NUC

enum NUC : Enum<NUC>

Definition of DNA and RNA Nucleotides, IUPAC ambiguity, and nucleotide properties

TODO - GAP may be included in the codes

Parameters

char

Single Char representation of nucleotide, e.g. NUC.A is 'A' (also used for byte level encoding)

twoBit

encoding scheme for two bit encoding for unambiguous nucleotides

fourBit

encoding scheme for four bit encoding for all nucleotides

ambiguous

indicates whether ambiguous code, e.g. A.ambiguous == false, R.ambiguous == true

Note two bit encoding uses A=0, C=1, G=3, T or U = 2

A 65 01000|00|1  0
C 67 01000|01|1  1
G 71 01000|11|1  3
T 84 01010|10|0  2

Entries

Adenosine

Cytosine

Guanine

Thymine

Uracil

aMino

puRine

Weak

Strong

pYrimidine

Keto

Not T, T+1

Not G, G+1

Not C, C+1

Not A, A+1

Any base

GAP

Types

Companion

object Companion

Properties

ambigDNA

val ambigDNA: Set<NUC>

Returns the set of unambiguous DNA nucleotides represented by this NUC, e.g. NUC.R.ambigRNA == [A,G]

ambigRNA

val ambigRNA: Set<NUC>

Returns the set of unambiguous RNA nucleotides represented by this NUC, e.g. NUC.R.ambigRNA == [A,G]

ambiguous

val ambiguous: Boolean

char

val char: Char

dnaAnalog

val dnaAnalog: NUC

DNA analog of a Nucleotide, identity except NUC.U returns NUC.T

dnaComplement

val dnaComplement: NUC

DNA complement of this nucleotide - includes ambiguous

dnaWeight

val dnaWeight: Double

Weight of nucleotide in Daltons, average weights for ambiguous

entries

val entries: EnumEntries<NUC>

Returns a representation of an immutable list of all enum entries, in the order they're declared.

fourBit

val fourBit: Byte

isDNA

val isDNA: Boolean

Could this be a DNA nucleotide. True unless NUC.U

isRNA

val isRNA: Boolean

Could this be a RNA nucleotide. True unless NUC.T

name

val name: String

ordinal

val ordinal: Int

rnaAnalog

val rnaAnalog: NUC

RNA analog of a Nucleotide, identity except NUC.T returns NUC.U

rnaComplement

val rnaComplement: NUC

DNA complement of this nucleotide - includes ambiguous

rnaWeight

val rnaWeight: Double

Weight of nucleotide in Daltons, average weights for ambiguous

twoBit

val twoBit: Byte

utf8

val utf8: <Error class: unknown class>

Functions

div

operator fun NUC.div(nuc: NUC): NUC

plus

operator fun NUC.plus(nuc: NUC): NucSeq

valueOf

fun valueOf(value: String): NUC

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.)

values

fun values(): Array<NUC>

Returns an array containing the constants of this enum type, in the order they're declared.