Newick Tree Parser

JavaScript library for parsing the Newick Tree format.

Usage:

import { Newick } from 'newick-tree-parser'
const newick = new Newick('some data')

Documentation:

NewickTools.dfs

Returns nodes data

import { NewickTools } from 'newick-tree-parser'
NewickTools.dfs(tree)

tree - string or parsed object

var tree = NewickTools.parse('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');
var data = NewickTools.dfs(tree);

Returns object

{
  A: 0.1,
  B: 0.2,
  C: 0.3,
  D: 0.4,
  E: 0.5
}

NewickTools.dfs(tree, nodeCallback)

• tree - string or parsed object
• nodeCallback - function (node)

var tree = NewickTools.parse('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');
var data = NewickTools.dfs(tree, function (e) {
  e.length *= 10;
  return e;
});

Returns object

{
  A: 1,
  B: 2,
  C: 3,
  D: 4,
  E: 5
}

NewickTools.equals

Check if two trees are equal

import { NewickTools } from 'newick-tree-parser'

NewickTools.equals(tree1, tree2)

tree1, tree2 - Newick instanse Returns boolean true or false

var tree1 = NewickTools.parse('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');
var tree2 = NewickTools.parse('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');

NewickTools.equals(tree1, tree2); // true;

tree2 = NewickTools.parse('(A:0.11,B:0.22,(C:0.33,D:0.44)E:0.55)F');

NewickTools.equals(tree1, tree2); // false

NewickTools.getRoot

Returns a root of the tree

import { NewickTools } from 'newick-tree-parser'

NewickTools.getRoot(s)

s - string on parsed object

var tree = NewickTools.parse('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');
var root = NewickTools.getRoot(tree);\

Returns string (root name)

'F'

NewickTools.map

Iterates tree's nodes and applies callback for each node

Alias for NewickTools.dfs(tree, callback)

import { NewickTools } from 'newick-tree-parser'

NewickTools.map(tree, callback)

tree - string or parsed object callback - function (node)

var tree = NewickTools.parse('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');
var mappedTree = NewickTools.map(tree, function (e) {
  e *= 10;
  e.name += ' mapped';
  return e;
});

Returns object

{
    name: "F mapped",
    branchset: [
    {
        name: "A mapped",
        length: 1
    },
    {
        name: "B mapped",
        length: 2
    },
    {
        name: "E mapped",
        length: 5,
        branchset: [
        {
            name: "C mapped",
            length: 3
        },
        {
            name: "D mapped",
            length: 4
        }]
    }]
}

NewickTools.normalize

Returns normalized tree in [0; 1]

import { NewickTools } from 'newick-tree-parser'

NewickTools.normalize(tree)

tree - string or parsed object

var tree = NewickTools.parse('(A:5,B:20)F;');
var normalizedTree = NewickTools.normalize(tree)

Returns object

{
  name:"F",
  branchset: [
    {name:"A", length: 0.2},
    {name:"B", length: 0.8}
  ]
}

NewickTools.parse

Parse Newick string into tree-object

import { NewickTools } from 'newick-tree-parser'

NewickTools.parse(s)

s - string

var tree = NewickTools.parse('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');

Returns object

{
    name: "F",
    branchset: [
    {
        name: "A",
        length: 0.1
    },
    {
        name: "B",
        length: 0.2
    },
    {
        name: "E",
        length: 0.5,
        branchset: [
        {
            name: "C",
            length: 0.3
        },
        {
            name: "D",
            length: 0.4
        }]
    }]
}

NewickTools.serialize

Serializes tree

import { NewickTools } from 'newick-tree-parser'

NewickTools.serialize(tree)

tree - string or parsed object

var tree = NewickTools.parse('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');
var serializedTree = NewickTools.serialize(tree)

Returns string

'(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;'

private.cast

Casts tree or string to tree-object

private

cast(s)

s - string or parsed object

var tree = '(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F';
tree = cast(tree);

Returns object

{
    name: "F",
    branchset: [
    {
        name: "A",
        length: 0.1
    },
    {
        name: "B",
        length: 0.2
    },
    {
        name: "E",
        length: 0.5,
        branchset: [
        {
            name: "C",
            length: 0.3
        },
        {
            name: "D",
            length: 0.4
        }]
    }]
}

private.getRoot

Returns a root of the tree

private

getRoot(s)

s - string or parsed object

var tree = Newick.parse('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');
tree = getRoot(tree);

Returns string (root name)

'F'

private.serialize

Serializes tree

private

serialize(node)

node - tree node

var tree = Newick.parse('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');
var serializedTree = Newick.serialize(tree)

Returns string

'(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F'

public.dfs

Returns nodes data

public method

var data = newick.dfs();
var tree = new Newick('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');
var data = newick.dfs();

Returns object

{
  A: 0.1,
  B: 0.2,
  C: 0.3,
  D: 0.4,
  E: 0.5
}

var data = newick.dfs(nodeCallback);

nodeCallback - function (node)

var tree = new Newick('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F');
var data = newick.dfs(function (e) {
  e.length *= 10;
  return e;
});

Returns object

{
  A: 1,
  B: 2,
  C: 3,
  D: 4,
  E: 5
}