ELynx.Character.Character

Creation date: Fri Oct 12 16:24:02 2018.

See header of Alphabet.

Documentation

class (Show a, Read a, Eq a, Ord a, Enum a, Bounded a, Unbox a) => Character a where

A set of characters forms an Alphabet. At the moment, Word8 is used, since none of the alphabets has more than 255 characters.

Methods

toWord :: a -> Word8

Write characters.

fromWord :: Word8 -> a

Read characters.

Instances

Character AminoAcid

Defined in ELynx.Character.AminoAcid

Methods

toWord :: AminoAcid -> Word8

fromWord :: Word8 -> AminoAcid

Character AminoAcidI

Defined in ELynx.Character.AminoAcidI

Methods

toWord :: AminoAcidI -> Word8

fromWord :: Word8 -> AminoAcidI

Character AminoAcidS

Defined in ELynx.Character.AminoAcidS

Methods

toWord :: AminoAcidS -> Word8

fromWord :: Word8 -> AminoAcidS

Character AminoAcidX

Defined in ELynx.Character.AminoAcidX

Methods

toWord :: AminoAcidX -> Word8

fromWord :: Word8 -> AminoAcidX

Character Nucleotide

Defined in ELynx.Character.Nucleotide

Methods

toWord :: Nucleotide -> Word8

fromWord :: Word8 -> Nucleotide

Character NucleotideI

Defined in ELynx.Character.NucleotideI

Methods

toWord :: NucleotideI -> Word8

fromWord :: Word8 -> NucleotideI

Character NucleotideX

Defined in ELynx.Character.NucleotideX

Methods

toWord :: NucleotideX -> Word8

fromWord :: Word8 -> NucleotideX

fromChar :: Character a => Char -> a

Conversion from Char.

toChar :: Character a => a -> Char

Conversion to Char.

fromString :: Character a => String -> [a]

Conversion from String.

toString :: Character a => [a] -> String

Conversion to String.

class Character a => CharacterX a where

An extended character type with gaps and unknowns.

Methods

gap :: a

Instances

CharacterX AminoAcidI

Defined in ELynx.Character.AminoAcidI

Methods

gap :: AminoAcidI

CharacterX AminoAcidS

Defined in ELynx.Character.AminoAcidS

Methods

gap :: AminoAcidS

CharacterX AminoAcidX

Defined in ELynx.Character.AminoAcidX

Methods

gap :: AminoAcidX

CharacterX NucleotideI

Defined in ELynx.Character.NucleotideI

Methods

gap :: NucleotideI

CharacterX NucleotideX

Defined in ELynx.Character.NucleotideX

Methods

gap :: NucleotideX

isGap :: CharacterX a => a -> Bool

Is the character a gap or unknown?

class CharacterX a => CharacterI a where

IUPAC characters with a mapping to extended characters.

Methods

unknown :: a

iupac :: [a]

toStandard :: a -> [a]

Instances

CharacterI AminoAcidI

Defined in ELynx.Character.AminoAcidI

Methods

unknown :: AminoAcidI

iupac :: [AminoAcidI]

toStandard :: AminoAcidI -> [AminoAcidI]

CharacterI NucleotideI

Defined in ELynx.Character.NucleotideI

Methods

unknown :: NucleotideI

iupac :: [NucleotideI]

toStandard :: NucleotideI -> [NucleotideI]

isUnknown :: CharacterI a => a -> Bool

Check if a IUPAC CharacterI is unknown (e.g., N for nucleotides).

isIUPAC :: CharacterI a => a -> Bool

Is the given character a IUPAC character?

isStandard :: CharacterI a => a -> Bool

Is the given character a standard character?

convert :: (Character a, Character b) => a -> b

Convert between character classes. May throw error.