ELynx.Data.Tree.PhyloTree

Creation date: Thu Jan 17 16:08:54 2019.

Phylogenetic nodes have a branch length and a label.

The easiest label type is Int: PhyloIntLabel.

Also, the ByteString label is needed often: PhyloByteStringLabel.

XXX: This is all too complicated. Maybe I should just define a standard tree object like > data PhyloTree a = Tree (PhyloLabel a) and that's it. Forget about type classes like Measurable, Named and so on.

Documentation

data PhyloLabel a

A primitive label type for phylogenetic trees with a name, possibly a branch support value, and a Double branch length.

Constructors

PhyloLabel

Fields

• pLabel :: a
• pBrSup :: Maybe Double
• pBrLen :: Double

Instances

Named PhyloByteStringLabel

Defined in ELynx.Data.Tree.PhyloTree

Methods

getName :: PhyloByteStringLabel -> ByteString

Named PhyloIntLabel

Defined in ELynx.Data.Tree.PhyloTree

Methods

getName :: PhyloIntLabel -> ByteString

Eq a => Eq (PhyloLabel a)

Defined in ELynx.Data.Tree.PhyloTree

Methods

(==) :: PhyloLabel a -> PhyloLabel a -> Bool

(/=) :: PhyloLabel a -> PhyloLabel a -> Bool

Ord a => Ord (PhyloLabel a)

Defined in ELynx.Data.Tree.PhyloTree

Methods

compare :: PhyloLabel a -> PhyloLabel a -> Ordering

(<) :: PhyloLabel a -> PhyloLabel a -> Bool

(<=) :: PhyloLabel a -> PhyloLabel a -> Bool

(>) :: PhyloLabel a -> PhyloLabel a -> Bool

(>=) :: PhyloLabel a -> PhyloLabel a -> Bool

max :: PhyloLabel a -> PhyloLabel a -> PhyloLabel a

min :: PhyloLabel a -> PhyloLabel a -> PhyloLabel a

Read a => Read (PhyloLabel a)

Defined in ELynx.Data.Tree.PhyloTree

Methods

readsPrec :: Int -> ReadS (PhyloLabel a)

readList :: ReadS [PhyloLabel a]

readPrec :: ReadPrec (PhyloLabel a)

readListPrec :: ReadPrec [PhyloLabel a]

Show a => Show (PhyloLabel a)

Defined in ELynx.Data.Tree.PhyloTree

Methods

showsPrec :: Int -> PhyloLabel a -> ShowS

show :: PhyloLabel a -> String

showList :: [PhyloLabel a] -> ShowS

Arbitrary a => Arbitrary (PhyloLabel a)

Defined in ELynx.Data.Tree.PhyloTree

Methods

arbitrary :: Gen (PhyloLabel a)

shrink :: PhyloLabel a -> [PhyloLabel a]

BranchSupportLabel (PhyloLabel a)

Defined in ELynx.Data.Tree.PhyloTree

Methods

getBranchSupport :: PhyloLabel a -> BranchSupport

setBranchSupport :: BranchSupport -> PhyloLabel a -> PhyloLabel a

Measurable (PhyloLabel a)

Defined in ELynx.Data.Tree.PhyloTree

Methods

getLen :: PhyloLabel a -> Double

setLen :: Double -> PhyloLabel a -> PhyloLabel a

lengthen :: Double -> PhyloLabel a -> PhyloLabel a

shorten :: Double -> PhyloLabel a -> PhyloLabel a

type PhyloIntLabel = PhyloLabel Int

Tree node with Int label.

type PhyloByteStringLabel = PhyloLabel ByteString

Tree node with ByteString label. Important for parsing Newick files.

removeBrLen :: Tree (PhyloLabel a) -> Tree a

Remove branch lengths from tree.