How do you imagine the "MSA Viewer HTML output" mode for the Jalview desktop to work?
Jalview would provide an export option that could either:
* write a single html page with bundled JSON/BSON data
* write a series of files: html page with references to local JSON/BSON files
The questions in my mind are:
1. should a bundled version of the BioJS msaviewer + dependencies be shipped with Jalview ?
-> alternative is to include external references to minified code
2. are the JSON/BSON structures employed by msaviewer sufficiently standard that we can commit time to create new parsers/emitters in Jalview ?
-> That would mean that we could also import data + visualisation settings from an existing msaviewer-enabled page.
-> alternately, we just write vanilla alignment, sequence feature and alignment annotation files and improve msaviewer so its compatible with Jalview's standard formats.
1. should a bundled version of the BioJS msaviewer + dependencies be shipped with Jalview ?
-> alternative is to include external references to minified code
I already upload the minified MSA code to a CDN, so just linking to sth. like [1] should be easier.
Do you think it is important that the rendered web page works without internet?
2. are the JSON/BSON structures employed by msaviewer sufficiently standard that we can commit time to create new parsers/emitters in Jalview ?
Nope. Imho a standard would require more than one person to agree on it.
we just write vanilla alignment, sequence feature and alignment annotation files and improve msaviewer so its compatible with Jalview's standard formats.
Currently the msaviewer only allows a user to import alignment files - it does not support the import of sequence features nor alignment annotation files.
I will work on this.
3. My idea was to show a basic configuration dialog to toggle some options of the msaviewer (before the generation of the JS files).
-> What is your preferred way to receive those changes? As git patch?
Best,
Seb
[1] cdn.biojs.net/msa/0.2/msa.min.gz.js
···
On 2014-09-12 10:42, Jim Procter wrote:
Hi Seb.
cc-ing jalview-dev...
On Thu Sep 11 19:59:42 2014, Sebastian Wilzbach wrote:
How do you imagine the "MSA Viewer HTML output" mode for the Jalview desktop to work?
Jalview would provide an export option that could either:
* write a single html page with bundled JSON/BSON data
* write a series of files: html page with references to local JSON/BSON files
The questions in my mind are:
1. should a bundled version of the BioJS msaviewer + dependencies be shipped with Jalview ?
-> alternative is to include external references to minified code
2. are the JSON/BSON structures employed by msaviewer sufficiently standard that we can commit time to create new parsers/emitters in Jalview ?
-> That would mean that we could also import data + visualisation settings from an existing msaviewer-enabled page.
-> alternately, we just write vanilla alignment, sequence feature and alignment annotation files and improve msaviewer so its compatible with Jalview's standard formats.
On 16 September 2014 04:34, Sebastian Wilzbach <sebi@wilzbach.me> wrote:
I already upload the minified MSA code to a CDN, so just linking to sth. like [1] should be easier.
Do you think it is important that the rendered web page works without internet?
That’s useful in some circumstances - particularly when connectivity is poor. The other issue is where the rendered alignment is to be deployed on a site where the domain policy is to avoid external code references, or - purely for speed, all dependencies are shipped locally.
are the JSON/BSON structures employed by msaviewer sufficiently standard that we can commit time to create new parsers/emitters in Jalview ?
Nope. Imho a standard would require more than one person to agree on it.
Point taken. How about stability/coverage ?
we just write vanilla alignment, sequence feature and alignment annotation files and improve msaviewer so its compatible with Jalview’s standard formats.
Currently the msaviewer only allows a user to import alignment files - it does not support the import of sequence features nor alignment annotation files.
I will work on this.
My idea was to show a basic configuration dialog to toggle some options of the msaviewer (before the generation of the JS files).
→ What is your preferred way to receive those changes? As git patch?
A git patch is fine - but I can also give you commit rights if you need them. Please work off the Release_2_8_2_Branch - that’s what Mungo and are currently working on.
The relevant Jalview issue is here: http://issues.jalview.org/browse/JAL-1541