Hi, I would suggest to include a summary of this discussion at wiki. In this way, other people interested will have access to the info. I also have a little experience with bioSW so, probably, I'm not the right person to do such a summary but I'll be glad to help as much as I can.
Thanks so much in advance. Cheers, David 2014-10-29 4:53 GMT+01:00 Sebastian Wilzbach <[email protected]>: > Hi Jim, > > sorry for being so unresponsive. > > > has just started looking at creating an msaviewer export. > > Wow great. I started to create a GFF and Annotation parser for the Jalview > format, but then completely run short of time. > (I did start my own naive and unfinished patch) > > https://github.com/greenify/biojs-io-gff > https://github.com/greenify/biojs-io-annots > > So again I am super sorry and will get more involved in #1541. > > http://issues.jalview.org/browse/JAL-1541 > > > a brief tour of the msaviewer web examples > > Project website (interactive example): http://biojs-msa.org/ > Integration in Galaxy: > https://github.com/greenify/tools-iuc/tree/master/visualizations/biojs-msa > > More examples: http://workmen.biojs.net/demo/biojs-vis-msa > MSA-Wiki: https://github.com/greenify/biojs-vis-msa/wiki > > @Tochukwu: I hope this you. Don't hesitate to contact me if you have > questions. > > > It would also be good to know exactly what is considered 'BioJS best > practice' [...] aren't going to break > > Tough question. JavaScript is a rapidly changing language, but what will > never change for the msaviewer is that: > > * the msaviewer is assumed to parse the input file(s) asynchronously > (those parsers are independent packages and unlikely to change) > * it is loaded into one div element > * one constructs an msaviewer instance with this DOM element > * it uses require to inject the component code > * one has to call `render` to draw the MSA on the page > > The additional configuration options the MSA receives are likely to change. > > > From our side, we'd really like it if MSA viewer could provide a link to > post data to the www.jalview.org/services/launchApp service so any data > in an MSA viewer could be opened in the Jalview Desktop. [..] creating an > HTTP api for the desktop > > As soon as I will find a bit of "leisure", I will definitely add the > "'View in Jalview' link". > > https://github.com/greenify/biojs-vis-msa/issues/64 > > > Any thoughts/strong opinions > > +1 for the HTTP API. I don't it is possible for Jalview to parse the > msaviewer page. > Currently everything is loaded asynchronously, so just saving the URL in > the msaviewer would avoid the effort for you to write an HTTP API. > (Anyway an POST API seems way more flexible than using GET parameters) > > Best, > > Seb > > On 2014-10-28 15:53, Jim Procter wrote: > > Hi Sebastian. > > > > Tochukwu - our newest Jalview developer, has just started looking at > creating an msaviewer export. He's not had much experience with working > with bioinformatics web resources so I'd really appreciate it if you could > give him a brief tour of the msaviewer web examples. It would also be good > to know exactly what is considered 'BioJS best practice' for deploying the > msaviewer so we can make sure any pages generated by Jalview aren't going > to break when BioJS or msaviewer is updated in the future. > > > > From our side, we'd really like it if MSA viewer could provide a link to > post data to the www.jalview.org/services/launchApp service so any data > in an MSA viewer could be opened in the Jalview Desktop. I've got a feeling > the easiest way to do this robustly is to look at creating an HTTP api for > the desktop so javascript code on the web page can launch an instance of > Jalview that listens on a localhost port, and posts JSON to it. Otherwise, > we'd have to work out how to either get Jalview to extract the data from > the page where msaviewer is deployed, or stash the data in msaviewer > somewhere and then pass the URL to Jalview via it's servlet JNLP launch > mechanism so it can load it. Any thoughts/strong opinions about the easiest > way to proceed ? > > > > Jim. > > _______________________________________________ > Jalview-dev mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev >
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