Bio.Phylogeny.Internal.Types

data Event

Constructors

• Clade
• Taxa
• Hybrid
• LateralGeneTransfer
• Recombination

Instances

• Eq Event

eventToString :: Event -> String

newtype PhylogenyNode

Constructors

• PhylogenyNode { attributes :: Map String Attribute, branchLength :: Number, event :: Event, name :: NodeName, ref :: NodeIdentifier }

Instances

• Eq PhylogenyNode
• Ord PhylogenyNode
• Show PhylogenyNode

type NodeIdentifier = Int

type NodeName = String

type Network = Graph NodeIdentifier PhylogenyNode

type Metadata = { description :: Maybe String, name :: Maybe String, parent :: NodeIdentifier, rooted :: Boolean }

type Phylogeny = { metadata :: Array Metadata, network :: Network }

newtype PartialPhylogeny

Constructors

• PartialPhylogeny { maxRef :: NodeIdentifier, metadata :: Array Metadata, network :: Map NodeIdentifier (Tuple PhylogenyNode (List NodeIdentifier)) }

Instances

• Semigroup PartialPhylogeny
• Monoid PartialPhylogeny

type PartialNode = { attributes :: Map String Attribute, branchLength :: Number, event :: Event, name :: NodeName, ref :: Maybe NodeIdentifier }

type Parser a = ParserT String Identity a

data Tree a

Constructors

• Leaf a
• Internal a (Array (Tree a))

Instances

• (Eq a) => Eq (Tree a)
• Functor Tree
• Semigroup (Tree a)
• Foldable Tree

  Pre-order tree traversal

• Traversable Tree

interpretIntermediate :: Int -> Tree PartialNode -> PartialPhylogeny

toPhylogeny :: PartialPhylogeny -> Phylogeny

toAnnotatedPhylogeny :: Array Metadata -> PartialPhylogeny -> Phylogeny