tree

Documentation

Overview

Package tree implements tree structure and newick parsing.

Index

• func IsSpecial(c rune) bool
• func NewickSplit(data []byte, atEOF bool) (advance int, token []byte, err error)
• type Mode
• type Node
  • func NewNode(parent *Node, nodeID int) (node *Node)
  • func (node *Node) AddChild(subNode *Node)
  • func (node *Node) BrString() (s string)
  • func (node *Node) ChildNodes() []*Node
  • func (node *Node) ClassString() (s string)
  • func (node *Node) Copy() *Node
  • func (node *Node) FullString() string
  • func (node *Node) IsRoot() bool
  • func (node *Node) IsTerminal() bool
  • func (node *Node) LongString() (s string)
  • func (node *Node) NSubNodes() (size int)
  • func (node *Node) ShortClassString() (s string)
  • func (node *Node) String() (s string)
  • func (node *Node) Walk(ch chan *Node, filter func(*Node) bool)
• type Tree
  • func ParseNewick(rd io.Reader) (tree *Tree, err error)
  • func (tree *Tree) ClassNodes(class int) <-chan *Node
  • func (tree *Tree) ClearCache()
  • func (tree *Tree) Copy() (newTree *Tree)
  • func (tree *Tree) IsRooted() bool
  • func (tree *Tree) MaxNodeID() (maxID int)
  • func (tree *Tree) NLeaves() (i int)
  • func (tree *Tree) NNodes() int
  • func (tree *Tree) NodeIDArray() []*Node
  • func (tree *Tree) NodeOrder() []*Node
  • func (tree *Tree) NonTerminals() <-chan *Node
  • func (tree *Tree) Root(branchID int) error
  • func (tree *Tree) Terminals() <-chan *Node
  • func (tree *Tree) Unroot() (int, error)
  • func (tree *Tree) Walker(filter func(*Node) bool) <-chan *Node

Functions

func IsSpecial

func IsSpecial(c rune) bool

IsSpecial returns true if character is a special character (i.e. not identifier).

func NewickSplit

func NewickSplit(data []byte, atEOF bool) (advance int, token []byte, err error)

NewickSplit is a function parsing a newick-formatted data.

Types

type Mode

type Mode int

Mode is a newick parsing mode variable.

const (
	// Default parsing mode.
	NORMAL Mode = iota
	// Parsing branch length.
	LENGTH
	// Parsing node class.
	CLASS
)

Newick parsing modes.

type Node

type Node struct {
	// Name is the node label.
	Name string
	// BranchLength is the length of the  branch going to the node.
	BranchLength float64
	// Parent is the parent node (nil for the root).
	Parent *Node

	// Id is the node ID.
	ID int
	// LeafId is the leaf id.
	LeafID int
	// Class is a node class (specified by # symbol in newick).
	Class int
	// contains filtered or unexported fields
}

Node is a node of a tree.

func NewNode

func NewNode(parent *Node, nodeID int) (node *Node)

NewNode creates a new Node.

func (*Node) AddChild

func (node *Node) AddChild(subNode *Node)

AddChild adds a child node.

func (*Node) BrString

func (node *Node) BrString() (s string)

BrString returns a newick string with branch labels for a node and its' subnodes.

func (*Node) ChildNodes

func (node *Node) ChildNodes() []*Node

ChildNodes returns a children nodes slice.

func (*Node) ClassString

func (node *Node) ClassString() (s string)

ClassString returns a newick string with class labels for a node and its' subnodes.

func (*Node) Copy

func (node *Node) Copy() *Node

Copy creates copy of node with empty parent and children.

func (*Node) FullString

func (node *Node) FullString() string

FullString returns extended string for the whole tree.

func (*Node) IsRoot

func (node *Node) IsRoot() bool

IsRoot returns true if current node is a root.

func (*Node) IsTerminal

func (node *Node) IsTerminal() bool

IsTerminal returns true if node is a leaf.

func (*Node) LongString

func (node *Node) LongString() (s string)

LongString returns an extended string with all the ids, classes, etc for one node.

func (*Node) NSubNodes

func (node *Node) NSubNodes() (size int)

NSubNodes returns a total number of subnodes for a current node.

func (*Node) ShortClassString

func (node *Node) ShortClassString() (s string)

ShortClassString returns a newick string with class labels for a node and its' subnodes without branch lengths.

func (*Node) String

func (node *Node) String() (s string)

String returns a newick string for a node and its' subnodes.

func (*Node) Walk

func (node *Node) Walk(ch chan *Node, filter func(*Node) bool)

Walk traverses the tree nodes and sends them into a channel. An optional filtering function may be provided.

type Tree

type Tree struct {
	// Node is the root node.
	*Node
	// contains filtered or unexported fields
}

Tree is a tree structure.

func ParseNewick

func ParseNewick(rd io.Reader) (tree *Tree, err error)

ParseNewick parses a newick formatted reader into the Tree type.

func (*Tree) ClassNodes

func (tree *Tree) ClassNodes(class int) <-chan *Node

ClassNodes returns a channel with all the nodes of a given class.

func (*Tree) ClearCache

func (tree *Tree) ClearCache()

ClearCache clears all precomputed parameters.

func (*Tree) Copy

func (tree *Tree) Copy() (newTree *Tree)

Copy creates independent copy of the tree.

func (*Tree) IsRooted

func (tree *Tree) IsRooted() bool

IsRooted returns true if the tree is rooted (i.e. bifurcation at the root).

func (*Tree) MaxNodeID

func (tree *Tree) MaxNodeID() (maxID int)

MaxNodeID returns maximum id of a node.

func (*Tree) NLeaves

func (tree *Tree) NLeaves() (i int)

NLeaves returns number of leaves.

func (*Tree) NNodes

func (tree *Tree) NNodes() int

NNodes returns number of nodes.

func (*Tree) NodeIDArray

func (tree *Tree) NodeIDArray() []*Node

NodeIDArray returns an array (slice). This array allows addressing nodes by their ids.

func (*Tree) NodeOrder

func (tree *Tree) NodeOrder() []*Node

NodeOrder returns an array (slice) with non-terminal nodes in post-order.

func (*Tree) NonTerminals

func (tree *Tree) NonTerminals() <-chan *Node

NonTerminals returns a channel with all the non-terminal nodes of a tree.

func (*Tree) Root

func (tree *Tree) Root(branchID int) error

Root roots the tree by replacing trifurcation at the root by a bifurcation.

func (*Tree) Terminals

func (tree *Tree) Terminals() <-chan *Node

Terminals returns a channel with all the terminal nodes of a tree.

func (*Tree) Unroot

func (tree *Tree) Unroot() (int, error)

Unroot unroots the tree (i.e. replaces bifurcation at the root with a trifurcation).

func (*Tree) Walker

func (tree *Tree) Walker(filter func(*Node) bool) <-chan *Node

Walker returns a channel iterating over nodes. An optional function is provided to filter nodes.