@jbrowse/plugin-sequence 2.6.3 → 2.7.1

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Files changed (7) hide show
  1. package/dist/ChromSizesAdapter/ChromSizesAdapter.d.ts +2 -6
  2. package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts +5 -5
  3. package/dist/DivSequenceRenderer/components/DivSequenceRendering.js +8 -8
  4. package/esm/ChromSizesAdapter/ChromSizesAdapter.d.ts +2 -6
  5. package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts +5 -5
  6. package/esm/DivSequenceRenderer/components/DivSequenceRendering.js +8 -8
  7. package/package.json +3 -3
package/dist/ChromSizesAdapter/ChromSizesAdapter.d.ts CHANGED
@@ -1,14 +1,10 @@
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  import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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  export default class extends BaseAdapter implements RegionsAdapter {
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- protected setupP?: Promise<{
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- [key: string]: number;
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- }>;
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+ protected setupP?: Promise<Record<string, number>>;
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  setupPre(): Promise<{
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  [k: string]: number;
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  }>;
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- setup(): Promise<{
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- [key: string]: number;
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- }>;
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+ setup(): Promise<Record<string, number>>;
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  getRegions(): Promise<{
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  refName: string;
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  start: number;
package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -1,7 +1,8 @@
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  import React from 'react';
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  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  import { Feature, Region } from '@jbrowse/core/util';
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- declare function Sequence(props: {
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+ import { Theme } from '@mui/material';
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+ declare const DivSequenceRendering: (props: {
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  exportSVG?: {
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  rasterizeLayers: boolean;
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  };
@@ -9,10 +10,9 @@ declare function Sequence(props: {
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  regions: Region[];
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  bpPerPx: number;
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  config: AnyConfigurationModel;
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- theme?: any;
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+ theme?: Theme;
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  showForward?: boolean;
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  showReverse?: boolean;
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  showTranslation?: boolean;
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- }): React.JSX.Element;
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- declare const _default: typeof Sequence;
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- export default _default;
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+ }) => React.JSX.Element;
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+ export default DivSequenceRendering;
package/dist/DivSequenceRenderer/components/DivSequenceRendering.js CHANGED
@@ -3,7 +3,6 @@ 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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- /* eslint-disable @typescript-eslint/no-explicit-any */
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  const react_1 = __importDefault(require("react"));
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  const ui_1 = require("@jbrowse/core/ui");
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  const mobx_react_1 = require("mobx-react");
@@ -53,6 +52,7 @@ function DNA(props) {
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  const len = feature.get('end') - feature.get('start');
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  const w = Math.max((rightPx - leftPx) / len, 0.8);
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  return (react_1.default.createElement(react_1.default.Fragment, null, seq.split('').map((letter, index) => {
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+ // @ts-expect-error
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  const color = theme.palette.bases[letter.toUpperCase()];
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  const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
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  return (react_1.default.createElement(react_1.default.Fragment, { key: index },
@@ -60,7 +60,7 @@ function DNA(props) {
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  render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ? theme.palette.getContrastText(color.main) : 'black' }, letter)) : null));
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  })));
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  }
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- const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) => {
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+ function SequenceSVG({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) {
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  const [region] = regions;
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  const theme = (0, ui_1.createJBrowseTheme)(configTheme);
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  const codonTable = (0, util_1.generateCodonTable)(util_1.defaultCodonTable);
@@ -85,16 +85,16 @@ const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showRe
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  showTranslation && (region.reversed ? showForward : showReverse)
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  ? [0, -1, -2].map(index => (react_1.default.createElement(Translation, { key: `rev-translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: !region.reversed })))
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  : null));
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- };
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- const Wrapper = ({ exportSVG, width, totalHeight, children, }) => {
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+ }
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+ function Wrapper({ exportSVG, width, totalHeight, children, }) {
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  return exportSVG ? (react_1.default.createElement(react_1.default.Fragment, null, children)) : (react_1.default.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: { width, height: totalHeight } }, children));
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- };
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- function Sequence(props) {
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+ }
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+ const DivSequenceRendering = (0, mobx_react_1.observer)(function (props) {
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  const { regions, bpPerPx } = props;
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  const [region] = regions;
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  const width = (region.end - region.start) / bpPerPx;
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  const totalHeight = 200;
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  return (react_1.default.createElement(Wrapper, { ...props, totalHeight: totalHeight, width: width },
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  react_1.default.createElement(SequenceSVG, { ...props })));
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- }
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- exports.default = (0, mobx_react_1.observer)(Sequence);
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+ });
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+ exports.default = DivSequenceRendering;
package/esm/ChromSizesAdapter/ChromSizesAdapter.d.ts CHANGED
@@ -1,14 +1,10 @@
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  import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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  export default class extends BaseAdapter implements RegionsAdapter {
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- protected setupP?: Promise<{
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- [key: string]: number;
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- }>;
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+ protected setupP?: Promise<Record<string, number>>;
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  setupPre(): Promise<{
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  [k: string]: number;
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  }>;
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- setup(): Promise<{
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- [key: string]: number;
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- }>;
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+ setup(): Promise<Record<string, number>>;
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  getRegions(): Promise<{
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  refName: string;
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  start: number;
package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -1,7 +1,8 @@
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  import React from 'react';
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  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  import { Feature, Region } from '@jbrowse/core/util';
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- declare function Sequence(props: {
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+ import { Theme } from '@mui/material';
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+ declare const DivSequenceRendering: (props: {
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  exportSVG?: {
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  rasterizeLayers: boolean;
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  };
@@ -9,10 +10,9 @@ declare function Sequence(props: {
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  regions: Region[];
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  bpPerPx: number;
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  config: AnyConfigurationModel;
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- theme?: any;
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+ theme?: Theme;
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  showForward?: boolean;
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  showReverse?: boolean;
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  showTranslation?: boolean;
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- }): React.JSX.Element;
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- declare const _default: typeof Sequence;
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- export default _default;
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+ }) => React.JSX.Element;
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+ export default DivSequenceRendering;
package/esm/DivSequenceRenderer/components/DivSequenceRendering.js CHANGED
@@ -1,4 +1,3 @@
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- /* eslint-disable @typescript-eslint/no-explicit-any */
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  import React from 'react';
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  import { createJBrowseTheme } from '@jbrowse/core/ui';
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  import { observer } from 'mobx-react';
@@ -48,6 +47,7 @@ function DNA(props) {
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  const len = feature.get('end') - feature.get('start');
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  const w = Math.max((rightPx - leftPx) / len, 0.8);
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  return (React.createElement(React.Fragment, null, seq.split('').map((letter, index) => {
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+ // @ts-expect-error
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  const color = theme.palette.bases[letter.toUpperCase()];
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  const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
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  return (React.createElement(React.Fragment, { key: index },
@@ -55,7 +55,7 @@ function DNA(props) {
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  render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ? theme.palette.getContrastText(color.main) : 'black' }, letter)) : null));
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  })));
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  }
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- const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) => {
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+ function SequenceSVG({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) {
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  const [region] = regions;
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  const theme = createJBrowseTheme(configTheme);
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  const codonTable = generateCodonTable(defaultCodonTable);
@@ -80,16 +80,16 @@ const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showRe
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  showTranslation && (region.reversed ? showForward : showReverse)
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  ? [0, -1, -2].map(index => (React.createElement(Translation, { key: `rev-translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: !region.reversed })))
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  : null));
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- };
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- const Wrapper = ({ exportSVG, width, totalHeight, children, }) => {
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+ }
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+ function Wrapper({ exportSVG, width, totalHeight, children, }) {
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  return exportSVG ? (React.createElement(React.Fragment, null, children)) : (React.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: { width, height: totalHeight } }, children));
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- };
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- function Sequence(props) {
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+ }
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+ const DivSequenceRendering = observer(function (props) {
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  const { regions, bpPerPx } = props;
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  const [region] = regions;
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  const width = (region.end - region.start) / bpPerPx;
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  const totalHeight = 200;
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  return (React.createElement(Wrapper, { ...props, totalHeight: totalHeight, width: width },
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  React.createElement(SequenceSVG, { ...props })));
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- }
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- export default observer(Sequence);
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+ });
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+ export default DivSequenceRendering;
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-sequence",
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- "version": "2.6.3",
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+ "version": "2.7.1",
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  "description": "JBrowse 2 sequence adapters, tracks, etc.",
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  "keywords": [
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  "jbrowse",
@@ -46,7 +46,7 @@
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  "@jbrowse/plugin-wiggle": "^2.0.0",
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  "@mui/material": "^5.0.0",
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  "mobx": "^6.0.0",
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- "mobx-react": "^7.0.0",
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+ "mobx-react": "^9.0.0",
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  "mobx-state-tree": "^5.0.0",
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  "react": ">=16.8.0",
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  "rxjs": "^7.0.0"
@@ -57,5 +57,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
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- "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
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+ "gitHead": "2cda1611eebd12517f2a3cfc1b612face27005d4"
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  }