tlynx-0.8.0.0: Handle phylogenetic trees
Copyright2021 Dominik Schrempf
LicenseGPL-3.0-or-later
Maintainer[email protected]
Stabilityunstable
Portabilityportable
Safe HaskellNone
LanguageHaskell2010

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

Instances

Instances details
FromJSON DistanceArguments Source # 
Instance details

Defined in TLynx.Distance.Options

Methods

parseJSON :: Value -> Parser DistanceArguments #

parseJSONList :: Value -> Parser [DistanceArguments] #

omittedField :: Maybe DistanceArguments #

ToJSON DistanceArguments Source # 
Instance details

Defined in TLynx.Distance.Options

Methods

toJSON :: DistanceArguments -> Value #

toEncoding :: DistanceArguments -> Encoding #

toJSONList :: [DistanceArguments] -> Value #

toEncodingList :: [DistanceArguments] -> Encoding #

omitField :: DistanceArguments -> Bool #

Generic DistanceArguments Source # 
Instance details

Defined in TLynx.Distance.Options

Associated Types

type Rep DistanceArguments 
Instance details

Defined in TLynx.Distance.Options

type Rep DistanceArguments = D1 ('MetaData "DistanceArguments" "TLynx.Distance.Options" "tlynx-0.8.0.0-JHadlx080MyGliqJ0mTjDo" '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])))))

Methods

from :: DistanceArguments -> Rep DistanceArguments x #

to :: Rep DistanceArguments x -> DistanceArguments #

Show DistanceArguments Source # 
Instance details

Defined in TLynx.Distance.Options

Methods

showsPrec :: Int -> DistanceArguments -> ShowS #

show :: DistanceArguments -> String #

showList :: [DistanceArguments] -> ShowS #

Reproducible DistanceArguments Source # 
Instance details

Defined in TLynx.Distance.Options

Methods

inFiles :: DistanceArguments -> [FilePath] #

outSuffixes :: DistanceArguments -> [String] #

getSeed :: DistanceArguments -> Maybe SeedOpt #

setSeed :: DistanceArguments -> SeedOpt -> DistanceArguments #

parser :: Parser DistanceArguments #

cmdName :: String #

cmdDsc :: [String] #

cmdFtr :: [String] #

Eq DistanceArguments Source # 
Instance details

Defined in TLynx.Distance.Options

Methods

(==) :: DistanceArguments -> DistanceArguments -> Bool #

(/=) :: DistanceArguments -> DistanceArguments -> Bool #

type Rep DistanceArguments Source # 
Instance details

Defined in TLynx.Distance.Options

type Rep DistanceArguments = D1 ('MetaData "DistanceArguments" "TLynx.Distance.Options" "tlynx-0.8.0.0-JHadlx080MyGliqJ0mTjDo" '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
FromJSON DistanceMeasure Source # 
Instance details

Defined in TLynx.Distance.Options

Methods

parseJSON :: Value -> Parser DistanceMeasure #

parseJSONList :: Value -> Parser [DistanceMeasure] #

omittedField :: Maybe DistanceMeasure #

ToJSON DistanceMeasure Source # 
Instance details

Defined in TLynx.Distance.Options

Methods

toJSON :: DistanceMeasure -> Value #

toEncoding :: DistanceMeasure -> Encoding #

toJSONList :: [DistanceMeasure] -> Value #

toEncodingList :: [DistanceMeasure] -> Encoding #

omitField :: DistanceMeasure -> Bool #

Generic DistanceMeasure Source # 
Instance details

Defined in TLynx.Distance.Options

Associated Types

type Rep DistanceMeasure 
Instance details

Defined in TLynx.Distance.Options

type Rep DistanceMeasure = D1 ('MetaData "DistanceMeasure" "TLynx.Distance.Options" "tlynx-0.8.0.0-JHadlx080MyGliqJ0mTjDo" '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)))

Methods

from :: DistanceMeasure -> Rep DistanceMeasure x #

to :: Rep DistanceMeasure x -> DistanceMeasure #

Show DistanceMeasure Source # 
Instance details

Defined in TLynx.Distance.Options

Methods

showsPrec :: Int -> DistanceMeasure -> ShowS #

show :: DistanceMeasure -> String #

showList :: [DistanceMeasure] -> ShowS #

Eq DistanceMeasure Source # 
Instance details

Defined in TLynx.Distance.Options

Methods

(==) :: DistanceMeasure -> DistanceMeasure -> Bool #

(/=) :: DistanceMeasure -> DistanceMeasure -> Bool #

type Rep DistanceMeasure Source # 
Instance details

Defined in TLynx.Distance.Options

type Rep DistanceMeasure = D1 ('MetaData "DistanceMeasure" "TLynx.Distance.Options" "tlynx-0.8.0.0-JHadlx080MyGliqJ0mTjDo" '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.