Copyright	(c) Dominik Schrempf 2018
License	GPL-3.0-or-later
Maintainer	dominik.schrempf@gmail.com
Stability	unstable
Portability	portable
Safe Haskell	None
Language	Haskell2010

ELynx.Data.Character.Character

Description

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

See header of Alphabet.

Synopsis

class (Show a, Read a, Eq a, Ord a, Enum a, Bounded a, Unbox a) => Character a where
- toWord :: a -> Word8
- fromWord :: Word8 -> a
fromChar :: Character a => Char -> a
toChar :: Character a => a -> Char
fromString :: Character a => String -> [a]
toString :: Character a => [a] -> String
class Character a => CharacterX a where
- gap :: a
isGap :: CharacterX a => a -> Bool
class CharacterX a => CharacterI a where
- unknown :: a
- iupac :: [a]
- toStandard :: a -> [a]
isUnknown :: CharacterI a => a -> Bool
isIUPAC :: CharacterI a => a -> Bool
isStandard :: CharacterI a => a -> Bool
convert :: (Character a, Character b) => a -> b

Documentation

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

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 Source #

Write characters.

fromWord :: Word8 -> a Source #

Read characters.

Instances

Instances details

Character AminoAcidX Source #
Instance details Defined in ELynx.Data.Character.AminoAcidX Methods toWord :: AminoAcidX -> Word8 Source # fromWord :: Word8 -> AminoAcidX Source #
Character AminoAcidS Source #
Instance details Defined in ELynx.Data.Character.AminoAcidS Methods toWord :: AminoAcidS -> Word8 Source # fromWord :: Word8 -> AminoAcidS Source #
Character AminoAcidI Source #
Instance details Defined in ELynx.Data.Character.AminoAcidI Methods toWord :: AminoAcidI -> Word8 Source # fromWord :: Word8 -> AminoAcidI Source #
Character AminoAcid Source #
Instance details Defined in ELynx.Data.Character.AminoAcid Methods toWord :: AminoAcid -> Word8 Source # fromWord :: Word8 -> AminoAcid Source #
Character Nucleotide Source #
Instance details Defined in ELynx.Data.Character.Nucleotide Methods toWord :: Nucleotide -> Word8 Source # fromWord :: Word8 -> Nucleotide Source #
Character NucleotideI Source #
Instance details Defined in ELynx.Data.Character.NucleotideI Methods toWord :: NucleotideI -> Word8 Source # fromWord :: Word8 -> NucleotideI Source #
Character NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods toWord :: NucleotideX -> Word8 Source # fromWord :: Word8 -> NucleotideX Source #

fromChar :: Character a => Char -> a Source #

Conversion from Char.

toChar :: Character a => a -> Char Source #

Conversion to Char.

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

Conversion from String.

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

Conversion to String.

class Character a => CharacterX a where Source #

An extended character type with gaps and unknowns.

Methods

gap :: a Source #

Instances

Instances details

CharacterX AminoAcidX Source #
Instance details Defined in ELynx.Data.Character.AminoAcidX Methods gap :: AminoAcidX Source #
CharacterX AminoAcidS Source #
Instance details Defined in ELynx.Data.Character.AminoAcidS Methods gap :: AminoAcidS Source #
CharacterX AminoAcidI Source #
Instance details Defined in ELynx.Data.Character.AminoAcidI Methods gap :: AminoAcidI Source #
CharacterX NucleotideI Source #
Instance details Defined in ELynx.Data.Character.NucleotideI Methods gap :: NucleotideI Source #
CharacterX NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods gap :: NucleotideX Source #

isGap :: CharacterX a => a -> Bool Source #

Is the character a gap or unknown?

class CharacterX a => CharacterI a where Source #

IUPAC characters with a mapping to extended characters.

Methods

unknown :: a Source #

iupac :: [a] Source #

toStandard :: a -> [a] Source #

Instances

Instances details

CharacterI AminoAcidI Source #
Instance details Defined in ELynx.Data.Character.AminoAcidI Methods unknown :: AminoAcidI Source # iupac :: [AminoAcidI] Source # toStandard :: AminoAcidI -> [AminoAcidI] Source #
CharacterI NucleotideI Source #
Instance details Defined in ELynx.Data.Character.NucleotideI Methods unknown :: NucleotideI Source # iupac :: [NucleotideI] Source # toStandard :: NucleotideI -> [NucleotideI] Source #

isUnknown :: CharacterI a => a -> Bool Source #

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

isIUPAC :: CharacterI a => a -> Bool Source #

Is the given character a IUPAC character?

isStandard :: CharacterI a => a -> Bool Source #

Is the given character a standard character?

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

Convert between character classes. May throw error.