Copyright	(c) Amy de Buitléir 2013-2016
License	BSD-style
Maintainer	amy@nualeargais.ie
Stability	experimental
Portability	portable
Safe Haskell	None
Language	Haskell98

ALife.Creatur.Genetics.BRGCWord8

Description

Utilities for working with genes that are encoded as a sequence of bytes, using a Binary Reflected Gray Code (BRGC).

A Gray code maps values to codes in a way that guarantees that the codes for two consecutive values will differ by only one bit. This feature can be useful in evolutionary programming because the genes resulting from a crossover operation are likely to be similar to the inputs. This helps to ensure that offspring are similar to their parents, as any radical changes from one generation to the next are the result of mutation alone.

Synopsis

Documentation

class Genetic g where Source #

A class representing anything which is represented in, and determined by, an agent's genome. This might include traits, parameters, "organs" (components of agents), or even entire agents. Instances of this class can be thought of as genes, i.e., instructions for building an agent.

Methods

put :: g -> Writer () Source #

Writes a gene to a sequence.

put :: (Generic g, GGenetic (Rep g)) => g -> Writer () Source #

Writes a gene to a sequence.

get :: Reader (Either [String] g) Source #

Reads the next gene in a sequence.

get :: (Generic g, GGenetic (Rep g)) => Reader (Either [String] g) Source #

Reads the next gene in a sequence.

getWithDefault :: g -> Reader g Source #

Instances

Genetic Bool Source #
Methods put :: Bool -> Writer () Source # get :: Reader (Either [String] Bool) Source # getWithDefault :: Bool -> Reader Bool Source #
Genetic Char Source #
Methods put :: Char -> Writer () Source # get :: Reader (Either [String] Char) Source # getWithDefault :: Char -> Reader Char Source #
Genetic Double Source #
Methods put :: Double -> Writer () Source # get :: Reader (Either [String] Double) Source # getWithDefault :: Double -> Reader Double Source #
Genetic Int Source #
Methods put :: Int -> Writer () Source # get :: Reader (Either [String] Int) Source # getWithDefault :: Int -> Reader Int Source #
Genetic Integer Source #
Methods put :: Integer -> Writer () Source # get :: Reader (Either [String] Integer) Source # getWithDefault :: Integer -> Reader Integer Source #
Genetic Word8 Source #
Methods put :: Word8 -> Writer () Source # get :: Reader (Either [String] Word8) Source # getWithDefault :: Word8 -> Reader Word8 Source #
Genetic Word16 Source #
Methods put :: Word16 -> Writer () Source # get :: Reader (Either [String] Word16) Source # getWithDefault :: Word16 -> Reader Word16 Source #
Genetic Word32 Source #
Methods put :: Word32 -> Writer () Source # get :: Reader (Either [String] Word32) Source # getWithDefault :: Word32 -> Reader Word32 Source #
Genetic Word64 Source #
Methods put :: Word64 -> Writer () Source # get :: Reader (Either [String] Word64) Source # getWithDefault :: Word64 -> Reader Word64 Source #
Genetic a => Genetic [a] Source #
Methods put :: [a] -> Writer () Source # get :: Reader (Either [String] [a]) Source # getWithDefault :: [a] -> Reader [a] Source #
Genetic a => Genetic (Maybe a) Source #
Methods put :: Maybe a -> Writer () Source # get :: Reader (Either [String] (Maybe a)) Source # getWithDefault :: Maybe a -> Reader (Maybe a) Source #
(Genetic a, Genetic b) => Genetic (Either a b) Source #
Methods put :: Either a b -> Writer () Source # get :: Reader (Either [String] (Either a b)) Source # getWithDefault :: Either a b -> Reader (Either a b) Source #
(Genetic a, Genetic b) => Genetic (a, b) Source #
Methods put :: (a, b) -> Writer () Source # get :: Reader (Either [String] (a, b)) Source # getWithDefault :: (a, b) -> Reader (a, b) Source #

type Sequence = [Word8] Source #

type Writer = StateT (Sequence, [String]) Identity Source #

write :: Genetic x => x -> Sequence Source #

runWriter :: Writer () -> (Sequence, [String]) Source #

type Reader = StateT (Sequence, Int, [String]) Identity Source #

read :: Genetic g => Sequence -> Either [String] g Source #

runReader :: Reader (Either [String] g) -> Sequence -> (Either [String] g, [String]) Source #

copy :: Reader Sequence Source #

Return the entire genome.

consumed :: Reader Sequence Source #

Return the portion of the genome that has been read.

type DiploidSequence = (Sequence, Sequence) Source #

type DiploidReader = StateT ((Sequence, Int, [String]), (Sequence, Int, [String])) Identity Source #

readAndExpress :: (Genetic g, Diploid g) => DiploidSequence -> Either [String] g Source #

runDiploidReader :: DiploidReader g -> DiploidSequence -> g Source #

getAndExpress :: (Genetic g, Diploid g) => DiploidReader (Either [String] g) Source #

Read the next pair of genes from twin sequences of genetic information, and return the resulting gene (after taking into account any dominance relationship) and the remaining (unread) portion of the two nucleotide strands.

getAndExpressWithDefault :: (Genetic g, Diploid g) => g -> DiploidReader g Source #

copy2 :: DiploidReader DiploidSequence Source #

Return the entire genome.

consumed2 :: DiploidReader DiploidSequence Source #

Return the portion of the genome that has been read.

putAndReport :: [Word8] -> String -> Writer () Source #

getAndReport :: Int -> ([Word8] -> Either String (g, String)) -> Reader (Either [String] g) Source #

putRawWord8 :: Word8 -> Writer () Source #

Write a Word8 value to the genome without encoding it

getRawWord8 :: Reader (Either [String] Word8) Source #

Read a Word8 value from the genome without decoding it

putRawWord8s :: [Word8] -> Writer () Source #

Write a raw sequence of Word8 values to the genome

getRawWord8s :: Int -> Reader (Either [String] [Word8]) Source #

Read a raw sequence of Word8 values from the genome