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VisBOL / visbol-js

SBOLv rendering in JavaScript
visbol.org
BSD 2-Clause "Simplified" License
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Complex formation involving RNA has exception in the browser #97

Open cjmyers opened 5 years ago

cjmyers commented 5 years ago

This file throws exception in the browser when rendering.

RGR_12_grna_rna_dCAS9_Mxi1_protein_complex_formation.zip

asadeg02 commented 5 years ago

@cjmyers I just looked into this one. In the code, (and of course based on the glyph specification) I have assumed there are only 3 types of complexes: rna-protein, protein-protein, small-molecule protein. but looking at the display list there is a non-covelant-binding in this sbol file which has a participant having an so term! I just fixed it to show 'SBGN' in this case! but I'm a little bit confused since I dont know what is the correct rendering for complex in this case! I thought (based on the spec), only non-DNA parts can form a complex!

asadeg02 commented 5 years ago

@cjmyers Below is the rendering I got after fixing it! it's still not good! the thing is that the way rendering for no-glyph-assigned has been implemented kind of messes up rendering when they are supposed to be attached to an interaction glyph since their center is not the same as the center of other glyphs vertically. The easiest solution for that is to change implementation of no glyph assigned glyph! bug

cjmyers commented 5 years ago

This is an rna part. RNA parts can have SO terms.

Chris

Sent from my iPhone

On Oct 30, 2018, at 10:52 PM, asadeg02 notifications@github.com wrote:

@cjmyers I just looked into this one. In the code, (and of course based on the glyph specification) I have assumed there are only 3 types of complexes: rna-protein, protein-protein, small-molecule protein. but looking at the display list there is a non-covelant-binding in this sbol file which has a participant having an so term! I just fixed it to show 'SBGN' in this case! but I'm a little bit confused since I dont know what is the correct rendering for complex in this case! I thought (based on the spe), only non-DNA parts can form a complex!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

cjmyers commented 5 years ago

This is related to the issue I checked in. It is an rna with a so role. This should still be rendered as an rna. Only dna region types should have glyph changed based on role.

Chris

Sent from my iPhone

On Oct 30, 2018, at 11:02 PM, asadeg02 notifications@github.com wrote:

@cjmyers Below is the rendering I got after fixing it! it's still not good! the thing is that the way rendering for no-glyph-assigned has been implemented kind of messes up rendering when they are supposed to be attached to an interaction glyph since their center is not the same as the center of other glyphs vertically. The easiest solution for that is to change implementation of no glyph assigned glyph!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

cjmyers commented 5 years ago

screen shot 2018-11-20 at 5 36 31 pm

Looks like it depends on which part is rendered first. If RNA is on right side, it overlaps the arrow. Can this overlap be removed?