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 @@
+((KF790010:0.001247,CY147300:0.000623):0.0,((CY168239:0.001872,(CY171039:0.001874,KF790389:0.000623):0.000624):0.0,((CY141224:0.001247,(CY147305:0.0,KF790037:0.000623):0.000623):0.0,(((KF790403:0.000623,KF761507:0.001876):0.0,KC526205:0.000623):0.0,((CY169303:0.0,(KF789585:0.000623,CY141202:0.000623):0.000623):0.000623,(((KJ667974:0.002501,KJ938675:0.001873):0.000623,CY134876:0.0):0.000623,((KF790414:0.001248,(KF790384:0.001245,KF790408:0.00125):0.0):0.0,((KF886352:0.001882,(KF790438:0.000623,CY134996:0.001873):0.000623):0.001875,(KF789591:0.001879,((KF790049:0.001255,(CY134956:0.000624,CY183153:0.000624):0.000626):0.001249,((CY168407:0.004394,CY183065:0.003128):0.0,(KF598733:0.002501,((KC892174:0.0,(KF685747:0.000624,CY168471:0.000625):0.00375):0.000624,(((KC892685:0.000624,KC892641:0.0):0.001874,KC893110:0.001249):0.0,(KC892480:0.0,(JX913043:0.001249,(KF551075:0.00125,((CY114509:0.0,(KC892889:0.0,KC893018:0.002498):0.005006):0.001877,(((KC892519:0.0,KC892498:0.000624):0.002497,KC892266:0.000623):0.001026,((KC892156:0.003756,(JX978746:0.001256,KC892407:0.001883):0.001875):0.00355,((KC535402:0.000623,(KC882488:0.002498,KC535387:0.001247):0.001872):0.0,(KC535363:0.000623,((KC535396:0.000623,(KC882883:0.0,KC882867:0.000623):0.003124):0.0,((KC535378:0.001872,KC535375:0.002498):0.0,(GQ385891:0.001248,((EU779522:0.001251,(CY037727:0.0,FJ179354:0.003124):0.0):0.000623,((GQ385889:0.005007,(FJ686933:0.001243,FJ179356:0.003117):0.0):0.000622,(CY173095:0.001245,(((CY173191:0.0,CY037703:0.001247):0.000622,CY035062:0.00249):0.0,((CY173255:0.001871,(CY044748:0.0,GQ385846:0.001247):0.000623):0.0,((CY027075:0.000623,(EU199367:0.0,CY172823:0.000623):0.0):0.000623,(((CY172847:0.000623,CY025643:0.0):0.000623,CY172839:0.000623):0.001247,(((CY026251:0.002497,CY092241:0.00125):0.000624,CY026019:0.000623):0.0,((CY025341:0.002502,(CY172775:0.001247,CY172903:0.000623):0.001248):0.000622,(EU199255:0.003134,(CY172431:0.000621,((CY172223:0.003127,(CY172191:0.001254,CY020069:0.000628):0.000621):0.0,((CY092217:0.003119,(CY025485:0.001283,EU516019:0.00059):0.008843):0.001868,(CY002080:0.000622,((CY002064:0.001873,(CY002456:0.000626,CY002048:0.002491):0.001243):0.003763,(AB434109:0.006307,(((CY088198:0.001245,CY088475:0.000621):0.0,CY000257:0.000621):0.002494,((CY112957:0.003135,CY006859:0.001253):0.000616,((CY000721:0.001243,(CY114493:0.0,CY090885:0.002483):0.002488):0.0,((CY001792:0.000621,(CY001600:0.00062,CY002368:0.001865):0.0):0.0,((CY002304:0.002489,(CY006163:0.001242,CY003632:0.00062):0.0):0.00062,(CY001920:0.003739,(CY001912:0.002498,((CY001504:0.0,CY006060:0.001241):0.00062,((CY001744:0.0,CY002136:0.00124):0.00062,((CY114309:0.003746,(CY006899:0.001874,CY112901:0.001863):0.002496):0.000618,(((CY006579:0.001245,CY006283:0.000621):0.001244,CY007979:0.001864):0.0,((CY006499:0.001241,(CY006491:0.001863,CY006635:0.00124):0.0):0.00062,(((CY036847:0.002495,CY010004:0.001867):0.000621,CY012200:0.000621):0.0,(((CY010028:0.001242,CY009732:0.001242):0.0,CY010012:0.002484):0.001875,(((CY010020:0.002497,CY011416:0.001237):0.001252,CY009484:0.00062):0.005658,((CY010036:0.0,(CY039879:0.002489,CY039880:0.000621):0.002487):0.003109,((CY010628:0.000619,(CY010716:0.002485,CY010516:0.001239):0.0):0.000619,((CY012728:0.0,CY013701:0.000621):0.001243,(((CY012760:0.001239,CY013200:0.001239):0.0,CY011888:0.005614):0.0,((CY013693:0.000619,(CY012184:0.002484,CY013669:0.00124):0.00124):0.0,((CY112669:0.004353,(CY112556:0.001861,CY011896:0.000619):0.00186):0.0,(CY112605:0.001243,(CY012224:0.006953,((CY012512:0.000619,(CY012896:0.00062,CY012232:0.00062):0.000621):0.0,(CY011848:0.0,(((CY011328:0.0,CY114221:0.000619):0.001241,CY011560:0.00124):0.0,((CY012456:0.000619,CY011824:0.00124):0.0,CY017283:0.000619):0.0):0.0):0.0):0.002439):0.008263):0.000618):0.0):0.0):0.000617):0.012609):0.000619):0.001215):0.003782):0.000613):0.006878):0.0):0.001862):0.0):0.0):0.001863):0.001862):0.001245):0.0):0.001241):0.021084):0.000623):0.00065):0.003713):0.002495):0.0):0.005637):0.00313):0.002515):0.001876):0.0):0.000623):0.0):0.003749):0.0):0.0):0.000623):0.000623):0.001872):0.002503):0.0):0.0):0.000623):0.001468):0.00189):0.002721):0.002524):0.0):0.000624):0.0):0.0):0.0):0.000623):0.001248):0.001255):0.000619):0.0):0.0):0.0):0.000623):0.0):0.0):0.0):0.0;
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 @@
-{
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- "dev": true,
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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",
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- "babel-loader": "^7.1.2",
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- "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}
/>
{this.state.data ? fastaToText(this.state.data) : null}
+{this.state.data ? fnaToText(this.state.data) : null}
+