@jbrowse/bandage-core 9.0.0 → 9.1.0
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/bubbles/bubbleHalos.js +9 -5
- package/dist/bubbles/bubbleLine.js +3 -1
- package/dist/bubbles/bubblesFromGraph.js +8 -4
- package/dist/bubbles/classifyBubble.js +2 -2
- package/dist/bubbles/superbubbles.js +21 -0
- package/dist/chunks/{chunk-ISEI2FH3.js → chunk-2AWUWGAD.js} +10 -4
- package/dist/chunks/{chunk-YOYLCLIG.js → chunk-2ZT7ZF7A.js} +6 -2
- package/dist/chunks/{chunk-TLQ7F2ZT.js → chunk-3TGUKQWQ.js} +4 -4
- package/dist/chunks/{chunk-LLP3FXPM.js → chunk-75HR3756.js} +24 -7
- package/dist/chunks/chunk-FUVI4WQP.js +273 -0
- package/dist/chunks/{chunk-MFKORG3F.js → chunk-FX4RDMDN.js} +5 -1
- package/dist/chunks/{chunk-4S47XRYA.js → chunk-GOZYKNQ2.js} +16 -11
- package/dist/chunks/{chunk-TL4B342F.js → chunk-MXDQGA7A.js} +1 -1
- package/dist/chunks/{chunk-SKKYLBRA.js → chunk-RRZMMYBG.js} +1 -1
- package/dist/chunks/{chunk-AMS3MAFP.js → chunk-UID3QBWH.js} +1 -1
- package/dist/chunks/{chunk-2WNBVB55.js → chunk-WBCOREDZ.js} +121 -74
- package/dist/chunks/{chunk-WOO7QYKB.js → chunk-XKWD2RY3.js} +8 -2
- package/dist/chunks/{chunk-6VBDMZBZ.js → chunk-XLCTQHBE.js} +1 -1
- package/dist/cli/figure.js +6 -6
- package/dist/figure.js +6 -6
- package/dist/figureSettings.js +3 -3
- package/dist/index.js +34 -24
- package/dist/layout/forceCache.js +3 -3
- package/dist/pipeline.js +2 -2
- package/dist/renderer/Canvas2DRenderer.js +1 -1
- package/dist/renderer/recordingCanvas.js +12 -1
- package/dist/tubeMap/connectors.js +3 -1
- package/dist/tubeMap/draw.js +3 -1
- package/dist/types/bubbles/bubbleHalos.d.ts +2 -0
- package/dist/types/bubbles/bubbleLine.d.ts +3 -0
- package/dist/types/bubbles/bubblesFromGraph.d.ts +12 -2
- package/dist/types/bubbles/superbubbles.d.ts +5 -0
- package/dist/types/index.d.ts +3 -2
- package/dist/types/renderer/Canvas2DRenderer.d.ts +6 -3
- package/dist/types/tubeMap/connectors.d.ts +1 -0
- package/dist/types/tubeMap/draw.d.ts +1 -0
- package/dist/types/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/dist/viewport.js +3 -3
- package/package.json +1 -1
- package/dist/chunks/{chunk-5OIVTEF7.js → chunk-OOXIMURX.js} +3 -3
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@@ -68,45 +68,81 @@ var Canvas2DRenderer = class {
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}
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ctx.lineCap = "round";
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ctx.lineJoin = "round";
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this.
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this.
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this.renderArrows(batch);
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}
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renderEdges(batch) {
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const t = this.transform;
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const ctx = this.ctx;
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const hl = this.highlightedEdge === null ? void 0 : batch.edgeCurveRuns.get(this.highlightedEdge);
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const factor = this.highlightFactor;
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const edgeRun = this.edgeRun(batch.edgeCurveRuns);
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for (const { color, items } of groupByPaint(batch.edgeCurves, (e, i) => ({
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color: inRun(
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color: inRun(edgeRun, i) ? brightenAbgr(e.color, factor) : e.color,
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weight: e.thickness,
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last: inRun(
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last: inRun(edgeRun, i)
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ctx.stroke();
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this.strokeCurves(items, color);
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}
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const lifted = this.liftedStrokes(batch);
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for (const { color, items } of groupByPaint(batch.nodeStrokes, (s, i) => {
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const f = lifted.get(i);
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return {
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color: f === void 0 ? s.color : brightenAbgr(s.color, f),
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weight: s.thickness,
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last: f !== void 0
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};
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})) {
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this.strokeNodes(items, color);
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}
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const arrowRun = this.edgeRun(batch.arrowRuns);
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for (const { color, items } of groupByPaint(batch.arrows, (a, i) => ({
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color: inRun(arrowRun, i) ? brightenAbgr(a.color, factor) : a.color,
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weight: 0,
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last: inRun(arrowRun, i)
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}))) {
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this.fillArrows(items, color);
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// Only what the highlights lift, over a transparent clear, for a hover layer
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// stacked on a canvas that drew the batch without them: a pointer move then
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// repaints one node or edge rather than the whole drawing
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renderHighlights() {
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const ctx = this.ctx;
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ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height);
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const batch = this.batch;
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if (!this.transform || !batch) {
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return;
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}
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ctx.lineCap = "round";
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ctx.lineJoin = "round";
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const factor = this.highlightFactor;
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const curves = runItems(batch.edgeCurves, this.edgeRun(batch.edgeCurveRuns));
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for (const { color, items } of groupByPaint(curves, (e) => ({
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color: brightenAbgr(e.color, factor),
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weight: e.thickness,
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last: false
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}))) {
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this.strokeCurves(items, color);
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}
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const lifted = [...this.liftedStrokes(batch)];
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for (const { color, items } of groupByPaint(lifted, ([i, f]) => ({
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color: brightenAbgr(batch.nodeStrokes[i].color, f),
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weight: batch.nodeStrokes[i].thickness,
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last: false
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}))) {
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this.strokeNodes(
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items.map(([i]) => batch.nodeStrokes[i]),
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color
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);
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}
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const arrows = runItems(batch.arrows, this.edgeRun(batch.arrowRuns));
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for (const { color, items } of groupByPaint(arrows, (a) => ({
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color: brightenAbgr(a.color, factor),
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weight: 0,
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last: false
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}))) {
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this.fillArrows(items, color);
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}
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}
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edgeRun(runs) {
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return this.highlightedEdge === null ? void 0 : runs.get(this.highlightedEdge);
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}
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// stroke index -> brighten factor, for the nodes the model lifted
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liftedStrokes(batch) {
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const lifted = /* @__PURE__ */ new Map();
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for (const [nodeId, factor] of this.nodeHighlights) {
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const run = batch.nodeStrokeRuns.get(nodeId);
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@@ -116,55 +152,63 @@ var Canvas2DRenderer = class {
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}
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}
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return lifted;
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}
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strokeCurves(items, color) {
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const t = this.transform;
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const ctx = this.ctx;
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ctx.strokeStyle = abgrToCssRgba(color);
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ctx.lineWidth = items[0].thickness * 2 * t.dpr;
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ctx.beginPath();
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for (const e of items) {
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const first = e.curves[0];
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ctx.moveTo(
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first.x0 * t.scaleX + t.translateX,
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first.y0 * t.scaleY + t.translateY
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);
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for (const c of e.curves) {
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ctx.bezierCurveTo(
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c.cx0 * t.scaleX + t.translateX,
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c.cy0 * t.scaleY + t.translateY,
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c.cx1 * t.scaleX + t.translateX,
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c.cy1 * t.scaleY + t.translateY,
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c.x1 * t.scaleX + t.translateX,
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c.y1 * t.scaleY + t.translateY
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strokeNodes(items, color) {
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const [tip, left, notch, right] = arrowheadOutline(a, t);
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ctx.moveTo(tip.x, tip.y);
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ctx.lineTo(left.x, left.y);
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ctx.lineTo(notch.x, notch.y);
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ctx.closePath();
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ctx.strokeStyle = abgrToCssRgba(color);
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ctx.lineWidth = items[0].thickness * 2 * t.dpr;
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ctx.beginPath();
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const p0 = s.points[0];
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ctx.moveTo(p0.x * t.scaleX + t.translateX, p0.y * t.scaleY + t.translateY);
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const p = s.points[i];
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ctx.lineTo(p.x * t.scaleX + t.translateX, p.y * t.scaleY + t.translateY);
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ctx.fill();
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ctx.stroke();
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}
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fillArrows(items, color) {
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const t = this.transform;
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const ctx = this.ctx;
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ctx.fillStyle = abgrToCssRgba(color);
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ctx.beginPath();
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for (const a of items) {
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const [tip, left, notch, right] = arrowheadOutline(a, t);
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ctx.moveTo(tip.x, tip.y);
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ctx.lineTo(left.x, left.y);
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ctx.lineTo(notch.x, notch.y);
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ctx.lineTo(right.x, right.y);
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ctx.closePath();
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}
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ctx.fill();
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}
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dispose() {
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this.batch = null;
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@@ -190,6 +234,9 @@ function arrowheadOutline(a, t) {
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{ x: backX + uy * halfWidth, y: backY - ux * halfWidth }
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];
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}
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function runItems(items, run) {
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return run ? items.slice(run.start, run.start + run.count) : [];
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}
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function inRun(run, i) {
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return run !== void 0 && i >= run.start && i < run.start + run.count;
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}
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} from "./chunk-FX4RDMDN.js";
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// src/bubbles/classifyBubble.ts
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if (inversion) {
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if (b.offReference) {
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return shortest === longest ? sameLength(shortest) : { kind: "complex", label: `${range}, ${routes(pathCount)}` };
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}
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const alleles = pathCount > 2 ? `, ${pathCount} alleles` : "";
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function sameLength(bp) {
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return bp <= 1 ? { kind: "snp", label: "SNP" } : { kind: "substitution", label: `${formatBp(bp)} sub` };
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}
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snp: "#5b6b7a",
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substitution: "#5b6b7a",
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package/dist/cli/figure.js
CHANGED
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import "../chunks/chunk-7XHHVYG7.js";
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figureSvg
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} from "../chunks/chunk-
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} from "../chunks/chunk-3TGUKQWQ.js";
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import "../chunks/chunk-LOCJN3BZ.js";
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import "../chunks/chunk-47DYCZOK.js";
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import "../chunks/chunk-WDTXW7T2.js";
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genesOnRow,
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placeRowGenes
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} from "../chunks/chunk-MIW3HYPE.js";
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import "../chunks/chunk-WBCOREDZ.js";
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import "../chunks/chunk-4BYTEJGW.js";
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import "../chunks/chunk-3S3YVOJ7.js";
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import "../chunks/chunk-BUBZ32IC.js";
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@@ -53,8 +53,8 @@ import "../chunks/chunk-2LQ5BWT7.js";
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|
package/dist/figureSettings.js
CHANGED
|
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|
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|
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|
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|
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|
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package/dist/index.js
CHANGED
|
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|
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1
|
import {
|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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26
|
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|
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|
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|
|
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|
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|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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47
|
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|
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48
|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
drawTubeMap,
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|
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|
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|
drawTubeMapRuler,
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|
drawingBounds,
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|
@@ -430,6 +438,7 @@ export {
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|
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|
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|
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@@ -485,6 +494,7 @@ export {
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|
svgCanvas,
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|
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|
|
@@ -1,13 +1,13 @@
|
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1
|
import {
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|
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2
|
createForceLayoutCache
|
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3
|
-
} from "../chunks/chunk-
|
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|
-
import "../chunks/chunk-
|
|
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|
+
} from "../chunks/chunk-RRZMMYBG.js";
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|
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|
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|
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import "../chunks/chunk-ST2IBUAN.js";
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|
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|
package/dist/pipeline.js
CHANGED
|
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|
|
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11
|
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|
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|
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|
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|
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|
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+
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@@ -4,6 +4,7 @@ function recordingCanvas() {
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|
|
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4
|
const fills = [];
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|
5
5
|
const lineWidths = [];
|
|
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|
const points = [];
|
|
7
|
+
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|
|
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8
|
const at = (x, y) => {
|
|
8
9
|
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|
|
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10
|
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|
|
@@ -27,6 +28,9 @@ function recordingCanvas() {
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|
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|
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|
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|
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|
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|
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|
|
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|
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|
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|
strokes.push(ctx.strokeStyle);
|
|
32
36
|
lineWidths.push(ctx.lineWidth);
|
|
@@ -37,7 +41,14 @@ function recordingCanvas() {
|
|
|
37
41
|
};
|
|
38
42
|
const canvas = document.createElement("canvas");
|
|
39
43
|
canvas.getContext = () => ctx;
|
|
40
|
-
return {
|
|
44
|
+
return {
|
|
45
|
+
canvas,
|
|
46
|
+
strokes,
|
|
47
|
+
fills,
|
|
48
|
+
lineWidths,
|
|
49
|
+
points,
|
|
50
|
+
clears: () => clears
|
|
51
|
+
};
|
|
41
52
|
}
|
|
42
53
|
export {
|
|
43
54
|
recordingCanvas
|
|
@@ -1,10 +1,12 @@
|
|
|
1
1
|
import {
|
|
2
2
|
connectorAt,
|
|
3
|
+
drawLitConnector,
|
|
3
4
|
drawTubeMapConnectors,
|
|
4
5
|
tubeMapConnectors
|
|
5
|
-
} from "../chunks/chunk-
|
|
6
|
+
} from "../chunks/chunk-2ZT7ZF7A.js";
|
|
6
7
|
export {
|
|
7
8
|
connectorAt,
|
|
9
|
+
drawLitConnector,
|
|
8
10
|
drawTubeMapConnectors,
|
|
9
11
|
tubeMapConnectors
|
|
10
12
|
};
|
package/dist/tubeMap/draw.js
CHANGED
|
@@ -1,5 +1,6 @@
|
|
|
1
1
|
import {
|
|
2
2
|
drawTubeMap,
|
|
3
|
+
drawTubeMapHighlight,
|
|
3
4
|
mismatchOnScreen,
|
|
4
5
|
mismatchesLegible,
|
|
5
6
|
parsePath,
|
|
@@ -7,12 +8,13 @@ import {
|
|
|
7
8
|
tubeMapMismatchAt,
|
|
8
9
|
tubeMapPicture,
|
|
9
10
|
tubeMapTrackAt
|
|
10
|
-
} from "../chunks/chunk-
|
|
11
|
+
} from "../chunks/chunk-75HR3756.js";
|
|
11
12
|
import "../chunks/chunk-XXT2JCAC.js";
|
|
12
13
|
import "../chunks/chunk-CWFNEKST.js";
|
|
13
14
|
import "../chunks/chunk-C44YRP5F.js";
|
|
14
15
|
export {
|
|
15
16
|
drawTubeMap,
|
|
17
|
+
drawTubeMapHighlight,
|
|
16
18
|
mismatchOnScreen,
|
|
17
19
|
mismatchesLegible,
|
|
18
20
|
parsePath,
|
|
@@ -17,4 +17,6 @@ export interface RouteLabel {
|
|
|
17
17
|
at: NodeSegment;
|
|
18
18
|
text: string;
|
|
19
19
|
}
|
|
20
|
+
export declare const WHOLE_FRACTION = 0.9;
|
|
21
|
+
export declare function coversGraph(members: number, nodes: number): boolean;
|
|
20
22
|
export declare function bubbleHalos(graph: Graph, bubbles: MinigraphBubble[], positions: Record<string, NodeSegment[]>, walkLabel?: (name: string) => string, repeats?: readonly RepeatSpan[]): BubbleHalo[];
|