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

TLynx.Parsers

Description

Creation date: Wed Apr 22 13:34:35 2020.

Synopsis

parseTree :: NewickFormat -> FilePath -> IO (Tree Phylo Name)
parseTrees :: NewickFormat -> FilePath -> IO (Forest Phylo Name)
data NewickFormat
newickFormat :: Parser NewickFormat
newickHelp :: [String]

Documentation

parseTree :: NewickFormat -> FilePath -> IO (Tree Phylo Name) Source #

Parse a Newick tree file or a Nexus file with Newick trees.

Error if no or more than one trees are found. Error if both file formats fail to parse.

parseTrees :: NewickFormat -> FilePath -> IO (Forest Phylo Name) Source #

Parse a Newick tree file or a Nexus file with Newick trees.

Error if both file formats fail to parse.

data NewickFormat #

Newick tree format.

Standard: Branch support values are stored in square brackets after branch lengths.
IqTree: Branch support values are stored as node names after the closing bracket of forests.
RevBayes: Key-value pairs are provided in square brackets after node names as well as branch lengths. NOTE: Key value pairs are ignored.

Instances

Instances details

FromJSON NewickFormat
Instance details Defined in ELynx.Tree.Import.Newick Methods parseJSON :: Value -> Parser NewickFormat # parseJSONList :: Value -> Parser [NewickFormat] #
ToJSON NewickFormat
Instance details Defined in ELynx.Tree.Import.Newick Methods toJSON :: NewickFormat -> Value # toEncoding :: NewickFormat -> Encoding # toJSONList :: [NewickFormat] -> Value # toEncodingList :: [NewickFormat] -> Encoding #
Bounded NewickFormat
Instance details Defined in ELynx.Tree.Import.Newick Methods minBound :: NewickFormat # maxBound :: NewickFormat #
Enum NewickFormat
Instance details Defined in ELynx.Tree.Import.Newick Methods succ :: NewickFormat -> NewickFormat # pred :: NewickFormat -> NewickFormat # toEnum :: Int -> NewickFormat # fromEnum :: NewickFormat -> Int # enumFrom :: NewickFormat -> [NewickFormat] # enumFromThen :: NewickFormat -> NewickFormat -> [NewickFormat] # enumFromTo :: NewickFormat -> NewickFormat -> [NewickFormat] # enumFromThenTo :: NewickFormat -> NewickFormat -> NewickFormat -> [NewickFormat] #
Generic NewickFormat
Instance details Defined in ELynx.Tree.Import.Newick Associated Types type Rep NewickFormat :: Type -> Type # Methods from :: NewickFormat -> Rep NewickFormat x # to :: Rep NewickFormat x -> NewickFormat #
Read NewickFormat
Instance details Defined in ELynx.Tree.Import.Newick Methods readsPrec :: Int -> ReadS NewickFormat # readList :: ReadS [NewickFormat] # readPrec :: ReadPrec NewickFormat # readListPrec :: ReadPrec [NewickFormat] #
Show NewickFormat
Instance details Defined in ELynx.Tree.Import.Newick Methods showsPrec :: Int -> NewickFormat -> ShowS # show :: NewickFormat -> String # showList :: [NewickFormat] -> ShowS #
Eq NewickFormat
Instance details Defined in ELynx.Tree.Import.Newick Methods (==) :: NewickFormat -> NewickFormat -> Bool # (/=) :: NewickFormat -> NewickFormat -> Bool #
type Rep NewickFormat
Instance details Defined in ELynx.Tree.Import.Newick type Rep NewickFormat = D1 ('MetaData "NewickFormat" "ELynx.Tree.Import.Newick" "elynx-tree-0.7.2.2-7v79cynrH4qIkHZDd1p2Yg" 'False) (C1 ('MetaCons "Standard" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "IqTree" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "RevBayes" 'PrefixI 'False) (U1 :: Type -> Type)))

newickFormat :: Parser NewickFormat Source #

Parse NewickFormat.

newickHelp :: [String] Source #

Help for different NewickFormats.