ELynx.Data.Tree.MeasurableTree

Creation date: Thu Jan 17 14:16:34 2019.

Documentation

class Measurable a where

A Node label with measurable and modifiable branch length to the parent.

Methods

getLen :: a -> Double

Length of attached branch.

setLen :: Double -> a -> a

Set attached branch length.

Instances

Measurable (PhyloLabel a)

If no branch length is available, 0 is returned. This is probably not the best (and final) behavior.

Defined in ELynx.Data.Tree.PhyloTree

Methods

getLen :: PhyloLabel a -> Double

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

distancesRootLeaves :: Measurable a => Tree a -> [Double]

Distances from the root node of a tree to its leaves (this are not the distances from the origin to the leaves, see distancesOriginLeaves).

distancesOriginLeaves :: Measurable a => Tree a -> [Double]

Distances from the origin of a tree to its leaves (this is not the distance from the root node to the leaves, which would be distanceOriginLeaves t - (getLen $ rootLabel t).). See also distancesRootLeaves.

averageDistanceOriginLeaves :: Measurable a => Tree a -> Double

Average distance from the origin of a tree to its leaves, see distancesOriginLeaves.

height :: Measurable a => Tree a -> Double

Height (max distance between origin and leaves) of a tree. Return 0 if the tree is empty.

rootHeight :: Measurable a => Tree a -> Double

Height of root node. Return 0 if the tree is empty.

lengthenStem :: Measurable a => Double -> Tree a -> Tree a

Lengthen the distance between root and origin.

shortenStem :: Measurable a => Double -> Tree a -> Tree a

Lengthen the distance between root and origin.

summarize :: Measurable a => Tree a -> ByteString

Summarize a tree with measureable branch lengths.

totalBranchLength :: Measurable a => Tree a -> Double

Total branch length of a tree.

normalize :: Measurable a => Tree a -> Tree a

Normalize tree so that sum of branch lengths is 1.0.

prune :: Measurable a => Tree a -> Tree a

Prune degree 2 nodes. Add branch lengths but forget pruned node label. See pruneWith.

removeMultifurcations :: Measurable a => Tree a -> Tree a

Remove multifurcations by copying multifurcating nodes and introducing branches of length 0.

ultrametric :: Measurable a => Tree a -> Bool

Check if a tree is ultrametric.