VepConsequence

gngs.VepConsequence

```
@groovy.transform.CompileStatic
final enum VepConsequence
extends java.lang.Enum<E<E>>
```
Models VEP Consequence type as sourced from https://asia.ensembl.org/info/genome/variation/prediction/predicted_data.html#consequences (Ensembl release 103 - February 2021). Also merges consequences initiator_codon_variant, non_coding_exon_variant and nc_transcript_variant that can only be found in deprecated gngs.VEPConsequences for backwards compatibility.

Field Summary

Fields
Modifiers	Name	Description
`static VepConsequence`	`CODING_SEQUENCE_VARIANT`
`static VepConsequence`	`DOWNSTREAM_GENE_VARIANT`
`static VepConsequence`	`FEATURE_ELONGATION`
`static VepConsequence`	`FEATURE_TRUNCATION`
`static VepConsequence`	`FIVE_PRIME_UTR_VARIANT`
`static VepConsequence`	`FRAMESHIFT_VARIANT`
`static VepConsequence`	`INCOMPLETE_TERMINAL_CODON_VARIANT`
`static VepConsequence`	`INFRAME_DELETION`
`static VepConsequence`	`INFRAME_INSERTION`
`static VepConsequence`	`INITIATOR_CODON_VARIANT`
`static VepConsequence`	`INTERGENIC_VARIANT`
`static VepConsequence`	`INTRON_VARIANT`
`static VepConsequence`	`MATURE_MIRNA_VARIANT`
`static VepConsequence`	`MAX_VALUE`
`static VepConsequence`	`MIN_VALUE`
`static VepConsequence`	`MISSENSE_VARIANT`
`static VepConsequence`	`NC_TRANSCRIPT_VARIANT`
`static VepConsequence`	`NMD_TRANSCRIPT_VARIANT`
`static VepConsequence`	`NON_CODING_EXON_VARIANT`
`static VepConsequence`	`NON_CODING_TRANSCRIPT_EXON_VARIANT`
`static VepConsequence`	`NON_CODING_TRANSCRIPT_VARIANT`
`static VepConsequence`	`PROTEIN_ALTERING_VARIANT`
`static VepConsequence`	`REGULATORY_REGION_ABLATION`
`static VepConsequence`	`REGULATORY_REGION_AMPLIFICATION`
`static VepConsequence`	`REGULATORY_REGION_VARIANT`
`static VepConsequence`	`SPLICE_ACCEPTOR_VARIANT`
`static VepConsequence`	`SPLICE_DONOR_VARIANT`
`static VepConsequence`	`SPLICE_REGION_VARIANT`
`static VepConsequence`	`START_LOST`
`static VepConsequence`	`START_RETAINED_VARIANT`
`static VepConsequence`	`STOP_GAINED`
`static VepConsequence`	`STOP_LOST`
`static VepConsequence`	`STOP_RETAINED_VARIANT`
`static VepConsequence`	`SYNONYMOUS_VARIANT`
`static VepConsequence`	`TFBS_ABLATION`
`static VepConsequence`	`TFBS_AMPLIFICATION`
`static VepConsequence`	`TF_BINDING_SITE_VARIANT`
`static VepConsequence`	`THREE_PRIME_UTR_VARIANT`
`static VepConsequence`	`TRANSCRIPT_ABLATION`
`static VepConsequence`	`TRANSCRIPT_AMPLIFICATION`
`static VepConsequence`	`UNKNOWN`
`static VepConsequence`	`UPSTREAM_GENE_VARIANT`

Properties Summary

Properties
Type	Name and description
`java.lang.String`	`description`
`java.lang.String`	`displayTerm`
`java.lang.String`	`ensemblColourHex`
`gngs.VepImpact`	`impact`
`java.lang.String`	`soAccession`
`java.lang.String`	`term`
`gngs.ConsequenceType`	`type`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`static VepConsequence`	`fromTerm(java.lang.String term)`
	`int`	`getRank()`
	`int`	`getSeverity()`
	`java.lang.String`	`getShortName()`
	`static java.lang.Object`	`knownValues()`
	`VepConsequence`	`next()`
	`VepConsequence`	`previous()`
	`static int`	`severityOf(java.lang.String consequence)`
	`static int`	`severityOfConsequence(VepConsequence consequence)`
	`java.util.Map<java.lang.String, java.lang.Object>`	`toMap()`
	`static VepConsequence`	`valueOf(java.lang.String name)`
	`static final VepConsequence[]`	`values()`

- Field Detail
  - public static final VepConsequence CODING_SEQUENCE_VARIANT
  - public static final VepConsequence DOWNSTREAM_GENE_VARIANT
  - public static final VepConsequence FEATURE_ELONGATION
  - public static final VepConsequence FEATURE_TRUNCATION
  - public static final VepConsequence FIVE_PRIME_UTR_VARIANT
  - public static final VepConsequence FRAMESHIFT_VARIANT
  - public static final VepConsequence INCOMPLETE_TERMINAL_CODON_VARIANT
  - public static final VepConsequence INFRAME_DELETION
  - public static final VepConsequence INFRAME_INSERTION
  - public static final VepConsequence INITIATOR_CODON_VARIANT
  - public static final VepConsequence INTERGENIC_VARIANT
  - public static final VepConsequence INTRON_VARIANT
  - public static final VepConsequence MATURE_MIRNA_VARIANT
  - public static final VepConsequence MAX_VALUE
  - public static final VepConsequence MIN_VALUE
  - public static final VepConsequence MISSENSE_VARIANT
  - public static final VepConsequence NC_TRANSCRIPT_VARIANT
  - public static final VepConsequence NMD_TRANSCRIPT_VARIANT
  - public static final VepConsequence NON_CODING_EXON_VARIANT
  - public static final VepConsequence NON_CODING_TRANSCRIPT_EXON_VARIANT
  - public static final VepConsequence NON_CODING_TRANSCRIPT_VARIANT
  - public static final VepConsequence PROTEIN_ALTERING_VARIANT
  - public static final VepConsequence REGULATORY_REGION_ABLATION
  - public static final VepConsequence REGULATORY_REGION_AMPLIFICATION
  - public static final VepConsequence REGULATORY_REGION_VARIANT
  - public static final VepConsequence SPLICE_ACCEPTOR_VARIANT
  - public static final VepConsequence SPLICE_DONOR_VARIANT
  - public static final VepConsequence SPLICE_REGION_VARIANT
  - public static final VepConsequence START_LOST
  - public static final VepConsequence START_RETAINED_VARIANT
  - public static final VepConsequence STOP_GAINED
  - public static final VepConsequence STOP_LOST
  - public static final VepConsequence STOP_RETAINED_VARIANT
  - public static final VepConsequence SYNONYMOUS_VARIANT
  - public static final VepConsequence TFBS_ABLATION
  - public static final VepConsequence TFBS_AMPLIFICATION
  - public static final VepConsequence TF_BINDING_SITE_VARIANT
  - public static final VepConsequence THREE_PRIME_UTR_VARIANT
  - public static final VepConsequence TRANSCRIPT_ABLATION
  - public static final VepConsequence TRANSCRIPT_AMPLIFICATION
  - public static final VepConsequence UNKNOWN
  - public static final VepConsequence UPSTREAM_GENE_VARIANT
- Property Detail
  - java.lang.String description
  - java.lang.String displayTerm
  - java.lang.String ensemblColourHex
  - gngs.VepImpact impact
  - java.lang.String soAccession
  - java.lang.String term
  - gngs.ConsequenceType type
- Method Detail
  - static VepConsequence fromTerm(java.lang.String term)
  - int getRank()
  - int getSeverity()
  - java.lang.String getShortName()
  - static java.lang.Object knownValues()
  - @groovy.transform.Generated VepConsequence next()
  - @groovy.transform.Generated VepConsequence previous()
  - static int severityOf(java.lang.String consequence)
  - static int severityOfConsequence(VepConsequence consequence)
  - java.util.Map<java.lang.String, java.lang.Object> toMap()
  - @groovy.transform.Generated static VepConsequence valueOf(java.lang.String name)
  - @groovy.transform.Generated static final VepConsequence[] values()

Summary:
Field
Property
Method

| Detail:
Field
Property
Method

Groovy Documentation

[Groovy] Enum VepConsequence

Field Summary

Properties Summary

Methods Summary

Field Detail

public static final VepConsequence CODING_SEQUENCE_VARIANT

public static final VepConsequence DOWNSTREAM_GENE_VARIANT

public static final VepConsequence FEATURE_ELONGATION

public static final VepConsequence FEATURE_TRUNCATION

public static final VepConsequence FIVE_PRIME_UTR_VARIANT

public static final VepConsequence FRAMESHIFT_VARIANT

public static final VepConsequence INCOMPLETE_TERMINAL_CODON_VARIANT

public static final VepConsequence INFRAME_DELETION

public static final VepConsequence INFRAME_INSERTION

public static final VepConsequence INITIATOR_CODON_VARIANT

public static final VepConsequence INTERGENIC_VARIANT

public static final VepConsequence INTRON_VARIANT

public static final VepConsequence MATURE_MIRNA_VARIANT

public static final VepConsequence MAX_VALUE

public static final VepConsequence MIN_VALUE

public static final VepConsequence MISSENSE_VARIANT

public static final VepConsequence NC_TRANSCRIPT_VARIANT

public static final VepConsequence NMD_TRANSCRIPT_VARIANT

public static final VepConsequence NON_CODING_EXON_VARIANT

public static final VepConsequence NON_CODING_TRANSCRIPT_EXON_VARIANT

public static final VepConsequence NON_CODING_TRANSCRIPT_VARIANT

public static final VepConsequence PROTEIN_ALTERING_VARIANT

public static final VepConsequence REGULATORY_REGION_ABLATION

public static final VepConsequence REGULATORY_REGION_AMPLIFICATION

public static final VepConsequence REGULATORY_REGION_VARIANT

public static final VepConsequence SPLICE_ACCEPTOR_VARIANT

public static final VepConsequence SPLICE_DONOR_VARIANT

public static final VepConsequence SPLICE_REGION_VARIANT

public static final VepConsequence START_LOST

public static final VepConsequence START_RETAINED_VARIANT

public static final VepConsequence STOP_GAINED

public static final VepConsequence STOP_LOST

public static final VepConsequence STOP_RETAINED_VARIANT

public static final VepConsequence SYNONYMOUS_VARIANT

public static final VepConsequence TFBS_ABLATION

public static final VepConsequence TFBS_AMPLIFICATION

public static final VepConsequence TF_BINDING_SITE_VARIANT

public static final VepConsequence THREE_PRIME_UTR_VARIANT

public static final VepConsequence TRANSCRIPT_ABLATION

public static final VepConsequence TRANSCRIPT_AMPLIFICATION

public static final VepConsequence UNKNOWN

public static final VepConsequence UPSTREAM_GENE_VARIANT

Property Detail

java.lang.String description

java.lang.String displayTerm

java.lang.String ensemblColourHex

gngs.VepImpact impact

java.lang.String soAccession

java.lang.String term

gngs.ConsequenceType type

Method Detail

static VepConsequence fromTerm(java.lang.String term)

int getRank()

int getSeverity()

java.lang.String getShortName()

static java.lang.Object knownValues()

@groovy.transform.Generated VepConsequence next()

@groovy.transform.Generated VepConsequence previous()

static int severityOf(java.lang.String consequence)

static int severityOfConsequence(VepConsequence consequence)

java.util.Map<java.lang.String, java.lang.Object> toMap()

@groovy.transform.Generated static VepConsequence valueOf(java.lang.String name)

@groovy.transform.Generated static final VepConsequence[] values()