From 2a34f97c8ec632756ae07d63f8a687e4ffb04ebd Mon Sep 17 00:00:00 2001 From: Colin Date: Fri, 17 Feb 2023 03:21:53 -0700 Subject: [PATCH] LGV ticks --- .../components/OverviewScalebar.tsx | 1 + .../LinearGenomeView.test.tsx.snap | 40 ++++++++++++++---- .../src/LinearGenomeView/util.test.ts | 11 +++-- .../src/LinearGenomeView/util.ts | 4 +- .../JBrowseLinearGenomeView.test.tsx.snap | 14 ++++-- ...-tsx-open-a-bigwig-line-track-2-1-snap.png | Bin 3617 -> 2448 bytes ...-tsx-open-a-bigwig-line-track-2-2-snap.png | Bin 0 -> 3617 bytes .../__image_snapshots__/dotplot_snapshot.svg | 2 +- .../__image_snapshots__/lgv_snapshot.svg | 2 +- .../__image_snapshots__/synteny_snapshot.svg | 2 +- .../__snapshots__/ExportSvg.test.tsx.snap | 6 +-- 11 files changed, 59 insertions(+), 23 deletions(-) create mode 100644 products/jbrowse-web/src/tests/__image_snapshots__/big-wig-test-tsx-open-a-bigwig-line-track-2-2-snap.png diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/OverviewScalebar.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/OverviewScalebar.tsx index b5bcb85e52..97fa39121b 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/OverviewScalebar.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/OverviewScalebar.tsx @@ -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")`, diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.tsx.snap b/plugins/linear-genome-view/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.tsx.snap index 3a6fa560b4..27892fd35a 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.tsx.snap +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.tsx.snap @@ -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;" />
@@ -32,7 +32,7 @@ exports[`renders one track, one region 1`] = ` ctgA

@@ -346,6 +346,10 @@ exports[`renders one track, one region 1`] = ` class="css-1dmfa10-contentBlock" style="width: 100px;" > +
+
@@ -584,12 +592,12 @@ exports[`renders two tracks, two regions 1`] = ` ctgA

@@ -600,7 +608,7 @@ exports[`renders two tracks, two regions 1`] = ` ctgB

@@ -916,6 +924,10 @@ exports[`renders two tracks, two regions 1`] = ` class="css-1dmfa10-contentBlock" style="width: 100px;" > +
+
+
+
diff --git a/plugins/linear-genome-view/src/LinearGenomeView/util.test.ts b/plugins/linear-genome-view/src/LinearGenomeView/util.test.ts index 1b98d96471..8375f82ee8 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/util.test.ts +++ b/plugins/linear-genome-view/src/LinearGenomeView/util.test.ts @@ -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 }, ]) }) }) diff --git a/plugins/linear-genome-view/src/LinearGenomeView/util.ts b/plugins/linear-genome-view/src/LinearGenomeView/util.ts index 84dc327e6d..d549042d07 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/util.ts +++ b/plugins/linear-genome-view/src/LinearGenomeView/util.ts @@ -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)) { diff --git a/products/jbrowse-react-linear-genome-view/src/JBrowseLinearGenomeView/__snapshots__/JBrowseLinearGenomeView.test.tsx.snap b/products/jbrowse-react-linear-genome-view/src/JBrowseLinearGenomeView/__snapshots__/JBrowseLinearGenomeView.test.tsx.snap index 08f735c775..82cd86dedf 100644 --- a/products/jbrowse-react-linear-genome-view/src/JBrowseLinearGenomeView/__snapshots__/JBrowseLinearGenomeView.test.tsx.snap +++ b/products/jbrowse-react-linear-genome-view/src/JBrowseLinearGenomeView/__snapshots__/JBrowseLinearGenomeView.test.tsx.snap @@ -104,7 +104,7 @@ exports[` renders successfully 1`] = ` style="width: 267px; left: 0px; background: rgba(66, 119, 127, 0.3); border-color: rgb(66, 119, 127);" />
@@ -115,7 +115,7 @@ exports[` renders successfully 1`] = ` ctgA

renders successfully 1`] = `

@@ -605,6 +605,10 @@ exports[` renders successfully 1`] = ` class="css-i794sq-tick-minorTick" style="left: 800px;" /> +
renders successfully 1`] = ` class="css-i794sq-tick-minorTick" style="left: 800px;" /> +
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