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Christian Zmasek
@cmzmasek

Hi:
I am trying to start a simple demo page for JalviewJS (since we are planning to use it in our ViPR and IRD resources (https://www.viprbrc.org/brc/home.spg?decorator=vipr).

Here is the page: http://phyloxml.org/jalviewjs/a.html

Unfortunately, I am getting a "java.lang.Class could not be loaded" error.

The HTML code is from: https://github.com/jalview/jalview-js/blob/master/JalviewJS.html

I wonder if you could tell me what I am doing wrong?

-Christian

Bob Hanson
@BobHanson
@cmzmasek Looks like you have not uploaded the swingjs/j2s folder to your server.
Bob Hanson
@BobHanson

@foreveremain @gmungoc I created a new branch JalviewJS/JAL-3563-sync-TestNG-test-bob to test out some ideas with allowing test processes to operate synchronously. This seems to be the problem with Jalview2xmlTest, where the test for how many mappings there are is run before the asynchronous process that creates them is run. I don't know why this is showing up now specifically on the JalviewJS branch. Seems to me it's a general problem. Of course, maybe this won't fix the problem. But it sure helped me on my own machine running these tests. Multiple threads were bombing out with NullPointerExceptions all over the place but, oddly enough, still passing the tests.

I'm pretty sure headless operations need to work synchronously as well, or am I wrong about that?

Bob Hanson
@BobHanson
@foreveremain Jim, when you get a chance, can you tell me why bamboo failed at https://builds.jalview.org/browse/JB-JDB200-JOB1-1/log
Jim Procter
@foreveremain
@cmzmasek - in principle a git clone https://../jalview-js.git gives you all you need (ie the swingjs/j2s folder) - did you do the clone into a web accessible directory ?
Jim Procter
@foreveremain
Hi @/all - I've pushed a test branch of jalview-js from our latest upstream jalview build - this is essentially Jalview 2.11.1.0 with added JalviewJS goodness. Do take a look and see if it works for you. We've still a few things to solve (excessive log output, etc!).. but this version is nearly ready!
jessielyons
@jessielyons
Hi Jim, I love your desktop jalview. I have a small project where I want to integrate the jalview javascript functionality as an automated function in my app. Jim, is there a standalone code you can provide which I can use where we can parse in the AA sequences and using jalview.js, we can spit out the phylogenetic tree and the colored MSA next to it as we can do in jalview desktop?
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