ELynx.Tree.Import.Newick

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

Code snippet:

import Data.Attoparsec.ByteString
import ELynx.Tree

getOneNewick = either error id . parseOnly (oneNewick Standard)

Documentation

data NewickFormat

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

Defined in ELynx.Tree.Import.Newick

Methods

minBound :: NewickFormat

maxBound :: NewickFormat

Enum NewickFormat

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

Defined in ELynx.Tree.Import.Newick

Methods

(==) :: NewickFormat -> NewickFormat -> Bool

(/=) :: NewickFormat -> NewickFormat -> Bool

Read NewickFormat

Defined in ELynx.Tree.Import.Newick

Methods

readsPrec :: Int -> ReadS NewickFormat

readList :: ReadS [NewickFormat]

readPrec :: ReadPrec NewickFormat

readListPrec :: ReadPrec [NewickFormat]

Show NewickFormat

Defined in ELynx.Tree.Import.Newick

Methods

showsPrec :: Int -> NewickFormat -> ShowS

show :: NewickFormat -> String

showList :: [NewickFormat] -> ShowS

Generic NewickFormat

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

Defined in ELynx.Tree.Import.Newick

Methods

toJSON :: NewickFormat -> Value

toEncoding :: NewickFormat -> Encoding

toJSONList :: [NewickFormat] -> Value

toEncodingList :: [NewickFormat] -> Encoding

FromJSON NewickFormat

Defined in ELynx.Tree.Import.Newick

Methods

parseJSON :: Value -> Parser NewickFormat

parseJSONList :: Value -> Parser [NewickFormat]

type Rep NewickFormat

Defined in ELynx.Tree.Import.Newick

type Rep NewickFormat = D1 ('MetaData "NewickFormat" "ELynx.Tree.Import.Newick" "elynx-tree-0.5.0.2-GziknJIwzW98btoIzMRbOK" '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)))

describeNewickFormat :: NewickFormat -> String

Short description of the supported Newick formats.

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

Newick tree parser. Also succeeds when more trees follow.

parseNewick :: NewickFormat -> ByteString -> Tree Phylo Name

See newick.

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

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

parseOneNewick :: NewickFormat -> ByteString -> Tree Phylo Name

See oneNewick.

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

One or more Newick trees parser.

parseSomeNewick :: NewickFormat -> ByteString -> [Tree Phylo Name]

See someNewick.