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Render start/stop codons on LASFD#731

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garrettjstevens merged 5 commits intomainfrom
691-render-startstop-codons-on-lasfd
Nov 12, 2025
Merged

Render start/stop codons on LASFD#731
garrettjstevens merged 5 commits intomainfrom
691-render-startstop-codons-on-lasfd

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@haessar haessar commented Nov 7, 2025 •
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Notes:

  • New Appearance toggle, with start:off, stop:on by default:
image
  • I've used high contrast colours (start: green, stop: black) to match those used in Artemis:
image
  • I've ensured the refSeq is loaded when much further zoomed out (like Artemis) to facilitate codon rendering. This is now tied to the zoom threshold value (set in Appearance):
image

@haessar haessar self-assigned this Nov 7, 2025
@haessar haessar linked an issue Nov 7, 2025 that may be closed by this pull request
Render start/stop codons on LASFD #691
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haessar commented Nov 7, 2025

You'll probably recognise a lot of the logic from jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/drawSequenceTrack.ts

@garrettjstevens garrettjstevens changed the title Rendering start/stop codons on LASFD Render start/stop codons on LASFD Nov 12, 2025
@garrettjstevens garrettjstevens merged commit 2398922 into main Nov 12, 2025
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cmdcolin pushed a commit to cmdcolin/Apollo3 that referenced this pull request Mar 16, 2026
@haessar
Render start/stop codons on LASFD (GMOD#731)
e1dd393 
* toggles

* rendering of high-contrast, feature-label-aware, start/stop codons on LASFD

* tie loading of refSeq to zoomThreshold level rather than hard-coded "3"

* make use of util functions

* Ensure codon rendering occurs after feature rendering, to avoid codons getting covered by features
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Render start/stop codons on LASFD

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