then you will need to write custom code
instead of just specifying urlTemplates in the config, you can make an array in the config called customScales, and each element of the array is an object with urlTemplates, and then when you receive a getFeatures query, it gets an object called basesPerSpan which could correspond roughly to which zoom level you want to access
@arpanda sounds good. Please see https://jbrowse.org/docs/faq.html#how-do-i-modify-jbrowse-source-code for how you can get started with modifying jbrowse source code
which includes plugins
just run
yarn watch in a command line window in the background while you modify the source code and then you can just refresh the browser and get your code changes like normal
When programmatically controlling a JBrowser embedded in an iframe, can you change the "loc" without reloading the browser? I wrapped an iframe/embedded jbrowser in a React component and am passing down new urls as props, but changing the url causes the embedded browser to reload.
I'm trying to link JBrowser views / charts in a dashboard. The goal is to be able to modify either the JBrowser or a chart and trigger an update in the other.
See
That link doesn't answer it directly
But it shows usage of the JBrowse global variable
Which you can call functions o
You could call JBrowse.navigateToLocation({ref,start,end}) I think
There are several different types of navigation functions depending on whether you want to search the enerate-names.pl index or not...can look at jbrowse's Browser.js if you want to dive deep(the JBrowse global variable in the iframe will be an instance of the Browser.js class)
@cmdcolin Thanks! This is very helpful, I have it working now. Is there a good place in the documentation or wiki detailing these types of JS functions for development? There's a lot of pages between the wiki and docs (which is not a complaint!) just not sure where best to poke around.
I made the FAQ some years ago to just try to brain dump lots of random ideas and answer hypotheticals
But it's not really any API documentation
And it's sort of true that the documentation was exploded into many different pages...I have been a little concerned about that, it used to be a single page wiki
(it actually is still available as the single page wiki just a little out of date)
unclear whether samples are tracks or different data folders
or what the requirements are lol
Sorry posting on mobile. There status 0 write generally mean CORS errors. Can you check the javascript console/devtools for console messages
@JHibbard if the iframe is on just a subdomain e.g. jbrowse.yoursite.org, which you view from a diff subdomainthen you can maybe set documentDomain=yoursite.org in the jbrowse.conf
@cmdcolin Thanks! It would be very convenient to have jbrowse run on a different domain, but if that's not possible with the embedded JBrowse do you have a feel for "how buggy" embedding directly into a div is? I remember someone on chat saying it was difficult but not elaborating much.
@JHibbard I did this as a quick mock up for a presentation I was giving last year: http://scottca.in/node/6 It has several JBrowse instances on a single page all in their own divs.
(Be sure to check out the worm div on the bottom of the page where you can flip the div so that the gene is in the same orientation as the other genes—obviously I just did that for fun :-)
If you wanted to change the view of any of these divs, you could just update the innerHTML of the named div that holds the instance, but that would require a complete redraw of the div (but hopefully not the whole page) so it would take a few seconds.
Here’s a gist for human and mouse from that page: https://gist.github.com/scottcain/aa99e669845a309b095eb00d2a9c771d
It seems that I've run into some sort of security thing in safari that doesn't happen in chrome or firefox. I wanted to create a page that would load several views of JBrowse so that I could check that all of the data are present and rendering properly, so I have this: http://scottca.in/node/8. In chrome this loads just fine (if a little slow, but I am asking a lot of the browser). In safari, it loads much of what I expect, but then towards the bottom, it loads a jbrowse window but stops drawing tracks. The error message is "SecurityError: Attempt to use history.replaceState() more than 100 times per 30.000000 seconds". It's not a big deal--I can use other browsers. I just spent some time trying to figure out what I did wrong, rather than looking at at the console to see the error message. Anyway, I thought it was interesting.
Not surprisingly, Safari also gave me a warning message that this page was using a significant amount of memory and closing it might help my browser performance. No kidding.