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LGV ticks
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@cmdcolin
cmdcolin committed Feb 17, 2023
1 parent b1b8a85 commit 2a34f97
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Showing 11 changed files with 59 additions and 23 deletions.
1 change: 1 addition & 0 deletions plugins/linear-genome-view/src/LinearGenomeView/components/OverviewScalebar.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ const useStyles = makeStyles()(theme => ({
position: 'absolute',
top: 0,
height: HEADER_OVERVIEW_HEIGHT,
overflow: 'hidden',
},
scalebarContigForward: {
backgroundImage: `url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M-.1 0L6 4.5L-.1 9' fill='none' stroke='${theme.palette.divider}'/%3E%3C/svg%3E")`,
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40 changes: 32 additions & 8 deletions ...-genome-view/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.tsx.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ exports[`renders one track, one region 1`] = `
style="width: 800px; left: 0px; background: rgba(66, 165, 245, 0.3); border-color: #42a5f5;"
/>
<div
class="css-osn2dd-scalebarContig"
class="css-2jeg0a-scalebarContig"
style="width: 0px; left: 0px; background-color: rgb(153, 153, 153);"
/>
<div>
Expand All @@ -32,7 +32,7 @@ exports[`renders one track, one region 1`] = `
ctgA
</p>
<div
class="css-1npsllo-scalebarContig-scalebarContigForward-scalebarBorder"
class="css-rtx9ov-scalebarContig-scalebarContigForward-scalebarBorder"
style="left: 0px; width: 800px; border-color: rgb(153, 102, 0);"
>
<p
Expand Down Expand Up @@ -68,7 +68,7 @@ exports[`renders one track, one region 1`] = `
</div>
</div>
<div
class="css-osn2dd-scalebarContig"
class="css-2jeg0a-scalebarContig"
style="width: 0px; left: 800px; background-color: rgb(153, 153, 153);"
/>
</div>
Expand Down Expand Up @@ -346,6 +346,10 @@ exports[`renders one track, one region 1`] = `
class="css-1dmfa10-contentBlock"
style="width: 100px;"
>
<div
class="css-i794sq-tick-minorTick"
style="left: -21px;"
/>
<div
class="css-1qcgmte-tick-majorTick"
style="left: -1px;"
Expand Down Expand Up @@ -374,6 +378,10 @@ exports[`renders one track, one region 1`] = `
class="css-i794sq-tick-minorTick"
style="left: 119px;"
/>
<div
class="css-i794sq-tick-minorTick"
style="left: 139px;"
/>
</div>
<div
class="css-a9ifge-boundaryPaddingBlock"
Expand Down Expand Up @@ -573,7 +581,7 @@ exports[`renders two tracks, two regions 1`] = `
style="width: 580px; left: 0px; background: rgba(66, 165, 245, 0.3); border-color: #42a5f5;"
/>
<div
class="css-osn2dd-scalebarContig"
class="css-2jeg0a-scalebarContig"
style="width: 0px; left: 0px; background-color: rgb(153, 153, 153);"
/>
<div>
Expand All @@ -584,12 +592,12 @@ exports[`renders two tracks, two regions 1`] = `
ctgA
</p>
<div
class="css-1npsllo-scalebarContig-scalebarContigForward-scalebarBorder"
class="css-rtx9ov-scalebarContig-scalebarContigForward-scalebarBorder"
style="left: 0px; width: 72.72727272727273px; border-color: rgb(153, 102, 0);"
/>
</div>
<div
class="css-osn2dd-scalebarContig"
class="css-2jeg0a-scalebarContig"
style="width: 0px; left: 72.72727272727273px; background-color: rgb(153, 153, 153);"
/>
<div>
Expand All @@ -600,7 +608,7 @@ exports[`renders two tracks, two regions 1`] = `
ctgB
</p>
<div
class="css-1npsllo-scalebarContig-scalebarContigForward-scalebarBorder"
class="css-rtx9ov-scalebarContig-scalebarContigForward-scalebarBorder"
style="left: 72.72727272727273px; width: 727.2727272727273px;"
>
<p
Expand Down Expand Up @@ -636,7 +644,7 @@ exports[`renders two tracks, two regions 1`] = `
</div>
</div>
<div
class="css-osn2dd-scalebarContig"
class="css-2jeg0a-scalebarContig"
style="width: 0px; left: 800px; background-color: rgb(153, 153, 153);"
/>
</div>
Expand Down Expand Up @@ -916,6 +924,10 @@ exports[`renders two tracks, two regions 1`] = `
class="css-1dmfa10-contentBlock"
style="width: 100px;"
>
<div
class="css-i794sq-tick-minorTick"
style="left: -21px;"
/>
<div
class="css-1qcgmte-tick-majorTick"
style="left: -1px;"
Expand Down Expand Up @@ -944,6 +956,10 @@ exports[`renders two tracks, two regions 1`] = `
class="css-i794sq-tick-minorTick"
style="left: 119px;"
/>
<div
class="css-i794sq-tick-minorTick"
style="left: 139px;"
/>
</div>
<div
class="css-1b6zgog-interRegionPaddingBlock"
Expand All @@ -953,6 +969,10 @@ exports[`renders two tracks, two regions 1`] = `
class="css-1dmfa10-contentBlock"
style="width: 800px;"
>
<div
class="css-i794sq-tick-minorTick"
style="left: -21px;"
/>
<div
class="css-1qcgmte-tick-majorTick"
style="left: -1px;"
Expand Down Expand Up @@ -1121,6 +1141,10 @@ exports[`renders two tracks, two regions 1`] = `
class="css-i794sq-tick-minorTick"
style="left: 819px;"
/>
<div
class="css-i794sq-tick-minorTick"
style="left: 839px;"
/>
</div>
</div>
</div>
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11 changes: 7 additions & 4 deletions plugins/linear-genome-view/src/LinearGenomeView/util.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -16,15 +16,18 @@ describe('tick calculation', () => {
{ type: 'minor', base: 8, index: 9 },
{ type: 'major', base: 9, index: 10 },
{ type: 'minor', base: 10, index: 11 },
{ type: 'minor', base: 11, index: 12 },
])
})
test('two', () => {
const result = Array.from(makeTicks(0, 50, 1))
expect(result).toEqual([
{ type: 'major', base: -1, index: 0 },
{ type: 'minor', base: 19, index: 1 },
{ type: 'minor', base: 39, index: 2 },
{ type: 'minor', base: 59, index: 3 },
{ type: 'minor', base: -21, index: 0 },
{ type: 'major', base: -1, index: 1 },
{ type: 'minor', base: 19, index: 2 },
{ type: 'minor', base: 39, index: 3 },
{ type: 'minor', base: 59, index: 4 },
{ type: 'minor', base: 79, index: 5 },
])
})
})
4 changes: 2 additions & 2 deletions plugins/linear-genome-view/src/LinearGenomeView/util.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -68,8 +68,8 @@ export function makeTicks(
let index = 0
const ticks = []
for (
let base = Math.ceil(minBase / iterPitch) * iterPitch;
base < maxBase;
let base = Math.floor(minBase / iterPitch) * iterPitch;
base < Math.ceil(maxBase / iterPitch) * iterPitch + 1;
base += iterPitch
) {
if (emitMinor && base % (gridPitch.majorPitch * 2)) {
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14 changes: 11 additions & 3 deletions ...nome-view/src/JBrowseLinearGenomeView/__snapshots__/JBrowseLinearGenomeView.test.tsx.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@ exports[`<JBrowseLinearGenomeView /> renders successfully 1`] = `
style="width: 267px; left: 0px; background: rgba(66, 119, 127, 0.3); border-color: rgb(66, 119, 127);"
/>
<div
class="css-osn2dd-scalebarContig"
class="css-2jeg0a-scalebarContig"
style="width: 0px; left: 0px; background-color: rgb(153, 153, 153);"
/>
<div>
Expand All @@ -115,7 +115,7 @@ exports[`<JBrowseLinearGenomeView /> renders successfully 1`] = `
ctgA
</p>
<div
class="css-1npsllo-scalebarContig-scalebarContigForward-scalebarBorder"
class="css-rtx9ov-scalebarContig-scalebarContigForward-scalebarBorder"
style="left: 0px; width: 800px; border-color: rgb(153, 102, 0);"
>
<p
Expand Down Expand Up @@ -157,7 +157,7 @@ exports[`<JBrowseLinearGenomeView /> renders successfully 1`] = `
</div>
</div>
<div
class="css-osn2dd-scalebarContig"
class="css-2jeg0a-scalebarContig"
style="width: 0px; left: 800px; background-color: rgb(153, 153, 153);"
/>
</div>
Expand Down Expand Up @@ -605,6 +605,10 @@ exports[`<JBrowseLinearGenomeView /> renders successfully 1`] = `
class="css-i794sq-tick-minorTick"
style="left: 800px;"
/>
<div
class="css-i794sq-tick-minorTick"
style="left: 820px;"
/>
</div>
<div
class="css-1dmfa10-contentBlock"
Expand Down Expand Up @@ -778,6 +782,10 @@ exports[`<JBrowseLinearGenomeView /> renders successfully 1`] = `
class="css-i794sq-tick-minorTick"
style="left: 800px;"
/>
<div
class="css-i794sq-tick-minorTick"
style="left: 820px;"
/>
</div>
</div>
</div>
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Binary file modified ...ests/__image_snapshots__/big-wig-test-tsx-open-a-bigwig-line-track-2-1-snap.png
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Binary file added ...ests/__image_snapshots__/big-wig-test-tsx-open-a-bigwig-line-track-2-2-snap.png
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2 changes: 1 addition & 1 deletion products/jbrowse-web/src/tests/__image_snapshots__/dotplot_snapshot.svg
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2 changes: 1 addition & 1 deletion products/jbrowse-web/src/tests/__image_snapshots__/lgv_snapshot.svg
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2 changes: 1 addition & 1 deletion products/jbrowse-web/src/tests/__image_snapshots__/synteny_snapshot.svg
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6 changes: 3 additions & 3 deletions products/jbrowse-web/src/tests/__snapshots__/ExportSvg.test.tsx.snap
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