@jbrowse/plugin-linear-genome-view 2.10.0 → 2.10.1

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.
@@ -1,16 +1,8 @@
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  import React from 'react';
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- import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
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  import { LinearGenomeViewModel } from '..';
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- declare const Polygon: ({ model, overview, useOffset, }: {
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- model: LGV;
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- overview: Base1DViewModel;
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- useOffset?: boolean | undefined;
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- }) => React.JSX.Element | null;
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  type LGV = LinearGenomeViewModel;
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  declare const OverviewScalebar: ({ model, children, }: {
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  model: LGV;
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  children: React.ReactNode;
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  }) => React.JSX.Element;
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- export { Polygon };
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- export { default as Cytobands } from './Cytobands';
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  export default OverviewScalebar;
@@ -26,7 +26,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  return (mod && mod.__esModule) ? mod : { "default": mod };
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
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- exports.Cytobands = exports.Polygon = void 0;
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  const react_1 = __importStar(require("react"));
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  const material_1 = require("@mui/material");
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  const mui_1 = require("tss-react/mui");
@@ -38,9 +37,10 @@ const blockTypes_1 = require("@jbrowse/core/util/blockTypes");
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  // locals
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  const __1 = require("..");
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  const util_2 = require("../util");
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+ const util_3 = require("./util");
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  const OverviewRubberband_1 = __importDefault(require("./OverviewRubberband"));
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  const Cytobands_1 = __importDefault(require("./Cytobands"));
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- const util_3 = require("./util");
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+ const OverviewScalebarPolygon_1 = __importDefault(require("./OverviewScalebarPolygon"));
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  const wholeSeqSpacer = 2;
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  const useStyles = (0, mui_1.makeStyles)()(theme => ({
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  scalebar: {
@@ -94,56 +94,14 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
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  position: 'absolute',
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  },
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  }));
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- const Polygon = (0, mobx_react_1.observer)(function ({ model, overview, useOffset = true, }) {
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- const theme = (0, material_1.useTheme)();
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- const multiplier = Number(useOffset);
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- const { interRegionPaddingWidth, offsetPx, dynamicBlocks, cytobandOffset } = model;
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- const { contentBlocks, totalWidthPxWithoutBorders } = dynamicBlocks;
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- const { tertiary, primary } = theme.palette;
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- const polygonColor = tertiary ? tertiary.light : primary.light;
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- // catches possible null from at's below
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- if (!contentBlocks.length) {
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- return null;
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- }
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- const first = contentBlocks.at(0);
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- const last = contentBlocks.at(-1);
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- const topLeft = (overview.bpToPx({
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- ...first,
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- coord: first.reversed ? first.end : first.start,
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- }) || 0) +
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- cytobandOffset * multiplier;
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- const topRight = (overview.bpToPx({
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- ...last,
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- coord: last.reversed ? last.start : last.end,
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- }) || 0) +
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- cytobandOffset * multiplier;
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- const startPx = Math.max(0, -offsetPx);
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- const endPx = startPx +
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- totalWidthPxWithoutBorders +
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- (contentBlocks.length * interRegionPaddingWidth) / 2;
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- const points = [
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- [startPx, __1.HEADER_BAR_HEIGHT],
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- [endPx, __1.HEADER_BAR_HEIGHT],
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- [topRight, 0],
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- [topLeft, 0],
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- ];
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- return (react_1.default.createElement("polygon", { points: points.toString(), fill: (0, material_1.alpha)(polygonColor, 0.3), stroke: (0, material_1.alpha)(polygonColor, 0.8) }));
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- });
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- exports.Polygon = Polygon;
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  const OverviewBox = (0, mobx_react_1.observer)(function ({ scale, model, block, overview, }) {
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  const { classes, cx } = useStyles();
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  const theme = (0, material_1.useTheme)();
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  const { cytobandOffset, showCytobands } = model;
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- const { start, end, reversed, refName, assemblyName } = block;
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- const { majorPitch } = (0, util_2.chooseGridPitch)(scale, 120, 15);
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+ const { reversed, refName, assemblyName } = block;
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  const { assemblyManager } = (0, util_1.getSession)(model);
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  const assembly = assemblyManager.get(assemblyName);
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  const refNameColor = assembly === null || assembly === void 0 ? void 0 : assembly.getRefNameColor(refName);
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- const tickLabels = [];
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- for (let i = 0; i < Math.floor((end - start) / majorPitch); i++) {
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- const offsetLabel = (i + 1) * majorPitch;
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- tickLabels.push(reversed ? end - offsetLabel : start + offsetLabel);
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- }
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  const canDisplayCytobands = showCytobands && (0, util_3.getCytobands)(assembly, block.refName).length;
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  return (react_1.default.createElement("div", null,
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  react_1.default.createElement(material_1.Typography, { style: {
@@ -161,16 +119,28 @@ const OverviewBox = (0, mobx_react_1.observer)(function ({ scale, model, block,
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  width: block.widthPx,
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  borderColor: refNameColor,
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  } },
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- !canDisplayCytobands
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- ? tickLabels.map((tickLabel, labelIdx) => (react_1.default.createElement(material_1.Typography, { key: `${JSON.stringify(block)}-${tickLabel}-${labelIdx}`, className: classes.scalebarLabel, variant: "body2", style: {
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- left: ((labelIdx + 1) * majorPitch) / scale,
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- pointerEvents: 'none',
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- color: refNameColor,
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- } }, (0, util_1.getTickDisplayStr)(tickLabel, overview.bpPerPx))))
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- : null,
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+ !canDisplayCytobands ? (react_1.default.createElement(TickLabels, { model: model, overview: overview, scale: scale, block: block })) : null,
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  canDisplayCytobands ? (react_1.default.createElement("svg", { style: { width: '100%' } },
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  react_1.default.createElement(Cytobands_1.default, { overview: overview, assembly: assembly, block: block }))) : null)));
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  });
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+ const TickLabels = (0, mobx_react_1.observer)(function ({ block, scale, overview, model, }) {
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+ const { classes } = useStyles();
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+ const { start, end, reversed, refName, assemblyName } = block;
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+ const { majorPitch } = (0, util_2.chooseGridPitch)(scale, 120, 15);
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+ const { assemblyManager } = (0, util_1.getSession)(model);
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+ const assembly = assemblyManager.get(assemblyName);
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+ const refNameColor = assembly === null || assembly === void 0 ? void 0 : assembly.getRefNameColor(refName);
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+ const tickLabels = [];
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+ for (let i = 0; i < Math.floor((end - start) / majorPitch); i++) {
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+ const offsetLabel = (i + 1) * majorPitch;
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+ tickLabels.push(reversed ? end - offsetLabel : start + offsetLabel);
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+ }
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+ return tickLabels.map((tickLabel, labelIdx) => (react_1.default.createElement(material_1.Typography, { key: `${JSON.stringify(block)}-${tickLabel}-${labelIdx}`, className: classes.scalebarLabel, variant: "body2", style: {
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+ left: ((labelIdx + 1) * majorPitch) / scale,
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+ pointerEvents: 'none',
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+ color: refNameColor,
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+ } }, (0, util_1.getTickDisplayStr)(tickLabel, overview.bpPerPx))));
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+ });
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  const Scalebar = (0, mobx_react_1.observer)(function ({ model, scale, overview, }) {
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  const { classes } = useStyles();
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  const theme = (0, material_1.useTheme)();
@@ -235,9 +205,7 @@ const OverviewScalebar = (0, mobx_react_1.observer)(function ({ model, children,
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  react_1.default.createElement(OverviewRubberband_1.default, { model: model, overview: overview, ControlComponent: react_1.default.createElement(Scalebar, { model: model, overview: overview, scale: scale }) }),
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  react_1.default.createElement("div", { className: classes.overview },
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  react_1.default.createElement("svg", { height: __1.HEADER_BAR_HEIGHT, className: classes.overviewSvg },
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- react_1.default.createElement(Polygon, { model: model, overview: overview })),
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+ react_1.default.createElement(OverviewScalebarPolygon_1.default, { model: model, overview: overview })),
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  children)));
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  });
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- var Cytobands_2 = require("./Cytobands");
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- Object.defineProperty(exports, "Cytobands", { enumerable: true, get: function () { return __importDefault(Cytobands_2).default; } });
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  exports.default = OverviewScalebar;
@@ -0,0 +1,9 @@
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+ import React from 'react';
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+ import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
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+ import { LinearGenomeViewModel } from '..';
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+ declare const OverviewScalebarPolygon: ({ model, overview, useOffset, }: {
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+ model: LinearGenomeViewModel;
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+ overview: Base1DViewModel;
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+ useOffset?: boolean | undefined;
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+ }) => React.JSX.Element | null;
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+ export default OverviewScalebarPolygon;
@@ -0,0 +1,46 @@
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+ "use strict";
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+ var __importDefault = (this && this.__importDefault) || function (mod) {
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+ return (mod && mod.__esModule) ? mod : { "default": mod };
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+ };
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+ Object.defineProperty(exports, "__esModule", { value: true });
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+ const react_1 = __importDefault(require("react"));
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+ const material_1 = require("@mui/material");
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+ const mobx_react_1 = require("mobx-react");
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+ // locals
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+ const __1 = require("..");
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+ const OverviewScalebarPolygon = (0, mobx_react_1.observer)(function ({ model, overview, useOffset = true, }) {
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+ const theme = (0, material_1.useTheme)();
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+ const multiplier = Number(useOffset);
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+ const { interRegionPaddingWidth, offsetPx, dynamicBlocks, cytobandOffset } = model;
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+ const { contentBlocks, totalWidthPxWithoutBorders } = dynamicBlocks;
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+ const { tertiary, primary } = theme.palette;
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+ const polygonColor = tertiary ? tertiary.light : primary.light;
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+ // catches possible null from at's below
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+ if (!contentBlocks.length) {
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+ return null;
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+ }
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+ const first = contentBlocks.at(0);
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+ const last = contentBlocks.at(-1);
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+ const topLeft = (overview.bpToPx({
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+ ...first,
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+ coord: first.reversed ? first.end : first.start,
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+ }) || 0) +
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+ cytobandOffset * multiplier;
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+ const topRight = (overview.bpToPx({
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+ ...last,
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+ coord: last.reversed ? last.start : last.end,
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+ }) || 0) +
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+ cytobandOffset * multiplier;
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+ const startPx = Math.max(0, -offsetPx);
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+ const endPx = startPx +
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+ totalWidthPxWithoutBorders +
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+ (contentBlocks.length * interRegionPaddingWidth) / 2;
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+ const points = [
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+ [startPx, __1.HEADER_BAR_HEIGHT],
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+ [endPx, __1.HEADER_BAR_HEIGHT],
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+ [topRight, 0],
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+ [topLeft, 0],
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+ ];
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+ return (react_1.default.createElement("polygon", { points: points.toString(), fill: (0, material_1.alpha)(polygonColor, 0.3), stroke: (0, material_1.alpha)(polygonColor, 0.8) }));
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+ });
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+ exports.default = OverviewScalebarPolygon;
@@ -10,9 +10,9 @@ const material_1 = require("@mui/material");
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  // locals
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  const __1 = require("..");
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  const Cytobands_1 = __importDefault(require("../components/Cytobands"));
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- const OverviewScalebar_1 = require("../components/OverviewScalebar");
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  const SVGRuler_1 = __importDefault(require("./SVGRuler"));
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  const SVGScalebar_1 = __importDefault(require("./SVGScalebar"));
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+ const OverviewScalebarPolygon_1 = __importDefault(require("../components/OverviewScalebarPolygon"));
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  function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }) {
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  const { width, assemblyNames, showCytobands, displayedRegions } = model;
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  const { assemblyManager } = (0, util_1.getSession)(model);
@@ -49,7 +49,7 @@ function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }) {
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  react_1.default.createElement(Cytobands_1.default, { overview: overview, assembly: assembly, block: block }),
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  react_1.default.createElement("rect", { stroke: "red", fill: "rgb(255,0,0,0.1)", width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: __1.HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
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  react_1.default.createElement("g", { transform: `translate(0,${__1.HEADER_OVERVIEW_HEIGHT})` },
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- react_1.default.createElement(OverviewScalebar_1.Polygon, { overview: overview, model: model, useOffset: false })))) : null,
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+ react_1.default.createElement(OverviewScalebarPolygon_1.default, { overview: overview, model: model, useOffset: false })))) : null,
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  react_1.default.createElement("g", { transform: `translate(0 ${fontSize + y})` },
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  react_1.default.createElement(SVGScalebar_1.default, { model: model, fontSize: fontSize })),
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  react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight + y})` },
@@ -1,16 +1,8 @@
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  import React from 'react';
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- import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
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  import { LinearGenomeViewModel } from '..';
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- declare const Polygon: ({ model, overview, useOffset, }: {
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- model: LGV;
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- overview: Base1DViewModel;
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- useOffset?: boolean | undefined;
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- }) => React.JSX.Element | null;
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  type LGV = LinearGenomeViewModel;
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  declare const OverviewScalebar: ({ model, children, }: {
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  model: LGV;
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  children: React.ReactNode;
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  }) => React.JSX.Element;
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- export { Polygon };
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- export { default as Cytobands } from './Cytobands';
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  export default OverviewScalebar;
@@ -9,9 +9,10 @@ import { ContentBlock } from '@jbrowse/core/util/blockTypes';
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  // locals
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  import { HEADER_BAR_HEIGHT, HEADER_OVERVIEW_HEIGHT, } from '..';
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  import { chooseGridPitch } from '../util';
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+ import { getCytobands } from './util';
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  import OverviewRubberband from './OverviewRubberband';
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  import Cytobands from './Cytobands';
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- import { getCytobands } from './util';
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+ import OverviewScalebarPolygon from './OverviewScalebarPolygon';
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  const wholeSeqSpacer = 2;
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  const useStyles = makeStyles()(theme => ({
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  scalebar: {
@@ -65,55 +66,14 @@ const useStyles = makeStyles()(theme => ({
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  position: 'absolute',
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  },
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  }));
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- const Polygon = observer(function ({ model, overview, useOffset = true, }) {
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- const theme = useTheme();
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- const multiplier = Number(useOffset);
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- const { interRegionPaddingWidth, offsetPx, dynamicBlocks, cytobandOffset } = model;
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- const { contentBlocks, totalWidthPxWithoutBorders } = dynamicBlocks;
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- const { tertiary, primary } = theme.palette;
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- const polygonColor = tertiary ? tertiary.light : primary.light;
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- // catches possible null from at's below
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- if (!contentBlocks.length) {
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- return null;
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- }
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- const first = contentBlocks.at(0);
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- const last = contentBlocks.at(-1);
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- const topLeft = (overview.bpToPx({
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- ...first,
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- coord: first.reversed ? first.end : first.start,
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- }) || 0) +
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- cytobandOffset * multiplier;
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- const topRight = (overview.bpToPx({
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- ...last,
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- coord: last.reversed ? last.start : last.end,
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- }) || 0) +
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- cytobandOffset * multiplier;
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- const startPx = Math.max(0, -offsetPx);
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- const endPx = startPx +
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- totalWidthPxWithoutBorders +
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- (contentBlocks.length * interRegionPaddingWidth) / 2;
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- const points = [
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- [startPx, HEADER_BAR_HEIGHT],
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- [endPx, HEADER_BAR_HEIGHT],
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- [topRight, 0],
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- [topLeft, 0],
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- ];
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- return (React.createElement("polygon", { points: points.toString(), fill: alpha(polygonColor, 0.3), stroke: alpha(polygonColor, 0.8) }));
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- });
103
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  const OverviewBox = observer(function ({ scale, model, block, overview, }) {
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  const { classes, cx } = useStyles();
105
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  const theme = useTheme();
106
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  const { cytobandOffset, showCytobands } = model;
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- const { start, end, reversed, refName, assemblyName } = block;
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- const { majorPitch } = chooseGridPitch(scale, 120, 15);
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+ const { reversed, refName, assemblyName } = block;
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  const { assemblyManager } = getSession(model);
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  const assembly = assemblyManager.get(assemblyName);
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  const refNameColor = assembly === null || assembly === void 0 ? void 0 : assembly.getRefNameColor(refName);
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- const tickLabels = [];
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- for (let i = 0; i < Math.floor((end - start) / majorPitch); i++) {
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- const offsetLabel = (i + 1) * majorPitch;
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- tickLabels.push(reversed ? end - offsetLabel : start + offsetLabel);
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- }
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  const canDisplayCytobands = showCytobands && getCytobands(assembly, block.refName).length;
118
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  return (React.createElement("div", null,
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  React.createElement(Typography, { style: {
@@ -131,16 +91,28 @@ const OverviewBox = observer(function ({ scale, model, block, overview, }) {
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  width: block.widthPx,
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  borderColor: refNameColor,
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  } },
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- !canDisplayCytobands
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- ? tickLabels.map((tickLabel, labelIdx) => (React.createElement(Typography, { key: `${JSON.stringify(block)}-${tickLabel}-${labelIdx}`, className: classes.scalebarLabel, variant: "body2", style: {
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- left: ((labelIdx + 1) * majorPitch) / scale,
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- pointerEvents: 'none',
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- color: refNameColor,
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- } }, getTickDisplayStr(tickLabel, overview.bpPerPx))))
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- : null,
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+ !canDisplayCytobands ? (React.createElement(TickLabels, { model: model, overview: overview, scale: scale, block: block })) : null,
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  canDisplayCytobands ? (React.createElement("svg", { style: { width: '100%' } },
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  React.createElement(Cytobands, { overview: overview, assembly: assembly, block: block }))) : null)));
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  });
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+ const TickLabels = observer(function ({ block, scale, overview, model, }) {
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+ const { classes } = useStyles();
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+ const { start, end, reversed, refName, assemblyName } = block;
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+ const { majorPitch } = chooseGridPitch(scale, 120, 15);
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+ const { assemblyManager } = getSession(model);
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+ const assembly = assemblyManager.get(assemblyName);
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+ const refNameColor = assembly === null || assembly === void 0 ? void 0 : assembly.getRefNameColor(refName);
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+ const tickLabels = [];
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+ for (let i = 0; i < Math.floor((end - start) / majorPitch); i++) {
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+ const offsetLabel = (i + 1) * majorPitch;
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+ tickLabels.push(reversed ? end - offsetLabel : start + offsetLabel);
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+ }
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+ return tickLabels.map((tickLabel, labelIdx) => (React.createElement(Typography, { key: `${JSON.stringify(block)}-${tickLabel}-${labelIdx}`, className: classes.scalebarLabel, variant: "body2", style: {
111
+ left: ((labelIdx + 1) * majorPitch) / scale,
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+ pointerEvents: 'none',
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+ color: refNameColor,
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+ } }, getTickDisplayStr(tickLabel, overview.bpPerPx))));
115
+ });
144
116
  const Scalebar = observer(function ({ model, scale, overview, }) {
145
117
  const { classes } = useStyles();
146
118
  const theme = useTheme();
@@ -205,9 +177,7 @@ const OverviewScalebar = observer(function ({ model, children, }) {
205
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  React.createElement(OverviewRubberband, { model: model, overview: overview, ControlComponent: React.createElement(Scalebar, { model: model, overview: overview, scale: scale }) }),
206
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  React.createElement("div", { className: classes.overview },
207
179
  React.createElement("svg", { height: HEADER_BAR_HEIGHT, className: classes.overviewSvg },
208
- React.createElement(Polygon, { model: model, overview: overview })),
180
+ React.createElement(OverviewScalebarPolygon, { model: model, overview: overview })),
209
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  children)));
210
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  });
211
- export { Polygon };
212
- export { default as Cytobands } from './Cytobands';
213
183
  export default OverviewScalebar;
@@ -0,0 +1,9 @@
1
+ import React from 'react';
2
+ import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
3
+ import { LinearGenomeViewModel } from '..';
4
+ declare const OverviewScalebarPolygon: ({ model, overview, useOffset, }: {
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+ model: LinearGenomeViewModel;
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+ overview: Base1DViewModel;
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+ useOffset?: boolean | undefined;
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+ }) => React.JSX.Element | null;
9
+ export default OverviewScalebarPolygon;
@@ -0,0 +1,41 @@
1
+ import React from 'react';
2
+ import { useTheme, alpha } from '@mui/material';
3
+ import { observer } from 'mobx-react';
4
+ // locals
5
+ import { HEADER_BAR_HEIGHT } from '..';
6
+ const OverviewScalebarPolygon = observer(function ({ model, overview, useOffset = true, }) {
7
+ const theme = useTheme();
8
+ const multiplier = Number(useOffset);
9
+ const { interRegionPaddingWidth, offsetPx, dynamicBlocks, cytobandOffset } = model;
10
+ const { contentBlocks, totalWidthPxWithoutBorders } = dynamicBlocks;
11
+ const { tertiary, primary } = theme.palette;
12
+ const polygonColor = tertiary ? tertiary.light : primary.light;
13
+ // catches possible null from at's below
14
+ if (!contentBlocks.length) {
15
+ return null;
16
+ }
17
+ const first = contentBlocks.at(0);
18
+ const last = contentBlocks.at(-1);
19
+ const topLeft = (overview.bpToPx({
20
+ ...first,
21
+ coord: first.reversed ? first.end : first.start,
22
+ }) || 0) +
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+ cytobandOffset * multiplier;
24
+ const topRight = (overview.bpToPx({
25
+ ...last,
26
+ coord: last.reversed ? last.start : last.end,
27
+ }) || 0) +
28
+ cytobandOffset * multiplier;
29
+ const startPx = Math.max(0, -offsetPx);
30
+ const endPx = startPx +
31
+ totalWidthPxWithoutBorders +
32
+ (contentBlocks.length * interRegionPaddingWidth) / 2;
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+ const points = [
34
+ [startPx, HEADER_BAR_HEIGHT],
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+ [endPx, HEADER_BAR_HEIGHT],
36
+ [topRight, 0],
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+ [topLeft, 0],
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+ ];
39
+ return (React.createElement("polygon", { points: points.toString(), fill: alpha(polygonColor, 0.3), stroke: alpha(polygonColor, 0.8) }));
40
+ });
41
+ export default OverviewScalebarPolygon;
@@ -5,9 +5,9 @@ import { useTheme } from '@mui/material';
5
5
  // locals
6
6
  import { HEADER_OVERVIEW_HEIGHT } from '..';
7
7
  import Cytobands from '../components/Cytobands';
8
- import { Polygon } from '../components/OverviewScalebar';
9
8
  import SVGRuler from './SVGRuler';
10
9
  import SVGScalebar from './SVGScalebar';
10
+ import OverviewScalebarPolygon from '../components/OverviewScalebarPolygon';
11
11
  export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }) {
12
12
  const { width, assemblyNames, showCytobands, displayedRegions } = model;
13
13
  const { assemblyManager } = getSession(model);
@@ -44,7 +44,7 @@ export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight
44
44
  React.createElement(Cytobands, { overview: overview, assembly: assembly, block: block }),
45
45
  React.createElement("rect", { stroke: "red", fill: "rgb(255,0,0,0.1)", width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
46
46
  React.createElement("g", { transform: `translate(0,${HEADER_OVERVIEW_HEIGHT})` },
47
- React.createElement(Polygon, { overview: overview, model: model, useOffset: false })))) : null,
47
+ React.createElement(OverviewScalebarPolygon, { overview: overview, model: model, useOffset: false })))) : null,
48
48
  React.createElement("g", { transform: `translate(0 ${fontSize + y})` },
49
49
  React.createElement(SVGScalebar, { model: model, fontSize: fontSize })),
50
50
  React.createElement("g", { transform: `translate(0 ${rulerHeight + y})` },
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-linear-genome-view",
3
- "version": "2.10.0",
3
+ "version": "2.10.1",
4
4
  "description": "JBrowse 2 linear genome view",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -63,5 +63,5 @@
63
63
  "access": "public"
64
64
  },
65
65
  "module": "esm/index.js",
66
- "gitHead": "223d8bfb68fd1bacaf22852639ad5920f1b7f43b"
66
+ "gitHead": "442b5f87efddfdf4ccf520b4d9dd01ddd370cb07"
67
67
  }