@jbrowse/plugin-alignments 2.3.1 → 2.3.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/BamAdapter/BamAdapter.js +2 -1
- package/dist/BamAdapter/BamAdapter.js.map +1 -1
- package/dist/CramAdapter/CramAdapter.js +3 -3
- package/dist/CramAdapter/CramAdapter.js.map +1 -1
- package/dist/LinearReadArcsDisplay/configSchema.js +8 -0
- package/dist/LinearReadArcsDisplay/configSchema.js.map +1 -1
- package/dist/LinearReadArcsDisplay/drawFeats.d.ts +1 -0
- package/dist/LinearReadArcsDisplay/drawFeats.js +45 -37
- package/dist/LinearReadArcsDisplay/drawFeats.js.map +1 -1
- package/dist/LinearReadArcsDisplay/model.d.ts +46 -15
- package/dist/LinearReadArcsDisplay/model.js +42 -0
- package/dist/LinearReadArcsDisplay/model.js.map +1 -1
- package/dist/LinearReadCloudDisplay/drawFeats.js +18 -32
- package/dist/LinearReadCloudDisplay/drawFeats.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +8 -8
- package/dist/PileupRPC/methods/GetGlobalValueForTag.js +3 -1
- package/dist/PileupRPC/methods/GetGlobalValueForTag.js.map +1 -1
- package/dist/PileupRPC/methods/GetReducedFeatures.js +2 -4
- package/dist/PileupRPC/methods/GetReducedFeatures.js.map +1 -1
- package/dist/PileupRPC/methods/GetVisibleModifications.js +2 -4
- package/dist/PileupRPC/methods/GetVisibleModifications.js.map +1 -1
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -4
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/dist/util.js +3 -3
- package/dist/util.js.map +1 -1
- package/esm/BamAdapter/BamAdapter.js +2 -1
- package/esm/BamAdapter/BamAdapter.js.map +1 -1
- package/esm/CramAdapter/CramAdapter.js +3 -3
- package/esm/CramAdapter/CramAdapter.js.map +1 -1
- package/esm/LinearReadArcsDisplay/configSchema.js +8 -0
- package/esm/LinearReadArcsDisplay/configSchema.js.map +1 -1
- package/esm/LinearReadArcsDisplay/drawFeats.d.ts +1 -0
- package/esm/LinearReadArcsDisplay/drawFeats.js +45 -37
- package/esm/LinearReadArcsDisplay/drawFeats.js.map +1 -1
- package/esm/LinearReadArcsDisplay/model.d.ts +46 -15
- package/esm/LinearReadArcsDisplay/model.js +42 -0
- package/esm/LinearReadArcsDisplay/model.js.map +1 -1
- package/esm/LinearReadCloudDisplay/drawFeats.js +19 -33
- package/esm/LinearReadCloudDisplay/drawFeats.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +8 -8
- package/esm/PileupRPC/methods/GetGlobalValueForTag.js +3 -1
- package/esm/PileupRPC/methods/GetGlobalValueForTag.js.map +1 -1
- package/esm/PileupRPC/methods/GetReducedFeatures.js +2 -4
- package/esm/PileupRPC/methods/GetReducedFeatures.js.map +1 -1
- package/esm/PileupRPC/methods/GetVisibleModifications.js +2 -4
- package/esm/PileupRPC/methods/GetVisibleModifications.js.map +1 -1
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -4
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/esm/util.js +3 -3
- package/esm/util.js.map +1 -1
- package/package.json +3 -3
- package/src/AlignmentsFeatureDetail/__snapshots__/{index.test.js.snap → index.test.tsx.snap} +0 -0
- package/src/AlignmentsFeatureDetail/{index.test.js → index.test.tsx} +4 -2
- package/src/BamAdapter/BamAdapter.test.ts +5 -4
- package/src/BamAdapter/BamAdapter.ts +2 -1
- package/src/CombinationTest.test.ts +3 -2
- package/src/CramAdapter/CramAdapter.test.ts +3 -2
- package/src/CramAdapter/CramAdapter.ts +11 -9
- package/src/LinearAlignmentsDisplay/models/{configSchema.test.js → configSchema.test.ts} +5 -1
- package/src/LinearReadArcsDisplay/configSchema.ts +10 -0
- package/src/LinearReadArcsDisplay/drawFeats.ts +73 -54
- package/src/LinearReadArcsDisplay/model.tsx +45 -0
- package/src/LinearReadCloudDisplay/drawFeats.ts +21 -33
- package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx +76 -73
- package/src/LinearSNPCoverageDisplay/models/{configSchema.test.js → configSchema.test.ts} +3 -1
- package/src/PileupRPC/methods/GetGlobalValueForTag.ts +4 -1
- package/src/PileupRPC/methods/GetReducedFeatures.ts +4 -5
- package/src/PileupRPC/methods/GetVisibleModifications.ts +4 -4
- package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +6 -4
- package/src/index.test.ts +0 -1
- package/src/util.ts +10 -8
- package/src/PileupRenderer/components/PileupRendering.test.js +0 -21
- package/src/PileupRenderer/components/__snapshots__/PileupRendering.test.js.snap +0 -23
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@@ -10,35 +10,50 @@ export function hasPairedReads(features) {
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}
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return false;
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}
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function jitter(n) {
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return Math.random() * 2 * n - n;
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}
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export default async function drawFeats(self, ctx) {
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const { chainData } = self;
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const { chainData, height, colorBy, drawInter, drawLongRange, lineWidthSetting, jitterVal, } = self;
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if (!chainData) {
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return;
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}
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const displayHeight = self.height;
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const view = getContainingView(self);
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const { assemblyManager } = getSession(self);
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self.setLastDrawnOffsetPx(view.offsetPx);
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ctx.lineWidth =
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ctx.lineWidth = lineWidthSetting;
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const { chains, stats } = chainData;
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const hasPaired = hasPairedReads(chainData);
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const assemblyName = view.assemblyNames[0];
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const asm = assemblyManager.get(assemblyName);
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const type = (
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const type = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) || 'insertSizeAndOrientation';
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if (!asm) {
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return;
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}
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function drawLineAtOffset(p, c) {
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// draws a vertical line off to middle of nowhere if the second end not found
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ctx.strokeStyle = c;
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ctx.beginPath();
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ctx.moveTo(p, 0);
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ctx.lineTo(p, height);
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ctx.stroke();
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}
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function draw(k1, k2, assembly, longRange) {
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const s1 = k1.strand;
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const s2 = k2.strand;
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const f1 = s1 === -1;
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const f2 = s2 === -1;
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const p1 = f1 ? k1.start : k1.end;
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const p2 = hasPaired ? (f2 ? k2.start : k2.end) : f2 ? k2.end : k2.start;
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const
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const
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const ra1 = assembly.getCanonicalRefName(k1.refName);
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const ra2 = assembly.getCanonicalRefName(k2.refName);
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const r1 = view.bpToPx({ refName: ra1, coord: p1 });
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const r2 = view.bpToPx({ refName: ra2, coord: p2 });
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if (r1 && r2) {
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const radius = (r2.offsetPx - r1.offsetPx) / 2;
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const absrad = Math.abs(radius);
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const p = r1.offsetPx - view.offsetPx;
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const p2 = r2.offsetPx - view.offsetPx;
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// bezier (used for non-long-range arcs) requires moveTo before beginPath
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// arc (used for long-range) requires moveTo after beginPath (or else a
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// unwanted line at y=0 is rendered along with the arc)
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@@ -65,7 +80,7 @@ export default async function drawFeats(self, ctx) {
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ctx.strokeStyle = getInsertSizeColor(k1, k2, stats) || 'grey';
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}
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else if (type === 'gradient') {
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ctx.strokeStyle = `hsl(${Math.log10(
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ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`;
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}
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}
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else {
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@@ -81,47 +96,45 @@ export default async function drawFeats(self, ctx) {
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}
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}
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else if (type === 'gradient') {
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ctx.strokeStyle = `hsl(${Math.log10(
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ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`;
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}
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}
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}
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const destX = p + radius * 2;
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const destY = Math.min(
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const destY = Math.min(height + jitter(jitterVal), absrad);
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if (longRange) {
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// avoid drawing gigantic circles that glitch out the rendering,
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// instead draw vertical lines
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if (absrad > 100000) {
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drawLineAtOffset(p + jitter(jitterVal), 'red');
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drawLineAtOffset(p2 + jitter(jitterVal), 'red');
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}
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else {
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ctx.arc(p + radius + jitter(jitterVal), 0, absrad, 0, Math.PI);
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ctx.stroke();
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}
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}
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else {
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ctx.bezierCurveTo(p, destY, destX, destY, destX, 0);
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ctx.bezierCurveTo(p + jitter(jitterVal), destY, destX, destY, destX + jitter(jitterVal), 0);
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ctx.stroke();
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}
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ctx.stroke();
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}
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else if (r1 &&
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const p = r1.offsetPx - view.offsetPx;
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ctx.strokeStyle = 'purple';
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ctx.beginPath();
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ctx.moveTo(p, 0);
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ctx.lineTo(p, displayHeight);
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ctx.stroke();
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else if (r1 && drawInter) {
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drawLineAtOffset(r1.offsetPx - view.offsetPx, 'purple');
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}
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}
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for (let i = 0; i < chains.length; i++) {
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let chain = chains[i];
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if (chain.length === 1 &&
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if (chain.length === 1 && drawLongRange) {
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// singleton feature
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const f = chain[0];
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// special case where we look at RPOS/RNEXT
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if (hasPaired) {
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// eslint-disable-next-line @typescript-eslint/no-non-null-assertion
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const refName =
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const refName = f.next_ref;
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// eslint-disable-next-line @typescript-eslint/no-non-null-assertion
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const coord = f.next_pos;
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draw(f, {
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refName,
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start: coord,
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end: coord,
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strand: f.strand,
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}, true);
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draw(f, { refName, start: coord, end: coord, strand: f.strand }, asm, true);
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}
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// special case where we look at SA
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else {
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for (let i = 0; i < features.length - 1; i++) {
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const f = features[i];
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const v1 = features[i + 1];
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draw(f,
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refName: (asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(v1.refName)) || v1.refName,
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start: v1.start,
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end: v1.end,
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strand: v1.strand,
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}, true);
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draw(f, v1, asm, true);
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}
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}
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}
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chain = chain.filter(f => !(f.flags & 2048));
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}
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for (let i = 0; i < chain.length - 1; i++) {
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draw(chain[i], chain[i + 1], false);
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draw(chain[i], chain[i + 1], asm, false);
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}
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}
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}
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{"version":3,"file":"drawFeats.js","sourceRoot":"","sources":["../../src/LinearReadArcsDisplay/drawFeats.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAGlE,SAAS;AACT,OAAO,EACL,mBAAmB,EACnB,kBAAkB,EAClB,gCAAgC,GACjC,MAAM,iBAAiB,CAAA;AAExB,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;
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icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
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muiName: string;
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muiName: string; /**
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* #action
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* used during tests to detect when we can complete a snapshot test
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* #property
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37
|
*/
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|
lineWidth: types.maybe(types.number),
|
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+
/**
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|
+
* #property
|
|
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|
+
*/
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|
+
jitter: types.maybe(types.number),
|
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|
/**
|
|
40
44
|
* #property
|
|
41
45
|
*/
|
|
@@ -132,6 +136,14 @@ function stateModelFactory(configSchema) {
|
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setLineWidth(n) {
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|
self.lineWidth = n;
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},
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+
/**
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+
* #action
|
|
141
|
+
* jitter val, helpful to jitter the x direction so you see better evidence when e.g. 100
|
|
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|
+
* long reads map to same x position
|
|
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|
+
*/
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|
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|
+
setJitter(n) {
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|
+
self.jitter = n;
|
|
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+
},
|
|
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147
|
}))
|
|
136
148
|
.views(self => {
|
|
137
149
|
const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
|
|
@@ -143,6 +155,13 @@ function stateModelFactory(configSchema) {
|
|
|
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155
|
var _a;
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156
|
return (_a = self.lineWidth) !== null && _a !== void 0 ? _a : getConf(self, 'lineWidth');
|
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|
},
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|
+
/**
|
|
159
|
+
* #getter
|
|
160
|
+
*/
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|
161
|
+
get jitterVal() {
|
|
162
|
+
var _a;
|
|
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|
+
return (_a = self.jitter) !== null && _a !== void 0 ? _a : getConf(self, 'jitter');
|
|
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|
+
},
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|
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|
/**
|
|
147
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|
* #getter
|
|
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167
|
*/
|
|
@@ -197,6 +216,29 @@ function stateModelFactory(configSchema) {
|
|
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197
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|
},
|
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|
],
|
|
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|
},
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|
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|
+
{
|
|
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|
+
label: 'Jitter x-positions',
|
|
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|
+
subMenu: [
|
|
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|
+
{
|
|
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|
+
type: 'checkbox',
|
|
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|
+
checked: this.jitterVal === 0,
|
|
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|
+
label: 'None',
|
|
226
|
+
onClick: () => self.setJitter(0),
|
|
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|
+
},
|
|
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|
+
{
|
|
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|
+
type: 'checkbox',
|
|
230
|
+
checked: this.jitterVal === 2,
|
|
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|
+
label: 'Small',
|
|
232
|
+
onClick: () => self.setJitter(2),
|
|
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|
+
},
|
|
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|
+
{
|
|
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|
+
type: 'checkbox',
|
|
236
|
+
checked: this.jitterVal === 10,
|
|
237
|
+
label: 'Large',
|
|
238
|
+
onClick: () => self.setJitter(10),
|
|
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|
+
},
|
|
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|
+
],
|
|
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|
+
},
|
|
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|
{
|
|
201
243
|
label: 'Draw inter-region vertical lines',
|
|
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|
type: 'checkbox',
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReadArcsDisplay/model.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AACnC,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,KAAK,EAAY,MAAM,iBAAiB,CAAA;AACpE,OAAO,EAEL,sBAAsB,EACtB,mBAAmB,EACnB,OAAO,GACR,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,UAAU,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAElE,OAAO,EACL,iBAAiB,GAElB,MAAM,oCAAoC,CAAA;AAE3C,QAAQ;AACR,OAAO,WAAW,MAAM,6BAA6B,CAAA;AACrD,OAAO,cAAc,MAAM,8BAA8B,CAAA;AAEzD,SAAS;AACT,OAAO,EAAE,WAAW,EAAE,MAAM,WAAW,CAAA;AACvC,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,EAAE,WAAW,EAAa,MAAM,uBAAuB,CAAA;AAG9D,QAAQ;AACR,MAAM,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,uBAAuB,CAAC,CAAC,CAAA;AAWlE;;;GAGG;AACH,SAAS,iBAAiB,CAAC,YAAwC;IACjE,OAAO,KAAK;SACT,OAAO,CACN,uBAAuB,EACvB,iBAAiB,EACjB,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,uBAAuB,CAAC;QAC5C;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QAEnD;;WAEG;QACH,QAAQ,EAAE,KAAK,CAAC,QAAQ,CAAC,WAAW,EAAE,EAAE,CAAC;QAEzC;;WAEG;QACH,SAAS,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAEpC;;WAEG;QACH,MAAM,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAEjC;;WAEG;QACH,OAAO,EAAE,KAAK,CAAC,KAAK,CAClB,KAAK,CAAC,KAAK,CAAC;YACV,IAAI,EAAE,KAAK,CAAC,MAAM;YAClB,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;YAC9B,KAAK,EAAE,KAAK,CAAC,MAAM,EAAE;SACtB,CAAC,CACH;QAED;;WAEG;QACH,SAAS,EAAE,IAAI;QAEf;;WAEG;QACH,aAAa,EAAE,IAAI;KACpB,CAAC,CACH;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,OAAO,EAAE,KAAK;QACd,KAAK,EAAE,KAAK;QACZ,SAAS,EAAE,SAAkC;QAC7C,GAAG,EAAE,IAAgC;QACrC,iBAAiB,EAAE,CAAC;KACrB,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;;WAGG;QACH,MAAM;YACJ,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;QACxB,CAAC;QACD;;;WAGG;QACH,MAAM,CAAC,GAA6B;YAClC,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QAED;;WAEG;QACH,cAAc,CAAC,CAAmB;YAChC,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACxB,CAAC;QAED;;WAEG;QACH,YAAY,CAAC,IAAe;YAC1B,IAAI,CAAC,SAAS,GAAG,IAAI,CAAA;QACvB,CAAC;QAED;;WAEG;QACH,YAAY,CAAC,CAAU;YACrB,IAAI,CAAC,SAAS,GAAG,CAAC,CAAA;QACpB,CAAC;QAED;;WAEG;QACH,gBAAgB,CAAC,CAAU;YACzB,IAAI,CAAC,aAAa,GAAG,CAAC,CAAA;QACxB,CAAC;QAED;;WAEG;QACH,UAAU,CAAC,CAAU;YACnB,IAAI,CAAC,OAAO,GAAG,CAAC,CAAA;QAClB,CAAC;QAED;;;WAGG;QACH,QAAQ,CAAC,CAAU;YACjB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QAChB,CAAC;QAED;;WAEG;QACH,WAAW,CAAC,MAAc;YACxB,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,MAAM,CAAC,CAAA;QAC9B,CAAC;QAED;;;WAGG;QACH,oBAAoB,CAAC,CAAS;YAC5B,IAAI,CAAC,iBAAiB,GAAG,CAAC,CAAA;QAC5B,CAAC;QAED;;;WAGG;QACH,YAAY,CAAC,CAAS;YACpB,IAAI,CAAC,SAAS,GAAG,CAAC,CAAA;QACpB,CAAC;QAED;;;;WAIG;QACH,SAAS,CAAC,CAAS;YACjB,IAAI,CAAC,MAAM,GAAG,CAAC,CAAA;QACjB,CAAC;KACF,CAAC,CAAC;SAEF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EACJ,cAAc,EAAE,mBAAmB,EACnC,WAAW,EAAE,gBAAgB,GAC9B,GAAG,IAAI,CAAA;QAER,OAAO;YACL;;eAEG;YACH,IAAI,gBAAgB;;gBAClB,OAAO,MAAA,IAAI,CAAC,SAAS,mCAAI,OAAO,CAAC,IAAI,EAAE,WAAW,CAAC,CAAA;YACrD,CAAC;YAED;;eAEG;YACH,IAAI,SAAS;;gBACX,OAAO,MAAA,IAAI,CAAC,MAAM,mCAAI,OAAO,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;YAC/C,CAAC;YACD;;eAEG;YACH,IAAI,KAAK;gBACP,OAAO,CAAC,CAAC,IAAI,CAAC,SAAS,CAAA;YACzB,CAAC;YACD,mEAAmE;YACnE,0CAA0C;YAC1C,IAAI,gBAAgB;gBAClB,OAAO,gBAAgB,CAAA;YACzB,CAAC;YACD,gEAAgE;YAChE,0BAA0B;YAC1B,WAAW;gBACT,OAAO;oBACL,GAAG,gBAAgB,EAAE;oBACrB,uDAAuD;oBACvD,QAAQ,EAAE,IAAI;oBACd,MAAM,EAAE,mBAAmB,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE;iBAClD,CAAA;YACH,CAAC;YAED;;eAEG;YACH,cAAc;gBACZ,OAAO;oBACL,GAAG,mBAAmB,EAAE;oBACxB;wBACE,KAAK,EAAE,WAAW;wBAClB,IAAI,EAAE,cAAc;wBACpB,OAAO,EAAE,GAAG,EAAE;4BACZ,UAAU,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;gCAC1C,cAAc;gCACd,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE;6BAC7B,CAAC,CAAA;wBACJ,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,YAAY;wBACnB,OAAO,EAAE;4BACP;gCACE,KAAK,EAAE,MAAM;gCACb,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC;6BACpC;4BACD;gCACE,KAAK,EAAE,MAAM;gCACb,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC;6BACpC;4BACD;gCACE,KAAK,EAAE,YAAY;gCACnB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC;6BACpC;yBACF;qBACF;oBACD;wBACE,KAAK,EAAE,oBAAoB;wBAC3B,OAAO,EAAE;4BACP;gCACE,IAAI,EAAE,UAAU;gCAChB,OAAO,EAAE,IAAI,CAAC,SAAS,KAAK,CAAC;gCAC7B,KAAK,EAAE,MAAM;gCACb,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC;6BACjC;4BACD;gCACE,IAAI,EAAE,UAAU;gCAChB,OAAO,EAAE,IAAI,CAAC,SAAS,KAAK,CAAC;gCAC7B,KAAK,EAAE,OAAO;gCACd,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC;6BACjC;4BACD;gCACE,IAAI,EAAE,UAAU;gCAChB,OAAO,EAAE,IAAI,CAAC,SAAS,KAAK,EAAE;gCAC9B,KAAK,EAAE,OAAO;gCACd,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;6BAClC;yBACF;qBACF;oBAED;wBACE,KAAK,EAAE,kCAAkC;wBACzC,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,SAAS;wBACvB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC;qBAClD;oBACD;wBACE,KAAK,EAAE,6BAA6B;wBACpC,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,aAAa;wBAC3B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC;qBAC1D;oBACD;wBACE,KAAK,EAAE,cAAc;wBACrB,IAAI,EAAE,WAAW;wBACjB,OAAO,EAAE;4BACP;gCACE,KAAK,EAAE,kCAAkC;gCACzC,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,0BAA0B,EAAE,CAAC;6BAC5D;4BA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@@ -1,5 +1,5 @@
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1
1
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import { getConf } from '@jbrowse/core/configuration';
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2
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-
import { getContainingView } from '@jbrowse/core/util';
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2
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+
import { getContainingView, getSession } from '@jbrowse/core/util';
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3
3
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// locals
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4
4
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import { getOrientationColor, getInsertSizeColor, getInsertSizeAndOrientationColor, } from '../shared/color';
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5
5
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// avoid drawing negative width features for SVG exports
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@@ -23,9 +23,15 @@ export default async function drawFeats(self, ctx) {
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if (!chainData) {
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return;
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}
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const { assemblyManager } = getSession(self);
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const featureHeight = getConf(self, 'featureHeight');
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const displayHeight = self.height;
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const view = getContainingView(self);
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const assemblyName = view.assemblyNames[0];
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const asm = assemblyManager.get(assemblyName);
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if (!asm) {
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return;
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}
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self.setLastDrawnOffsetPx(view.offsetPx);
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36
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const { chains, stats } = chainData;
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37
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const coords = [];
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@@ -37,22 +43,12 @@ export default async function drawFeats(self, ctx) {
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if (chain[0].flags & 1 && chain.length > 1) {
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|
const v0 = chain[0];
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const v1 = chain[1];
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-
const
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41
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-
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-
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});
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const
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-
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coord: v0.end,
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47
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});
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48
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-
const r2s = view.bpToPx({
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49
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refName: v1.refName,
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50
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coord: v1.start,
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51
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});
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52
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-
const r2e = view.bpToPx({
|
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53
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refName: v1.refName,
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54
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-
coord: v1.end,
|
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55
|
-
});
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46
|
+
const ra1 = asm.getCanonicalRefName(v0.refName);
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47
|
+
const ra2 = asm.getCanonicalRefName(v1.refName);
|
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48
|
+
const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
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49
|
+
const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
|
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50
|
+
const r2s = view.bpToPx({ refName: ra2, coord: v1.start });
|
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51
|
+
const r2e = view.bpToPx({ refName: ra2, coord: v1.end });
|
|
56
52
|
let distance = 0;
|
|
57
53
|
if (r1s !== undefined &&
|
|
58
54
|
r1e !== undefined &&
|
|
@@ -80,22 +76,12 @@ export default async function drawFeats(self, ctx) {
|
|
|
80
76
|
for (let i = 1; i < chain.length; i++) {
|
|
81
77
|
const v0 = chain[i - 1];
|
|
82
78
|
const v1 = chain[i];
|
|
83
|
-
const
|
|
84
|
-
|
|
85
|
-
|
|
86
|
-
});
|
|
87
|
-
const
|
|
88
|
-
|
|
89
|
-
coord: v0.end,
|
|
90
|
-
});
|
|
91
|
-
const r2s = view.bpToPx({
|
|
92
|
-
refName: v1.refName,
|
|
93
|
-
coord: v1.start,
|
|
94
|
-
});
|
|
95
|
-
const r2e = view.bpToPx({
|
|
96
|
-
refName: v1.refName,
|
|
97
|
-
coord: v1.end,
|
|
98
|
-
});
|
|
79
|
+
const ra1 = asm.getCanonicalRefName(v0.refName);
|
|
80
|
+
const ra2 = asm.getCanonicalRefName(v1.refName);
|
|
81
|
+
const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
|
|
82
|
+
const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
|
|
83
|
+
const r2s = view.bpToPx({ refName: ra2, coord: v1.start });
|
|
84
|
+
const r2e = view.bpToPx({ refName: ra2, coord: v1.end });
|
|
99
85
|
let distance = 0;
|
|
100
86
|
if (r1s !== undefined &&
|
|
101
87
|
r1e !== undefined &&
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"drawFeats.js","sourceRoot":"","sources":["../../src/LinearReadCloudDisplay/drawFeats.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;
|
|
1
|
+
{"version":3,"file":"drawFeats.js","sourceRoot":"","sources":["../../src/LinearReadCloudDisplay/drawFeats.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,iBAAiB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAGlE,SAAS;AACT,OAAO,EACL,mBAAmB,EACnB,kBAAkB,EAClB,gCAAgC,GACjC,MAAM,iBAAiB,CAAA;AAexB,wDAAwD;AACxD,SAAS,WAAW,CAClB,CAAS,EACT,CAAS,EACT,KAAa,EACb,MAAc,EACd,GAA6B,EAC7B,KAAc;IAEd,IAAI,KAAK,GAAG,CAAC,EAAE;QACb,CAAC,IAAI,KAAK,CAAA;QACV,KAAK,GAAG,CAAC,KAAK,CAAA;KACf;IACD,IAAI,MAAM,GAAG,CAAC,EAAE;QACd,CAAC,IAAI,MAAM,CAAA;QACX,MAAM,GAAG,CAAC,MAAM,CAAA;KACjB;IAED,IAAI,KAAK,EAAE;QACT,GAAG,CAAC,SAAS,GAAG,KAAK,CAAA;KACtB;IACD,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;AACnC,CAAC;AAED,MAAM,CAAC,OAAO,CAAC,KAAK,UAAU,SAAS,CACrC,IAMC,EACD,GAA6B;;IAE7B,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,CAAA;IAC1B,IAAI,CAAC,SAAS,EAAE;QACd,OAAM;KACP;IACD,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IAC5C,MAAM,aAAa,GAAG,OAAO,CAAC,IAAI,EAAE,eAAe,CAAC,CAAA;IACpD,MAAM,aAAa,GAAG,IAAI,CAAC,MAAM,CAAA;IACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;IAC3C,MAAM,YAAY,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IAC1C,MAAM,GAAG,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAC7C,IAAI,CAAC,GAAG,EAAE;QACR,OAAM;KACP;IAED,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;IAExC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAA;IACnC,MAAM,MAAM,GAAiB,EAAE,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACtC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QACvB,wEAAwE;QACxE,qEAAqE;QACrE,uCAAuC;QACvC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE;YAC1C,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,GAAG,GAAG,GAAG,CAAC,mBAAmB,CAAC,EAAE,CAAC,OAAO,CAAC,CAAA;YAC/C,MAAM,GAAG,GAAG,GAAG,CAAC,mBAAmB,CAAC,EAAE,CAAC,OAAO,CAAC,CAAA;YAC/C,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAA;YAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;YACxD,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAA;YAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;YAExD,IAAI,QAAQ,GAAG,CAAC,CAAA;YAEhB,IACE,GAAG,KAAK,SAAS;gBACjB,GAAG,KAAK,SAAS;gBACjB,GAAG,KAAK,SAAS;gBACjB,GAAG,KAAK,SAAS,EACjB;gBACA,IAAI,EAAE,CAAC,OAAO,KAAK,EAAE,CAAC,OAAO,EAAE;oBAC7B,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,CAAA;oBACtC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,CAAA;oBAClC,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;iBAC3B;gBACD,MAAM,CAAC,IAAI,CAAC;oBACV,GAAG,EAAE,GAAG,CAAC,QAAQ;oBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;oBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;oBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;oBACjB,EAAE;oBACF,EAAE;oBACF,QAAQ;iBACT,CAAC,CAAA;aACH;SACF;aAAM;YACL,wEAAwE;YACxE,0BAA0B;YAC1B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACrC,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;gBACvB,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBACnB,MAAM,GAAG,GAAG,GAAG,CAAC,mBAAmB,CAAC,EAAE,CAAC,OAAO,CAAC,CAAA;gBAC/C,MAAM,GAAG,GAAG,GAAG,CAAC,mBAAmB,CAAC,EAAE,CAAC,OAAO,CAAC,CAAA;gBAC/C,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAA;gBAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;gBACxD,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAA;gBAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;gBAExD,IAAI,QAAQ,GAAG,CAAC,CAAA;gBAEhB,IACE,GAAG,KAAK,SAAS;oBACjB,GAAG,KAAK,SAAS;oBACjB,GAAG,KAAK,SAAS;oBACjB,GAAG,KAAK,SAAS,EACjB;oBACA,IAAI,EAAE,CAAC,OAAO,KAAK,EAAE,CAAC,OAAO,EAAE;wBAC7B,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,CAAA;wBAClC,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;qBAC3B;oBACD,MAAM,CAAC,IAAI,CAAC;wBACV,GAAG,EAAE,GAAG,CAAC,QAAQ;wBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;wBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;wBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;wBACjB,EAAE;wBACF,EAAE;wBACF,QAAQ;qBACT,CAAC,CAAA;iBACH;aACF;SACF;KACF;IAED,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACtC,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QAC9B,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;KAC9B;IACD,MAAM,UAAU,GAAG,aAAa,GAAG,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,MAAM,GAAG,CAAC,aAAa,GAAG,EAAE,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;IAEnD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACtC,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,EAAE,EAAE,EAAE,QAAQ,EAAE,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QAC1D,MAAM,IAAI,GAAG,CAAA,MAAA,IAAI,CAAC,OAAO,0CAAE,IAAI,KAAI,0BAA0B,CAAA;QAE7D,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,MAAM,CAAA;QACvC,GAAG,CAAC,SAAS,GAAG,OAAO,CAAA;QACvB,MAAM,CAAC,GAAG,GAAG,GAAG,GAAG,CAAA;QACnB,WAAW,CAAC,GAAG,GAAG,IAAI,CAAC,QAAQ,EAAE,GAAG,GAAG,UAAU,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;QAE7D,IAAI,IAAI,KAAK,0BAA0B,EAAE;YACvC,GAAG,CAAC,SAAS,GAAG,gCAAgC,CAAC,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,CAAA;SAChE;aAAM,IAAI,IAAI,KAAK,aAAa,EAAE;YACjC,GAAG,CAAC,SAAS,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;SACxC;aAAM,IAAI,IAAI,KAAK,YAAY,EAAE;YAChC,GAAG,CAAC,SAAS,GAAG,kBAAkB,CAAC,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,MAAM,CAAA;SAC5D;aAAM,IAAI,IAAI,KAAK,UAAU,EAAE;YAC9B,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,CAAA;YACtC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,CAAA;YAClC,GAAG,CAAC,SAAS,GAAG,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,WAAW,CAAA;SACnE;QAED,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;QACjC,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;QACjC,WAAW,CAAC,GAAG,GAAG,IAAI,CAAC,QAAQ,EAAE,GAAG,EAAE,EAAE,EAAE,aAAa,EAAE,GAAG,CAAC,CAAA;QAC7D,WAAW,CAAC,GAAG,GAAG,IAAI,CAAC,QAAQ,EAAE,GAAG,EAAE,EAAE,EAAE,aAAa,EAAE,GAAG,CAAC,CAAA;KAC9D;AACH,CAAC"}
|
|
@@ -4,7 +4,7 @@ import { Tooltip } from '@jbrowse/plugin-wiggle';
|
|
|
4
4
|
const en = (n) => n.toLocaleString('en-US');
|
|
5
5
|
const toP = (s = 0) => +(+s).toFixed(1);
|
|
6
6
|
const pct = (n, total) => `${toP((n / (total || 1)) * 100)}%`;
|
|
7
|
-
const TooltipContents = React.forwardRef(({ feature }, reactRef)
|
|
7
|
+
const TooltipContents = React.forwardRef(function ({ feature }, reactRef) {
|
|
8
8
|
const start = feature.get('start');
|
|
9
9
|
const end = feature.get('end');
|
|
10
10
|
const name = feature.get('refName');
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"Tooltip.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/components/Tooltip.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAA;AAyBhD,MAAM,EAAE,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;AACnD,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAA;AACvC,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,KAAa,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAA;
|
|
1
|
+
{"version":3,"file":"Tooltip.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/components/Tooltip.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAA;AAyBhD,MAAM,EAAE,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;AACnD,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAA;AACvC,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,KAAa,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAA;AAI7E,MAAM,eAAe,GAAG,KAAK,CAAC,UAAU,CAAwB,UAC9D,EAAE,OAAO,EAAE,EACX,QAAQ;IAER,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAClC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;IACnC,MAAM,EACJ,OAAO,EACP,GAAG,EACH,KAAK,EACL,GAAG,EACH,IAAI,EAAE,GAAG,EACT,GAAG,EAAE,EAAE,EACP,GAAG,EAAE,EAAE,EACP,GAAG,IAAI,EACR,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAY,CAAA;IACrC,MAAM,GAAG,GAAG,CAAC,IAAI,EAAE,KAAK,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;SACvE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,IAAI,CAAC,GAAG,CAAC,CAAA;IAEZ,OAAO,CACL,6BAAK,GAAG,EAAE,QAAQ;QAChB;YACE,qCAAU,GAAG,CAAW;YACxB;gBACE;oBACE,uCAAa;oBACb,wCAAc;oBACd,6CAAmB;oBACnB,0CAAgB;oBAChB,yCAAe,CACZ,CACC;YACR;gBACE;oBACE,wCAAc;oBACd,gCAAK,GAAG,CAAM,CACX;gBACL;oBACE;;wBAAS,OAAO,CAAC,CAAC,CAAC,IAAI,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAM;oBAC1D,gCAAK,GAAG,CAAM;oBACd,gCAAK,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,CAAM;oBACxB;wBACG,GAAG,CAAC,CAAC,CAAC,GAAG,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE;wBACtB,EAAE,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,EAAE,CAClB;oBACL,+BAAM,CACH;gBAEJ,MAAM,CAAC,OAAO,CAAC,IAAwC,CAAC,CAAC,GAAG,CAC3D,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CACf,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAC3C,4BAAI,GAAG,EAAE,IAAI;oBACX,gCAAK,IAAI,CAAC,WAAW,EAAE,CAAM;oBAC7B,gCAAK,KAAK,CAAC,KAAK,CAAM;oBACtB,gCACG,IAAI,KAAK,OAAO,IAAI,IAAI,KAAK,MAAM;wBAClC,CAAC,CAAC,KAAK;wBACP,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CACtB;oBACL;wBACG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;wBACtC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAClC;oBACL,gCAAK,GAAG,CAAM,CACX,CACN,CAAC,CACL,CACK,CACF,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAIF,MAAM,kBAAkB,GAAG,QAAQ,CACjC,CAAC,KAMA,EAAE,EAAE;IACH,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,iBAAiB,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IACzC,OAAO,IAAI,IAAI,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAClD,oBAAC,OAAO,IAAC,eAAe,EAAE,eAAe,KAAM,KAAK,GAAI,CACzD,CAAA;AACH,CAAC,CACF,CAAA;AAED,eAAe,kBAAkB,CAAA"}
|
|
@@ -45,7 +45,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
45
45
|
}) => any;
|
|
46
46
|
renderProps: any;
|
|
47
47
|
} & {
|
|
48
|
-
doReload(): void;
|
|
48
|
+
doReload(): void; /**
|
|
49
|
+
* #action
|
|
50
|
+
*/
|
|
49
51
|
afterAttach(): void;
|
|
50
52
|
setStatus(message: string): void;
|
|
51
53
|
setLoading(abortController: AbortController): void;
|
|
@@ -56,9 +58,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
56
58
|
layout: any;
|
|
57
59
|
maxHeightReached: boolean;
|
|
58
60
|
renderProps: any;
|
|
59
|
-
} | undefined): void;
|
|
60
|
-
* #getter
|
|
61
|
-
*/
|
|
61
|
+
} | undefined): void;
|
|
62
62
|
setError(error: unknown): void;
|
|
63
63
|
reload(): void;
|
|
64
64
|
beforeDestroy(): void;
|
|
@@ -152,13 +152,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
152
152
|
rendererTypeName: string;
|
|
153
153
|
error: unknown;
|
|
154
154
|
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
155
|
-
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
156
|
-
* #getter
|
|
157
|
-
*/
|
|
155
|
+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
158
156
|
type: import("mobx-state-tree").ISimpleType<string>;
|
|
159
157
|
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
160
158
|
}, {
|
|
161
|
-
rendererTypeName: string;
|
|
159
|
+
rendererTypeName: string; /**
|
|
160
|
+
* #method
|
|
161
|
+
*/
|
|
162
162
|
error: unknown;
|
|
163
163
|
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
164
164
|
}> | null;
|
|
@@ -1,5 +1,7 @@
|
|
|
1
1
|
import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
|
|
2
2
|
import { toArray } from 'rxjs/operators';
|
|
3
|
+
import { firstValueFrom } from 'rxjs';
|
|
4
|
+
// locals
|
|
3
5
|
import PileupBaseRPC from '../base';
|
|
4
6
|
import { getTag } from '../../util';
|
|
5
7
|
export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
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@@ -11,7 +13,7 @@ export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
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11
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const { adapterConfig, sessionId, regions, tag } = await this.deserializeArguments(args, rpcDriver);
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const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
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const features = dataAdapter.getFeaturesInMultipleRegions(regions);
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14
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-
const featuresArray = await features.pipe(toArray())
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16
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+
const featuresArray = await firstValueFrom(features.pipe(toArray()));
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return [
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...new Set(featuresArray
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.map(feature => getTag(feature, tag))
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