Safe Haskell	None
Language	Haskell2010

ELynx.Import.Tree.Newick

Description

module header.

Synopsis

data NewickFormat
- = Standard
- | IqTree
- | RevBayes
description :: NewickFormat -> String
newick :: NewickFormat -> Parser (Tree Phylo ByteString)
oneNewick :: NewickFormat -> Parser (Tree Phylo ByteString)
someNewick :: NewickFormat -> Parser (Forest Phylo ByteString)

Documentation

data NewickFormat Source #

Newick tree format.

>>> unlines $ map (("- " <>) . description) (allValues :: [NewickFormat])
- 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 is provided in square brackets after node names as well as branch lengths. XXX: Key value pairs are ignored at the moment.

Constructors

Standard
IqTree
RevBayes

Instances

Bounded NewickFormat Source #
Instance details Defined in ELynx.Import.Tree.Newick Methods minBound :: NewickFormat # maxBound :: NewickFormat #
Enum NewickFormat Source #
Instance details Defined in ELynx.Import.Tree.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] #
Eq NewickFormat Source #
Instance details Defined in ELynx.Import.Tree.Newick Methods (==) :: NewickFormat -> NewickFormat -> Bool # (/=) :: NewickFormat -> NewickFormat -> Bool #
Read NewickFormat Source #
Instance details Defined in ELynx.Import.Tree.Newick Methods readsPrec :: Int -> ReadS NewickFormat # readList :: ReadS [NewickFormat] # readPrec :: ReadPrec NewickFormat # readListPrec :: ReadPrec [NewickFormat] #
Show NewickFormat Source #
Instance details Defined in ELynx.Import.Tree.Newick Methods showsPrec :: Int -> NewickFormat -> ShowS # show :: NewickFormat -> String # showList :: [NewickFormat] -> ShowS #
Generic NewickFormat Source #
Instance details Defined in ELynx.Import.Tree.Newick Associated Types type Rep NewickFormat :: Type -> Type # Methods from :: NewickFormat -> Rep NewickFormat x # to :: Rep NewickFormat x -> NewickFormat #
ToJSON NewickFormat Source #
Instance details Defined in ELynx.Import.Tree.Newick Methods toJSON :: NewickFormat -> Value # toEncoding :: NewickFormat -> Encoding # toJSONList :: [NewickFormat] -> Value # toEncodingList :: [NewickFormat] -> Encoding #
FromJSON NewickFormat Source #
Instance details Defined in ELynx.Import.Tree.Newick Methods parseJSON :: Value -> Parser NewickFormat # parseJSONList :: Value -> Parser [NewickFormat] #
type Rep NewickFormat Source #
Instance details Defined in ELynx.Import.Tree.Newick type Rep NewickFormat = D1 (MetaData "NewickFormat" "ELynx.Import.Tree.Newick" "elynx-tree-0.3.4-LQCElpJLZESF8ouYw4ZWeR" 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)))

description :: NewickFormat -> String Source #

Short description of the supported Newick formats.

newick :: NewickFormat -> Parser (Tree Phylo ByteString) Source #

Parse a single Newick tree. Also succeeds when more trees follow.

oneNewick :: NewickFormat -> Parser (Tree Phylo ByteString) Source #

Parse a single Newick tree. Fails when end of file is not reached.

someNewick :: NewickFormat -> Parser (Forest Phylo ByteString) Source #

Parse one or more Newick trees until end of file.