search

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
Other
461 stars 199 forks source link

Custom JBrowse feature glyphs do not work with NeatHTMLFeatures #735

Closed thomasvangurp closed 6 years ago

thomasvangurp commented 8 years ago

I've used the "hourglass hgred" features as a subclass to annotate conserved domains in proteins: deena_bioinformatics_test_jbrowse_uti_cns_0005289_447339__447721 However, when activating the NeatHTMLFeatures plugin the hourglass tags disappear. deena_bioinformatics_test_jbrowse_uti_cns_0005289_447339__447721

Any idea how to fix this? Would it be possible to exclude certain tracks from using the NeatHTMLFeatures plugin?

nathandunn commented 8 years ago

I had two thoughts about this:

  1. this plugin could be a subclassed track
  2. we allow more configuration of the plugin to exclude certain options

I can take a look at the second one.

nathandunn commented 8 years ago
  1. configure at the track of the plugin level
enuggetry commented 8 years ago

I suspect it's probably the gradient function that is causing this. Thiere is an option to turn off gradients, with gradientFeatures=0. Then, gradients can be turned ON per track. This is spelled out in the last half of the readme file. https://github.com/GMOD/jbrowse/blob/master/plugins/NeatHTMLFeatures/README.md

enuggetry commented 8 years ago

What I said there, wasn't quite true, but now it is true. Introns remain ON all the time, now. gradientFeatures=0 disable gradient features only.

as of this: https://github.com/GMOD/jbrowse/commit/85c048a4663378a2e48524a30225799849bcefc3

nathandunn commented 8 years ago

I added a related PR: https://github.com/GMOD/jbrowse/pull/737

allows turning off the linear gradient, but is otherwise unchanged.

cmdcolin commented 7 years ago

I made some experiments at making neatfeatures a subclassed track type here, something I think @nathandunn referred to above https://github.com/GMOD/jbrowse/tree/track_type_neatfeatures

rbuels commented 6 years ago

Since NeatHTMLFeatures is also no longer on by default, this seems like it's probably not a big issue anymore. Closing for now, please reopen if this is still a problem.