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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.
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more refseq dropdown configuration options #349

Open rbuels opened 10 years ago

rbuels commented 10 years ago

Set order explicitly. Configure sorting callback. Set exact content explicitly.

rbuels commented 10 years ago

On 09/27/2013 08:09 AM, Dan Morandir wrote:

Not exactly, it will still show more refSeqs than I want... let's say I have reference sequences in my refSeqs.json file for human and rhesus, 95 of them are rhesus and 5 are human, and I only want to show the human

  1. As it is currently, even if I arrange the refSeq names alphabetically, the dropdown menu would show 5 human and 25 rhesus refSeqs.

If there's not an option to specify the refSeqs I want to show in the dropdown menu, do you consider it feasible for me to write a script for JBrowse that will create that option? It's not an urgent need, it's mostly just a hypothetical situation.

Thanks for your fast response, Mr. Buels.

Date: Fri, 27 Sep 2013 07:58:04 -0400 From: rbuels@gmail.com To: el_morando@hotmail.com; gmod-ajax@lists.sourceforge.net Subject: Re: [Gmod-ajax] About refSeq dropdown menus

There isn't an option for that, but you can set the sorting order of the dropdown menu, which lets you sort them either alphabetically, or (which is I suspect what you might want here) by length. See

http://gmod.org/wiki/JBrowse_Configuration_Guide#Reference_Sequence_Display_Order

So if you set "refSeqOrder": "length descending" in your jbrowse_conf.json, does that do what you need?

Robert Buels Lead Developer JBrowse - http://jbrowse.org

On 09/27/2013 07:51 AM, Dan Morandir wrote:

Good day, and thanks in advance to everyone:

Let's say I have kind of... 100 reference sequences in my refSeqs.json. Given that I always have a dropdown menu forced on my views, and knowing that it won't show more than 30 at any given time, is there any argument/script/plugin/something that will allow me to show only some selected reference sequences in my dropdown menu?

As an example, I want to show reference sequences #5, 32, 7, 87 and 36 on the dropdown menu, and not any of the others.

cmdcolin commented 10 years ago

I have some interest in this feature from my lab group as well. Another possibility for this feature is to "map refseq names to a refseq id" to present easier names in the dropdown since our refseq identifiers are coded. We might just create pages outside of jbrowse to manage this issue, but it's an idea.

djcline commented 10 years ago

It would also be nice if the dropdown had some reasonable maximum size and used a scroll bar. If you have hundreds of sequences it is currently a pain having to use the scroll bar for the whole window to move around the dropdown.

colindaven commented 9 years ago

The scrollbar idea is great. Even with Pacbio assemblies we are frequently going to be working with >100 reference sequences.

cmdcolin commented 6 years ago

Looks like several of these were added, everything except callback sorting