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

data DistanceArguments = DistanceArguments {
- argsDistance :: DistanceMeasure
- argsNormalize :: Bool
- argsIntersect :: Bool
- argsSummaryStatistics :: Bool
- argsMasterTreeFile :: Maybe FilePath
- argsNewickFormat :: NewickFormat
- argsInFiles :: [FilePath]
}
data DistanceMeasure
- = Symmetric
- | IncompatibleSplit Double
- | BranchScore
distanceArguments :: Parser DistanceArguments
distanceFooter :: [String]

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

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-0.4.0-8tcIvrUCDfo4d2N61gOzrk" 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 Double	Incompatible split distance; collapse nodes with branch support below given value.
BranchScore	Branch score distance.

Instances

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-0.4.0-8tcIvrUCDfo4d2N61gOzrk" False) (C1 (MetaCons "Symmetric" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "IncompatibleSplit" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Double)) :+: C1 (MetaCons "BranchScore" PrefixI False) (U1 :: Type -> Type)))

distanceArguments :: Parser DistanceArguments Source #

COmmand line parser.

distanceFooter :: [String] Source #

Information about provided distance types.