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"Show all regions" for dotplot and synteny views and refactor synteny rendering RPC to optimize scrolling #3440

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merged 28 commits into from
Jan 9, 2023

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@cmdcolin cmdcolin commented Jan 6, 2023

This performs a "Show all regions" operation for dotplot and synteny views

It also does some miscellaneous refactoring to make the header bar a bit less overwhelming, putting some of the "icons" (e.g. the chain icon for linking the views) into a submenu with text descriptions (because, chain icon isn't really obvious by itself)

Fixes #3380

Screenshot from 2023-01-06 09-39-28

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Jan 6, 2023
@cmdcolin cmdcolin added enhancement New feature or request and removed needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) labels Jan 6, 2023
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codecov bot commented Jan 6, 2023

Codecov Report

Merging #3440 (0578cdf) into main (aa43be2) will decrease coverage by 0.21%.
The diff coverage is 64.13%.

❗ Current head 0578cdf differs from pull request most recent head 6da562e. Consider uploading reports for the commit 6da562e to get more accurate results

@@            Coverage Diff             @@
##             main    #3440      +/-   ##
==========================================
- Coverage   61.50%   61.28%   -0.22%     
==========================================
  Files         821      818       -3     
  Lines       29448    29529      +81     
  Branches     7072     7065       -7     
==========================================
- Hits        18113    18098      -15     
- Misses      11172    11262      +90     
- Partials      163      169       +6     
Impacted Files Coverage Δ
...dotplot-view/src/DotplotView/components/Header.tsx 47.50% <0.00%> (-1.22%) ⬇️
...view/src/LinearComparativeDisplay/configSchemaF.ts 100.00% <ø> (ø)
...arative-view/src/LinearComparativeDisplay/index.ts 66.66% <0.00%> (-33.34%) ⬇️
...ive-view/src/LinearSyntenyDisplay/configSchemaF.ts 100.00% <ø> (ø)
...comparative-view/src/LinearSyntenyDisplay/index.ts 100.00% <ø> (ø)
plugins/linear-comparative-view/src/index.tsx 87.50% <ø> (-0.74%) ⬇️
plugins/linear-comparative-view/src/util.ts 0.00% <ø> (-28.31%) ⬇️
...aseLinearDisplay/models/serverSideRenderedBlock.ts 95.93% <ø> (ø)
...ircular-genome-view/src/createModel/createModel.ts 37.50% <ø> (ø)
...-linear-genome-view/src/createModel/createModel.ts 38.46% <ø> (ø)
... and 42 more

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@cmdcolin cmdcolin changed the title "Show all regions" for dotplot and synteny views "Show all regions" for dotplot and synteny views and refactor synteny rendering RPC to optimize scrolling Jan 9, 2023
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cmdcolin commented Jan 9, 2023

This PR now combines #3442 and #3441

the result is that the "LinearSyntenyRenderer" concept is removed, instead doing all drawing in the LinearSyntenyDisplay (inside an autorun, similar to the LinearAlignmentArcsDisplay)

the difference in performance is not "super significantly improved", but is maybe 2x faster, with the hope in helping whole genome overviews with many lines especially

this branch, grape vs peach whole genome overview:

https://jbrowse.org/code/jb2/show_all_regions/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-mHWrHxj8y9&password=2b8k7

main:

https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-mHWrHxj8y9&password=2b8k7

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cmdcolin commented Jan 9, 2023

might go ahead with merge :)

@cmdcolin cmdcolin merged commit 0f9bf14 into main Jan 9, 2023
@cmdcolin cmdcolin deleted the show_all_regions branch January 9, 2023 21:00
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Add "show all regions" for dotplot/synteny views
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