Copyright	(c) Dominik Schrempf 2020
License	GPL-3.0-or-later
Maintainer	dominik.schrempf@gmail.com
Stability	unstable
Portability	portable
Safe Haskell	None
Language	Haskell2010

TLynx.Distance.Options

Description

Creation date: Thu Aug 29 13:02:22 2019.

Synopsis

Documentation

data DistanceArguments Source #

Arguments needed to compute distance measures.

Constructors

DistanceArguments
Fields argsDistance :: DistanceMeasure argsNormalize :: Bool argsIntersect :: Bool argsSummaryStatistics :: Bool argsMasterTreeFile :: Maybe FilePath argsNewickFormat :: NewickFormat argsInFiles :: [FilePath]

Instances

Instances details

Eq DistanceArguments Source #
Instance details Defined in TLynx.Distance.Options Methods (==) :: DistanceArguments -> DistanceArguments -> Bool # (/=) :: DistanceArguments -> DistanceArguments -> Bool #
Show DistanceArguments Source #
Instance details Defined in TLynx.Distance.Options Methods showsPrec :: Int -> DistanceArguments -> ShowS # show :: DistanceArguments -> String # showList :: [DistanceArguments] -> ShowS #
Generic DistanceArguments Source #
Instance details Defined in TLynx.Distance.Options Associated Types type Rep DistanceArguments :: Type -> Type # Methods from :: DistanceArguments -> Rep DistanceArguments x # to :: Rep DistanceArguments x -> DistanceArguments #
ToJSON DistanceArguments Source #
Instance details Defined in TLynx.Distance.Options Methods toJSON :: DistanceArguments -> Value # toEncoding :: DistanceArguments -> Encoding # toJSONList :: [DistanceArguments] -> Value # toEncodingList :: [DistanceArguments] -> Encoding #
FromJSON DistanceArguments Source #
Instance details Defined in TLynx.Distance.Options Methods parseJSON :: Value -> Parser DistanceArguments # parseJSONList :: Value -> Parser [DistanceArguments] #
Reproducible DistanceArguments Source #
Instance details Defined in TLynx.Distance.Options Methods inFiles :: DistanceArguments -> [FilePath] # outSuffixes :: DistanceArguments -> [String] # getSeed :: DistanceArguments -> Maybe Seed # setSeed :: DistanceArguments -> Vector Word32 -> DistanceArguments # parser :: Parser DistanceArguments # cmdName :: String # cmdDsc :: [String] # cmdFtr :: [String] #
type Rep DistanceArguments Source #
Instance details Defined in TLynx.Distance.Options type Rep DistanceArguments = D1 ('MetaData "DistanceArguments" "TLynx.Distance.Options" "tlynx-0.5.1.0-Cp2GVRVR5JRgZoSqGsPKo" 'False) (C1 ('MetaCons "DistanceArguments" 'PrefixI 'True) ((S1 ('MetaSel ('Just "argsDistance") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 DistanceMeasure) :: (S1 ('MetaSel ('Just "argsNormalize") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Bool) :: S1 ('MetaSel ('Just "argsIntersect") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Bool))) :: ((S1 ('MetaSel ('Just "argsSummaryStatistics") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Bool) :: S1 ('MetaSel ('Just "argsMasterTreeFile") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe FilePath))) :: (S1 ('MetaSel ('Just "argsNewickFormat") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 NewickFormat) :: S1 ('MetaSel ('Just "argsInFiles") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [FilePath])))))

data DistanceMeasure Source #

Supported distance measures.

Constructors

Symmetric	Symmetric distance.
IncompatibleSplit Support	Incompatible split distance; collapse nodes with branch support below given value.
BranchScore	Branch score distance.

Instances

Instances details

Eq DistanceMeasure Source #
Instance details Defined in TLynx.Distance.Options Methods (==) :: DistanceMeasure -> DistanceMeasure -> Bool # (/=) :: DistanceMeasure -> DistanceMeasure -> Bool #
Show DistanceMeasure Source #
Instance details Defined in TLynx.Distance.Options Methods showsPrec :: Int -> DistanceMeasure -> ShowS # show :: DistanceMeasure -> String # showList :: [DistanceMeasure] -> ShowS #
Generic DistanceMeasure Source #
Instance details Defined in TLynx.Distance.Options Associated Types type Rep DistanceMeasure :: Type -> Type # Methods from :: DistanceMeasure -> Rep DistanceMeasure x # to :: Rep DistanceMeasure x -> DistanceMeasure #
ToJSON DistanceMeasure Source #
Instance details Defined in TLynx.Distance.Options Methods toJSON :: DistanceMeasure -> Value # toEncoding :: DistanceMeasure -> Encoding # toJSONList :: [DistanceMeasure] -> Value # toEncodingList :: [DistanceMeasure] -> Encoding #
FromJSON DistanceMeasure Source #
Instance details Defined in TLynx.Distance.Options Methods parseJSON :: Value -> Parser DistanceMeasure # parseJSONList :: Value -> Parser [DistanceMeasure] #
type Rep DistanceMeasure Source #
Instance details Defined in TLynx.Distance.Options type Rep DistanceMeasure = D1 ('MetaData "DistanceMeasure" "TLynx.Distance.Options" "tlynx-0.5.1.0-Cp2GVRVR5JRgZoSqGsPKo" 'False) (C1 ('MetaCons "Symmetric" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "IncompatibleSplit" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Support)) :+: C1 ('MetaCons "BranchScore" 'PrefixI 'False) (U1 :: Type -> Type)))

distanceArguments :: Parser DistanceArguments Source #

COmmand line parser.

distanceFooter :: [String] Source #

Information about provided distance types.