Package org.snpeff.snpEffect
Enum Class EffectType
- All Implemented Interfaces:
Serializable
,Comparable<EffectType>
,Constable
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
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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 TypeMethodDescriptionReturn effect impactboolean
isFusion()
static EffectType
parse
(EffFormatVersion formatVersion, String str) Parse a string to an EffectTypetoSequenceOntology
(EffFormatVersion formatVersion, Variant variant) static EffectType
Returns the enum constant of this class with the specified name.static EffectType[]
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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CHROMOSOME_LARGE_DELETION
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CHROMOSOME_LARGE_INVERSION
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CHROMOSOME_LARGE_DUPLICATION
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GENE_REARRANGEMENT
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GENE_DELETED
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TRANSCRIPT_DELETED
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EXON_DELETED
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EXON_DELETED_PARTIAL
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GENE_FUSION
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GENE_FUSION_REVERESE
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GENE_FUSION_HALF
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FRAME_SHIFT
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STOP_GAINED
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STOP_LOST
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START_LOST
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SPLICE_SITE_ACCEPTOR
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SPLICE_SITE_DONOR
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RARE_AMINO_ACID
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EXON_DUPLICATION
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EXON_DUPLICATION_PARTIAL
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EXON_INVERSION
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EXON_INVERSION_PARTIAL
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PROTEIN_PROTEIN_INTERACTION_LOCUS
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PROTEIN_STRUCTURAL_INTERACTION_LOCUS
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NON_SYNONYMOUS_CODING
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GENE_DUPLICATION
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TRANSCRIPT_DUPLICATION
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UTR_5_DELETED
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UTR_3_DELETED
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SPLICE_SITE_BRANCH_U12
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GENE_INVERSION
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TRANSCRIPT_INVERSION
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CODON_INSERTION
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CODON_CHANGE_PLUS_CODON_INSERTION
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CODON_DELETION
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CODON_CHANGE_PLUS_CODON_DELETION
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NON_SYNONYMOUS_STOP
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NON_SYNONYMOUS_START
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SPLICE_SITE_REGION
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SPLICE_SITE_BRANCH
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SYNONYMOUS_CODING
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SYNONYMOUS_START
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SYNONYMOUS_STOP
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CODON_CHANGE
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START_GAINED
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MOTIF
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MOTIF_DELETED
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FEATURE_FUSION
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FRAME_SHIFT_BEFORE_CDS_START
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FRAME_SHIFT_AFTER_CDS_END
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UTR_5_PRIME
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UTR_3_PRIME
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REGULATION
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MICRO_RNA
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UPSTREAM
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DOWNSTREAM
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NEXT_PROT
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INTRON_CONSERVED
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INTRON
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INTRAGENIC
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INTERGENIC_CONSERVED
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INTERGENIC
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CDS
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EXON
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TRANSCRIPT
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GENE
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SEQUENCE
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CHROMOSOME_ELONGATION
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CUSTOM
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CHROMOSOME
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GENOME
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NONE
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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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parse
Parse a string to an EffectType -
effectImpact
Return effect impact -
getGeneRegion
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isFusion
public boolean isFusion() -
toSequenceOntology
-