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Separate out PileupDisplay functionality shared with SyntenyDisplay into a Mixin #3781

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merged 5 commits into from Jul 6, 2023

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carolinebridge
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Removes "nonsense" operations from the synteny view by separating shared functionality between it and pileup into a mixin they both implement separately.

…ny to inherit separately with their own implementations
@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Jun 30, 2023
@carolinebridge carolinebridge marked this pull request as ready for review June 30, 2023 19:47
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codecov bot commented Jun 30, 2023

Codecov Report

Merging #3781 (8e5a9de) into lgv-synteny-color (4b8386f) will increase coverage by 64.06%.
The diff coverage is 60.86%.

@@                  Coverage Diff                   @@
##           lgv-synteny-color    #3781       +/-   ##
======================================================
+ Coverage                   0   64.06%   +64.06%     
======================================================
  Files                      0      989      +989     
  Lines                      0    29781    +29781     
  Branches                   0     7130     +7130     
======================================================
+ Hits                       0    19080    +19080     
- Misses                     0    10536    +10536     
- Partials                   0      165      +165     
Impacted Files Coverage Δ
...c/LinearPileupDisplay/components/ColorByCustom.tsx 0.00% <0.00%> (ø)
...lugins/alignments/src/LinearPileupDisplay/index.ts 100.00% <ø> (ø)
...lugins/alignments/src/LinearPileupDisplay/model.ts 82.40% <ø> (ø)
...ns/alignments/src/PileupRenderer/PileupRenderer.ts 97.05% <ø> (ø)
...ments/src/PileupRenderer/getAlignmentShapeColor.ts 45.65% <ø> (ø)
plugins/alignments/src/index.ts 100.00% <ø> (ø)
plugins/alignments/src/PileupRenderer/colorBy.ts 9.75% <50.00%> (ø)
...earPileupDisplay/SharedLinearPileupDisplayMixin.ts 61.26% <61.26%> (ø)
plugins/alignments/src/shared/color.ts 95.65% <100.00%> (ø)
...ar-comparative-view/src/LGVSyntenyDisplay/model.ts 23.17% <100.00%> (ø)

... and 979 files with indirect coverage changes

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@carolinebridge carolinebridge force-pushed the pileup-synteny-display-refactor branch from 472f8e3 to 0ac6233 Compare July 5, 2023 17:26
@@ -22,7 +22,7 @@ import { makeImageData } from './makeImageData'
import { readConfObject } from '@jbrowse/core/configuration'

export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
colorBy?: { type: string; tag?: string; extra?: any }
colorBy?: { type: string; tag?: string; extra?: {} }
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can extra be typed with Record<string,unknown> or ExtraColorBy or something?


function ColorByCustomDlg(props: {
model: {
colorBy: any
colorBy: IColorByModel
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is it possibly undefined e.g. colorBy?: IColorByModel?

@cmdcolin cmdcolin merged commit 2c858fb into lgv-synteny-color Jul 6, 2023
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cmdcolin commented Jul 6, 2023

looks good to me, looks like this merges into the other PR currently. can address comments there perhaps, they are typescript nits

@cmdcolin cmdcolin deleted the pileup-synteny-display-refactor branch July 10, 2023 18:14
cmdcolin pushed a commit that referenced this pull request Jul 25, 2023
…nto a Mixin (#3781)

* separating out shared functionality into a mixin for pileup and synteny to inherit separately with their own implementations

* fixing lint with strict typing

* mv interface to shared file and add maybe type back

* revert change to package.json
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2 participants