search

VisBOL / visbol-js

SBOLv rendering in JavaScript
visbol.org
BSD 2-Clause "Simplified" License
10 stars 3 forks source link

Hide strings of no glyph assigned or generic sequence features #75

Open cjmyers opened 6 years ago

cjmyers commented 6 years ago

A string of say 2 or more no glyph assigned OR generic sequence features could be combined under a single "..." glyph. These could potentially be expanded by clicking on them, assuming they do not overrun the total glyph limit.

dany-fu commented 6 years ago

1) What are generic sequence features?

2) Testing no-glyph-assigned is a bit problematic as it goes back to a discussion we had over email about a month back. Currently SBOLDesigner generates xml files with NGA with the SO term for "Unspecified" <sbol:role rdf:resource="http://identifiers.org/so/SO:0000110"/>

I could simply delete this line in the SBOL file and have Visbol default to NGA if no roles exist (currently it defaults to Unspecified). I tested a file with no <sbol:role> and it doesn't seem to break anything, but is that too hacky?

cjmyers commented 6 years ago

A missing role is one example, and it should be rendered with the "question-mark" glyph. However, as I think you pointed out "sequence feature" SO:0000110 is also specified to be rendered with that glyph. SBOLDesigner though does have an issue that it uses the "[]" NGA glyph for that one.

In SBOLDesigner though, you can select any SO term and change the role to another term when you instantiate the NGA. If this term does not map to a glyph in SBOLv, then this is rendered in both SBOLDesigner and Visbol using the "[]" glyph.

So my rough idea above was to replace strings of "question-mark" and/or "[]" with the "..." glyph, since the visualizations sometimes get cluttered with these uninteresting glyphs. However, these still need a means to expand them back. The reason for this is this is currently the only way you can see those annotations and potentially click through to other pages describing those components.

In any case, this idea is a little bit rough. I think it should be lower priority to the simple upper bound on the number of glyphs and means to open up the hidden areas (i.e., issues #73 and #74).

cjmyers commented 5 years ago

Should be able to select glyphs not to render. A key one to hide would be glyphs for features with no glyph (current showing up as a box). Might also want to hide things like scars, spacers, insulators, etc.