Comments (2)
Dear @MrTomRod,
Thanks for your interest in alignment.js!
Can you clarify exactly what you mean by standalone library? Since you are seeking to avoid node/yarn, and also from looking at the link you provided, I assume you are developing a more classical web application. As such, this will require bundled JavaScript and CSS files that can be accessed via script
and link
tags, respectively.
If so, this is actually something I was working on earlier this week and am near finished. I'd be happy to bump it up in priority and organize a release with some documentation of the features that you'll need.
It also seems like you'll want an amino-acid alignment with a phylogenetic tree. All these features are there, they just need to be put together.
Please let me know your exact use case, I am happy to chat further and believe this project could suit your needs.
Best,
Stephen
from alignment.js.
That sounds fantastic!
No need to hurry, I don't have too much time at the moment. Of course, if I end up using your library, I will cite your work.
My requirements
- visualize nucleic acid and protein alignments (e.g. multi-fasta format)
- visualize phylogenetic tree (e.g. Newick format)
- ability to scroll in the MSA horizontally without specialized mouse (add scroll bar to canvas?)
- ideally: control the looks (width of the plot, font size, size of the nucleic acid/protein boxes)
- fix small bug, see below (Top: Chrome, bottom: Firefox)
What I meant with standalone library
CSS files that can be accessed via script and link tags, respectively
I think you have the right idea. My software is based on Django. This is, more or less, how I use my current library:
<link rel="stylesheet" type="text/css" href="/alignment-js.css">
<script src="/alignment-js.js"></script>
<script>
const targetDiv = document.getElementById ('target')
alignmentJs({
data: {
alignment: /* some alignment file, e.g. in aligned FASTA format */
">A\nAAAGAG..AATCC...",
newick: "(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);"
}
},
config: {
parent: targetDiv
}
})
</script>
Something similar would be great. I don't think I can use your library as a node component via Django. (?)
Thanks a lot for your time,
MrTomRod
from alignment.js.
Related Issues (16)
- Case sensitivity HOT 1
- [Safari] Scrolling fails HOT 1
- Automatically detect amino acid alignments
- Slight format change request HOT 1
- Command line tool for prototyping alignment.js widgets
- Line plots
- Sequence Logos
- Large tree and guide tree components with React phylotree
- Highlight FASTA parser in documentation
- Allow alignment to be used with node HOT 1
- Distribute assets over NPM
- Fasta Viewer Imported Into React App Issue HOT 6
- Tree And MSA Not Aligning As Expected HOT 4
- Integrate phylotree.js and alignment.js HOT 2
- Fix webpack
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from alignment.js.