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v0.0.0-...-318585b Latest Latest Go to latest Published: Mar 10, 2014 License: GPL-2.0 Imports: 11 Imported by: 0

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Repository

github.com/adamzy/txtgo

Links

Open Source Insights

Documentation ¶

Index ¶

Variables
func BinaryCost(gt *Tree, st *SpeciesTree) (dup, loss, dc int, err error)
func RF(gt *Tree, st *SpeciesTree) (rf int, err error)
func RefineGt(gt *Tree, st *SpeciesTree, method string, weights ...float64) error
type InvalidEdgeLengthError
- func (err InvalidEdgeLengthError) Error() string
type InvalidMethodError
- func (err InvalidMethodError) Error() string
type InvalidTreeError
- func (err InvalidTreeError) Error() string
type Lcamap
- func LcaMap(t *Tree, st *SpeciesTree) (*Lcamap, error)
type NoTaxaError
- func (err NoTaxaError) Error() string
type Node
- func (n *Node) AddChild(c *Node)
- func (node *Node) IsBinary() bool
- func (node *Node) IsInternal() bool
- func (node *Node) IsLeaf() bool
- func (node *Node) IsRoot() bool
- func (n *Node) NewChild() (child *Node)
- func (node *Node) Post2List() []*Node
- func (n *Node) String() string
type SpeciesTree
type Taxonmap
type Tree
- func ExampleTree(nleaves int) *Tree
- func LineTree(nleaves int) *Tree
- func LineTree2(nleaves int) *Tree
- func Make(s string) (*Tree, error)
- func SimuTree(size int) *Tree
- func SimuTreeRandomTaxon(size, ntaxon int) *Tree
- func YuleTree(size int) *Tree
- func (t *Tree) AssignLeafName()
- func (t *Tree) ContractByLength(length float64)
- func (t *Tree) ContractSingleChild()
- func (t *Tree) IsBinary() bool
- func (t *Tree) LCAer() func(a, b *Node) *Node
- func (t *Tree) PruneFromTaxon(taxon Taxonmap)
- func (t *Tree) PruneFromTree(gt *Tree)
- func (t *Tree) RandomContract(rate float64)
- func (t *Tree) SpeciesTree() (*SpeciesTree, error)
- func (t *Tree) TaxonMap() (taxon Taxonmap, unique bool)
- func (t *Tree) Update()
- func (t *Tree) UpdateInfo()

Constants ¶

This section is empty.

Variables ¶

View Source

var (
	NotEnoughWeightsError     = errors.New("Not enough weight parameters.")
	NotBinarySpeciesTreeError = errors.New("Species tree is not binary.")
)

View Source

var (
	SpeciesTreeNotUniquelyLabeledError = errors.New("Species tree is not uniquely labeled.")
)

Functions ¶

func BinaryCost ¶

func BinaryCost(gt *Tree, st *SpeciesTree) (dup, loss, dc int, err error)

BinaryCost finds the duplication, loss, and deep coalescence cost for input binary gene tree and species tree.

func RF ¶

func RF(gt *Tree, st *SpeciesTree) (rf int, err error)

RF finds the Robinson-Folds distance for uniquely labeled binary gene tree and species tree.

func RefineGt ¶

func RefineGt(gt *Tree, st *SpeciesTree, method string, weights ...float64) error

A dispatch function

Types ¶

type InvalidEdgeLengthError ¶

type InvalidEdgeLengthError struct {
	EdgeLength string
}

func (InvalidEdgeLengthError) Error ¶

func (err InvalidEdgeLengthError) Error() string

type InvalidMethodError ¶

type InvalidMethodError struct {
	Method string
}

func (InvalidMethodError) Error ¶

func (err InvalidMethodError) Error() string

type InvalidTreeError ¶

type InvalidTreeError struct {
	TreeString string
}

func (InvalidTreeError) Error ¶

func (err InvalidTreeError) Error() string

type Lcamap ¶

type Lcamap struct {
	G   *Tree
	S   *SpeciesTree
	Map []*Node
}

func LcaMap ¶

func LcaMap(t *Tree, st *SpeciesTree) (*Lcamap, error)

Generate `Lcamap` for gene tree and species tree. Assume that every internal genetree node has at least two children

type NoTaxaError ¶

type NoTaxaError struct {
	Taxa string
}

func (NoTaxaError) Error ¶

func (err NoTaxaError) Error() string

type Node ¶

type Node struct {
	Father   *Node
	Children []*Node
	// contains filtered or unexported fields
}

func (*Node) AddChild ¶

func (n *Node) AddChild(c *Node)

func (*Node) IsBinary ¶

func (node *Node) IsBinary() bool

func (*Node) IsInternal ¶

func (node *Node) IsInternal() bool

func (*Node) IsLeaf ¶

func (node *Node) IsLeaf() bool

func (*Node) IsRoot ¶

func (node *Node) IsRoot() bool

func (*Node) NewChild ¶

func (n *Node) NewChild() (child *Node)

func (*Node) Post2List ¶

func (node *Node) Post2List() []*Node

Postorder iterate the tree and put nodes into a list

func (*Node) String ¶

func (n *Node) String() string

Represent the tree (rooted at `n`) in newick format.

type SpeciesTree ¶

type SpeciesTree struct {
	*Tree
	Taxon Taxonmap
	Lca   func(a, b *Node) *Node
}

type Taxonmap ¶

type Taxonmap map[string]*Node

A map that maps taxa to (one of) the corresponding leaf node

type Tree ¶

type Tree struct {
	*Node
	Nodes []*Node
}

func ExampleTree ¶

func ExampleTree(nleaves int) *Tree

func LineTree ¶

func LineTree(nleaves int) *Tree

func LineTree2 ¶

func LineTree2(nleaves int) *Tree

func Make ¶

func Make(s string) (*Tree, error)

Make a tree from a string

func SimuTree ¶

func SimuTree(size int) *Tree

func SimuTreeRandomTaxon ¶

func SimuTreeRandomTaxon(size, ntaxon int) *Tree

func YuleTree ¶

func YuleTree(size int) *Tree

func (*Tree) AssignLeafName ¶

func (t *Tree) AssignLeafName()

func (*Tree) ContractByLength ¶

func (t *Tree) ContractByLength(length float64)

Contract tree branches whose lengthes are less than the given one.

func (*Tree) ContractSingleChild ¶

func (t *Tree) ContractSingleChild()

Contract tree branches which have only one child.

func (*Tree) IsBinary ¶

func (t *Tree) IsBinary() bool

A tree is binary tree <=> every internal node has two children. Overwrite `node.IsBinary` method.

func (*Tree) LCAer ¶

func (t *Tree) LCAer() func(a, b *Node) *Node

Make a LCAer function for species tree t.

Usage:
    Lca := st.LCAer()
    Lca(a, b)

func (*Tree) PruneFromTaxon ¶

func (t *Tree) PruneFromTaxon(taxon Taxonmap)

Prune tree according to the taxonmap

func (*Tree) PruneFromTree ¶

func (t *Tree) PruneFromTree(gt *Tree)

Prune tree according to another tree

func (*Tree) RandomContract ¶

func (t *Tree) RandomContract(rate float64)

Randomly contract tree branches according to the given rate.

func (*Tree) SpeciesTree ¶

func (t *Tree) SpeciesTree() (*SpeciesTree, error)

func (*Tree) TaxonMap ¶

func (t *Tree) TaxonMap() (taxon Taxonmap, unique bool)

`TaxonMap` return the `Taxonmap` for a tree, and the uniqueness of its taxon.

func (*Tree) Update ¶

func (t *Tree) Update()

Update everything of a tree from `tree.Node`, including `tree.Nodes, size, node.id, level`. Useful after the tree was manually edited

func (*Tree) UpdateInfo ¶

func (t *Tree) UpdateInfo()

Update node.Level and node.Id for tree `t`

Source Files ¶

View all Source files

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