seth.ner.wrapper

Enum Type

java.lang.Object

java.lang.Enum<Type>

seth.ner.wrapper.Type

All Implemented Interfaces:

Serializable, Comparable<Type>

public enum Type
extends Enum<Type>

Mutation types found by SETHNER, MutationFinder currently extracts only Substitutions

Enum Constant Summary

Enum Constants

Enum Constant and Description
CONVERSION Gene conversion
COPY_NUMBER_VARIATION Introduced by the "cnv" module to find CNVs of genes.
DBSNP_MENTION Literal dbSNP Mention (e.g., rs1232)
DELETION Deletion of a amino-acid or nucleotide (e.g., p.F123del or DeltaF508)
DELETION_INSERTION Mutation resulting in both insertion and deletion (e.g., p.Val134_K144delinsE)
DUPLICATION Duplication of genetic material (e.g., c.123dupC)
FRAMESHIFT Mutation which leads to a shifted reading frame and therefore to a completely different translation product (e.g., R123fs or p.N310fs)
INSERTION Addition of a nucleotide into the DNA which can can lead to added amino acids (e.g., 123insA)
INVERSION Inversion of DNA fragment (e.g., c12_15inv)
OTHER Fall back mutation-type
SHORT_SEQUENCE_REPEAT Short reperat of the same fragment (e.g., c1210-12T[9])
SILENT Used to specify silent mutations, with no impact on protein sequence (e.g., p.Arg12=)
STRUCTURAL_ABNORMALITY Wide range mutations.
SUBSTITUTION Replacement of wildtype by mutation
TRANSLOCATION

Method Summary

Modifier and Type	Method and Description
static Type	valueOf(String name) Returns the enum constant of this type with the specified name.
static Type[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

SUBSTITUTION

public static final Type SUBSTITUTION

Replacement of wildtype by mutation

DBSNP_MENTION

public static final Type DBSNP_MENTION

Literal dbSNP Mention (e.g., rs1232)

DELETION

public static final Type DELETION

Deletion of a amino-acid or nucleotide (e.g., p.F123del or DeltaF508)

STRUCTURAL_ABNORMALITY

public static final Type STRUCTURAL_ABNORMALITY

Wide range mutations. I.e., trisomy or deletions of chromosomes and regions (e.g., 46,XX,-13 or chr17:123533-12131314)

FRAMESHIFT

public static final Type FRAMESHIFT

Mutation which leads to a shifted reading frame and therefore to a completely different translation product (e.g., R123fs or p.N310fs)

INSERTION

public static final Type INSERTION

Addition of a nucleotide into the DNA which can can lead to added amino acids (e.g., 123insA)

DUPLICATION

public static final Type DUPLICATION

Duplication of genetic material (e.g., c.123dupC)

DELETION_INSERTION

public static final Type DELETION_INSERTION

Mutation resulting in both insertion and deletion (e.g., p.Val134_K144delinsE)

SHORT_SEQUENCE_REPEAT

public static final Type SHORT_SEQUENCE_REPEAT

Short reperat of the same fragment (e.g., c1210-12T[9])

SILENT

public static final Type SILENT

Used to specify silent mutations, with no impact on protein sequence (e.g., p.Arg12=)

INVERSION

public static final Type INVERSION

Inversion of DNA fragment (e.g., c12_15inv)

CONVERSION

public static final Type CONVERSION

Gene conversion

TRANSLOCATION

public static final Type TRANSLOCATION

COPY_NUMBER_VARIATION

public static final Type COPY_NUMBER_VARIATION

Introduced by the "cnv" module to find CNVs of genes. (currently not used; for details check "package cnveth").

OTHER

public static final Type OTHER

Fall back mutation-type

Method Detail

values

public static Type[] 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 (Type c : Type.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static Type valueOf(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:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null