diff --git a/.babelrc b/.babelrc deleted file mode 100644 index 441b240..0000000 --- a/.babelrc +++ /dev/null @@ -1,3 +0,0 @@ -{ - "presets": ["env", "react", "stage-1"] -} diff --git a/.gitignore b/.gitignore index bd8503c..18da204 100644 --- a/.gitignore +++ b/.gitignore @@ -10,3 +10,4 @@ dist/alignment.js *.svg *.ttf *.eot +tags* diff --git a/README.md b/README.md index a0f5783..b62cb1c 100644 --- a/README.md +++ b/README.md @@ -43,3 +43,22 @@ Start the development server: ``` yarn start ``` + +Visit `localhost:8000` in a browser (will read from environment variable `$PORT`). + +Note that this starts `webpack` in watch mode; refresh to observe changes. + +## Deployment + +### Application + +``` +yarn build-app +yarn serve +``` + +### Library + +``` +yarn build-lib +``` diff --git a/dist/data/H3trunk.new b/dist/data/H3trunk.new new file mode 100644 index 0000000..b9f83ee --- /dev/null +++ b/dist/data/H3trunk.new @@ -0,0 +1 @@ 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diff --git a/dist/data/Simple.fasta b/dist/data/Simple.fasta index 8637359..a4dada3 100644 --- a/dist/data/Simple.fasta +++ b/dist/data/Simple.fasta @@ -1,9 +1,6 @@ >Seq1 -ATCGTA -ATTGCA +ATCGTAATTGCA >Seq2 -CTCGTA -ATGGCC +CTCGTAATGGCC >Seq3 -GTCGTC -AATGCT +GTCGTCAATGCT diff --git a/extract_genbank_information.py b/extract_genbank_information.py new file mode 100644 index 0000000..1b65e5e --- /dev/null +++ b/extract_genbank_information.py @@ -0,0 +1,78 @@ +import sys +import json +import argparse +from itertools import chain + +try: + from Bio import SeqIO +except ImportError: + print('BioPython not installed!') + print('Please visit https://biopython.org/wiki/Download for instructions.') + sys.exit(1) + + +parser = argparse.ArgumentParser( + description='Write GenBank information to a JSON file for alignment.js.' +) + +parser.add_argument( + '-i', '--input', + metavar='INPUT', + type=str, + help='Input GenBank file', + required=True +) + +parser.add_argument( + '-o', '--output', + metavar='OUTPUT', + type=str, + help='Output JSON file', + required=True +) + + +args = parser.parse_args() + + +def extract_site_information(feature): + return list(chain(*[ + [ + { + 'name': feature.qualifiers['site_type'][0], + 'site': site, + 'type': 'site' + } + for site in part + ] + for part in feature.location.parts + ])) + + +def extract_region_information(feature): + return { + 'name': feature.qualifiers['region_name'][0], + 'start': int(feature.location.start), + 'end': int(feature.location.end), + 'type': 'region' + } + + +def extract_functional_information(features): + all_information = [] + for feature in features: + if feature.type == 'Site': + result = extract_site_information(feature) + all_information.append(result) + elif feature.type == 'Region': + result = extract_region_information(feature) + all_information.append([result]) + return sum(all_information, []) + + +record = next(SeqIO.parse(args.input, 'genbank')) +information = extract_functional_information(record.features) + +with open(args.output, 'w') as json_file: + json.dump(information, json_file, indent=2) + diff --git a/package-lock.json b/package-lock.json deleted file mode 100644 index 0b218d1..0000000 --- a/package-lock.json +++ /dev/null @@ -1,17734 +0,0 @@ -{ - "name": "alignment.js", - "version": "1.0.9", - "lockfileVersion": 1, - "requires": true, - "dependencies": { - "@samverschueren/stream-to-observable": { - "version": "0.3.0", - "resolved": - "https://registry.npmjs.org/@samverschueren/stream-to-observable/-/stream-to-observable-0.3.0.tgz", - "integrity": - "sha512-MI4Xx6LHs4Webyvi6EbspgyAb4D2Q2VtnCQ1blOJcoLS6mVa8lNN2rkIy1CVxfTUpoyIbCTkXES1rLXztFD1lg==", - "dev": true, - "requires": { - "any-observable": "^0.3.0" - } - }, - "abbrev": { - "version": "1.1.1", - "resolved": "https://registry.npmjs.org/abbrev/-/abbrev-1.1.1.tgz", - "integrity": - 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"camelcase": { - "version": "4.1.0", - "resolved": - "https://registry.npmjs.org/camelcase/-/camelcase-4.1.0.tgz", - "integrity": "sha1-1UVjW+HjPFQmScaRc+Xeas+uNN0=", - "dev": true - } - } - } - } -} diff --git a/package.json b/package.json index 0736fc6..9920779 100644 --- a/package.json +++ b/package.json @@ -1,37 +1,47 @@ { "name": "alignment.js", - "version": "1.1.1", + "version": "0.0.1", "main": "lib/alignment.js", "license": "MIT", "dependencies": { + "@babel/plugin-proposal-class-properties": "^7.4.4", + "@gmod/bam": "^1.0.18", "bootstrap": "^4.1.1", - "d3": "^4.12.2", + "d3": "5", + "d3-save-svg": "^0.0.2", + "express": "^4.16.4", + "file-saver": "^2.0.0", "jquery": "^3.3.1", - "phylotree": "0.2.0-alpha.1", + "phylotree": "1.0.0-alpha.14", "popper.js": "^1.14.3", "react": "^16.2.0", "react-dom": "^16.2.0", + "react-phylotree": "^0.0.1", + "react-router-dom": "^4.3.1", + "save-svg-as-png": "^1.4.14", "text-width": "^1.2.0", "underscore": "^1.8.3" }, "devDependencies": { + "@babel/cli": "^7.4.4", + "@babel/core": "^7.4.5", + "@babel/preset-env": "^7.4.5", + "@babel/preset-react": "^7.0.0", "autoprefixer": "^8.4.1", - "babel-core": "^6.26.0", - "babel-loader": "^7.1.2", - "babel-preset-env": "^1.6.1", - "babel-preset-es2015": "^6.24.1", - "babel-preset-react": "^6.24.1", - "babel-preset-stage-1": "^6.24.1", + "babel-eslint": "^10.0.1", + "babel-loader": "8", + "concurrently": "^4.1.0", "css-loader": "^0.28.11", "eslint": "4.18.2", "eslint-config-airbnb": "16.1.0", "eslint-plugin-import": "2.9.0", "eslint-plugin-jsx-a11y": "6.0.3", "eslint-plugin-react": "7.7.0", - "extract-text-webpack-plugin": "^3.0.2", + "extract-text-webpack-plugin": "^4.0.0-beta.0", "file-loader": "^1.1.6", - "html-webpack-plugin": "^2.30.1", + "html-webpack-plugin": "3", "husky": "^0.14.3", + "jest": "^23.6.0", "lint-staged": "^7.2.0", "node-sass": "^4.9.0", "npx": "^9.7.1", @@ -41,20 +51,33 @@ "sass-loader": "^7.0.1", "style-loader": "^0.21.0", "uglifyjs-webpack-plugin": "^1.1.4", - "webpack": "^3.10.0", - "webpack-dev-server": "^2.9.7", + "webpack": "4", + "webpack-cli": "^3.1.2", + "webpack-dev-server": "^3.1.10", "webpack-merge": "^4.1.1" }, "scripts": { - "start": "npx webpack-dev-server --open --config webpack.dev.js", + "develop": "npx webpack-dev-server --config webpack.dev.js --open", + "serve": "node src/server.js", "build-app": "npx webpack --config webpack.prod.js", "build-lib": "npx webpack --config webpack.lib.js", "precommit": "pretty-quick --staged", - "format": "prettier 'src/**/*.{js,jsx}' --write" + "format": "prettier 'src/**/*.{js,jsx}' --write", + "test": "jest" + }, + "babel": { + "presets": ["@babel/preset-env", "@babel/preset-react"], + "plugins": ["@babel/plugin-proposal-class-properties"], + "env": { + "test": { + "presets": ["@babel/preset-env", "@babel/preset-react"] + } + } }, "files": ["lib/alignment.js", "lib/alignment.css"], "repository": { "type": "git", "url": "https://github.com/veg/alignment.js" - } + }, + "sideEffects": false } diff --git a/src/components/Alignment.jsx b/src/Alignment.jsx similarity index 67% rename from src/components/Alignment.jsx rename to src/Alignment.jsx index 125f4b4..ec46ebc 100644 --- a/src/components/Alignment.jsx +++ b/src/Alignment.jsx @@ -1,16 +1,13 @@ import React, { Component } from "react"; -const d3 = require("d3"); -const $ = require("jquery"); -const _ = require("underscore"); -import fastaParser from "./../helpers/fasta"; -import computeLabelWidth from "../helpers/computeLabelWidth"; -import BaseAlignment from "./BaseAlignment.jsx"; -import SiteAxis from "./SiteAxis.jsx"; -import Placeholder from "./Placeholder.jsx"; -import SequenceAxis from "./SequenceAxis.jsx"; -import ScrollBroadcaster from "./../helpers/ScrollBroadcaster"; -import { nucleotide_color, nucleotide_text_color } from "./../helpers/colors"; +import fastaParser from "./helpers/fasta"; +import computeLabelWidth from "./helpers/computeLabelWidth"; +import BaseAlignment from "./components/BaseAlignment.jsx"; +import SiteAxis from "./components/SiteAxis.jsx"; +import Placeholder from "./components/Placeholder.jsx"; +import SequenceAxis from "./components/SequenceAxis.jsx"; +import ScrollBroadcaster from "./helpers/ScrollBroadcaster"; +import { nucleotide_color, nucleotide_text_color } from "./helpers/colors"; class Alignment extends Component { constructor(props) { @@ -18,34 +15,31 @@ class Alignment extends Component { this.label_width = 200; this.initialize(this.props); } - componentDidMount() { - this.setScrollingEvents(this.props); - } setScrollingEvents(props) { if (props.fasta) { const { width, height, axis_height } = props; - this.scroll_broadcaster = new ScrollBroadcaster( - { width: this.full_pixel_width, height: this.full_pixel_height }, - { width: width - this.label_width, height: height - axis_height }, - { x_pixel: this.x_pixel, y_pixel: this.y_pixel }, - [ + const { full_pixel_width, full_pixel_height, label_width } = this; + this.scroll_broadcaster = new ScrollBroadcaster({ + width: full_pixel_width, + height: full_pixel_height, + x_pad: width - label_width, + y_pad: height - axis_height, + x_pixel: this.x_pixel || 0, + y_pixel: this.y_pixel || 0, + bidirectional: [ "alignmentjs-alignment", "alignmentjs-axis-div", "alignmentjs-labels-div" ] - ); - const { scroll_broadcaster } = this; - scroll_broadcaster.setListeners(); - $("#alignmentjs-main-div").off("wheel"); - $("#alignmentjs-main-div").on("wheel", function(e) { - e.preventDefault(); - scroll_broadcaster.handleWheel(e); }); + if (props.excavator) { + props.excavator.broadcaster = this.scroll_broadcaster; + } } } - componentWillUpdate(nextProps) { + shouldComponentUpdate(nextProps) { this.initialize(nextProps); - this.setScrollingEvents(nextProps); + return true; } initialize(props) { if (props.fasta) { @@ -68,6 +62,7 @@ class Alignment extends Component { height / 2 : 0; } + this.setScrollingEvents(props); } render() { const { full_pixel_width, full_pixel_height, label_width } = this, @@ -88,6 +83,7 @@ class Alignment extends Component { site_size={this.props.site_size} sequence_data={this.sequence_data} x_pixel={this.x_pixel} + scroll_broadcaster={this.scroll_broadcaster} /> ); @@ -116,7 +115,11 @@ Alignment.defaultProps = { text_color: nucleotide_text_color, label_padding: 10, site_size: 20, - axis_height: 20 + axis_height: 25, + width: 960, + height: 500, + sender: "main", + molecule: mol => mol }; -module.exports = Alignment; +export default Alignment; diff --git a/src/SVGAlignment.jsx b/src/SVGAlignment.jsx new file mode 100644 index 0000000..2ee98e6 --- /dev/null +++ b/src/SVGAlignment.jsx @@ -0,0 +1,47 @@ +import React from "react"; + +import BaseSVGAlignment from "./components/BaseSVGAlignment.jsx"; +import SVGSiteAxis from "./components/SVGSiteAxis.jsx"; +import { BaseSequenceAxis } from "./components/SequenceAxis.jsx"; +import computeLabelWidth from "./helpers/computeLabelWidth"; + +function SVGAlignment(props) { + const { sequence_data, label_padding, site_size } = props; + if (!sequence_data) { + return ; + } + const { number_of_sites, number_of_sequences } = sequence_data, + label_width = computeLabelWidth(sequence_data, label_padding), + width = label_width + site_size * number_of_sites, + height = props.axis_height + site_size * number_of_sequences; + + return ( + + + + + + + ); +} + +SVGAlignment.defaultProps = { + label_padding: 10, + site_size: 20, + axis_height: 25 +}; + +export default SVGAlignment; diff --git a/src/app.jsx b/src/app.jsx new file mode 100644 index 0000000..c078e8c --- /dev/null +++ b/src/app.jsx @@ -0,0 +1,208 @@ +import React, { Component } from "react"; +import ReactDOM from "react-dom"; +import { BrowserRouter, Route, NavLink } from "react-router-dom"; +import "bootstrap"; +import "bootstrap/scss/bootstrap.scss"; +const $ = require("jquery"); + +import Home from "./app/home.jsx"; +import * as FASTA from "./app/FASTA.jsx"; +import * as FNA from "./app/FNA.jsx"; +import * as BAM from "./app/BAM.jsx"; +import Components from "./app/Components.jsx"; +import "./app/styles.scss"; + +function Divider(props) { + return [ +
, + props.header ? ( +
+ {props.header} +
+ ) : null + ]; +} + +function Link(props) { + return ( + + {props.header} + + ); +} + +function Dropdown(props) { + return ( + + ); +} + +function FASTALinks(props) { + return ( + + + + + + + + + + ); +} + +function FNALinks(props) { + return ( + + + + + + + + ); +} + +function BAMLinks(props) { + return ( + + + + + + ); +} + +function NavBar(props) { + const show_import_export = props.viewing == "alignment"; + return ( +
+ +
+ ); +} + +class App extends Component { + constructor(props) { + super(props); + this.state = { + data: null + }; + } + + render() { + return ( +
+ +
+ } /> + + } /> + + + + + + + + + + + + + +
+
+ ); + } +} + +function Main(props) { + return ( + + + + ); +} + +/* Temporary fix for a breaking change in Chrome to React + * See https://github.com/facebook/react/issues/14856 + */ +const EVENTS_TO_MODIFY = [ + "touchstart", + "touchmove", + "touchend", + "touchcancel", + "wheel" +]; + +const originalAddEventListener = document.addEventListener.bind(); +document.addEventListener = (type, listener, options, wantsUntrusted) => { + let modOptions = options; + if (EVENTS_TO_MODIFY.includes(type)) { + if (typeof options === "boolean") { + modOptions = { + capture: options, + passive: false + }; + } else if (typeof options === "object") { + modOptions = { + ...options, + passive: false + }; + } + } + + return originalAddEventListener(type, listener, modOptions, wantsUntrusted); +}; + +const originalRemoveEventListener = document.removeEventListener.bind(); +document.removeEventListener = (type, listener, options) => { + let modOptions = options; + if (EVENTS_TO_MODIFY.includes(type)) { + if (typeof options === "boolean") { + modOptions = { + capture: options, + passive: false + }; + } else if (typeof options === "object") { + modOptions = { + ...options, + passive: false + }; + } + } + return originalRemoveEventListener(type, listener, modOptions); +}; +// End of temporary fix + +ReactDOM.render( +
, + document.body.appendChild(document.createElement("div")) +); diff --git a/src/app/BAM.jsx b/src/app/BAM.jsx new file mode 100644 index 0000000..872ac6e --- /dev/null +++ b/src/app/BAM.jsx @@ -0,0 +1,89 @@ +import React, { Component } from "react"; +import { BamFile } from "@gmod/bam"; + +import Alignment from "../Alignment.jsx"; +import BAMReader from "../helpers/bam.js"; + +function VariantCaller(props) { + return

Variant calling example will go here.

; +} + +class BAMViewer extends Component { + constructor(props) { + super(props); + this.state = { + window_start: 0, + window_width: 200, + site_size: 15, + fasta: null + }; + } + componentDidMount() { + const bam_file = new BamFile({ + bamUrl: "data/sorted.bam", + baiUrl: "data/sorted.bam.bai" + }); + this.bam = new BAMReader(bam_file); + const { window_start, window_width } = this.state, + window_end = window_start + window_width; + this.bam + .fasta_window(window_start, window_end) + .then(fasta => this.setState({ fasta })); + } + render() { + const width = 1400, + toolbar_style = { + display: "flex", + justifyContent: "space-between", + width: width + }; + return ( +
+

BAM viewer

+
+ + + this.setState({ window_start: e.target.value })} + /> + + + + this.setState({ window_width: e.target.value })} + /> + + + + this.setState({ site_size: e.target.value })} + /> + +
+ +
+ ); + } +} + +export { BAMViewer, VariantCaller }; diff --git a/src/app/Components.jsx b/src/app/Components.jsx new file mode 100644 index 0000000..2221465 --- /dev/null +++ b/src/app/Components.jsx @@ -0,0 +1,54 @@ +import React, { Component } from "react"; +import { text } from "d3"; +import Phylotree from "react-phylotree"; +import { phylotree } from "phylotree"; + +class DataFetcher extends Component { + constructor(props) { + super(props); + this.state = { + data: null + }; + } + componentDidMount() { + const { source } = this.props; + text(source).then(data => this.setState({ data })); + } + render() { + if (!this.state.data) { + return null; + } + const { modifier, child_prop, children } = this.props, + data = modifier(this.state.data), + child_props = {}; + child_props[child_prop] = data; + return React.cloneElement(children, child_props); + } +} + +DataFetcher.defaultProps = { + modifier: data => data, + child_prop: "data" +}; + +const dimensions = { + width: 500, + height: 500 +}; + +function BaseSVGTreeInstance(props) { + const instantiate_phylotree = newick => new phylotree(newick); + return ( + + + + + + ); +} + +export { BaseSVGTreeInstance }; diff --git a/src/app/FASTA.jsx b/src/app/FASTA.jsx new file mode 100644 index 0000000..bb19d3f --- /dev/null +++ b/src/app/FASTA.jsx @@ -0,0 +1,191 @@ +import React, { Component } from "react"; +import { text } from "d3-fetch"; +import { saveAs } from "file-saver"; +import { saveSvgAsPng as savePNG } from "save-svg-as-png"; + +import fastaParser, { fastaToText } from "../helpers/fasta"; +import Alignment from "../Alignment.jsx"; +import Button from "../components/Button.jsx"; +import FileUploadButton from "./FileUploadButton.jsx"; +import Modal from "./Modal.jsx"; +import SVGAlignment from "../SVGAlignment.jsx"; +import { nucleotide_color, nucleotide_difference } from "../helpers/colors"; +import AminoAcid from "./FASTA/amino_acid.jsx"; +import Highlight from "./FASTA/highlight.jsx"; +import SVGAlignmentExample from "./FASTA/svg_example.jsx"; +import StartAtSiteAndSequence from "./FASTA/start_at_site_and_sequence.jsx"; +import Lowercase from "./FASTA/lowercase.jsx"; + +class FASTAViewer extends Component { + constructor(props) { + super(props); + this.state = { + data: null, + site_size: 20, + show_differences: "", + saving: false + }; + } + componentDidMount() { + text("data/CD2.fasta").then(data => this.loadFASTA(data)); + } + loadFASTA(fasta) { + this.setState({ + data: fastaParser(fasta), + show_differences: "" + }); + } + saveFASTA() { + const blob = new Blob([fastaToText(this.state.data)], { + type: "text/plain:charset=utf-8;" + }); + saveAs(blob, "sequences.fasta"); + } + siteColor() { + if (!this.state.show_differences) return nucleotide_color; + const desired_record = this.state.data.filter( + datum => datum.header == this.state.show_differences + )[0]; + return nucleotide_difference(desired_record); + } + molecule() { + if (!this.state.show_differences) return molecule => molecule; + const data = this.state.saving + ? this.state.trimmed_sequence_data + : this.state.data, + desired_record = data.filter( + datum => datum.header == this.state.show_differences + )[0]; + return (mol, site, header) => { + if (mol == "-") return "-"; + if (header == desired_record.header) return mol; + return mol == desired_record.seq[site - 1] ? "." : mol; + }; + } + handleFileChange = e => { + const files = e.target.files; + if (files.length == 1) { + const file = files[0], + reader = new FileReader(); + reader.onload = e => { + this.loadFASTA(e.target.result); + }; + reader.readAsText(file); + } + }; + scrollExcavator = () => { + return this.scrollExcavator.broadcaster.location(); + }; + trimData = (start_site, end_site) => { + return this.state.data.map(record => { + const new_record = { + header: record.header, + seq: record.seq.slice(start_site, end_site) + }; + return new_record; + }); + }; + saveAsPNG = () => { + const saving = true; + const { x_pixel, x_pad, x_fraction, y_fraction } = this.scrollExcavator(), + start_site = Math.floor(x_pixel / this.state.site_size), + end_site = Math.ceil((x_pixel + x_pad) / this.state.site_size), + axis_bounds = [start_site, end_site], + trimmed_sequence_data = this.trimData(start_site, end_site); + trimmed_sequence_data.number_of_sequences = trimmed_sequence_data.length; + trimmed_sequence_data.number_of_sites = trimmed_sequence_data[0].seq.length; + this.setState({ saving, trimmed_sequence_data, axis_bounds }, () => { + savePNG(document.getElementById("alignment-js-svg"), "alignment.png"); + this.setState({ saving: false }, () => { + this.scrollExcavator.broadcaster.broadcast( + x_fraction, + y_fraction, + "main" + ); + }); + }); + }; + render() { + const toolbar_style = { + display: "flex", + justifyContent: "space-between", + width: 960 + }; + const options = this.state.data + ? this.state.data.map(datum => { + return ( + + ); + }) + : null; + return ( +
+

FASTA Viewer Application

+
+ +
+
+ {this.state.saving ? ( + + ) : ( + + )} +
+ +
+ ); + } +} + +export { + FASTAViewer, + AminoAcid, + Highlight, + StartAtSiteAndSequence, + Lowercase, + SVGAlignmentExample +}; diff --git a/src/app/FASTA/amino_acid.jsx b/src/app/FASTA/amino_acid.jsx new file mode 100644 index 0000000..c27b5ef --- /dev/null +++ b/src/app/FASTA/amino_acid.jsx @@ -0,0 +1,40 @@ +import React, { Component } from "react"; +import { text } from "d3"; + +import Alignment from "../../Alignment.jsx"; +import fastaParser from "../../helpers/fasta.js"; +import { + amino_acid_color, + amino_acid_text_color +} from "../../helpers/colors.js"; + +class AminoAcid extends Component { + constructor(props) { + super(props); + this.state = { + sequence_data: null + }; + } + componentDidMount() { + text("data/CD2_AA.fasta").then(data => { + const sequence_data = fastaParser(data); + this.setState({ sequence_data }); + }); + } + render() { + return ( +
+
+

Amino Acid Alignment

+
+ +
+ ); + } +} + +export default AminoAcid; diff --git a/src/app/FASTA/highlight.jsx b/src/app/FASTA/highlight.jsx new file mode 100644 index 0000000..e5dc12e --- /dev/null +++ b/src/app/FASTA/highlight.jsx @@ -0,0 +1,47 @@ +import React, { Component } from "react"; +import { text } from "d3"; + +import Alignment from "../../Alignment.jsx"; +import fastaParser from "../../helpers/fasta.js"; +import { nucleotide_color } from "../../helpers/colors.js"; + +function highlight_codon_color(character, position, header) { + if (header == "DUCK_VIETNAM_272_2005" && Math.floor((position - 1) / 3) == 3) + return "red"; + return character == "-" ? "white" : "GhostWhite"; +} + +function highlight_codon_text_color(character, position, header) { + return character == "G" ? "Gold" : nucleotide_color(character); +} + +class Highlight extends Component { + constructor(props) { + super(props); + this.state = { + sequence_data: null + }; + } + componentDidMount() { + text("data/Flu.fasta").then(data => { + const sequence_data = fastaParser(data); + this.setState({ sequence_data }); + }); + } + render() { + return ( +
+
+

Highlighting specific sites

+
+ +
+ ); + } +} + +export default Highlight; diff --git a/src/app/FASTA/lowercase.jsx b/src/app/FASTA/lowercase.jsx new file mode 100644 index 0000000..202bf5f --- /dev/null +++ b/src/app/FASTA/lowercase.jsx @@ -0,0 +1,32 @@ +import React, { Component } from "react"; +import { text } from "d3"; + +import Alignment from "../../Alignment.jsx"; +import fastaParser from "../../helpers/fasta.js"; + +class Lowercase extends Component { + constructor(props) { + super(props); + this.state = { + sequence_data: null + }; + } + componentDidMount() { + text("data/CVF.fasta").then(data => { + const sequence_data = fastaParser(data); + this.setState({ sequence_data }); + }); + } + render() { + return ( +
+
+

Display an alignment with lower case letters

+
+ +
+ ); + } +} + +export default Lowercase; diff --git a/src/app/FASTA/start_at_site_and_sequence.jsx b/src/app/FASTA/start_at_site_and_sequence.jsx new file mode 100644 index 0000000..3cc3c38 --- /dev/null +++ b/src/app/FASTA/start_at_site_and_sequence.jsx @@ -0,0 +1,36 @@ +import React, { Component } from "react"; +import { text } from "d3"; + +import Alignment from "../../Alignment.jsx"; +import fastaParser from "../../helpers/fasta.js"; + +class StartAtSiteAndSequence extends Component { + constructor(props) { + super(props); + this.state = { + sequence_data: null + }; + } + componentDidMount() { + text("data/H3trunk.fasta").then(data => { + const sequence_data = fastaParser(data); + this.setState({ sequence_data }); + }); + } + render() { + return ( +
+
+

Begin centered on a given sequence (CY010004) and site (100).

+
+ +
+ ); + } +} + +export default StartAtSiteAndSequence; diff --git a/src/app/FASTA/svg_example.jsx b/src/app/FASTA/svg_example.jsx new file mode 100644 index 0000000..c1e037d --- /dev/null +++ b/src/app/FASTA/svg_example.jsx @@ -0,0 +1,46 @@ +import React, { Component } from "react"; +import { text } from "d3-fetch"; + +import fastaParser from "../../helpers/fasta"; +import SVGAlignment from "../../SVGAlignment.jsx"; +import Button from "../../components/Button.jsx"; +import { save as saveSVG } from "d3-save-svg"; +import { saveSvgAsPng as savePNG } from "save-svg-as-png"; + +class SVGAlignmentExample extends Component { + constructor(props) { + super(props); + this.state = { + sequence_data: null + }; + } + savePNG() { + savePNG(document.getElementById("alignment-js-svg"), "alignment.png"); + } + saveSVG() { + saveSVG.save(document.getElementById("alignment-js-svg"), { + filename: "alignment.svg" + }); + } + componentDidMount() { + text("data/CD2-slim.fasta").then(data => { + const sequence_data = fastaParser(data); + this.setState({ sequence_data }); + }); + } + render() { + return ( +
+
+

SVG Alignment

+
+ + +
+ ); + } +} + +export default SVGAlignmentExample; diff --git a/src/app/FNA.jsx b/src/app/FNA.jsx new file mode 100644 index 0000000..c200a39 --- /dev/null +++ b/src/app/FNA.jsx @@ -0,0 +1,136 @@ +import React, { Component } from "react"; +import { text } from "d3-fetch"; +import { saveAs } from "file-saver"; + +import { fnaParser, fnaToText } from "../helpers/fasta"; +import { BaseSVGTreeInstance } from "./Components.jsx"; +import Button from "../components/Button.jsx"; +import FileUploadButton from "./FileUploadButton.jsx"; +import Modal from "./Modal.jsx"; +import { nucleotide_color, nucleotide_difference } from "../helpers/colors"; + +function Immunology(props) { + return

Immunology example will go here.

; +} + +function HIV(props) { + return

HIV example will go here.

; +} + +class FNAViewer extends Component { + constructor(props) { + super(props); + this.state = { + data: null, + site_size: 20, + show_differences: "" + }; + } + componentDidMount() { + text("data/CD2.fna").then(data => this.loadFNA(data)); + } + loadFNA(fasta) { + this.setState({ + data: fnaParser(fasta, true), + show_differences: "" + }); + } + saveFNA() { + const blob = new Blob([fnaToText(this.state.data)], { + type: "text/plain:charset=utf-8;" + }); + saveAs(blob, "sequences.fna"); + } + siteColor() { + if (!this.state.show_differences) return nucleotide_color; + const desired_record = this.state.data.fasta.filter( + datum => datum.header == this.state.show_differences + )[0]; + return nucleotide_difference(desired_record); + } + molecule() { + if (!this.state.show_differences) return molecule => molecule; + const desired_record = this.state.data.fasta.filter( + datum => datum.header == this.state.show_differences + )[0]; + return (mol, site, header) => { + if (mol == "-") return "-"; + if (header == desired_record.header) return mol; + return mol == desired_record.seq[site - 1] ? "." : mol; + }; + } + handleFileChange = e => { + const files = e.target.files; + if (files.length == 1) { + const file = files[0], + reader = new FileReader(); + reader.onload = e => { + this.loadFNA(e.target.result); + }; + reader.readAsText(file); + } + document.body.click(); + }; + render() { + const toolbar_style = { + display: "flex", + justifyContent: "space-between", + width: 960 + }; + const options = this.state.data + ? this.state.data.fasta.map(datum => { + return ( + + ); + }) + : null; + return ( +
+

FNA Viewer Application

+
+ +
+ + +
+ ); + } +} + +export { FNAViewer, Immunology, HIV, BaseSVGTreeInstance }; diff --git a/src/app/FileUploadButton.jsx b/src/app/FileUploadButton.jsx new file mode 100644 index 0000000..f077dac --- /dev/null +++ b/src/app/FileUploadButton.jsx @@ -0,0 +1,31 @@ +import React, { Component } from "react"; + +function FileUploadButton(props) { + const button_style = { + position: "relative", + overflow: "hidden" + }; + const input_style = { + position: "absolute", + top: 0, + right: 0, + minWidth: "100%", + minHeight: "100%", + fontSize: "100px", + textAlign: "right", + filter: "alpha(opacity=0)", + opacity: 0, + outline: "none", + background: "white", + cursor: "inherit", + display: "block" + }; + return ( + + ); +} + +export default FileUploadButton; diff --git a/src/components/navComponents/Modal.jsx b/src/app/Modal.jsx similarity index 91% rename from src/components/navComponents/Modal.jsx rename to src/app/Modal.jsx index 86e074f..09560dd 100644 --- a/src/components/navComponents/Modal.jsx +++ b/src/app/Modal.jsx @@ -5,7 +5,7 @@ function Modal(props) { return ( -
{props.body}
+
{props.children}
+ ); +} + +export default Button; diff --git a/src/components/LargeTreeAlignment.jsx b/src/components/LargeTreeAlignment.jsx deleted file mode 100644 index 8fd881a..0000000 --- a/src/components/LargeTreeAlignment.jsx +++ /dev/null @@ -1,307 +0,0 @@ -import React, { Component } from "react"; -const d3 = require("phylotree/node_modules/d3"); - -import "phylotree/phylotree.css"; -require("phylotree"); - -import BaseAlignment from "./BaseAlignment.jsx"; -import SiteAxis from "./SiteAxis.jsx"; -import SequenceAxis from "./SequenceAxis.jsx"; -import fastaParser from "./../helpers/fasta"; -import ScrollBroadcaster from "./../helpers/ScrollBroadcaster"; -import computeLabelWidth from "../helpers/computeLabelWidth"; - -import "./LargeTreeAlignment.css"; - -class LargeTreeAlignment extends Component { - constructor(props) { - super(props); - this.column_sizes = [700, 700, 200, 700]; - this.row_sizes = [20, 700]; - if (props.fasta) { - this.preprocess(props); - } - } - preprocess(props) { - const { site_size } = this.props; - this.sequence_data = fastaParser(props.fasta); - const number_of_sequences = this.sequence_data.length; - this.tree_size = number_of_sequences * site_size; - this.main_tree = d3.layout - .phylotree() - .options({ - "left-right-spacing": "fit-to-size", - "top-bottom-spacing": "fit-to-size", - "show-scale": false, - "align-tips": true, - "show-labels": false, - selectable: false - }) - .size([this.tree_size, this.tree_size]) - .node_circle_size(0); - this.parsed = d3.layout.newick_parser(props.newick); - this.main_tree(this.parsed); - - const label_width = computeLabelWidth( - this.sequence_data, - this.props.label_padding - ); - - this.column_sizes[3] += this.column_sizes[2] - label_width; - this.column_sizes[2] = label_width; - - var i = 0; - this.main_tree.traverse_and_compute(function(n) { - var d = 1; - if (!n.name) { - n.name = "Node" + i++; - } - if (n.children && n.children.length) { - d += d3.max(n.children, function(d) { - return d["count_depth"]; - }); - } - n["count_depth"] = d; - }); - - this.main_tree.resort_children( - function(a, b) { - return a["count_depth"] - b["count_depth"]; - }, - null, - null, - true - ); - - const ordered_leaf_names = this.main_tree - .get_nodes(true) - .filter(d3.layout.phylotree.is_leafnode) - .map(d => d.name); - - this.sequence_data.sort((a, b) => { - const a_index = ordered_leaf_names.indexOf(a.header), - b_index = ordered_leaf_names.indexOf(b.header); - return a_index - b_index; - }); - } - postprocess(props) { - this.main_tree.svg(d3.select("#alignmentjs-largeTreeAlignment")).layout(); - - const guide_height = this.row_sizes[1], - guide_width = this.column_sizes[0]; - - this.guide_tree = d3.layout - .phylotree() - .svg(d3.select("#alignmentjs-guideTree")) - .options({ - "left-right-spacing": "fit-to-size", - // fit to given size top-to-bottom - "top-bottom-spacing": "fit-to-size", - // fit to given size left-to-right - collapsible: false, - // turn off the menu on internal nodes - transitions: false, - // turn off d3 animations - "show-scale": false, - // disable brush - brush: false, - // disable selections on this tree - selectable: false - }) - .size([guide_height, guide_width]) - .node_circle_size(0); - - this.guide_tree(this.parsed).layout(); - - this.guide_x_scale = d3.scale - .linear() - .domain([0, this.tree_size]) - .range([0, guide_width]); - this.guide_y_scale = d3.scale - .linear() - .domain([0, this.tree_size]) - .range([0, guide_height]); - this.rect = d3 - .select("#alignmentjs-guideTree") - .append("rect") - .attr("x", 0) - .attr("y", 0) - .attr("id", "guide-rect") - .style("opacity", 0.6) - .style("stroke-width", "1px") - .style("stroke", "red") - .style("fill", "pink") - .attr("width", this.guide_x_scale(guide_width)) - .attr("height", this.guide_y_scale(guide_height)); - - const { sequence_data } = this, - { site_size } = props, - height = this.row_sizes[1], - width = this.column_sizes[3], - full_pixel_width = site_size * sequence_data.number_of_sites, - full_pixel_height = site_size * sequence_data.number_of_sequences; - this.scroll_broadcaster = new ScrollBroadcaster( - { width: full_pixel_width, height: full_pixel_height }, - { width: width, height: height }, - { x_pixel: 0, y_pixel: 0 }, - [ - "alignmentjs-alignment", - "alignmentjs-labels-div", - "alignmentjs-largeTreeAlignment-div", - "alignmentjs-guideTree-div", - "alignmentjs-axis-div" - ] - ); - - const { scroll_broadcaster, guide_x_scale, guide_y_scale, rect } = this; - scroll_broadcaster.setListeners(); - - $("#alignmentjs-guideTree-div").off("wheel"); - $("#alignmentjs-guideTree-div").on("wheel", function(e) { - e.preventDefault(); - const guide_x = +d3.select("#guide-rect").attr("x"); - const new_guide_x = Math.min( - Math.max(guide_x + guide_x_scale(e.originalEvent.deltaX), 0), - guide_width - guide_x_scale(guide_width) - ); - rect.attr("x", new_guide_x); - - const guide_y = +d3.select("#guide-rect").attr("y"); - const new_guide_y = Math.min( - Math.max(guide_y + guide_y_scale(e.originalEvent.deltaY), 0), - guide_height - guide_y_scale(guide_height) - ); - rect.attr("y", new_guide_y); - - const new_x_pixel = guide_x_scale.invert(new_guide_x), - new_y_pixel = guide_y_scale.invert(new_guide_y); - $("#alignmentjs-largeTreeAlignment-div").scrollLeft(new_x_pixel); - $("#alignmentjs-largeTreeAlignment-div").scrollTop(new_y_pixel); - - const e_mock = { - originalEvent: { - deltaX: 0, - deltaY: e.originalEvent.deltaY - } - }; - scroll_broadcaster.handleWheel(e_mock, "tree"); - }); - - $("#alignmentjs-largeTreeAlignment-div").off("wheel"); - $("#alignmentjs-largeTreeAlignment-div").on("wheel", function(e) { - const guide_x = +d3.select("#guide-rect").attr("x"); - const new_guide_x = Math.min( - Math.max(guide_x + guide_x_scale(e.originalEvent.deltaX), 0), - guide_width - guide_x_scale(guide_width) - ); - rect.attr("x", new_guide_x); - - const guide_y = +d3.select("#guide-rect").attr("y"); - const new_guide_y = Math.min( - Math.max(guide_y + guide_y_scale(e.originalEvent.deltaY), 0), - guide_height - guide_y_scale(guide_height) - ); - rect.attr("y", new_guide_y); - - const e_mock = { - originalEvent: { - deltaX: 0, - deltaY: e.originalEvent.deltaY - } - }; - scroll_broadcaster.handleWheel(e_mock, "tree"); - }); - - $("#alignmentjs-alignment").on("wheel", function(e) { - e.preventDefault(); - const guide_y = +d3.select("#guide-rect").attr("y"); - const new_guide_y = Math.min( - Math.max(guide_y + guide_y_scale(e.originalEvent.deltaY), 0), - guide_height - guide_y_scale(guide_height) - ); - rect.attr("y", new_guide_y); - scroll_broadcaster.handleWheel(e, "alignment"); - }); - - d3.select("#alignmentjs-guideTree").on("click", null); - d3.select("#alignmentjs-guideTree").on("click", function() { - const coords = d3.mouse(this), - new_x_pixel = guide_x_scale.invert(coords[0]), - new_y_pixel = guide_y_scale.invert(coords[1]), - current_x_fraction = scroll_broadcaster.x_fraction, - new_y_fraction = new_y_pixel / scroll_broadcaster.full_pixel_height; - scroll_broadcaster.broadcast(current_x_fraction, new_y_fraction); - rect.attr("x", coords[0]); - rect.attr("y", coords[1]); - $("#alignmentjs-largeTreeAlignment-div").scrollLeft(new_x_pixel); - $("#alignmentjs-largeTreeAlignment-div").scrollTop(new_y_pixel); - }); - - document - .getElementById("alignmentjs-largeTreeAlignment-div") - .addEventListener("alignmentjs_wheel_event", e => { - if (e.detail.sender == "alignment") { - $("#alignmentjs-largeTreeAlignment-div").scrollTop(e.detail.y_pixel); - } - }); - } - componentDidMount() { - if (this.props.fasta) { - this.postprocess(this.props); - } - } - componentWillUpdate(nextProps) { - this.preprocess(nextProps); - } - componentDidUpdate() { - this.postprocess(this.props); - } - render() { - if (!this.props.fasta) { - return
; - } - const template_css = { - display: "grid", - gridTemplateColumns: this.column_sizes.join("px ") + "px", - gridTemplateRows: this.row_sizes.join("px ") + "px" - }; - return ( -
-
-
-
- -
- -
-
- -
- - -
- ); - } -} - -LargeTreeAlignment.defaultProps = { - label_padding: 10, - site_size: 20 -}; - -module.exports = LargeTreeAlignment; diff --git a/src/components/Placeholder.jsx b/src/components/Placeholder.jsx index 659cb7c..129fbf9 100644 --- a/src/components/Placeholder.jsx +++ b/src/components/Placeholder.jsx @@ -9,4 +9,4 @@ function Placeholder(props) { ); } -module.exports = Placeholder; +export default Placeholder; diff --git a/src/components/SVGSiteAxis.jsx b/src/components/SVGSiteAxis.jsx new file mode 100644 index 0000000..1180b15 --- /dev/null +++ b/src/components/SVGSiteAxis.jsx @@ -0,0 +1,59 @@ +import React, { Component } from "react"; +import { range } from "d3"; + +function Tick(props) { + const translateX = + props.site_size / 2 + (props.site - 1 - props.offset) * props.site_size; + return ( + + + + {props.site} + + + ); +} + +function SVGSiteAxis(props) { + const site_start = props.axis_bounds[0] + 1 || 1, + offset = site_start - 1, + sites = range( + site_start, + props.axis_bounds[1] || props.number_of_sites + 1, + 2 + ), + half_site_size = props.site_size / 2, + x2 = props.number_of_sites * props.site_size - half_site_size; + return ( + + + {sites.map(site => ( + + ))} + + ); +} + +SVGSiteAxis.defaultProps = { + axis_bounds: [null, null] +}; + +export default SVGSiteAxis; diff --git a/src/components/Scaffold.jsx b/src/components/Scaffold.jsx index a32331a..89edc75 100644 --- a/src/components/Scaffold.jsx +++ b/src/components/Scaffold.jsx @@ -1,6 +1,5 @@ import React, { Component } from "react"; const d3 = require("d3"); -const $ = require("jquery"); class Scaffold extends Component { componentDidMount() { @@ -12,33 +11,43 @@ class Scaffold extends Component { .attr("x", e.detail.x_fraction * this.props.width) .attr("y", e.detail.y_fraction * this.props.height); }); - const { width, height, scroll_broadcaster } = this.props, + const { width, height, scroll_broadcaster, sender } = this.props, guide_svg = d3.select("#alignmentjs-scaffold"); guide_svg.on("click", function() { const coords = d3.mouse(this), x_fraction = coords[0] / width, y_fraction = coords[1] / height; - scroll_broadcaster.broadcast(x_fraction, y_fraction); + scroll_broadcaster.broadcast(x_fraction, y_fraction, sender); }); } + handleWheel(e) { + e.preventDefault(); + this.props.scroll_broadcaster.handleWheel(e, this.props.sender); + } render() { if (!this.props.sequence_data) { return
; } - const { sequence_data, scroll_broadcaster, width, height } = this.props, + const { + sequence_data, + scroll_broadcaster, + width, + height, + sender + } = this.props, + { + x_pad, + y_pad, + width: alignment_width, + height: alignment_height + } = scroll_broadcaster[sender], number_of_sites = sequence_data[0].seq.length, number_of_sequences = sequence_data.length, - guide_width = - this.props.width * - scroll_broadcaster.viewport_pixel_width / - scroll_broadcaster.full_pixel_width, - guide_height = - this.props.height * - scroll_broadcaster.viewport_pixel_height / - scroll_broadcaster.full_pixel_height, + guide_width = this.props.width * x_pad / alignment_width, + guide_height = this.props.height * y_pad / alignment_height, line_style = { stroke: "red", strokeWidth: "1px" }; return ( -
+
this.handleWheel(e)}> {sequence_data.map((row, index) => { @@ -81,4 +90,8 @@ class Scaffold extends Component { } } -module.exports = Scaffold; +Scaffold.defaultProps = { + sender: "main" +}; + +export default Scaffold; diff --git a/src/components/ScaffoldViewer.jsx b/src/components/ScaffoldViewer.jsx index 228a66a..8ca26d6 100644 --- a/src/components/ScaffoldViewer.jsx +++ b/src/components/ScaffoldViewer.jsx @@ -1,7 +1,4 @@ import React, { Component } from "react"; -const d3 = require("d3"); -const $ = require("jquery"); -const _ = require("underscore"); import fastaParser from "./../helpers/fasta"; import computeLabelWidth from "../helpers/computeLabelWidth"; @@ -19,23 +16,35 @@ class ScaffoldViewer extends Component { this.label_width = 200; this.initialize(this.props); } - componentDidMount() { - this.setScrollingEvents(this.props); - } setScrollingEvents(props) { if (props.fasta) { - const { scroll_broadcaster } = this; - scroll_broadcaster.setListeners(); - $("#alignmentjs-main-div").off("wheel"); - $("#alignmentjs-main-div").on("wheel", function(e) { - e.preventDefault(); - scroll_broadcaster.handleWheel(e); + const { + width, + height, + axis_height, + alignment_width, + alignment_height + } = props; + const { full_pixel_width, full_pixel_height, label_width } = this; + this.scroll_broadcaster = new ScrollBroadcaster({ + width: full_pixel_width, + height: full_pixel_height, + x_pad: alignment_width, + y_pad: alignment_height, + x_pixel: this.x_pixel, + y_pixel: this.y_pixel, + bidirectional: [ + "alignmentjs-reference-alignment", + "alignmentjs-alignment", + "alignmentjs-axis-div", + "alignmentjs-labels-div", + "alignmentjs-scaffold-div" + ] }); } } componentWillUpdate(nextProps) { this.initialize(nextProps); - this.setScrollingEvents(nextProps); } initialize(props) { if (props.fasta) { @@ -47,23 +56,8 @@ class ScaffoldViewer extends Component { this.full_pixel_width = site_size * sequence_data.number_of_sites; this.full_pixel_height = site_size * (sequence_data.number_of_sequences - 1); - - this.scroll_broadcaster = new ScrollBroadcaster( - { width: this.full_pixel_width, height: this.full_pixel_height }, - { - width: this.props.alignment_width, - height: this.props.alignment_height - }, - { x_pixel: this.x_pixel, y_pixel: this.y_pixel }, - [ - "alignmentjs-reference-alignment", - "alignmentjs-alignment", - "alignmentjs-axis-div", - "alignmentjs-labels-div", - "alignmentjs-scaffold-div" - ] - ); } + this.setScrollingEvents(props); } render() { if (!this.sequence_data) { @@ -87,6 +81,7 @@ class ScaffoldViewer extends Component { width={alignment_width} height={20} sequence_data={this.sequence_data} + scroll_broadcaster={this.scroll_broadcaster} />
record.header); + return ( + + {labels.map((label, i) => { + return ( + + {label} + + ); + })} + + ); +} + +BaseSequenceAxis.defaultProps = { + translateX: 0, + translateY: 0 +}; + class SequenceAxis extends Component { constructor(props) { super(props); @@ -18,6 +50,10 @@ class SequenceAxis extends Component { componentDidUpdate(nextProps) { $(`#${this.div_id}`).scrollTop(this.props.y_pixel); } + handleWheel(e) { + e.preventDefault(); + this.props.scroll_broadcaster.handleWheel(e, this.props.sender); + } render() { if (!this.props.sequence_data) { return
; @@ -30,24 +66,16 @@ class SequenceAxis extends Component { width: width, height: height }, - alignment_height = site_size * number_of_sequences, - labels = this.props.sequence_data.map(record => record.header); + alignment_height = site_size * number_of_sequences; return ( -
+
this.handleWheel(e)} + > - {labels.map((label, i) => { - return ( - - {label} - - ); - })} +
); @@ -57,7 +85,9 @@ class SequenceAxis extends Component { SequenceAxis.defaultProps = { label_padding: 10, site_size: 20, - id: "alignmentjs" + id: "alignmentjs", + sender: "main" }; -module.exports = SequenceAxis; +export default SequenceAxis; +export { BaseSequenceAxis }; diff --git a/src/components/SiteAxis.jsx b/src/components/SiteAxis.jsx index 7a2f355..210b47f 100644 --- a/src/components/SiteAxis.jsx +++ b/src/components/SiteAxis.jsx @@ -31,7 +31,7 @@ class SiteAxis extends Component { axis_svg .append("g") .attr("class", "axis") - .attr("transform", `translate(0, ${height - 1})`) + .attr("transform", `translate(0, ${height - 2})`) .call(axis); $("#alignmentjs-axis-div").scrollLeft(this.props.x_pixel); @@ -48,12 +48,17 @@ class SiteAxis extends Component { componentDidUpdate() { this.initialize(); } + handleWheel(e) { + e.preventDefault(); + this.props.scroll_broadcaster.handleWheel(e, this.props.sender); + } render() { return (
this.handleWheel(e)} > { + this.x_pixel = e.detail.x_pixel; }); } } @@ -91,6 +86,7 @@ class SiteBarPlotExample extends Component { height / 2 : 0; } + this.setScrollingEvents(props); } getSiteNucleotideData = sequence_data => { @@ -133,6 +129,7 @@ class SiteBarPlotExample extends Component { height={barPlotHeight} max_value={1} axis_label={"Nucleotide %"} + scroll_broadcaster={this.scroll_broadcaster} />
@@ -184,7 +185,8 @@ SiteBarPlotExample.defaultProps = { text_color: nucleotide_text_color, label_padding: 10, site_size: 20, - axis_height: 20 + axis_height: 20, + sender: "main" }; class SwitchNucleotideButtons extends React.Component { @@ -228,4 +230,4 @@ class SwitchNucleotideButtons extends React.Component { } } -module.exports = SiteBarPlotExample; +export default SiteBarPlotExample; diff --git a/src/components/SitePlotAxis.jsx b/src/components/SitePlotAxis.jsx index 1de3f10..5f64a05 100644 --- a/src/components/SitePlotAxis.jsx +++ b/src/components/SitePlotAxis.jsx @@ -4,24 +4,25 @@ const d3 = require("d3"); class SitePlotAxis extends React.Component { componentDidMount() { if (this.props.data != null) { - this.createBarPlotAxis(); + this.createPlotAxis(); } } componentDidUpdate(prevProps, prevState) { - if (prevProps.data == null) { - this.createBarPlotAxis(); + if (prevProps.data != null) { + d3.select(".baseSitePlotAxis").html(""); + this.createPlotAxis(); } } - createBarPlotAxis() { + createPlotAxis() { var { data, label_width, padding } = this.props; var label_width = this.props.label_width; - var max_value = this.props.max_value && d3.max(data); + var max_value = this.props.max_value || d3.max(data); var padding = this.props.padding; var height = this.props.height - padding.bottom; - var bar_axis = d3.axisLeft().scale( + var plot_axis = d3.axisLeft().scale( d3 .scaleLinear() .domain([max_value, 0]) @@ -29,7 +30,7 @@ class SitePlotAxis extends React.Component { ); var axis = d3 - .select(".baseSiteBarPlotAxis") + .select(".baseSitePlotAxis") .attr("width", label_width) .attr("height", height + padding.bottom); @@ -37,7 +38,7 @@ class SitePlotAxis extends React.Component { .append("g") .attr("class", "axis") .attr("transform", `translate(${label_width - 1}, ${padding.top})`) - .call(bar_axis); + .call(plot_axis); axis .append("text") @@ -50,25 +51,26 @@ class SitePlotAxis extends React.Component { render() { return ( -
- -
+ ); } } SitePlotAxis.defaultProps = { id: "alignmentjs", - padding: { top: 10, right: 0, bottom: 15, left: 5 } + padding: { top: 10, right: 0, bottom: 15, left: 5 }, + sender: "main", + label_width: 30, + translateX: 0, + translateY: 0 }; -module.exports = SitePlotAxis; +export default SitePlotAxis; diff --git a/src/components/navComponents/DropDownOfAlignmentsToView.jsx b/src/components/navComponents/DropDownOfAlignmentsToView.jsx deleted file mode 100644 index 9d68022..0000000 --- a/src/components/navComponents/DropDownOfAlignmentsToView.jsx +++ /dev/null @@ -1,40 +0,0 @@ -import React, { Component } from "react"; -const _ = require("underscore"); -import "bootstrap"; - -function DropDownOfAlignmentsToView(props) { - return ( -
-
  • - -
    - {_.keys(props.alignmentsToView) - .slice(1) - .map(name => { - return ( - props.loadData(name)} - > - {name} - - ); - })} -
    -
  • -
    - ); -} - -module.exports = DropDownOfAlignmentsToView; diff --git a/src/components/navComponents/Export.jsx b/src/components/navComponents/Export.jsx deleted file mode 100644 index ac5681a..0000000 --- a/src/components/navComponents/Export.jsx +++ /dev/null @@ -1,33 +0,0 @@ -import React, { Component } from "react"; -const $ = require("jquery"); - -import Modal from "./Modal.jsx"; - -class Export extends Component { - constructor(props) { - super(props); - } - - showExportModal() { - $("#exportModal").modal("show"); - } - - render() { - return ( -
    -
  • - this.showExportModal()}> - Export - -
  • - {this.props.fasta}
    } - /> -
    - ); - } -} - -module.exports = Export; diff --git a/src/components/navComponents/Import.jsx b/src/components/navComponents/Import.jsx deleted file mode 100644 index 6e2a0f9..0000000 --- a/src/components/navComponents/Import.jsx +++ /dev/null @@ -1,88 +0,0 @@ -import React, { Component } from "react"; -const $ = require("jquery"); - -import Modal from "./Modal.jsx"; - -class Import extends Component { - constructor(props) { - super(props); - } - - showImportModal() { - $("#importModal").modal("show"); - } - - render() { - return ( -
    - - -
    - ); - } -} - -module.exports = Import; diff --git a/src/helpers/ScrollBroadcaster.js b/src/helpers/ScrollBroadcaster.js index b3ad12d..8bb0718 100644 --- a/src/helpers/ScrollBroadcaster.js +++ b/src/helpers/ScrollBroadcaster.js @@ -1,87 +1,75 @@ class ScrollBroadcaster { - /* ScrollBroadcaster is a class used to coordinate the scrolling of multiple DOM elements. - * It follows the publish–subscribe pattern. - * - * The following conventions/names are used: - * - DOM elements have a full width/height described in terms of pixels. - * - When only a part of a DOM element is shown/rendered that part is refered to as the viewport. - * - Scrolling can be thought of as moving the viewport around the DOM element. - * - The location of the viewport on the DOM element is described by the location of the top left corner of the viewport in two ways: - * 1. pixel: How many pixels over/down from the top left corner of the complete DOM element. - * 2. fraction: What fraction of the way across/down relative to the complete DOM element. - * (NOTE: because the top left corner of the viewport can never reach the bottom or right of the DOM element - * the "fraction" will never be 100%... two variables `upper_x_fraction` & `upper_y_fraction` are - * therefore used to describe the maximum fraction that the upper left corner can reach. - */ - - constructor( - full_pixel_dimensions, - viewport_pixel_dimensions, - initial_pixels, - listener_ids - ) { - // How many pixels wide/high the full DOM element (this is always the BaseAlignment component). - this.full_pixel_width = full_pixel_dimensions.width; - this.full_pixel_height = full_pixel_dimensions.height; - // How many pixels wide/high the viewport is (again, always the viewport for the BaseAlignment component). - this.viewport_pixel_width = viewport_pixel_dimensions.width; - this.viewport_pixel_height = viewport_pixel_dimensions.height; - // How far the viewport is scrolled over/down. - this.x_fraction = initial_pixels.x_pixel / this.full_pixel_width || 0; - this.y_fraction = initial_pixels.y_pixel / this.full_pixel_height || 0; - // The maximum fraction (i.e. when scrolled all the way right/down). - this.upper_x_fraction = Math.max( - 1 - this.viewport_pixel_width / this.full_pixel_width, - 0 - ); - this.upper_y_fraction = Math.max( - 1 - this.viewport_pixel_height / this.full_pixel_height, - 0 - ); - // The ids of the DOM elements that are being listned to (an array). - this.listener_ids = listener_ids; + constructor(broadcast_units) { + if (!Array.isArray(broadcast_units)) { + if (!broadcast_units.name) { + broadcast_units.name = "main"; + } + broadcast_units = [broadcast_units]; + } else if (broadcast_units.length == 1 && !broadcast_units[0].name) { + broadcast_units.name = "main"; + } + broadcast_units.forEach(unit => { + this[unit.name] = {}; + this[unit.name].width = unit.width; + this[unit.name].height = unit.height; + this[unit.name].x_pad = unit.x_pad; + this[unit.name].y_pad = unit.y_pad; + this[unit.name].bidirectional = unit.bidirectional; + this[unit.name].horizontal = unit.horizontal; + this[unit.name].vertical = unit.vertical; + this[unit.name].x_fraction = unit.x_pixel / unit.width || 0; + this[unit.name].y_fraction = unit.y_pixel / unit.height || 0; + this[unit.name].upper_x_fraction = + Math.max(unit.width - unit.x_pad, 0) / unit.width; + this[unit.name].upper_y_fraction = + Math.max(unit.height - unit.y_pad, 0) / unit.height; + }); } - - setListeners() { - this.listeners = this.listener_ids.map(id => document.getElementById(id)); + handleWheel(e, sender) { + const unit = this[sender], + old_x_pixel = unit.width * unit.x_fraction, + old_y_pixel = unit.height * unit.y_fraction, + new_x_pixel = old_x_pixel + e.deltaX, + new_y_pixel = old_y_pixel + e.deltaY, + x_fraction_candidate = new_x_pixel / unit.width, + y_fraction_candidate = new_y_pixel / unit.height; + this.broadcast(x_fraction_candidate, y_fraction_candidate, sender); } - broadcast(x_fraction_candidate, y_fraction_candidate, sender) { - // Make sure the viewport doens't go off the element. - this.x_fraction = Math.min( + const unit = this[sender]; + unit.x_fraction = Math.min( Math.max(0, x_fraction_candidate), - this.upper_x_fraction + unit.upper_x_fraction ); - this.y_fraction = Math.min( + unit.y_fraction = Math.min( Math.max(0, y_fraction_candidate), - this.upper_y_fraction + unit.upper_y_fraction ); - // The "detail" object contains the location of the top left corner of the viewport in terms of pixel and fraction. const detail = { - x_fraction: this.x_fraction, - y_fraction: this.y_fraction, - x_pixel: this.x_fraction * this.full_pixel_width, - y_pixel: this.y_fraction * this.full_pixel_height, + x_fraction: unit.x_fraction, + y_fraction: unit.y_fraction, + x_pixel: unit.x_fraction * unit.width, + y_pixel: unit.y_fraction * unit.height, sender: sender }; - // Broadcast the current "detail" on the "alignmentjs_wheel_event" channel. const wheel_event = new CustomEvent("alignmentjs_wheel_event", { detail: detail }); - this.listeners.forEach(element => element.dispatchEvent(wheel_event)); + unit.bidirectional.forEach(recipient => { + const element = document.getElementById(recipient); + element.dispatchEvent(wheel_event); + }); } - - handleWheel(e, sender) { - // Calculate the new location based on how far has been scrolled. - const old_x_pixel = this.full_pixel_width * this.x_fraction; - const old_y_pixel = this.full_pixel_height * this.y_fraction; - const new_x_pixel = old_x_pixel + e.originalEvent.deltaX; - const new_y_pixel = old_y_pixel + e.originalEvent.deltaY; - const x_fraction_candidate = new_x_pixel / this.full_pixel_width; - const y_fraction_candidate = new_y_pixel / this.full_pixel_height; - // Broadcast the new location with the broadcaster method. - this.broadcast(x_fraction_candidate, y_fraction_candidate, sender); + location() { + return { + x_pixel: this["main"].width * this["main"].x_fraction, + y_pixel: this["main"].height * this["main"].y_fraction, + x_fraction: this["main"].x_fraction, + y_fraction: this["main"].y_fraction, + x_pad: this["main"].x_pad, + y_pad: this["main"].y_pad + }; } } -module.exports = ScrollBroadcaster; +export default ScrollBroadcaster; diff --git a/src/helpers/bam.js b/src/helpers/bam.js new file mode 100644 index 0000000..624c0ed --- /dev/null +++ b/src/helpers/bam.js @@ -0,0 +1,75 @@ +class BAMReader { + constructor(bam_file) { + this.bam_file = bam_file; + } + bamToFasta(bam_record, window_start, window_end) { + const query = bam_record.getReadBases(), + cigar_information = bam_record + .cigar() + .split(/(\d+|[A-Z])/) + .filter(x => x), + number_of_cigar_pairs = cigar_information.length / 2; + var alignment = "", + position = 0, + action, + stride, + match, + insertion, + deletion; + + for (var i = 0; i < number_of_cigar_pairs; i++) { + stride = +cigar_information[2 * i]; + action = cigar_information[2 * i + 1]; + match = action == "M"; + insertion = action == "I"; + deletion = action == "D"; + if (match || insertion) { + if (match) { + alignment += query.slice(position, position + stride); + } + position += stride; + } else if (deletion) { + if (alignment.length > 0 || i < number_of_cigar_pairs) { + alignment += "-".repeat(stride); + } + } + } + + const reference_start = bam_record.get("start"), + reference_end = bam_record.get("end"), + left_pad_amount = Math.max(0, reference_start - window_start), + left_pad = "-".repeat(left_pad_amount), + right_pad_amount = Math.max(0, window_end - reference_end), + right_pad = "-".repeat(right_pad_amount), + left_trim_amount = Math.max(0, window_start - reference_start), + right_trim_amount = Math.max(0, reference_end - window_end), + full_length = alignment.length, + inner_fasta = alignment.slice( + left_trim_amount, + full_length - right_trim_amount + ); + + const fasta_record = { + header: bam_record.get("name"), + seq: left_pad + inner_fasta + right_pad + }; + + return fasta_record; + } + async fasta_window(start_site, end_site) { + const header = await this.bam_file.getHeader(), + reference = header[1].data[0].value; + return await this.bam_file + .getRecordsForRange(reference, start_site, end_site) + .then(records => { + const fasta = records.map(bam_record => { + return this.bamToFasta(bam_record, start_site, end_site); + }); + fasta.number_of_sequences = fasta.length; + fasta.number_of_sites = fasta[0].seq.length; + return fasta; + }); + } +} + +export default BAMReader; diff --git a/src/helpers/colors.js b/src/helpers/colors.js index 507a461..9e0d7ea 100644 --- a/src/helpers/colors.js +++ b/src/helpers/colors.js @@ -92,6 +92,7 @@ const nucleotide_colors = { t: "DeepSkyBlue", v: "Gold", w: "HotPink", + x: "black", y: "IndianRed", A: "lightblue", C: "pink", @@ -112,6 +113,7 @@ const nucleotide_colors = { T: "DeepSkyBlue", V: "Gold", W: "HotPink", + X: "black", Y: "IndianRed" }, nucleotide_color = (character, position, header) => { @@ -120,27 +122,27 @@ const nucleotide_colors = { nucleotide_text_color = (character, position, header) => { return nucleotide_text_colors[character]; }, - highlight_codon_color = (character, position, header) => { - if ( - header == "DUCK_VIETNAM_272_2005" && - Math.floor((position - 1) / 3) == 3 - ) - return "red"; - return character == "-" ? "white" : "GhostWhite"; - }, - highlight_codon_text_color = (character, position, header) => { - return character == "G" ? "Gold" : nucleotide_colors[character]; - }, amino_acid_color = (character, position, header) => { return amino_acid_colors[character]; }, amino_acid_text_color = (character, position, header) => { - return "black"; + return character.toUpperCase() != "X" ? "black" : "white"; + }, + nucleotide_difference = desired_record => { + const desired_header = desired_record.header, + desired_sequence = desired_record.seq; + return (mol, site, header) => { + const desired_color = nucleotide_colors[mol]; + if (mol == "-") return nucleotide_colors["-"]; + if (header == desired_header) return desired_color; + return mol == desired_sequence[site - 1] ? "white" : desired_color; + }; }; -module.exports.nucleotide_color = nucleotide_color; -module.exports.nucleotide_text_color = nucleotide_text_color; -module.exports.highlight_codon_color = highlight_codon_color; -module.exports.highlight_codon_text_color = highlight_codon_text_color; -module.exports.amino_acid_color = amino_acid_color; -module.exports.amino_acid_text_color = amino_acid_text_color; +export { + nucleotide_color, + nucleotide_text_color, + nucleotide_difference, + amino_acid_color, + amino_acid_text_color +}; diff --git a/src/helpers/computeLabelWidth.js b/src/helpers/computeLabelWidth.js index 2ef3f4c..31b6d3f 100644 --- a/src/helpers/computeLabelWidth.js +++ b/src/helpers/computeLabelWidth.js @@ -7,4 +7,4 @@ function computeLabelWidth(sequence_data, padding) { return padding + label_width; } -module.exports = computeLabelWidth; +export default computeLabelWidth; diff --git a/src/helpers/fasta.js b/src/helpers/fasta.js index ea1fae3..2f5e4d5 100644 --- a/src/helpers/fasta.js +++ b/src/helpers/fasta.js @@ -1,4 +1,7 @@ +import sortFASTAAndNewick from "./jointSort.js"; + function fastaParser(fasta) { + if (typeof fasta == "object") return fasta; var seqs = [], header, in_header, @@ -27,4 +30,41 @@ function fastaParser(fasta) { return seqs; } -module.exports = fastaParser; +function fastaToText(fasta) { + return ( + fasta.map(entry => ">" + entry.header + "\n" + entry.seq).join("\n") + "\n" + ); +} + +function fnaParser(fna, sortFASTA) { + var i = fna.length - 2, + current_char = fna[i]; + while (current_char != "\n") { + i--; + current_char = fna[i]; + } + const parsed_fasta = fastaParser(fna.slice(0, i + 1)), + newick = fna.slice(i + 1, fna.length - 1); + if (sortFASTA) { + sortFASTAAndNewick(parsed_fasta, newick, 20); + } + return { + fasta: parsed_fasta, + newick: newick + }; +} + +function fnaToText(fna) { + return ( + fna.fasta + .map(record => { + return ">" + record.header + "\n" + record.seq; + }) + .join("\n") + + "\n" + + fna.newick + ); +} + +export default fastaParser; +export { fastaToText, fnaParser, fnaToText }; diff --git a/src/helpers/jointSort.js b/src/helpers/jointSort.js new file mode 100644 index 0000000..cbd6c89 --- /dev/null +++ b/src/helpers/jointSort.js @@ -0,0 +1,65 @@ +/* +const d3 = require("phylotree/node_modules/d3"); +require("phylotree"); + +import fastaParser from "./fasta"; + +function sortFASTAAndNewick(sequence_data, newick, size) { + const number_of_sequences = sequence_data.length, + phylotree = d3.layout + .phylotree() + .options({ + "left-right-spacing": "fit-to-size", + "top-bottom-spacing": "fit-to-size", + "show-scale": false, + "align-tips": true, + "show-labels": false, + selectable: false + }) + .size(size) + .node_circle_size(0), + tree_json = d3.layout.newick_parser(newick); + phylotree(tree_json); + + var i = 0; + phylotree.traverse_and_compute(function(n) { + var d = 1; + if (!n.name) { + n.name = "Node" + i++; + } + if (n.children && n.children.length) { + d += d3.max(n.children, function(d) { + return d["count_depth"]; + }); + } + n["count_depth"] = d; + }); + + phylotree.resort_children( + function(a, b) { + return a["count_depth"] - b["count_depth"]; + }, + null, + null, + true + ); + + const ordered_leaf_names = phylotree + .get_nodes(true) + .filter(d3.layout.phylotree.is_leafnode) + .map(d => d.name); + + sequence_data.sort((a, b) => { + const a_index = ordered_leaf_names.indexOf(a.header), + b_index = ordered_leaf_names.indexOf(b.header); + return a_index - b_index; + }); + + return { + phylotree, + tree_json + }; +} + +module.exports = sortFASTAAndNewick; +*/ diff --git a/src/helpers/nucleotideComposition.js b/src/helpers/nucleotideComposition.js index a32974f..b55dbcd 100644 --- a/src/helpers/nucleotideComposition.js +++ b/src/helpers/nucleotideComposition.js @@ -32,4 +32,4 @@ function siteComposition(alignmentData, callback) { } } -module.exports.siteComposition = siteComposition; +export { siteComposition }; diff --git a/src/index.jsx b/src/index.jsx deleted file mode 100644 index ba45a04..0000000 --- a/src/index.jsx +++ /dev/null @@ -1,208 +0,0 @@ -import React, { Component } from "react"; -import ReactDOM from "react-dom"; -import "bootstrap"; -const d3 = require("d3"); -const _ = require("underscore"); -const $ = require("jquery"); - -import Alignment from "./components/Alignment.jsx"; -import LargeTreeAlignment from "./components/LargeTreeAlignment.jsx"; -import ScaffoldViewer from "./components/ScaffoldViewer.jsx"; -import { - highlight_codon_color, - highlight_codon_text_color, - amino_acid_color, - amino_acid_text_color -} from "./helpers/colors"; -import NavBar from "./components/navComponents/NavBar.jsx"; -import SiteBarPlotExample from "./components/SiteBarPlotExample.jsx"; -require("./app.scss"); - -const examples = { - loading: {}, - CD2: { - purpose: "Display a nucleotide alignment." - }, - CD2_AA: { - purpose: "Display an amino acid alignment.", - props: { - site_color: amino_acid_color, - text_color: amino_acid_text_color - } - }, - Flu: { - purpose: "Highlight individual sites in an alignment.", - props: { - site_color: highlight_codon_color, - text_color: highlight_codon_text_color - } - }, - CVF: { - purpose: "Display an alignment with lower case letters." - }, - Simple: { - purpose: "Display a very small alignment." - }, - H3trunk: { - purpose: "Begin centered on a given sequence (CY010004) and site (100).", - props: { - centerOnSite: 100, - centerOnHeader: "CY010004" - } - }, - H3full: { - purpose: "Display a large alignment." - } -}; - -const messages = { - scaffold: "NGS Scaffold viewer", - siteBarPlot: "Example Bar Plot (nucleotide composition)", - largeTreeAlignment: "Large phylogenetic tree and alignment." -}; - -class App extends Component { - constructor(props) { - super(props); - this.state = { - fasta: null, - dataset: "loading", - viewing: "largeTreeAlignment" - }; - } - - componentDidMount() { - this.loadData("largeTreeAlignment"); - } - - handleFileChange = e => { - const files = e.target.files; - if (files.length == 1) { - const file = files[0], - reader = new FileReader(); - reader.onload = e => { - this.setState({ fasta: e.target.result }); - }; - reader.readAsText(file); - } - document.body.click(); - }; - - handleTextUpdate = () => { - $("#importModal").modal("hide"); - this.setState({ - fasta: document.getElementById("input_textarea").value - }); - }; - - loadData = dataset => { - if (dataset == "largeTreeAlignment") { - d3.text("data/H3full.fasta", (fasta_error, fasta_data) => { - d3.text("data/H3full.new", (newick_error, newick_data) => { - this.setState({ - fasta: fasta_data, - newick: newick_data, - viewing: "largeTreeAlignment" - }); - }); - }); - } else { - d3.text(`data/${dataset}.fasta`, (error, data) => { - this.setState({ - dataset: dataset, - fasta: data, - viewing: "alignment" - }); - }); - } - }; - - changeView = view => { - const views = { - scaffold: { data: "data/scaffold.fasta" }, - siteBarPlot: { data: "data/CD2.fasta" } - }; - if (view == "largeTreeAlignment") { - d3.text("data/H3full.fasta", (fasta_error, fasta_data) => { - d3.text("data/H3full.new", (newick_error, newick_data) => { - this.setState({ - viewing: view, - fasta: fasta_data, - newick: newick_data - }); - }); - }); - } else { - d3.text(views[view].data, (error, data) => { - this.setState({ - fasta: data, - viewing: view - }); - }); - } - }; - - render() { - const message = - this.state.viewing == "alignment" - ? examples[this.state.dataset].purpose - : messages[this.state.viewing]; - return ( -
    - - -
    -
    -
    -

    {message}

    -
    - -
    - {this.state.viewing == "alignment" ? ( - - ) : this.state.viewing == "scaffold" ? ( - - ) : this.state.viewing == "siteBarPlot" ? ( - - ) : ( - - )} -
    -
    -
    -
    - ); - } -} - -ReactDOM.render( - , - document.body.appendChild(document.createElement("div")) -); diff --git a/src/library.js b/src/library.js index dce4712..1e80890 100644 --- a/src/library.js +++ b/src/library.js @@ -1,16 +1,23 @@ -import Alignment from "./components/Alignment.jsx"; +import Alignment from "./Alignment.jsx"; import BaseAlignment from "./components/BaseAlignment.jsx"; +import BaseSVGAlignment from "./components/BaseSVGAlignment.jsx"; import SiteAxis from "./components/SiteAxis.jsx"; +import SitePlotAxis from "./components/SitePlotAxis.jsx"; import SequenceAxis from "./components/SequenceAxis.jsx"; import fastaParser from "./helpers/fasta"; +import computeLabelWidth from "./helpers/computeLabelWidth"; import ScrollBroadcaster from "./helpers/ScrollBroadcaster"; +import colors from "./helpers/colors"; -require("./app.scss"); - -module.exports = Alignment; -module.exports.Alignment = Alignment; -module.exports.BaseAlignment = BaseAlignment; -module.exports.SiteAxis = SiteAxis; -module.exports.SequenceAxis = SequenceAxis; -module.exports.fastaParser = fastaParser; -module.exports.ScrollBroadcaster = ScrollBroadcaster; +export default Alignment; +export { + BaseAlignment, + BaseSVGAlignment, + SiteAxis, + SitePlotAxis, + SequenceAxis, + fastaParser, + computeLabelWidth, + ScrollBroadcaster, + colors +}; diff --git a/src/server.js b/src/server.js new file mode 100644 index 0000000..a9c8cf9 --- /dev/null +++ b/src/server.js @@ -0,0 +1,15 @@ +const express = require("express"), + path = require("path"); + +const port = process.env.PORT || 8000; +const app = express(); + +app.use(express.static("dist")); + +app.get(/./, (req, res) => { + res.sendFile(path.resolve(".", "dist", "index.html")); +}); + +app.listen(port, () => { + console.log("Listening on port", port, "..."); +}); diff --git a/src/components/LargeTreeAlignment.css b/src/styles/LargeTreeAlignment.css similarity index 100% rename from src/components/LargeTreeAlignment.css rename to src/styles/LargeTreeAlignment.css diff --git a/tests/fasta.test.js b/tests/fasta.test.js new file mode 100644 index 0000000..5df9407 --- /dev/null +++ b/tests/fasta.test.js @@ -0,0 +1,40 @@ +const path = require("path"), + fs = require("fs"); + +import fastaParser, { + fastaToText, + fnaParser, + fnaToText +} from "./../src/helpers/fasta"; + +const internalFastaDataStructure = [ + { header: "Seq1", seq: "ATCGTAATTGCA" }, + { header: "Seq2", seq: "CTCGTAATGGCC" }, + { header: "Seq3", seq: "GTCGTCAATGCT" } + ], + simple_fasta_path = path.resolve( + __dirname, + "..", + "dist", + "data", + "Simple.fasta" + ), + simple_fna_path = path.resolve(__dirname, "..", "dist", "data", "Simple.fna"), + fasta = fs.readFileSync(simple_fasta_path).toString(), + fna = fs.readFileSync(simple_fna_path).toString(); +internalFastaDataStructure.number_of_sequences = 3; +internalFastaDataStructure.number_of_sites = 12; + +test("Imports simple fasta correctly.", () => { + const parsedFasta = fastaParser(fasta); + expect(parsedFasta).toEqual(internalFastaDataStructure); +}); + +test.only("Import simple fna correctly.", () => { + const internalFnaDataStructure = { + fasta: internalFastaDataStructure, + newick: "((Seq1,Seq2),Seq3);" + }, + parsed_fna = fnaParser(fna); + expect(parsed_fna).toEqual(internalFnaDataStructure); +}); diff --git a/webpack.common.js b/webpack.common.js index c1383cd..ea78692 100644 --- a/webpack.common.js +++ b/webpack.common.js @@ -4,7 +4,7 @@ const HtmlWebpackPlugin = require("html-webpack-plugin"); const ExtractTextPlugin = require("extract-text-webpack-plugin"); module.exports = { - entry: path.resolve("src", "index.jsx"), + entry: path.resolve("src", "app.jsx"), plugins: [ new HtmlWebpackPlugin({ title: "Javascript Alignment Viewer" @@ -21,10 +21,7 @@ module.exports = { { test: /\.(js|jsx)?$/, exclude: /node_modules/, - loader: "babel-loader", - query: { - presets: ["es2015", "react", "stage-1"] - } + loader: "babel-loader" }, { test: /\.css$/, @@ -50,5 +47,8 @@ module.exports = { output: { filename: "bundle.js", path: path.resolve(__dirname, "dist") + }, + stats: { + colors: true } }; diff --git a/webpack.dev.js b/webpack.dev.js index 1bf5915..2126ab1 100644 --- a/webpack.dev.js +++ b/webpack.dev.js @@ -1,10 +1,12 @@ -const path = require('path'), - merge = require('webpack-merge'), - common = require('./webpack.common.js'); +const path = require("path"), + merge = require("webpack-merge"), + common = require("./webpack.common.js"); module.exports = merge(common, { - devtool: 'inline-source-map', + mode: "development", + devtool: "inline-source-map", devServer: { - contentBase: path.resolve(__dirname, 'dist') - } + contentBase: path.resolve(__dirname, "dist"), + historyApiFallback: true + } }); diff --git a/webpack.lib.js b/webpack.lib.js index bdc0ead..9ff59ab 100644 --- a/webpack.lib.js +++ b/webpack.lib.js @@ -1,7 +1,7 @@ -const UglifyJsWebpackPlugin = require('uglifyjs-webpack-plugin'), - merge = require('webpack-merge'), - path = require('path'), - common = require('./webpack.common.js'); +const UglifyJsWebpackPlugin = require("uglifyjs-webpack-plugin"), + merge = require("webpack-merge"), + path = require("path"), + common = require("./webpack.common.js"); module.exports = merge(common, { output: { @@ -10,11 +10,5 @@ module.exports = merge(common, { libraryTarget: "commonjs2", filename: "alignment.js" }, - entry: path.resolve(__dirname, 'src', 'library.js'), - externals: [ - 'react', - 'react-bootstrap', - 'd3', - 'underscore' - ] + entry: path.resolve(__dirname, "src", "library.js") }); diff --git a/webpack.prod.js b/webpack.prod.js index 753e438..721b372 100644 --- a/webpack.prod.js +++ b/webpack.prod.js @@ -1,9 +1,8 @@ -const UglifyJsWebpackPlugin = require('uglifyjs-webpack-plugin'), - merge = require('webpack-merge'), - common = require('./webpack.common.js'); +const UglifyJsWebpackPlugin = require("uglifyjs-webpack-plugin"), + merge = require("webpack-merge"), + common = require("./webpack.common.js"); module.exports = merge(common, { - plugins: [ - new UglifyJsWebpackPlugin() - ] + mode: "production", + plugins: [new UglifyJsWebpackPlugin()] }); diff --git a/yarn.lock b/yarn.lock index f2cd7bd..b749abc 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2,219 +2,1202 @@ # yarn lockfile v1 +"@babel/cli@^7.4.4": + version "7.4.4" + resolved "https://registry.yarnpkg.com/@babel/cli/-/cli-7.4.4.tgz#5454bb7112f29026a4069d8e6f0e1794e651966c" + integrity sha512-XGr5YjQSjgTa6OzQZY57FAJsdeVSAKR/u/KA5exWIz66IKtv/zXtHy+fIZcMry/EgYegwuHE7vzGnrFhjdIAsQ== + dependencies: + commander "^2.8.1" + convert-source-map "^1.1.0" + fs-readdir-recursive "^1.1.0" + glob "^7.0.0" + lodash "^4.17.11" + mkdirp "^0.5.1" + output-file-sync "^2.0.0" + slash "^2.0.0" + source-map "^0.5.0" + optionalDependencies: + chokidar "^2.0.4" + +"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.0.0-beta.35": + version "7.0.0" + resolved 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"^3.5.0" chownr "^1.0.1" @@ -1400,6 +2029,7 @@ cacache@^9.2.9: cacache@~9.2.9: version "9.2.9" resolved "https://registry.yarnpkg.com/cacache/-/cacache-9.2.9.tgz#f9d7ffe039851ec94c28290662afa4dd4bb9e8dd" + integrity sha512-ghg1j5OyTJ6qsrqU++dN23QiTDxb5AZCFGsF3oB+v9v/gY+F4X8L/0gdQMEjd+8Ot3D29M2etX5PKozHRn2JQw== dependencies: bluebird "^3.5.0" chownr "^1.0.1" @@ -1418,6 +2048,7 @@ cacache@~9.2.9: cache-base@^1.0.1: version "1.0.1" resolved "https://registry.yarnpkg.com/cache-base/-/cache-base-1.0.1.tgz#0a7f46416831c8b662ee36fe4e7c59d76f666ab2" + integrity sha512-AKcdTnFSWATd5/GCPRxr2ChwIJ85CeyrEyjRHlKxQ56d4XJMGym0uAiKn0xbLOGOl3+yRpOTi484dVCEc5AUzQ== dependencies: collection-visit "^1.0.0" component-emitter "^1.2.1" @@ -1432,20 +2063,43 @@ cache-base@^1.0.1: call-limit@~1.1.0: version "1.1.0" resolved "https://registry.yarnpkg.com/call-limit/-/call-limit-1.1.0.tgz#6fd61b03f3da42a2cd0ec2b60f02bd0e71991fea" + integrity sha1-b9YbA/PaQqLNDsK2DwK9DnGZH+o= + +caller-callsite@^2.0.0: + version 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- resolved "https://registry.yarnpkg.com/create-ecdh/-/create-ecdh-4.0.0.tgz#888c723596cdf7612f6498233eebd7a35301737d" + version "4.0.3" + resolved "https://registry.yarnpkg.com/create-ecdh/-/create-ecdh-4.0.3.tgz#c9111b6f33045c4697f144787f9254cdc77c45ff" + integrity sha512-GbEHQPMOswGpKXM9kCWVrremUcBmjteUaQ01T9rkKCPDXfUHX0IoP9LpHYo2NPFampa4e+/pFDc3jQdxrxQLaw== dependencies: bn.js "^4.1.0" elliptic "^6.0.0" @@ -1936,21 +2685,25 @@ create-ecdh@^4.0.0: create-error-class@^3.0.0: version "3.0.2" resolved "https://registry.yarnpkg.com/create-error-class/-/create-error-class-3.0.2.tgz#06be7abef947a3f14a30fd610671d401bca8b7b6" + integrity sha1-Br56vvlHo/FKMP1hBnHUAbyot7Y= dependencies: capture-stack-trace "^1.0.0" create-hash@^1.1.0, create-hash@^1.1.2: - version "1.1.3" - resolved "https://registry.yarnpkg.com/create-hash/-/create-hash-1.1.3.tgz#606042ac8b9262750f483caddab0f5819172d8fd" + version "1.2.0" + resolved 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"https://registry.yarnpkg.com/postcss-merge-rules/-/postcss-merge-rules-2.1.2.tgz#d1df5dfaa7b1acc3be553f0e9e10e87c61b5f721" + integrity sha1-0d9d+qexrMO+VT8OnhDofGG19yE= dependencies: browserslist "^1.5.2" caniuse-api "^1.5.2" @@ -5998,10 +8312,12 @@ postcss-merge-rules@^2.0.3: postcss-message-helpers@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/postcss-message-helpers/-/postcss-message-helpers-2.0.0.tgz#a4f2f4fab6e4fe002f0aed000478cdf52f9ba60e" + integrity sha1-pPL0+rbk/gAvCu0ABHjN9S+bpg4= postcss-minify-font-values@^1.0.2: version "1.0.5" resolved "https://registry.yarnpkg.com/postcss-minify-font-values/-/postcss-minify-font-values-1.0.5.tgz#4b58edb56641eba7c8474ab3526cafd7bbdecb69" + integrity sha1-S1jttWZB66fIR0qzUmyv17vey2k= dependencies: object-assign "^4.0.1" postcss "^5.0.4" @@ -6010,6 +8326,7 @@ postcss-minify-font-values@^1.0.2: postcss-minify-gradients@^1.0.1: version "1.0.5" resolved "https://registry.yarnpkg.com/postcss-minify-gradients/-/postcss-minify-gradients-1.0.5.tgz#5dbda11373703f83cfb4a3ea3881d8d75ff5e6e1" + integrity sha1-Xb2hE3NwP4PPtKPqOIHY11/15uE= dependencies: postcss "^5.0.12" postcss-value-parser "^3.3.0" @@ -6017,6 +8334,7 @@ postcss-minify-gradients@^1.0.1: postcss-minify-params@^1.0.4: version "1.2.2" resolved "https://registry.yarnpkg.com/postcss-minify-params/-/postcss-minify-params-1.2.2.tgz#ad2ce071373b943b3d930a3fa59a358c28d6f1f3" + integrity sha1-rSzgcTc7lDs9kwo/pZo1jCjW8fM= dependencies: alphanum-sort "^1.0.1" postcss "^5.0.2" @@ -6026,6 +8344,7 @@ postcss-minify-params@^1.0.4: postcss-minify-selectors@^2.0.4: version "2.1.1" resolved "https://registry.yarnpkg.com/postcss-minify-selectors/-/postcss-minify-selectors-2.1.1.tgz#b2c6a98c0072cf91b932d1a496508114311735bf" + integrity sha1-ssapjAByz5G5MtGkllCBFDEXNb8= dependencies: alphanum-sort "^1.0.2" has "^1.0.1" @@ -6033,14 +8352,16 @@ postcss-minify-selectors@^2.0.4: postcss-selector-parser "^2.0.0" postcss-modules-extract-imports@^1.2.0: - version "1.2.0" - resolved "https://registry.yarnpkg.com/postcss-modules-extract-imports/-/postcss-modules-extract-imports-1.2.0.tgz#66140ecece38ef06bf0d3e355d69bf59d141ea85" + version "1.2.1" + resolved "https://registry.yarnpkg.com/postcss-modules-extract-imports/-/postcss-modules-extract-imports-1.2.1.tgz#dc87e34148ec7eab5f791f7cd5849833375b741a" + integrity sha512-6jt9XZwUhwmRUhb/CkyJY020PYaPJsCyt3UjbaWo6XEbH/94Hmv6MP7fG2C5NDU/BcHzyGYxNtHvM+LTf9HrYw== dependencies: postcss "^6.0.1" postcss-modules-local-by-default@^1.2.0: version "1.2.0" resolved "https://registry.yarnpkg.com/postcss-modules-local-by-default/-/postcss-modules-local-by-default-1.2.0.tgz#f7d80c398c5a393fa7964466bd19500a7d61c069" + integrity sha1-99gMOYxaOT+nlkRmvRlQCn1hwGk= dependencies: css-selector-tokenizer "^0.7.0" postcss "^6.0.1" @@ -6048,6 +8369,7 @@ postcss-modules-local-by-default@^1.2.0: postcss-modules-scope@^1.1.0: version "1.1.0" resolved "https://registry.yarnpkg.com/postcss-modules-scope/-/postcss-modules-scope-1.1.0.tgz#d6ea64994c79f97b62a72b426fbe6056a194bb90" + integrity sha1-1upkmUx5+XtipytCb75gVqGUu5A= dependencies: css-selector-tokenizer "^0.7.0" postcss "^6.0.1" @@ -6055,6 +8377,7 @@ postcss-modules-scope@^1.1.0: postcss-modules-values@^1.3.0: version "1.3.0" resolved "https://registry.yarnpkg.com/postcss-modules-values/-/postcss-modules-values-1.3.0.tgz#ecffa9d7e192518389f42ad0e83f72aec456ea20" + integrity sha1-7P+p1+GSUYOJ9CrQ6D9yrsRW6iA= dependencies: icss-replace-symbols "^1.1.0" postcss "^6.0.1" @@ -6062,12 +8385,14 @@ postcss-modules-values@^1.3.0: postcss-normalize-charset@^1.1.0: version "1.1.1" resolved "https://registry.yarnpkg.com/postcss-normalize-charset/-/postcss-normalize-charset-1.1.1.tgz#ef9ee71212d7fe759c78ed162f61ed62b5cb93f1" + integrity sha1-757nEhLX/nWceO0WL2HtYrXLk/E= dependencies: postcss "^5.0.5" postcss-normalize-url@^3.0.7: version "3.0.8" resolved 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postcss-reduce-initial@^1.0.0: version "1.0.1" resolved "https://registry.yarnpkg.com/postcss-reduce-initial/-/postcss-reduce-initial-1.0.1.tgz#68f80695f045d08263a879ad240df8dd64f644ea" + integrity sha1-aPgGlfBF0IJjqHmtJA343WT2ROo= dependencies: postcss "^5.0.4" postcss-reduce-transforms@^1.0.3: version "1.0.4" resolved "https://registry.yarnpkg.com/postcss-reduce-transforms/-/postcss-reduce-transforms-1.0.4.tgz#ff76f4d8212437b31c298a42d2e1444025771ae1" + integrity sha1-/3b02CEkN7McKYpC0uFEQCV3GuE= dependencies: has "^1.0.1" postcss "^5.0.8" @@ -6105,6 +8434,7 @@ postcss-reduce-transforms@^1.0.3: postcss-selector-parser@^2.0.0, postcss-selector-parser@^2.2.2: version "2.2.3" resolved "https://registry.yarnpkg.com/postcss-selector-parser/-/postcss-selector-parser-2.2.3.tgz#f9437788606c3c9acee16ffe8d8b16297f27bb90" + integrity sha1-+UN3iGBsPJrO4W/+jYsWKX8nu5A= dependencies: flatten "^1.0.2" indexes-of "^1.0.1" @@ -6113,6 +8443,7 @@ postcss-selector-parser@^2.0.0, postcss-selector-parser@^2.2.2: postcss-svgo@^2.1.1: version "2.1.6" resolved "https://registry.yarnpkg.com/postcss-svgo/-/postcss-svgo-2.1.6.tgz#b6df18aa613b666e133f08adb5219c2684ac108d" + integrity sha1-tt8YqmE7Zm4TPwittSGcJoSsEI0= dependencies: is-svg "^2.0.0" postcss "^5.0.14" @@ -6122,18 +8453,21 @@ postcss-svgo@^2.1.1: postcss-unique-selectors@^2.0.2: version "2.0.2" resolved "https://registry.yarnpkg.com/postcss-unique-selectors/-/postcss-unique-selectors-2.0.2.tgz#981d57d29ddcb33e7b1dfe1fd43b8649f933ca1d" + integrity sha1-mB1X0p3csz57Hf4f1DuGSfkzyh0= dependencies: alphanum-sort "^1.0.1" postcss "^5.0.4" uniqs "^2.0.0" postcss-value-parser@^3.0.1, postcss-value-parser@^3.0.2, postcss-value-parser@^3.1.1, postcss-value-parser@^3.1.2, postcss-value-parser@^3.2.3, postcss-value-parser@^3.3.0: - version "3.3.0" - resolved "https://registry.yarnpkg.com/postcss-value-parser/-/postcss-value-parser-3.3.0.tgz#87f38f9f18f774a4ab4c8a232f5c5ce8872a9d15" + version "3.3.1" + resolved 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