cjmyers
commented
1 month ago It used to be that VisBOL showed all levels of hierarchy in one image, but this was a bit cumbersome. We decided that instead that it would show the has hierarchy decoration and allow one to click on the object to dive into it on SynBioHub. If we simply show the parent icon, then you would lose the ability to click into the sub-components. We could go back to showing all levels of hierarchy, but again this may be too cumbersome. A possible compromise would be to show the parent icon when there are no sub-components. This would mean that we do not render the glpyhs for sequence annotations that do not reference a component.
PRO: this means that renderings of components with no sub-components would be rendered with their core functionality glyph. The renderings of glyphs for sequence annotations without sub-components is often problematic, since these are typically overlapping sequence features and not actual sub-parts.
CON: all SBOL files created from GenBank would be rendered as an Engineered Region glyph. This is less nice for people to see for these cases. However, the renderings of SBOL generated by GenBank are not always that intuitive anyway, since they are a mix of sequence features and sub-parts. Ideally, SBOL files generated from GenBank should be further curated using SeqImprove or similar anyway.
Thoughts?
It would be great if the visualisation used parent icons if they exist. E.g. Core promoter element being shown by a promoter as it is a child of promoter.