Package org.snpeff.snpEffect
Enum EffectType
- java.lang.Object
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- java.lang.Enum<EffectType>
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- org.snpeff.snpEffect.EffectType
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- 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
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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 VariantEffect.EffectImpact
effectImpact()
Return effect impactEffectType
getGeneRegion()
boolean
isFusion()
static EffectType
parse(EffFormatVersion formatVersion, java.lang.String str)
Parse a string to an EffectTypejava.lang.String
toSequenceOntology(EffFormatVersion formatVersion, Variant variant)
static EffectType
valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.static EffectType[]
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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CHROMOSOME_LARGE_DELETION
public static final EffectType CHROMOSOME_LARGE_DELETION
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CHROMOSOME_LARGE_INVERSION
public static final EffectType CHROMOSOME_LARGE_INVERSION
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CHROMOSOME_LARGE_DUPLICATION
public static final EffectType CHROMOSOME_LARGE_DUPLICATION
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GENE_REARRANGEMENT
public static final EffectType GENE_REARRANGEMENT
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GENE_DELETED
public static final EffectType GENE_DELETED
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TRANSCRIPT_DELETED
public static final EffectType TRANSCRIPT_DELETED
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EXON_DELETED
public static final EffectType EXON_DELETED
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EXON_DELETED_PARTIAL
public static final EffectType EXON_DELETED_PARTIAL
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GENE_FUSION
public static final EffectType GENE_FUSION
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GENE_FUSION_REVERESE
public static final EffectType GENE_FUSION_REVERESE
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GENE_FUSION_HALF
public static final EffectType GENE_FUSION_HALF
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FRAME_SHIFT
public static final EffectType FRAME_SHIFT
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STOP_GAINED
public static final EffectType STOP_GAINED
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STOP_LOST
public static final EffectType STOP_LOST
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START_LOST
public static final EffectType START_LOST
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SPLICE_SITE_ACCEPTOR
public static final EffectType SPLICE_SITE_ACCEPTOR
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SPLICE_SITE_DONOR
public static final EffectType SPLICE_SITE_DONOR
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RARE_AMINO_ACID
public static final EffectType RARE_AMINO_ACID
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EXON_DUPLICATION
public static final EffectType EXON_DUPLICATION
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EXON_DUPLICATION_PARTIAL
public static final EffectType EXON_DUPLICATION_PARTIAL
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EXON_INVERSION
public static final EffectType EXON_INVERSION
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EXON_INVERSION_PARTIAL
public static final EffectType EXON_INVERSION_PARTIAL
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PROTEIN_PROTEIN_INTERACTION_LOCUS
public static final EffectType PROTEIN_PROTEIN_INTERACTION_LOCUS
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PROTEIN_STRUCTURAL_INTERACTION_LOCUS
public static final EffectType PROTEIN_STRUCTURAL_INTERACTION_LOCUS
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NON_SYNONYMOUS_CODING
public static final EffectType NON_SYNONYMOUS_CODING
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GENE_DUPLICATION
public static final EffectType GENE_DUPLICATION
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TRANSCRIPT_DUPLICATION
public static final EffectType TRANSCRIPT_DUPLICATION
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UTR_5_DELETED
public static final EffectType UTR_5_DELETED
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UTR_3_DELETED
public static final EffectType UTR_3_DELETED
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SPLICE_SITE_BRANCH_U12
public static final EffectType SPLICE_SITE_BRANCH_U12
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GENE_INVERSION
public static final EffectType GENE_INVERSION
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TRANSCRIPT_INVERSION
public static final EffectType TRANSCRIPT_INVERSION
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CODON_INSERTION
public static final EffectType CODON_INSERTION
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CODON_CHANGE_PLUS_CODON_INSERTION
public static final EffectType CODON_CHANGE_PLUS_CODON_INSERTION
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CODON_DELETION
public static final EffectType CODON_DELETION
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CODON_CHANGE_PLUS_CODON_DELETION
public static final EffectType CODON_CHANGE_PLUS_CODON_DELETION
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NON_SYNONYMOUS_STOP
public static final EffectType NON_SYNONYMOUS_STOP
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NON_SYNONYMOUS_START
public static final EffectType NON_SYNONYMOUS_START
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SPLICE_SITE_REGION
public static final EffectType SPLICE_SITE_REGION
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SPLICE_SITE_BRANCH
public static final EffectType SPLICE_SITE_BRANCH
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SYNONYMOUS_CODING
public static final EffectType SYNONYMOUS_CODING
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SYNONYMOUS_START
public static final EffectType SYNONYMOUS_START
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SYNONYMOUS_STOP
public static final EffectType SYNONYMOUS_STOP
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CODON_CHANGE
public static final EffectType CODON_CHANGE
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START_GAINED
public static final EffectType START_GAINED
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MOTIF
public static final EffectType MOTIF
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MOTIF_DELETED
public static final EffectType MOTIF_DELETED
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FEATURE_FUSION
public static final EffectType FEATURE_FUSION
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UTR_5_PRIME
public static final EffectType UTR_5_PRIME
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UTR_3_PRIME
public static final EffectType UTR_3_PRIME
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REGULATION
public static final EffectType REGULATION
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MICRO_RNA
public static final EffectType MICRO_RNA
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UPSTREAM
public static final EffectType UPSTREAM
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DOWNSTREAM
public static final EffectType DOWNSTREAM
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NEXT_PROT
public static final EffectType NEXT_PROT
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INTRON_CONSERVED
public static final EffectType INTRON_CONSERVED
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INTRON
public static final EffectType INTRON
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INTRAGENIC
public static final EffectType INTRAGENIC
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INTERGENIC_CONSERVED
public static final EffectType INTERGENIC_CONSERVED
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INTERGENIC
public static final EffectType INTERGENIC
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CDS
public static final EffectType CDS
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EXON
public static final EffectType EXON
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TRANSCRIPT
public static final EffectType TRANSCRIPT
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GENE
public static final EffectType GENE
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SEQUENCE
public static final EffectType SEQUENCE
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CHROMOSOME_ELONGATION
public static final EffectType CHROMOSOME_ELONGATION
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CUSTOM
public static final EffectType CUSTOM
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CHROMOSOME
public static final EffectType CHROMOSOME
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GENOME
public static final EffectType GENOME
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NONE
public static final EffectType NONE
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Method Detail
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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
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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 namejava.lang.NullPointerException
- if the argument is null
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parse
public static EffectType parse(EffFormatVersion formatVersion, java.lang.String str)
Parse a string to an EffectType
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effectImpact
public VariantEffect.EffectImpact effectImpact()
Return effect impact
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getGeneRegion
public EffectType getGeneRegion()
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isFusion
public boolean isFusion()
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toSequenceOntology
public java.lang.String toSequenceOntology(EffFormatVersion formatVersion, Variant variant)
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