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GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
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Wrapped sequence view #823

Open BevanR opened 8 years ago

BevanR commented 8 years ago

Does JBrowse support a wrapped view of sequences with vertical scroll instead of horizontal scroll?

If not, is such a feature on the radar?

Would a contribution for it be welcome?

Apologies for the duplicate post. I couldn't tell if the mailing list or GitHub is more appropriate.

E.g.

screen shot 2016-10-25 at 8 55 03 am

BevanR commented 7 years ago
hexylena commented 7 years ago

Edit: I somehow completely mis-read this

BevanR commented 7 years ago

I added a screenshot example to make it clearer.

nathandunn commented 7 years ago

@BevanR Trying to clarify what you want here. You are talking modifying the popup area under "Region Sequence" not the zoomed in sequence values?

screen shot 2016-11-14 at 10 02 22 am
BevanR commented 7 years ago

No. I'm talking about the entire sequence. Here is another example from Geneious. This one is zoomed out most of the way:

screen shot 2016-11-15 at 8 47 32 am

This is the same chromosome zoomed in a lot, but still in wrapped view;

screen shot 2016-11-15 at 8 49 25 am

nathandunn commented 7 years ago

Thanks for the clarification. We'll try to get back to you by the end of this week.

enuggetry commented 7 years ago

Sorry for the delayed response, I think I completely missed this thread. We don't have anything like this on the roadmap, so we'd welcome the contribution. In general, this looks like it wouldn't fit our existing view model (GenomeView class). So, I think the extension would be a class that substitutes the GenomeView class. You could take advantage of some of the location selection/zoom navigation. Unfortunately, there is no built-in framework to handle a view selection of this sort, yet. However, we do plan to do some work here. @ihh has been working on a radial view called Rotunda https://github.com/gmod/jbrowse/tree/rotunda (a purely SVG/D3 view), which we plan in integrate with some form of semantical selection. Thus, I see the framework opening up accommodate alternate genome views like yours.

I think it's safe to say that you can implement in either Javascript framework, dojo or jquery, with GUI elements like dialog boxes leaning towards Bootstrap (not completely decided). Implement your view to respect a DIV container.

nathandunn commented 7 years ago

Also, if you have an existing code-base in Java (if you are working within you're own Geneious plugin), you could use GWT to start building the component. The newer GWT uses JSInterop to do javascript integration. That being said, I think forking off of @ihh 's rotunda would be a better starting point if you are starting from scratch.