Copyright	(c) Dominik Schrempf 2021
License	GPL-3.0-or-later
Maintainer	dominik.schrempf@gmail.com
Stability	unstable
Portability	portable
Safe Haskell	None
Language	Haskell2010

ELynx.Tree.Import.Newick

Description

Creation date: Thu Jan 17 14:56:27 2019.

Some functions are inspired by Biobase.Newick.Import.

Specifications

In particular, no conversion from _ to (space) is done right now.

For a description of rooted Trees, please see the Rooted

Synopsis

data NewickFormat
- = Standard
- | IqTree
- | RevBayes
newick :: NewickFormat -> Parser (Tree Phylo Name)
oneNewick :: NewickFormat -> Parser (Tree Phylo Name)
parseOneNewick :: NewickFormat -> ByteString -> Either String (Tree Phylo Name)
readOneNewick :: NewickFormat -> FilePath -> IO (Tree Phylo Name)
someNewick :: NewickFormat -> Parser (Forest Phylo Name)
parseSomeNewick :: NewickFormat -> ByteString -> Either String [Tree Phylo Name]
readSomeNewick :: NewickFormat -> FilePath -> IO [Tree Phylo Name]

Documentation

data NewickFormat Source #

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.

Constructors

Standard
IqTree
RevBayes

Instances

Instances details

Bounded NewickFormat Source #
Instance details Defined in ELynx.Tree.Import.Newick Methods minBound :: NewickFormat # maxBound :: NewickFormat #
Enum NewickFormat Source #
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] #
Eq NewickFormat Source #
Instance details Defined in ELynx.Tree.Import.Newick Methods (==) :: NewickFormat -> NewickFormat -> Bool # (/=) :: NewickFormat -> NewickFormat -> Bool #
Read NewickFormat Source #
Instance details Defined in ELynx.Tree.Import.Newick Methods readsPrec :: Int -> ReadS NewickFormat # readList :: ReadS [NewickFormat] # readPrec :: ReadPrec NewickFormat # readListPrec :: ReadPrec [NewickFormat] #
Show NewickFormat Source #
Instance details Defined in ELynx.Tree.Import.Newick Methods showsPrec :: Int -> NewickFormat -> ShowS # show :: NewickFormat -> String # showList :: [NewickFormat] -> ShowS #
Generic NewickFormat Source #
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 #
ToJSON NewickFormat Source #
Instance details Defined in ELynx.Tree.Import.Newick Methods toJSON :: NewickFormat -> Value # toEncoding :: NewickFormat -> Encoding # toJSONList :: [NewickFormat] -> Value # toEncodingList :: [NewickFormat] -> Encoding #
FromJSON NewickFormat Source #
Instance details Defined in ELynx.Tree.Import.Newick Methods parseJSON :: Value -> Parser NewickFormat # parseJSONList :: Value -> Parser [NewickFormat] #
type Rep NewickFormat Source #
Instance details Defined in ELynx.Tree.Import.Newick type Rep NewickFormat = D1 ('MetaData "NewickFormat" "ELynx.Tree.Import.Newick" "elynx-tree-0.6.0.0-FQkEU9t6m33732ommPyIXg" '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)))

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

Newick tree parser. Also succeeds when more trees follow.

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

One Newick tree parser. Fails when end of input is not reached.

parseOneNewick :: NewickFormat -> ByteString -> Either String (Tree Phylo Name) Source #

See oneNewick.

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

See oneNewick; may fail with error.

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

One or more Newick trees parser.

parseSomeNewick :: NewickFormat -> ByteString -> Either String [Tree Phylo Name] Source #

See someNewick.

readSomeNewick :: NewickFormat -> FilePath -> IO [Tree Phylo Name] Source #

See someNewick; may fail with error.