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

ELynx.Tree.Measurable

Contents

Non-negative length
Functions on trees

Description

Creation date: Thu Jan 17 14:16:34 2019.

Non-negativity of lengths is not completely ensured. See the documentation of Length.

Synopsis

data Length
toLength :: Double -> Either String Length
toLengthUnsafe :: Double -> Length
checkLength :: Length -> Either String Length
class Measurable e where
- getLen :: e -> Length
- setLen :: Length -> e -> e
- modLen :: (Length -> Length) -> e -> e
height :: Measurable e => Tree e a -> Length
rootHeight :: Measurable e => Tree e a -> Length
distancesOriginLeaves :: Measurable e => Tree e a -> [Length]
totalBranchLength :: Measurable e => Tree e a -> Length
normalizeBranchLengths :: Measurable e => Tree e a -> Tree e a
normalizeHeight :: Measurable e => Tree e a -> Tree e a
ultrametric :: Measurable e => Tree e a -> Bool
makeUltrametric :: Measurable e => Tree e a -> Tree e a

Non-negative length

data Length Source #

Non-negative length.

However, non-negativity is only checked with toLength, and negative values can be obtained using the Num and related instances.

Safe operations with conversion from and to length are roughly 50 percent slower.

benchmarking length/length sum foldl' with safe conversion
time                 110.4 ms   (109.8 ms .. 111.0 ms)
                     1.000 R²   (1.000 R² .. 1.000 R²)
mean                 110.2 ms   (110.0 ms .. 110.6 ms)
std dev              501.8 μs   (359.1 μs .. 730.0 μs)

benchmarking length/length sum foldl' num instance
time                 89.37 ms   (85.13 ms .. 94.27 ms)
                     0.996 R²   (0.992 R² .. 1.000 R²)
mean                 86.53 ms   (85.63 ms .. 88.52 ms)
std dev              2.239 ms   (1.069 ms .. 3.421 ms)

benchmarking length/double sum foldl'
time                 85.47 ms   (84.88 ms .. 86.42 ms)
                     1.000 R²   (0.999 R² .. 1.000 R²)
mean                 85.56 ms   (85.26 ms .. 86.02 ms)
std dev              611.9 μs   (101.5 μs .. 851.7 μs)

Instances

Instances details

Enum Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods succ :: Length -> Length # pred :: Length -> Length # toEnum :: Int -> Length # fromEnum :: Length -> Int # enumFrom :: Length -> [Length] # enumFromThen :: Length -> Length -> [Length] # enumFromTo :: Length -> Length -> [Length] # enumFromThenTo :: Length -> Length -> Length -> [Length] #
Eq Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods (==) :: Length -> Length -> Bool # (/=) :: Length -> Length -> Bool #
Floating Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods pi :: Length # exp :: Length -> Length # log :: Length -> Length # sqrt :: Length -> Length # (**) :: Length -> Length -> Length # logBase :: Length -> Length -> Length # sin :: Length -> Length # cos :: Length -> Length # tan :: Length -> Length # asin :: Length -> Length # acos :: Length -> Length # atan :: Length -> Length # sinh :: Length -> Length # cosh :: Length -> Length # tanh :: Length -> Length # asinh :: Length -> Length # acosh :: Length -> Length # atanh :: Length -> Length # log1p :: Length -> Length # expm1 :: Length -> Length # log1pexp :: Length -> Length # log1mexp :: Length -> Length #
Fractional Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods (/) :: Length -> Length -> Length # recip :: Length -> Length # fromRational :: Rational -> Length #
Num Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods (+) :: Length -> Length -> Length # (-) :: Length -> Length -> Length # (*) :: Length -> Length -> Length # negate :: Length -> Length # abs :: Length -> Length # signum :: Length -> Length # fromInteger :: Integer -> Length #
Ord Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods compare :: Length -> Length -> Ordering # (<) :: Length -> Length -> Bool # (<=) :: Length -> Length -> Bool # (>) :: Length -> Length -> Bool # (>=) :: Length -> Length -> Bool # max :: Length -> Length -> Length # min :: Length -> Length -> Length #
Read Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods readsPrec :: Int -> ReadS Length # readList :: ReadS [Length] # readPrec :: ReadPrec Length # readListPrec :: ReadPrec [Length] #
Real Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods toRational :: Length -> Rational #
RealFloat Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods floatRadix :: Length -> Integer # floatDigits :: Length -> Int # floatRange :: Length -> (Int, Int) # decodeFloat :: Length -> (Integer, Int) # encodeFloat :: Integer -> Int -> Length # exponent :: Length -> Int # significand :: Length -> Length # scaleFloat :: Int -> Length -> Length # isNaN :: Length -> Bool # isInfinite :: Length -> Bool # isDenormalized :: Length -> Bool # isNegativeZero :: Length -> Bool # isIEEE :: Length -> Bool # atan2 :: Length -> Length -> Length #
RealFrac Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods properFraction :: Integral b => Length -> (b, Length) # truncate :: Integral b => Length -> b # round :: Integral b => Length -> b # ceiling :: Integral b => Length -> b # floor :: Integral b => Length -> b #
Show Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods showsPrec :: Int -> Length -> ShowS # show :: Length -> String # showList :: [Length] -> ShowS #
Generic Length Source #
Instance details Defined in ELynx.Tree.Measurable Associated Types type Rep Length :: Type -> Type # Methods from :: Length -> Rep Length x # to :: Rep Length x -> Length #
Semigroup Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods (<>) :: Length -> Length -> Length # sconcat :: NonEmpty Length -> Length # stimes :: Integral b => b -> Length -> Length #
Monoid Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods mempty :: Length # mappend :: Length -> Length -> Length # mconcat :: [Length] -> Length #
NFData Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods rnf :: Length -> () #
ToJSON Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods toJSON :: Length -> Value # toEncoding :: Length -> Encoding # toJSONList :: [Length] -> Value # toEncodingList :: [Length] -> Encoding #
FromJSON Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods parseJSON :: Value -> Parser Length # parseJSONList :: Value -> Parser [Length] #
Splittable Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods split :: Length -> Length Source #
Measurable Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods getLen :: Length -> Length Source # setLen :: Length -> Length -> Length Source # modLen :: (Length -> Length) -> Length -> Length Source #
type Rep Length Source #
Instance details Defined in ELynx.Tree.Measurable type Rep Length = D1 ('MetaData "Length" "ELynx.Tree.Measurable" "elynx-tree-0.5.0-LNeltioHkaNAWvI1l3dP6J" 'True) (C1 ('MetaCons "Length" 'PrefixI 'True) (S1 ('MetaSel ('Just "fromLength") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Double)))

toLength :: Double -> Either String Length Source #

Nothing if length is negative.

toLengthUnsafe :: Double -> Length Source #

Do not check if support value is negative.

checkLength :: Length -> Either String Length Source #

Nothing if length is negative.

class Measurable e where Source #

A data type with measurable and modifiable length.

Methods

getLen :: e -> Length Source #

Get length.

setLen :: Length -> e -> e Source #

Set length.

modLen :: (Length -> Length) -> e -> e Source #

Modify length.

Instances

Instances details

Measurable Length Source #
Instance details Defined in ELynx.Tree.Measurable Methods getLen :: Length -> Length Source # setLen :: Length -> Length -> Length Source # modLen :: (Length -> Length) -> Length -> Length Source #
Measurable PhyloExplicit Source #
Instance details Defined in ELynx.Tree.Phylogeny Methods getLen :: PhyloExplicit -> Length Source # setLen :: Length -> PhyloExplicit -> PhyloExplicit Source # modLen :: (Length -> Length) -> PhyloExplicit -> PhyloExplicit Source #