Copyright	2021 Dominik Schrempf
License	GPL-3.0-or-later
Maintainer	dominik.schrempf@gmail.com
Stability	unstable
Portability	portable
Safe Haskell	Safe-Inferred
Language	Haskell2010

SLynx.Simulate.Options

Description

Creation date: Sun Oct 7 17:29:45 2018.

Available options: -h,--help Show this help text -v,--version Show version -t,--tree-file NAME Specify tree file NAME -s,--substitution-model MODEL Set the phylogenetic substitution model; available models are shown below -m,--mixture-model MODEL Set the phylogenetic mixture model; available models are shown below -l,--length NUMBER Set alignment length to NUMBER -e,--edm-file NAME empirical distribution model file NAME in Phylobayes format -w,--mixture-model-weights [DOUBLE,DOUBLE,...] weights of mixture model components -g,--gamma-rate-heterogeneity (NCAT, SHAPE) number of gamma rate categories and shape parameter -e,--seed [INT] Set seed for the random number generator; list of 32 bit integers with up to 256 elements (default: [0]) -q,--quiet Be quiet -o,--output-file NAME Specify output file NAME

Documentation

type GammaRateHeterogeneityParams = (Int, Double) Source #

Number of gamma rate categories and alpha parameter.

data MixtureModelGlobalNormalization Source #

Constructors

GlobalNormalization
LocalNormalization

Instances

Instances details

FromJSON MixtureModelGlobalNormalization Source #
Instance details Defined in SLynx.Simulate.Options Methods parseJSON :: Value -> Parser MixtureModelGlobalNormalization # parseJSONList :: Value -> Parser [MixtureModelGlobalNormalization] #
ToJSON MixtureModelGlobalNormalization Source #
Instance details Defined in SLynx.Simulate.Options Methods toJSON :: MixtureModelGlobalNormalization -> Value # toEncoding :: MixtureModelGlobalNormalization -> Encoding # toJSONList :: [MixtureModelGlobalNormalization] -> Value # toEncodingList :: [MixtureModelGlobalNormalization] -> Encoding #
Generic MixtureModelGlobalNormalization Source #
Instance details Defined in SLynx.Simulate.Options Associated Types type Rep MixtureModelGlobalNormalization :: Type -> Type # Methods from :: MixtureModelGlobalNormalization -> Rep MixtureModelGlobalNormalization x # to :: Rep MixtureModelGlobalNormalization x -> MixtureModelGlobalNormalization #
Read MixtureModelGlobalNormalization Source #
Instance details Defined in SLynx.Simulate.Options Methods readsPrec :: Int -> ReadS MixtureModelGlobalNormalization # readList :: ReadS [MixtureModelGlobalNormalization] # readPrec :: ReadPrec MixtureModelGlobalNormalization # readListPrec :: ReadPrec [MixtureModelGlobalNormalization] #
Show MixtureModelGlobalNormalization Source #
Instance details Defined in SLynx.Simulate.Options Methods showsPrec :: Int -> MixtureModelGlobalNormalization -> ShowS # show :: MixtureModelGlobalNormalization -> String # showList :: [MixtureModelGlobalNormalization] -> ShowS #
Eq MixtureModelGlobalNormalization Source #
Instance details Defined in SLynx.Simulate.Options Methods (==) :: MixtureModelGlobalNormalization -> MixtureModelGlobalNormalization -> Bool # (/=) :: MixtureModelGlobalNormalization -> MixtureModelGlobalNormalization -> Bool #
type Rep MixtureModelGlobalNormalization Source #
Instance details Defined in SLynx.Simulate.Options type Rep MixtureModelGlobalNormalization = D1 ('MetaData "MixtureModelGlobalNormalization" "SLynx.Simulate.Options" "slynx-0.7.2.2-LEEFMVV1Ckz1AmAXiyZfpK" 'False) (C1 ('MetaCons "GlobalNormalization" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "LocalNormalization" 'PrefixI 'False) (U1 :: Type -> Type))

data SimulateArguments Source #

Arguments needed to simulate sequences.

Constructors

SimulateArguments
Fields argsTreeFile :: FilePath argsSubstitutionModelString :: Maybe String argsMixtureModelString :: Maybe String argsMixtureModelGlobalNormalization :: MixtureModelGlobalNormalization argsEDMFile :: Maybe FilePath argsSiteprofilesFiles :: Maybe [FilePath] argsMixtureWeights :: Maybe [Double] argsGammaParams :: Maybe GammaRateHeterogeneityParams argsLength :: Int argsSeed :: SeedOpt

Instances

Instances details

FromJSON SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Methods parseJSON :: Value -> Parser SimulateArguments # parseJSONList :: Value -> Parser [SimulateArguments] #
ToJSON SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Methods toJSON :: SimulateArguments -> Value # toEncoding :: SimulateArguments -> Encoding # toJSONList :: [SimulateArguments] -> Value # toEncodingList :: [SimulateArguments] -> Encoding #
Generic SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Associated Types type Rep SimulateArguments :: Type -> Type # Methods from :: SimulateArguments -> Rep SimulateArguments x # to :: Rep SimulateArguments x -> SimulateArguments #
Show SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Methods showsPrec :: Int -> SimulateArguments -> ShowS # show :: SimulateArguments -> String # showList :: [SimulateArguments] -> ShowS #
Reproducible SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Methods inFiles :: SimulateArguments -> [FilePath] # outSuffixes :: SimulateArguments -> [String] # getSeed :: SimulateArguments -> Maybe SeedOpt # setSeed :: SimulateArguments -> SeedOpt -> SimulateArguments # parser :: Parser SimulateArguments # cmdName :: String # cmdDsc :: [String] # cmdFtr :: [String] #
Eq SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Methods (==) :: SimulateArguments -> SimulateArguments -> Bool # (/=) :: SimulateArguments -> SimulateArguments -> Bool #
type Rep SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options type Rep SimulateArguments = D1 ('MetaData "SimulateArguments" "SLynx.Simulate.Options" "slynx-0.7.2.2-LEEFMVV1Ckz1AmAXiyZfpK" 'False) (C1 ('MetaCons "SimulateArguments" 'PrefixI 'True) (((S1 ('MetaSel ('Just "argsTreeFile") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 FilePath) :: S1 ('MetaSel ('Just "argsSubstitutionModelString") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe String))) :: (S1 ('MetaSel ('Just "argsMixtureModelString") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe String)) :: (S1 ('MetaSel ('Just "argsMixtureModelGlobalNormalization") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 MixtureModelGlobalNormalization) :: S1 ('MetaSel ('Just "argsEDMFile") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe FilePath))))) :: ((S1 ('MetaSel ('Just "argsSiteprofilesFiles") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe [FilePath])) :: S1 ('MetaSel ('Just "argsMixtureWeights") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe [Double]))) :: (S1 ('MetaSel ('Just "argsGammaParams") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe GammaRateHeterogeneityParams)) :: (S1 ('MetaSel ('Just "argsLength") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :*: S1 ('MetaSel ('Just "argsSeed") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 SeedOpt))))))

simulateArguments :: Parser SimulateArguments Source #

Sub command parser.

simulateFooter :: [String] Source #

The model specification is somewhat complicated, so we need to provide additional help.