elynx-seq-0.0.1: Handle molecular sequences

Copyright	(c) Dominik Schrempf 2019
License	GPL-3
Maintainer	dominik.schrempf@gmail.com
Stability	unstable
Portability	portable
Safe Haskell	None
Language	Haskell2010

ELynx.Data.MarkovProcess.SubstitutionModel

Contents

Types
Lenses and other accessors
Building substitution models
Transformations
Output

Description

Creation date: Tue Jan 29 19:10:46 2019.

To be imported qualified.

Synopsis

type Name = String
type Params = [Double]
data SubstitutionModel
alphabet :: Lens' SubstitutionModel Alphabet
name :: Lens' SubstitutionModel Name
stationaryDistribution :: Lens' SubstitutionModel StationaryDistribution
exchangeabilityMatrix :: Lens' SubstitutionModel ExchangeabilityMatrix
getRateMatrix :: SubstitutionModel -> RateMatrix
totalRate :: SubstitutionModel -> Double
substitutionModel :: Alphabet -> Name -> Params -> StationaryDistribution -> ExchangeabilityMatrix -> SubstitutionModel
unnormalized :: Alphabet -> Name -> Params -> StationaryDistribution -> ExchangeabilityMatrix -> SubstitutionModel
scale :: Double -> SubstitutionModel -> SubstitutionModel
normalize :: SubstitutionModel -> SubstitutionModel
appendName :: Name -> SubstitutionModel -> SubstitutionModel
summarize :: SubstitutionModel -> [ByteString]

Types

type Name = String Source #

Name of substitution model; abstracted and subject to change.

type Params = [Double] Source #

Parameters of substitution model. May be the empty list.

data SubstitutionModel Source #

Complete definition of a substitution model. Create instances with substitutionModel.

Instances

Read SubstitutionModel Source #
Instance details Defined in ELynx.Data.MarkovProcess.SubstitutionModel Methods readsPrec :: Int -> ReadS SubstitutionModel # readList :: ReadS [SubstitutionModel] # readPrec :: ReadPrec SubstitutionModel # readListPrec :: ReadPrec [SubstitutionModel] #
Show SubstitutionModel Source #
Instance details Defined in ELynx.Data.MarkovProcess.SubstitutionModel Methods showsPrec :: Int -> SubstitutionModel -> ShowS # show :: SubstitutionModel -> String # showList :: [SubstitutionModel] -> ShowS #

Lenses and other accessors

alphabet :: Lens' SubstitutionModel Alphabet Source #

name :: Lens' SubstitutionModel Name Source #

stationaryDistribution :: Lens' SubstitutionModel StationaryDistribution Source #

exchangeabilityMatrix :: Lens' SubstitutionModel ExchangeabilityMatrix Source #

getRateMatrix :: SubstitutionModel -> RateMatrix Source #

Calculate rate matrix from substitution model.

totalRate :: SubstitutionModel -> Double Source #

Get scale of substitution model.

Building substitution models

substitutionModel :: Alphabet -> Name -> Params -> StationaryDistribution -> ExchangeabilityMatrix -> SubstitutionModel Source #

Create normalized SubstitutionModel. See normalize.

unnormalized :: Alphabet -> Name -> Params -> StationaryDistribution -> ExchangeabilityMatrix -> SubstitutionModel Source #

Create UNNORMALIZED SubstitutionModel. See substitutionModel.

Transformations

scale :: Double -> SubstitutionModel -> SubstitutionModel Source #

Scale the rate of a substitution model by given factor.

normalize :: SubstitutionModel -> SubstitutionModel Source #

Normalize a substitution model, so that, on average, one substitution happens per unit time.

appendName :: Name -> SubstitutionModel -> SubstitutionModel Source #

Abbend to name.

Output

summarize :: SubstitutionModel -> [ByteString] Source #

Summarize a substitution model; lines to be printed to screen or log.