ihh / abrowse Goto Github PK

Currently large numbers of sequences freeze ABrowse, e.g. see examples at https://www.ebi.ac.uk/~gsalazar/abrowse/

It should be possible to collapse leaf nodes (and hide the corresponding alignment rows) as well as internal nodes

If no tree is available (and/or there are too many sequences to compute the tree without noticeable lag for the user), it should fall back to being a non-phylogenetic alignment browser

We need a way for users on the web to mark up an alignment (or individual residues in individual sequences) with notes, and to up- and down-vote others' notes.

This may belong in a separate app; we could do something with AWS Lambda and DynamoDB, for example.

c.f. #5

This was identified by InterPro as an issue because they use NGL rather than PV. However, at the moment InterPro are using react-msa-viewer for other reasons (mostly performance), so it seems like performance-related issues (#6, #7) are higher-priority than switching out the PDB viewer, at least for the moment.

Stockholm format allows per-column and per-sequence annotations, and these are recognized by the parser, but are currently not plotted in ABrowse.

It would be good to show these. Common uses are to annotate functional sites, secondary structure, and so on.

It would also be good to show interval-based annotations on the individual sequences (e.g. GFF) but this would be a slightly different kind of feature....

Currently long sequences freeze ABrowse, e.g. see examples at https://www.ebi.ac.uk/~gsalazar/abrowse/

This would result in more colored area and would make it easier to see conservation.

As part of addressing #6 and #7, it may be necessary to reduce the amount of data that comes down the wire when viewing any part of the alignment. This may necessitate a compressed alignment format. I have a sketch of a design for this, so please contact me for more info as necessary. -Ian

I want to integrate this into my website, but it was quite annoying to do so:

• Install npm, node and yarn (I've never used any of them before)
• ran 'yarn build', but:
• got an error, had to npm install react-scripts , which took forever
• got an error, had to npm install react-dom
• got an error, had to npm install react
• got an error, had to yarn add workerize-loader, which took forever
• got an error, had to yarn add lodash
• then, it worked. But I ended up with ugly-named js files which I am unsure how to use:

tree abrowse/build
├── 6bc8976516bbabed843b.worker.js
├── 6bc8976516bbabed843b.worker.js.LICENSE.txt
├── 6bc8976516bbabed843b.worker.js.map
├── asset-manifest.json
├── favicon.ico
├── index.html
├── logo192.png
├── logo512.png
├── manifest.json
├── PF01601_full.txt
├── precache-manifest.af30cb89b07353510a274f9994be19d8.js
├── robots.txt
├── service-worker.js
└── static
    ├── css
    │   ├── main.de0a18cb.chunk.css
    │   └── main.de0a18cb.chunk.css.map
    └── js
        ├── 2.4133e705.chunk.js
        ├── 2.4133e705.chunk.js.LICENSE.txt
        ├── 2.4133e705.chunk.js.map
        ├── main.78e0e997.chunk.js
        ├── main.78e0e997.chunk.js.map
        ├── runtime-main.099d901a.js
        └── runtime-main.099d901a.js.map

How should I proceed?

If a clade of the tree contains under a given threshold of total branch length, it should be collapsed from the beginning.