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Add ability to get stitched together CDS, protein, and cDNA sequences in feature details #1758

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merged 14 commits into from
Mar 4, 2021
Merged

Add ability to get stitched together CDS, protein, and cDNA sequences in feature details #1758

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1986780
Add sequence dialog
cmdcolin Mar 3, 2021
6c3363b
Allow getting protein translations
cmdcolin Mar 3, 2021
fd18d8a
Fix for negative strand features
cmdcolin Mar 4, 2021
8553931
Updates
cmdcolin Mar 4, 2021
c19d9a1
Simplification to avoid special case reverse strand features
cmdcolin Mar 4, 2021
f566140
Simplify types
cmdcolin Mar 4, 2021
f7e0dc4
Add a config for what types are included in sequenceTypes in jbrowse …
cmdcolin Mar 4, 2021
e5f293c
Use accordion border to help see nested subcategories
cmdcolin Mar 4, 2021
495adab
Remove duplicate features with note
cmdcolin Mar 4, 2021
bc06592
Fixup tests
cmdcolin Mar 4, 2021
d06760f
More test fixes
cmdcolin Mar 4, 2021
a508148
Increase some timeouts
cmdcolin Mar 4, 2021
fb76863
More timeouts
cmdcolin Mar 4, 2021
7966a19
Fix tsc
cmdcolin Mar 4, 2021
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382 changes: 321 additions & 61 deletions packages/core/BaseFeatureWidget/BaseFeatureDetail.tsx
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216 changes: 76 additions & 140 deletions packages/core/BaseFeatureWidget/__snapshots__/index.test.js.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,179 +2,115 @@

exports[`open up a widget 1`] = `
<div
class="MuiPaper-root makeStyles-paperRoot MuiPaper-elevation1 MuiPaper-rounded"
class="MuiPaper-root MuiAccordion-root makeStyles-accordionBorder MuiAccordion-expanded MuiAccordion-rounded MuiPaper-elevation1 MuiPaper-rounded"
>
<div
class="MuiPaper-root MuiAccordion-root MuiAccordion-expanded MuiAccordion-rounded MuiPaper-elevation1 MuiPaper-rounded"
style="margin-top: 4px;"
aria-disabled="false"
aria-expanded="true"
class="MuiButtonBase-root MuiAccordionSummary-root MuiAccordionSummary-expanded"
role="button"
tabindex="0"
>
<div
aria-disabled="false"
aria-expanded="true"
class="MuiButtonBase-root MuiAccordionSummary-root MuiAccordionSummary-expanded"
role="button"
tabindex="0"
class="MuiAccordionSummary-content MuiAccordionSummary-expanded"
>
<div
class="MuiAccordionSummary-content MuiAccordionSummary-expanded"
<span
class="MuiTypography-root MuiTypography-button"
>
<span
class="MuiTypography-root MuiTypography-button"
>

Primary data
</span>
</div>
<div
aria-disabled="false"
aria-hidden="true"
class="MuiButtonBase-root MuiIconButton-root MuiAccordionSummary-expandIcon MuiAccordionSummary-expanded MuiIconButton-edgeEnd"

</span>
</div>
<div
aria-disabled="false"
aria-hidden="true"
class="MuiButtonBase-root MuiIconButton-root MuiAccordionSummary-expandIcon MuiAccordionSummary-expanded MuiIconButton-edgeEnd"
>
<span
class="MuiIconButton-label"
>
<span
class="MuiIconButton-label"
<svg
aria-hidden="true"
class="MuiSvgIcon-root makeStyles-expandIcon"
focusable="false"
viewBox="0 0 24 24"
>
<svg
aria-hidden="true"
class="MuiSvgIcon-root makeStyles-expandIcon"
focusable="false"
viewBox="0 0 24 24"
>
<path
d="M16.59 8.59L12 13.17 7.41 8.59 6 10l6 6 6-6z"
/>
</svg>
</span>
</div>
<path
d="M16.59 8.59L12 13.17 7.41 8.59 6 10l6 6 6-6z"
/>
</svg>
</span>
</div>
</div>
<div
class="MuiCollapse-container MuiCollapse-entered"
style="min-height: 0px;"
>
<div
class="MuiCollapse-container MuiCollapse-entered"
style="min-height: 0px;"
class="MuiCollapse-wrapper"
>
<div
class="MuiCollapse-wrapper"
class="MuiCollapse-wrapperInner"
>
<div
class="MuiCollapse-wrapperInner"
role="region"
>
<div
role="region"
class="MuiAccordionDetails-root makeStyles-expansionPanelDetails"
>
<div>
Core details
</div>
<div
class="MuiAccordionDetails-root makeStyles-expansionPanelDetails"
class="makeStyles-field"
>
<div
class="makeStyles-field"
class="makeStyles-fieldName"
>
<div
class="makeStyles-fieldName"
>
Position
</div>
<div
class="makeStyles-fieldValue"
>
<div>
ctgA:3..102 (+)
</div>
</div>
Position
</div>
<div
class="makeStyles-field"
class="makeStyles-fieldValue"
>
<div
class="makeStyles-fieldName"
>
Length
<div>
ctgA:3..102 (+)
</div>
<div
class="makeStyles-fieldValue"
>
<div>
100
</div>
</div>
</div>
<div
class="makeStyles-field"
>
<div
class="makeStyles-fieldName"
>
Length
</div>
<div
class="makeStyles-fieldValue"
>
<div>
100
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<hr
class="MuiDivider-root"
/>
<div
class="MuiPaper-root MuiAccordion-root MuiAccordion-expanded MuiAccordion-rounded MuiPaper-elevation1 MuiPaper-rounded"
style="margin-top: 4px;"
>
<div
aria-disabled="false"
aria-expanded="true"
class="MuiButtonBase-root MuiAccordionSummary-root MuiAccordionSummary-expanded"
role="button"
tabindex="0"
>
<div
class="MuiAccordionSummary-content MuiAccordionSummary-expanded"
>
<span
class="MuiTypography-root MuiTypography-button"
>

Attributes
</span>
</div>
<div
aria-disabled="false"
aria-hidden="true"
class="MuiButtonBase-root MuiIconButton-root MuiAccordionSummary-expandIcon MuiAccordionSummary-expanded MuiIconButton-edgeEnd"
>
<span
class="MuiIconButton-label"
>
<svg
aria-hidden="true"
class="MuiSvgIcon-root makeStyles-expandIcon"
focusable="false"
viewBox="0 0 24 24"
>
<path
d="M16.59 8.59L12 13.17 7.41 8.59 6 10l6 6 6-6z"
<hr
class="MuiDivider-root"
/>
</svg>
</span>
</div>
</div>
<div
class="MuiCollapse-container MuiCollapse-entered"
style="min-height: 0px;"
>
<div
class="MuiCollapse-wrapper"
>
<div
class="MuiCollapse-wrapperInner"
>
<div
role="region"
>
<div>
Attributes
</div>
<div
class="MuiAccordionDetails-root makeStyles-expansionPanelDetails"
class="makeStyles-field"
>
<div
class="makeStyles-field"
class="makeStyles-fieldName"
>
<div
class="makeStyles-fieldName"
>
score
</div>
<div
class="makeStyles-fieldValue"
>
<div>
37
</div>
score
</div>
<div
class="makeStyles-fieldValue"
>
<div>
37
</div>
</div>
</div>
Expand Down
18 changes: 14 additions & 4 deletions packages/core/BaseFeatureWidget/index.test.js
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Original file line number Diff line number Diff line change
@@ -1,17 +1,27 @@
import { render } from '@testing-library/react'
import React from 'react'
import { types } from 'mobx-state-tree'
import { ConfigurationSchema } from '@jbrowse/core/configuration'
import PluginManager from '../PluginManager'
import { stateModelFactory } from '.'
import { BaseFeatureDetails as ReactComponent } from './BaseFeatureDetail'

test('open up a widget', () => {
console.warn = jest.fn()
const pluginManager = new PluginManager([])
const model = stateModelFactory(pluginManager).create({
type: 'BaseFeatureWidget',

const Session = types.model({
pluginManager: types.optional(types.frozen(), {}),
configuration: ConfigurationSchema('test', {}),
widget: stateModelFactory(pluginManager),
})
const model = Session.create({
widget: { type: 'BaseFeatureWidget' },
})
const { container, getByText } = render(<ReactComponent model={model} />)
model.setFeatureData({
const { container, getByText } = render(
<ReactComponent model={model.widget} />,
)
model.widget.setFeatureData({
start: 2,
end: 102,
strand: 1,
Expand Down
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