min & max stoichiometry labels #212
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complexviewer v2.0.0-beta
fix for PRO chain and isoform annotations
superfam fix
| { | ||
| "ac": "CPX-37", | ||
| "name": "CPX-37", | ||
| "url": "https://www.ebi.ac.uk/complexportal/complex/CPX-37" |
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There's a small bug in complex portal (which I have fixed but not deployed yet) causing the min and max stoichiometry not being set properly when the min is 0.
The correct version of this file is
CPX-37.json
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yes, the min/max label appears for the correct version of the file
| participant.setPosition(-500, -500); | ||
| this.proteinUpper.appendChild(participant.upperGroup); | ||
| } | ||
| participant.setPosition(-500, -500); |
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I just got this code locally and I tried to run it, and this is causing errors for complex CPX-5602
app.js:254 Uncaught TypeError: Failed to execute 'appendChild' on 'Node': parameter 1 is not of type 'Node'.
at App.init (app.js:254:1)
at App.readMIJSON (app.js:489:1)
at index.html?_ijt=vs1f11ftplrbgklh33n43qk7rd&_ij_reload=RELOAD_ON_SAVE:175:16
at d3.v3.min.js:1:9203
at Object.<anonymous> (d3.v3.min.js:1:9034)
at Object.t (d3.v3.min.js:1:740)
at XMLHttpRequest.i (d3.v3.min.js:1:7909)
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odd, for me CPX-5602 is working,
i tested in FireFox and Chrome
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it's like you don't have the most recent version of complex.js
the new version of complex.js should initialise this.upperGroup on line 12
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You're right, I forgot those changes. It is working now. The only thing is that because we don't have labels for complexes, when we have stoichiometry, it's just the stoichiometry being displayed.
So, if we change the code (in line 10 of complex.js) to
const complexIdMatch = interactorRef.match(/^.*(CPX-[0-9]+).*$/);
const complexId = complexIdMatch ? complexIdMatch[1] : "";
this.init(id, app, interactor, complexId);
Then we have the complex id of subcomplexes, and it would look like this
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Yes, i mentioned in the issue that "you could now also have similar labels for complexes giving their names if you wanted".
I thought it might be perceived as cluttered things up, but if you prefer this then lets do it like that.
Like this then, with complex names shown?
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I have some other trivial changes in my dev branch - removing comments, linting and also added:
setAllLinkCoordinates() {
this.setLabelPosition();
super.setAllLinkCoordinates();
}
to the Complex class, i think that is neater than way i had it before.
You can see the changes here: colin-combe/ComplexViewer@master...dev
Do you want me to add these changes to this pull request?
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I just had a look at the changes and they mostly seem like cleaning up and it's not that many. I would say add them to this PR.
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they are added to this PR.
This PR can probably be merged and the new version deployed on npm?
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can also mark as a release on GH which we (I) haven't done for a while
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Yeah, we can. Latest, and only, one is 2.2.0, in November 2022. Maybe it's time to mark another released version.
#19