Full JS version of Dotlet
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components
core centralised actions Jul 22, 2016
docs Screenshot in the readme Sep 7, 2016
pages intermediate Sep 2, 2016
public
test Zoom bug fixes Sep 5, 2016
utils .gitignore Jul 14, 2016
.editorconfig My panel; cleanup; start personalizing Jul 14, 2016
.eslintrc pure render mixin Jul 21, 2016
.gitattributes .gitignore Jul 14, 2016
.gitignore
.gitlab-ci.yaml intermediate Jul 17, 2016
.travis.yml .gitignore Jul 14, 2016
LICENSE.txt GNU Affero license Sep 2, 2016
README.md
firebase.json .gitignore Jul 14, 2016
main.js react-d3 for density plot. Footer styling Jul 21, 2016
package.json Get version directly from package.json Sep 9, 2016
routes.json
run.js Fixed Minimap bug. Tooltips. Renamed title. Sep 5, 2016
webpack.config.js Inputs. CSS loaders stuff. Jul 15, 2016

README.md

Dotlet reborn

Dotlet is a web app that produces a dot plot representing the alignment of two protein/nucleotide sequences.

It is a pure client-side Javascript application written with React.


Dotlet screenshot

History

The original app was written in Java by Marco Pagni and Thomas Junier (Vital-IT). Java applets are no more supported by modern web browsers, so it has to be rewritten with a more modern design, new technologies, and hopefully performance improvements.

Original app: https://myhits.isb-sib.ch/cgi-bin/dotlet

Archive Java source files: ftp://ftp.isrec.isb-sib.ch/pub/software/java/dotlet/

Publication: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/2/178

Vital-IT, 2016 - julien.delafontaine@sib.swiss

Technology

Started from Kriasoft's react-static-boilerplate:

  • React - redux
  • Webpack - babel - browsersync - hot loader
  • Material Design
  • CSS modules

Build from source

Install node.js and npm, then from the root directory, run

npm install     
node run build [--release] 

Start the test server

node run start [--release]

Run tests

npm run test[:watch]

Deploy in production

rm -rf public/dist/*
node run build --release
scp -r public/* <DESTINATION>

where <DESTINATION> is the DocumentRoot in your server configuration.

Structure

/

  • run.js: Node tasks and some global config.
  • main.js: The main call to ReactDOM.render and binds the router.
  • webpack.config.js: Build configuration.
  • package.json: Project config file. Lists JS dependencies to be installed with npm install in /node_modules. Lists npm run <action> aliases, such as npm run test:watch.

/public

  • Everything that is to be copied for distribution. .ejs files get compiled to html/xml. In particular, don't try to edit the classic index.html, but index.ejs instead.
  • /dist: bundled JS with all dependencies and inlined assets. If some assets are over some size limit, they appear outside of the bundle.

/pages: Routes. Only home is actually used in this project.

/node_modules: JS dependencies, automatically generated by npm install.

/core: Things you don't want to touch.

/components

  • /actions: Redux reducers and action creators.
  • /common: Common helper functions.
  • /constants: Common variable definitions, to avoid typos.
  • /DensityPanel: The part showing the scores density as a bar chart.
  • /DotterPanel: The main dot plot canvas.
  • /GreyScale: All what concerns the scaling of grey shades.
  • /InfoPanel: The summary showing the currently inspected position and score.
  • /InputPanel: The top menu with input fields.
  • /Layout: MDL layout structure. Header and footer.
  • /TwoSeqsPanel: The bottom part showing the currently inspected alignment.
  • /utils: Helper components.