    Author:
    pcingola
    • Enum Constant Detail

      • CHROMOSOME_LARGE_DELETION

        public static final EffectType CHROMOSOME_LARGE_DELETION
      • CHROMOSOME_LARGE_INVERSION

        public static final EffectType CHROMOSOME_LARGE_INVERSION
      • CHROMOSOME_LARGE_DUPLICATION

        public static final EffectType CHROMOSOME_LARGE_DUPLICATION
      • GENE_REARRANGEMENT

        public static final EffectType GENE_REARRANGEMENT
      • GENE_DELETED

        public static final EffectType GENE_DELETED
      • TRANSCRIPT_DELETED

        public static final EffectType TRANSCRIPT_DELETED
      • EXON_DELETED

        public static final EffectType EXON_DELETED
      • EXON_DELETED_PARTIAL

        public static final EffectType EXON_DELETED_PARTIAL
      • GENE_FUSION

        public static final EffectType GENE_FUSION
      • GENE_FUSION_REVERESE

        public static final EffectType GENE_FUSION_REVERESE
      • GENE_FUSION_HALF

        public static final EffectType GENE_FUSION_HALF
      • FRAME_SHIFT

        public static final EffectType FRAME_SHIFT
      • STOP_GAINED

        public static final EffectType STOP_GAINED
      • STOP_LOST

        public static final EffectType STOP_LOST
      • START_LOST

        public static final EffectType START_LOST
      • SPLICE_SITE_ACCEPTOR

        public static final EffectType SPLICE_SITE_ACCEPTOR
      • SPLICE_SITE_DONOR

        public static final EffectType SPLICE_SITE_DONOR
      • RARE_AMINO_ACID

        public static final EffectType RARE_AMINO_ACID
      • EXON_DUPLICATION

        public static final EffectType EXON_DUPLICATION
      • EXON_DUPLICATION_PARTIAL

        public static final EffectType EXON_DUPLICATION_PARTIAL
      • EXON_INVERSION

        public static final EffectType EXON_INVERSION
      • EXON_INVERSION_PARTIAL

        public static final EffectType EXON_INVERSION_PARTIAL
      • PROTEIN_PROTEIN_INTERACTION_LOCUS

        public static final EffectType PROTEIN_PROTEIN_INTERACTION_LOCUS
      • PROTEIN_STRUCTURAL_INTERACTION_LOCUS

        public static final EffectType PROTEIN_STRUCTURAL_INTERACTION_LOCUS
      • NON_SYNONYMOUS_CODING

        public static final EffectType NON_SYNONYMOUS_CODING
      • GENE_DUPLICATION

        public static final EffectType GENE_DUPLICATION
      • TRANSCRIPT_DUPLICATION

        public static final EffectType TRANSCRIPT_DUPLICATION
      • UTR_5_DELETED

        public static final EffectType UTR_5_DELETED
      • UTR_3_DELETED

        public static final EffectType UTR_3_DELETED
      • SPLICE_SITE_BRANCH_U12

        public static final EffectType SPLICE_SITE_BRANCH_U12
      • GENE_INVERSION

        public static final EffectType GENE_INVERSION
      • TRANSCRIPT_INVERSION

        public static final EffectType TRANSCRIPT_INVERSION
      • CODON_INSERTION

        public static final EffectType CODON_INSERTION
      • CODON_CHANGE_PLUS_CODON_INSERTION

        public static final EffectType CODON_CHANGE_PLUS_CODON_INSERTION
      • CODON_DELETION

        public static final EffectType CODON_DELETION
      • CODON_CHANGE_PLUS_CODON_DELETION

        public static final EffectType CODON_CHANGE_PLUS_CODON_DELETION
      • NON_SYNONYMOUS_STOP

        public static final EffectType NON_SYNONYMOUS_STOP
      • NON_SYNONYMOUS_START

        public static final EffectType NON_SYNONYMOUS_START
      • SPLICE_SITE_REGION

        public static final EffectType SPLICE_SITE_REGION
      • SPLICE_SITE_BRANCH

        public static final EffectType SPLICE_SITE_BRANCH
      • SYNONYMOUS_CODING

        public static final EffectType SYNONYMOUS_CODING
      • SYNONYMOUS_START

        public static final EffectType SYNONYMOUS_START
      • SYNONYMOUS_STOP

        public static final EffectType SYNONYMOUS_STOP
      • CODON_CHANGE

        public static final EffectType CODON_CHANGE
      • START_GAINED

        public static final EffectType START_GAINED
      • MOTIF_DELETED

        public static final EffectType MOTIF_DELETED
      • FEATURE_FUSION

        public static final EffectType FEATURE_FUSION
      • FRAME_SHIFT_BEFORE_CDS_START

        public static final EffectType FRAME_SHIFT_BEFORE_CDS_START
      • FRAME_SHIFT_AFTER_CDS_END

        public static final EffectType FRAME_SHIFT_AFTER_CDS_END
      • UTR_5_PRIME

        public static final EffectType UTR_5_PRIME
      • UTR_3_PRIME

        public static final EffectType UTR_3_PRIME
      • REGULATION

        public static final EffectType REGULATION
      • MICRO_RNA

        public static final EffectType MICRO_RNA
      • UPSTREAM

        public static final EffectType UPSTREAM
      • DOWNSTREAM

        public static final EffectType DOWNSTREAM
      • NEXT_PROT

        public static final EffectType NEXT_PROT
      • INTRON_CONSERVED

        public static final EffectType INTRON_CONSERVED
      • INTRAGENIC

        public static final EffectType INTRAGENIC
      • INTERGENIC_CONSERVED

        public static final EffectType INTERGENIC_CONSERVED
      • INTERGENIC

        public static final EffectType INTERGENIC
      • TRANSCRIPT

        public static final EffectType TRANSCRIPT
      • SEQUENCE

        public static final EffectType SEQUENCE
      • CHROMOSOME_ELONGATION

        public static final EffectType CHROMOSOME_ELONGATION
      • CHROMOSOME

        public static final EffectType CHROMOSOME
    • Method Detail

      • values

        public static EffectType[] 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 (EffectType c : EffectType.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static EffectType 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
      • parse

        public static EffectType parse​(EffFormatVersion formatVersion,
                                       java.lang.String str)
        Parse a string to an EffectType
      • getGeneRegion

        public EffectType getGeneRegion()
      • isFusion

        public boolean isFusion()
      • toSequenceOntology

        public java.lang.String toSequenceOntology​(EffFormatVersion formatVersion,
                                                   Variant variant)