@jbrowse/bandage-core 11.9.0 → 11.11.0
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/chunks/{chunk-3BDQQTXY.js → chunk-4KBZ7WPP.js} +13 -2
- package/dist/chunks/{chunk-T2UNTWU5.js → chunk-7553WCL3.js} +6 -6
- package/dist/chunks/chunk-DAEEMZ74.js +34 -0
- package/dist/chunks/{chunk-UEWIGD52.js → chunk-EB4Q35QD.js} +2 -1
- package/dist/chunks/{chunk-ZWBQ4RRK.js → chunk-F47LKG5B.js} +23 -9
- package/dist/chunks/{chunk-GDZQFELP.js → chunk-GXCMBPC6.js} +16 -7
- package/dist/chunks/{chunk-GYJMPVOU.js → chunk-I5HVXRAO.js} +1 -1
- package/dist/chunks/{chunk-3BOREHCJ.js → chunk-JPT44REW.js} +14 -14
- package/dist/chunks/{chunk-JO2T77NW.js → chunk-KYTV5EAZ.js} +4 -4
- package/dist/chunks/{chunk-VTGQCLGI.js → chunk-LNLYK3Y5.js} +1 -1
- package/dist/chunks/{chunk-N3DCLT7M.js → chunk-N4QOWBRR.js} +1 -1
- package/dist/chunks/{chunk-2MXFG3W7.js → chunk-PYK4JKYW.js} +1 -0
- package/dist/chunks/{chunk-I5CHAYDZ.js → chunk-R36RBFNH.js} +4 -3
- package/dist/chunks/{chunk-IXLT3JJX.js → chunk-SVP2CQTA.js} +4 -4
- package/dist/cli/figure.js +28 -27
- package/dist/edgeWidths.js +10 -0
- package/dist/figure.js +13 -12
- package/dist/figureData.js +12 -11
- package/dist/figureScene.js +7 -6
- package/dist/figureSettings.js +1 -1
- package/dist/index.js +89 -81
- package/dist/layout/walkRowDraw.js +5 -4
- package/dist/layout/walkStrip.js +6 -5
- package/dist/layoutModes.js +3 -3
- package/dist/referenceStrip.js +4 -3
- package/dist/renderer/GeometryBuilder.js +3 -2
- package/dist/renderer/walkLanes.js +1 -1
- package/dist/tubeMap/nodeColors.js +4 -3
- package/dist/types/edgeWidths.d.ts +13 -0
- package/dist/types/figure.d.ts +2 -0
- package/dist/types/figureData.d.ts +1 -1
- package/dist/types/figureScene.d.ts +1 -1
- package/dist/types/figureSettings.d.ts +2 -0
- package/dist/types/index.d.ts +2 -0
- package/dist/types/renderer/GeometryBuilder.d.ts +2 -0
- package/dist/types/renderer/walkLanes.d.ts +1 -0
- package/dist/types/version.d.ts +1 -1
- package/dist/types/walkEncoding.d.ts +4 -0
- package/dist/types/walkHighlight.d.ts +2 -0
- package/dist/version.js +1 -1
- package/dist/walkEncoding.js +4 -3
- package/dist/walkHighlight.js +5 -4
- package/package.json +1 -1
- package/dist/chunks/{chunk-ARXDNQLF.js → chunk-WE7CLY2E.js} +3 -3
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@@ -367,7 +367,12 @@ function repeats(passes) {
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}
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function walkThreads(route, passes, nodePositions, yToX, reach) {
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if (!repeats(passes)) {
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return {
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return {
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span: passes,
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nodeThreads: /* @__PURE__ */ new Map(),
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threadPasses: /* @__PURE__ */ new Map(),
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linkThreads: /* @__PURE__ */ new Map()
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};
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}
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const index = /* @__PURE__ */ new Map();
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const ids = [];
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@@ -449,12 +454,18 @@ function walkThreads(route, passes, nodePositions, yToX, reach) {
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});
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const span = /* @__PURE__ */ new Map();
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const nodeThreads = /* @__PURE__ */ new Map();
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const threadPasses = /* @__PURE__ */ new Map();
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ids.forEach((id, k) => {
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span.set(id, widths[k]);
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nodeThreads.set(
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id,
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taken[k] ? [...taken[k]].sort((a, b) => a - b) : ONE_THREAD
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);
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const passOf = [];
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threadOf[k]?.forEach((thread, visit) => {
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passOf[thread] = visit - 1;
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});
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threadPasses.set(id, passOf);
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});
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const linkThreads = /* @__PURE__ */ new Map();
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steps.forEach((nodes, piece) => {
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@@ -479,7 +490,7 @@ function walkThreads(route, passes, nodePositions, yToX, reach) {
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}
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}
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});
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return { span, nodeThreads, linkThreads };
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return { span, nodeThreads, threadPasses, linkThreads };
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}
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function bandSpans(lanes, spans, { reach, taper }) {
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const out = /* @__PURE__ */ new Map();
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@@ -3,7 +3,7 @@ import {
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} from "./chunk-CO6RGQAD.js";
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import {
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layoutModeByValue
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} from "./chunk-
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} from "./chunk-WE7CLY2E.js";
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import {
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parseRegion
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} from "./chunk-FNDNSDKW.js";
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} from "./chunk-HEYIAMTC.js";
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import {
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version
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} from "./chunk-
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} from "./chunk-N4QOWBRR.js";
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import {
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axisScaleOf
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} from "./chunk-3DHGSHC3.js";
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import {
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figureScene
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} from "./chunk-
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} from "./chunk-R36RBFNH.js";
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import {
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encodingStops
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} from "./chunk-
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} from "./chunk-EB4Q35QD.js";
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import {
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laneSlideAt,
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passesKey,
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threadsPasses
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} from "./chunk-
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} from "./chunk-4KBZ7WPP.js";
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import {
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abgrAlpha,
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abgrBlue,
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} from "./chunk-G2FD7S3C.js";
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import {
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FIGURE_DEFAULTS
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} from "./chunk-
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} from "./chunk-PYK4JKYW.js";
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import {
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engineSettingsOf,
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fitTransform,
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// src/edgeWidths.ts
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var EDGE_WIDTHS = [
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{
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value: "uniform",
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label: "Uniform",
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description: "Every link the same thickness."
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},
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{
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value: "walks",
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label: "By walks",
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description: "Thicker the more walks take a link, on the square root of its count against the busiest link in the cut. A graph without walks draws uniform."
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}
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];
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var MIN_FACTOR = 0.5;
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var MAX_FACTOR = 4;
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function busiestEdge(graph) {
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let most = 0;
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for (const edge of graph.edges) {
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most = Math.max(most, edge.pathIds?.length ?? 0);
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}
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return most;
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}
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function edgeWidthFactor(walks, busiest, edgeWidth) {
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if (edgeWidth === "uniform" || busiest === 0) {
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return 1;
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}
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return MIN_FACTOR + (MAX_FACTOR - MIN_FACTOR) * Math.sqrt(walks / busiest);
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}
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export {
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EDGE_WIDTHS,
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busiestEdge,
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edgeWidthFactor
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};
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import {
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REFERENCE_RAMP_ALT_COLOR,
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hslToRgb
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} from "./chunk-
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} from "./chunk-GXCMBPC6.js";
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import {
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packAbgr
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} from "./chunk-G2FD7S3C.js";
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{ value: "red", label: "Yellow to red", ends: ["#ffd24a", "#b3121b"] },
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{ value: "purple", label: "Pink to plum", ends: ["#f5a3d8", "#5e1a6e"] },
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{ value: "green", label: "Lime to forest", ends: ["#b6e36c", "#0b5d3b"] },
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{ value: "orange", label: "Peach to rust", ends: ["#ffc285", "#8f3a00"] },
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{ value: "rainbow", label: "Rainbow" }
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];
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var FAMILIES = ["blue", "red", "purple", "green"];
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encodedColor,
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resolveEncoding,
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splitFamilies
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} from "./chunk-
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} from "./chunk-EB4Q35QD.js";
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} from "./chunk-GXCMBPC6.js";
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import {
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} from "./chunk-LG2UK4MB.js";
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@@ -55,6 +55,7 @@ function highlightOf(graph, name, { byId, edgeAt }) {
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const nodeIds = /* @__PURE__ */ new Set();
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const edgeIndexes = /* @__PURE__ */ new Set();
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const progress = /* @__PURE__ */ new Map();
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const passProgress = /* @__PURE__ */ new Map();
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const passes = /* @__PURE__ */ new Map();
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}
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}
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function laneColors(byId, walk, encoding, ramp) {
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const colors = /* @__PURE__ */ new Map();
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(t) => encodedColor(encoding, encoding.field === "progress" ? t : atNode)
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);
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const threadColor = (lane, nodeId, thread) => liftedWalks[lane]?.passColors.get(nodeId)?.[threads?.[lane]?.threadPasses.get(nodeId)?.[thread] ?? 0];
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const lanePointsOf = (nodeId, segments) => lines?.shifts.has(nodeId) ? segments.map((p, i) => {
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const ribbonThickness = connectorThickness / 2 * (isDeletion ? DELETION_THICKNESS_FACTOR : 1);
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const edgeColor = !highlight || onWalk ? plainEdgeColor : fadeAbgr(plainEdgeColor, FADED_ALPHA);
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691
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const arrowOn = (curves) => {
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const head = showArrows ? arrowheadFor({
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curves,
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694
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-
edgeHalfWidth: connectorThickness / 2,
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+
edgeHalfWidth: isDeletion || ribbons ? connectorThickness / 2 : edgeThickness,
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nodeHalfWidth: intoHalfWidth,
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scale,
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yToX,
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@@ -746,7 +754,7 @@ function buildGeometry(options) {
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laneStroke(
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curves,
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thickness,
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749
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-
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+
threadColor(lane, edge.from, pass) ?? threadColor(lane, edge.to, toPass) ?? plainEdgeColor,
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lane,
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pass,
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from.normal,
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@@ -782,7 +790,7 @@ function buildGeometry(options) {
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const ribbonColor = pathColorByName(edge.pathIds[pathIdx]);
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stroke(
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curves,
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785
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-
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+
ribbonThickness,
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highlight && (highlight.walks.length ? !highlight.names.has(edge.pathIds[pathIdx]) : !onWalk) ? fadeAbgr(ribbonColor, FADED_ALPHA) : ribbonColor
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);
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if (pathIdx === arrowRibbon) {
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@@ -834,11 +842,12 @@ function buildGeometry(options) {
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}
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const onThreads = threads?.[lane]?.nodeThreads.get(nodeId) ?? ONE_PASS;
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for (const pass of onThreads) {
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const color2 = threadColor(lane, nodeId, pass) ?? laneColor;
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if (lanes.length === 1) {
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nodeStrokes.push({
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points: segments,
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thickness,
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-
color:
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color: color2,
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walk: lane,
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pass
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});
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@@ -848,7 +857,7 @@ function buildGeometry(options) {
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nodeStrokes.push({
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points: offsetPolyline(points, normals, offsetX, yToX),
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thickness,
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-
color:
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+
color: color2,
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walk: lane,
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pass,
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normals,
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@@ -1,19 +1,19 @@
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1
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+
import {
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2
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svgCanvas
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3
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} from "./chunk-V4YML3GR.js";
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1
4
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import {
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2
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stripGeneGaps,
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walkStripFrame,
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walkStripLabelsTree
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-
} from "./chunk-
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+
} from "./chunk-KYTV5EAZ.js";
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import {
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Canvas2DRenderer
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} from "./chunk-4DMSPNYV.js";
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-
import {
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-
svgCanvas
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-
} from "./chunk-V4YML3GR.js";
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import {
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walkRowsKey,
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walkRowsKeyTree,
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walkRowsTree
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-
} from "./chunk-
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+
} from "./chunk-SVP2CQTA.js";
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import {
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EXON_COLOR,
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exonOutlineTree,
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@@ -25,30 +25,26 @@ import {
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import {
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nodesUnderBox
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} from "./chunk-4JDO7ZLN.js";
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-
import {
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-
escapeAttr,
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-
serializeEl
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-
} from "./chunk-H2H4Y3TV.js";
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import {
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genePins
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} from "./chunk-HEYIAMTC.js";
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import {
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version
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-
} from "./chunk-
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} from "./chunk-N4QOWBRR.js";
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import {
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axisScaleOf
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} from "./chunk-3DHGSHC3.js";
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import {
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figureScene
|
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-
} from "./chunk-
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+
} from "./chunk-R36RBFNH.js";
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import {
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41
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encodingStops
|
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46
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-
} from "./chunk-
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+
} from "./chunk-EB4Q35QD.js";
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import {
|
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48
44
|
THREAD_PX,
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49
45
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passesKey,
|
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50
46
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threadsPasses
|
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-
} from "./chunk-
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47
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+
} from "./chunk-4KBZ7WPP.js";
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import {
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53
49
|
rangeText
|
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} from "./chunk-IZKM4NY7.js";
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@@ -60,7 +56,7 @@ import {
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60
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} from "./chunk-ZANALBSX.js";
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import {
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FIGURE_DEFAULTS
|
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-
} from "./chunk-
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+
} from "./chunk-PYK4JKYW.js";
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import {
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65
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FIT_PADDING,
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66
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fitTransform
|
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@@ -72,6 +68,10 @@ import {
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72
68
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occupancy,
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placeLabels
|
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74
70
|
} from "./chunk-AB35TJST.js";
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+
import {
|
|
72
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+
escapeAttr,
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73
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+
serializeEl
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74
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+
} from "./chunk-H2H4Y3TV.js";
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75
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import {
|
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76
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|
FACET_GAP_PX,
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77
77
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FACET_PAD_PX,
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|
@@ -3,10 +3,7 @@ import {
|
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3
3
|
boxesGenes,
|
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4
4
|
rowPitch,
|
|
5
5
|
rowSpan
|
|
6
|
-
} from "./chunk-
|
|
7
|
-
import {
|
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8
|
-
el
|
|
9
|
-
} from "./chunk-H2H4Y3TV.js";
|
|
6
|
+
} from "./chunk-SVP2CQTA.js";
|
|
10
7
|
import {
|
|
11
8
|
READOUT_ROOM,
|
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12
9
|
longestBar
|
|
@@ -20,6 +17,9 @@ import {
|
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|
20
17
|
import {
|
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21
18
|
partitionPoint
|
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22
19
|
} from "./chunk-HOAIOEI7.js";
|
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20
|
+
import {
|
|
21
|
+
el
|
|
22
|
+
} from "./chunk-H2H4Y3TV.js";
|
|
23
23
|
|
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24
24
|
// src/layout/walkStrip.ts
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|
25
25
|
function walkStripApplies(o) {
|
|
@@ -4,11 +4,11 @@ import {
|
|
|
4
4
|
import {
|
|
5
5
|
facetLifts,
|
|
6
6
|
walkLift
|
|
7
|
-
} from "./chunk-
|
|
7
|
+
} from "./chunk-F47LKG5B.js";
|
|
8
8
|
import {
|
|
9
9
|
buildGeometry,
|
|
10
10
|
computeReferenceRamp
|
|
11
|
-
} from "./chunk-
|
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11
|
+
} from "./chunk-GXCMBPC6.js";
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12
12
|
import {
|
|
13
13
|
walkKey
|
|
14
14
|
} from "./chunk-IZKM4NY7.js";
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@@ -21,7 +21,7 @@ import {
|
|
|
21
21
|
} from "./chunk-VQ353UDK.js";
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22
22
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import {
|
|
23
23
|
FIGURE_DEFAULTS
|
|
24
|
-
} from "./chunk-
|
|
24
|
+
} from "./chunk-PYK4JKYW.js";
|
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25
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import {
|
|
26
26
|
drawingBounds
|
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27
27
|
} from "./chunk-JVT3XTKN.js";
|
|
@@ -110,6 +110,7 @@ function figureScene(graph, layout, o) {
|
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110
110
|
connectorThickness: o.connectorThickness ?? FIGURE_DEFAULTS.connectorThickness,
|
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111
111
|
drawPaths: false,
|
|
112
112
|
nodeWidth,
|
|
113
|
+
edgeWidth: o.edgeWidth ?? FIGURE_DEFAULTS.edgeWidth,
|
|
113
114
|
linearLayout: o.linearLayout,
|
|
114
115
|
highlight,
|
|
115
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|
axis,
|
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@@ -1,9 +1,6 @@
|
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1
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-
import {
|
|
2
|
-
el
|
|
3
|
-
} from "./chunk-H2H4Y3TV.js";
|
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4
1
|
import {
|
|
5
2
|
REFERENCE_RAMP_ALT_CSS
|
|
6
|
-
} from "./chunk-
|
|
3
|
+
} from "./chunk-GXCMBPC6.js";
|
|
7
4
|
import {
|
|
8
5
|
RAMP_GRADIENT_CSS,
|
|
9
6
|
RAMP_GRADIENT_STOPS,
|
|
@@ -20,6 +17,9 @@ import {
|
|
|
20
17
|
import {
|
|
21
18
|
ROW_HEIGHT_PX
|
|
22
19
|
} from "./chunk-CPMHA4W5.js";
|
|
20
|
+
import {
|
|
21
|
+
el
|
|
22
|
+
} from "./chunk-H2H4Y3TV.js";
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23
23
|
import {
|
|
24
24
|
panSNContig
|
|
25
25
|
} from "./chunk-2JL2JVZ2.js";
|
package/dist/cli/figure.js
CHANGED
|
@@ -6,41 +6,25 @@ import {
|
|
|
6
6
|
backboneGenes
|
|
7
7
|
} from "../chunks/chunk-376YFQOY.js";
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8
|
import "../chunks/chunk-EQDQ7P4Y.js";
|
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9
|
-
import {
|
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10
|
-
figureSvg
|
|
11
|
-
} from "../chunks/chunk-3BOREHCJ.js";
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12
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-
import "../chunks/chunk-JO2T77NW.js";
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13
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-
import "../chunks/chunk-4DMSPNYV.js";
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14
|
-
import "../chunks/chunk-RBCE2OQH.js";
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15
|
-
import "../chunks/chunk-V4YML3GR.js";
|
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16
|
-
import {
|
|
17
|
-
genesOnRow,
|
|
18
|
-
placeRowGenes
|
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19
|
-
} from "../chunks/chunk-IXLT3JJX.js";
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20
|
-
import "../chunks/chunk-JSUCGZ6K.js";
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21
|
-
import "../chunks/chunk-TQ26XEFL.js";
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22
|
-
import "../chunks/chunk-4JDO7ZLN.js";
|
|
23
|
-
import "../chunks/chunk-7YSIP3O2.js";
|
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24
|
-
import "../chunks/chunk-H2H4Y3TV.js";
|
|
25
9
|
import {
|
|
26
10
|
laidOutGraph,
|
|
27
11
|
walkLayers
|
|
28
|
-
} from "../chunks/chunk-
|
|
12
|
+
} from "../chunks/chunk-7553WCL3.js";
|
|
29
13
|
import {
|
|
30
14
|
LAYOUT_ENGINE_VALUES,
|
|
31
15
|
isLayoutEngineKind
|
|
32
16
|
} from "../chunks/chunk-CO6RGQAD.js";
|
|
33
17
|
import {
|
|
34
18
|
LAYOUT_MODES
|
|
35
|
-
} from "../chunks/chunk-
|
|
19
|
+
} from "../chunks/chunk-WE7CLY2E.js";
|
|
20
|
+
import "../chunks/chunk-XR2HMGAS.js";
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36
21
|
import "../chunks/chunk-BDS5VZYZ.js";
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37
22
|
import "../chunks/chunk-KKHXMJEE.js";
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38
|
-
import "../chunks/chunk-XR2HMGAS.js";
|
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39
23
|
import "../chunks/chunk-GJLZ2MKE.js";
|
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40
24
|
import "../chunks/chunk-MYLAJDKB.js";
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41
25
|
import "../chunks/chunk-5OJZV6YT.js";
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|
42
|
-
import "../chunks/chunk-UAFATXYA.js";
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43
26
|
import "../chunks/chunk-3GLG3ZLE.js";
|
|
27
|
+
import "../chunks/chunk-UAFATXYA.js";
|
|
44
28
|
import {
|
|
45
29
|
cutGbzRegion,
|
|
46
30
|
gbzLocations,
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|
@@ -50,15 +34,30 @@ import {
|
|
|
50
34
|
} from "../chunks/chunk-FNDNSDKW.js";
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51
35
|
import "../chunks/chunk-ZKSC7QVE.js";
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|
52
36
|
import "../chunks/chunk-HNWJ4B7S.js";
|
|
37
|
+
import {
|
|
38
|
+
figureSvg
|
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39
|
+
} from "../chunks/chunk-JPT44REW.js";
|
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40
|
+
import "../chunks/chunk-V4YML3GR.js";
|
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41
|
+
import "../chunks/chunk-KYTV5EAZ.js";
|
|
42
|
+
import "../chunks/chunk-4DMSPNYV.js";
|
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43
|
+
import "../chunks/chunk-RBCE2OQH.js";
|
|
44
|
+
import {
|
|
45
|
+
genesOnRow,
|
|
46
|
+
placeRowGenes
|
|
47
|
+
} from "../chunks/chunk-SVP2CQTA.js";
|
|
48
|
+
import "../chunks/chunk-JSUCGZ6K.js";
|
|
49
|
+
import "../chunks/chunk-TQ26XEFL.js";
|
|
50
|
+
import "../chunks/chunk-4JDO7ZLN.js";
|
|
51
|
+
import "../chunks/chunk-7YSIP3O2.js";
|
|
53
52
|
import "../chunks/chunk-HEYIAMTC.js";
|
|
54
|
-
import "../chunks/chunk-
|
|
53
|
+
import "../chunks/chunk-N4QOWBRR.js";
|
|
55
54
|
import "../chunks/chunk-3DHGSHC3.js";
|
|
56
|
-
import "../chunks/chunk-
|
|
55
|
+
import "../chunks/chunk-R36RBFNH.js";
|
|
57
56
|
import "../chunks/chunk-LOCJN3BZ.js";
|
|
58
|
-
import "../chunks/chunk-
|
|
59
|
-
import "../chunks/chunk-
|
|
60
|
-
import "../chunks/chunk-
|
|
61
|
-
import "../chunks/chunk-
|
|
57
|
+
import "../chunks/chunk-F47LKG5B.js";
|
|
58
|
+
import "../chunks/chunk-EB4Q35QD.js";
|
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|
+
import "../chunks/chunk-GXCMBPC6.js";
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|
+
import "../chunks/chunk-4KBZ7WPP.js";
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61
|
import "../chunks/chunk-G2FD7S3C.js";
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|
63
62
|
import "../chunks/chunk-IZKM4NY7.js";
|
|
64
63
|
import "../chunks/chunk-GQZVR5DW.js";
|
|
@@ -71,7 +70,7 @@ import {
|
|
|
71
70
|
import "../chunks/chunk-LODKC7PJ.js";
|
|
72
71
|
import "../chunks/chunk-VQ353UDK.js";
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|
73
72
|
import "../chunks/chunk-ZANALBSX.js";
|
|
74
|
-
import "../chunks/chunk-
|
|
73
|
+
import "../chunks/chunk-PYK4JKYW.js";
|
|
75
74
|
import "../chunks/chunk-JVT3XTKN.js";
|
|
76
75
|
import "../chunks/chunk-OPPVSPEF.js";
|
|
77
76
|
import "../chunks/chunk-NAYS472K.js";
|
|
@@ -101,6 +100,8 @@ import "../chunks/chunk-ZPZ7GNBT.js";
|
|
|
101
100
|
import "../chunks/chunk-BSOZW3FC.js";
|
|
102
101
|
import "../chunks/chunk-RJWPJCIB.js";
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|
103
102
|
import "../chunks/chunk-HOAIOEI7.js";
|
|
103
|
+
import "../chunks/chunk-DAEEMZ74.js";
|
|
104
|
+
import "../chunks/chunk-H2H4Y3TV.js";
|
|
104
105
|
import "../chunks/chunk-BLUEFYIR.js";
|
|
105
106
|
import "../chunks/chunk-2JL2JVZ2.js";
|
|
106
107
|
|
package/dist/figure.js
CHANGED
|
@@ -1,25 +1,24 @@
|
|
|
1
1
|
import {
|
|
2
2
|
figureSvg
|
|
3
|
-
} from "./chunks/chunk-
|
|
4
|
-
import "./chunks/chunk-
|
|
3
|
+
} from "./chunks/chunk-JPT44REW.js";
|
|
4
|
+
import "./chunks/chunk-V4YML3GR.js";
|
|
5
|
+
import "./chunks/chunk-KYTV5EAZ.js";
|
|
5
6
|
import "./chunks/chunk-4DMSPNYV.js";
|
|
6
7
|
import "./chunks/chunk-RBCE2OQH.js";
|
|
7
|
-
import "./chunks/chunk-
|
|
8
|
-
import "./chunks/chunk-IXLT3JJX.js";
|
|
8
|
+
import "./chunks/chunk-SVP2CQTA.js";
|
|
9
9
|
import "./chunks/chunk-JSUCGZ6K.js";
|
|
10
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export {
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