@jbrowse/plugin-sequence 2.6.2 → 2.7.0

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.
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 @@
1
1
  import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
2
2
  export default class extends BaseAdapter implements RegionsAdapter {
3
- protected setupP?: Promise<{
4
- [key: string]: number;
5
- }>;
3
+ protected setupP?: Promise<Record<string, number>>;
6
4
  setupPre(): Promise<{
7
5
  [k: string]: number;
8
6
  }>;
9
- setup(): Promise<{
10
- [key: string]: number;
11
- }>;
7
+ setup(): Promise<Record<string, number>>;
12
8
  getRegions(): Promise<{
13
9
  refName: string;
14
10
  start: number;
package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -1,7 +1,8 @@
1
1
  import React from 'react';
2
2
  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
3
3
  import { Feature, Region } from '@jbrowse/core/util';
4
- declare function Sequence(props: {
4
+ import { Theme } from '@mui/material';
5
+ declare const DivSequenceRendering: (props: {
5
6
  exportSVG?: {
6
7
  rasterizeLayers: boolean;
7
8
  };
@@ -9,10 +10,9 @@ declare function Sequence(props: {
9
10
  regions: Region[];
10
11
  bpPerPx: number;
11
12
  config: AnyConfigurationModel;
12
- theme?: any;
13
+ theme?: Theme;
13
14
  showForward?: boolean;
14
15
  showReverse?: boolean;
15
16
  showTranslation?: boolean;
16
- }): React.JSX.Element;
17
- declare const _default: typeof Sequence;
18
- export default _default;
17
+ }) => React.JSX.Element;
18
+ export default DivSequenceRendering;
package/dist/DivSequenceRenderer/components/DivSequenceRendering.js CHANGED
@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
- /* eslint-disable @typescript-eslint/no-explicit-any */
7
6
  const react_1 = __importDefault(require("react"));
8
7
  const ui_1 = require("@jbrowse/core/ui");
9
8
  const mobx_react_1 = require("mobx-react");
@@ -53,6 +52,7 @@ function DNA(props) {
53
52
  const len = feature.get('end') - feature.get('start');
54
53
  const w = Math.max((rightPx - leftPx) / len, 0.8);
55
54
  return (react_1.default.createElement(react_1.default.Fragment, null, seq.split('').map((letter, index) => {
55
+ // @ts-expect-error
56
56
  const color = theme.palette.bases[letter.toUpperCase()];
57
57
  const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
58
58
  return (react_1.default.createElement(react_1.default.Fragment, { key: index },
@@ -60,7 +60,7 @@ function DNA(props) {
60
60
  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));
61
61
  })));
62
62
  }
63
- const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) => {
63
+ function SequenceSVG({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) {
64
64
  const [region] = regions;
65
65
  const theme = (0, ui_1.createJBrowseTheme)(configTheme);
66
66
  const codonTable = (0, util_1.generateCodonTable)(util_1.defaultCodonTable);
@@ -85,16 +85,16 @@ const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showRe
85
85
  showTranslation && (region.reversed ? showForward : showReverse)
86
86
  ? [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 })))
87
87
  : null));
88
- };
89
- const Wrapper = ({ exportSVG, width, totalHeight, children, }) => {
88
+ }
89
+ function Wrapper({ exportSVG, width, totalHeight, children, }) {
90
90
  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));
91
- };
92
- function Sequence(props) {
91
+ }
92
+ const DivSequenceRendering = (0, mobx_react_1.observer)(function (props) {
93
93
  const { regions, bpPerPx } = props;
94
94
  const [region] = regions;
95
95
  const width = (region.end - region.start) / bpPerPx;
96
96
  const totalHeight = 200;
97
97
  return (react_1.default.createElement(Wrapper, { ...props, totalHeight: totalHeight, width: width },
98
98
  react_1.default.createElement(SequenceSVG, { ...props })));
99
- }
100
- exports.default = (0, mobx_react_1.observer)(Sequence);
99
+ });
100
+ exports.default = DivSequenceRendering;
package/esm/ChromSizesAdapter/ChromSizesAdapter.d.ts CHANGED
@@ -1,14 +1,10 @@
1
1
  import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
2
2
  export default class extends BaseAdapter implements RegionsAdapter {
3
- protected setupP?: Promise<{
4
- [key: string]: number;
5
- }>;
3
+ protected setupP?: Promise<Record<string, number>>;
6
4
  setupPre(): Promise<{
7
5
  [k: string]: number;
8
6
  }>;
9
- setup(): Promise<{
10
- [key: string]: number;
11
- }>;
7
+ setup(): Promise<Record<string, number>>;
12
8
  getRegions(): Promise<{
13
9
  refName: string;
14
10
  start: number;
package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -1,7 +1,8 @@
1
1
  import React from 'react';
2
2
  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
3
3
  import { Feature, Region } from '@jbrowse/core/util';
4
- declare function Sequence(props: {
4
+ import { Theme } from '@mui/material';
5
+ declare const DivSequenceRendering: (props: {
5
6
  exportSVG?: {
6
7
  rasterizeLayers: boolean;
7
8
  };
@@ -9,10 +10,9 @@ declare function Sequence(props: {
9
10
  regions: Region[];
10
11
  bpPerPx: number;
11
12
  config: AnyConfigurationModel;
12
- theme?: any;
13
+ theme?: Theme;
13
14
  showForward?: boolean;
14
15
  showReverse?: boolean;
15
16
  showTranslation?: boolean;
16
- }): React.JSX.Element;
17
- declare const _default: typeof Sequence;
18
- export default _default;
17
+ }) => React.JSX.Element;
18
+ export default DivSequenceRendering;
package/esm/DivSequenceRenderer/components/DivSequenceRendering.js CHANGED
@@ -1,4 +1,3 @@
1
- /* eslint-disable @typescript-eslint/no-explicit-any */
2
1
  import React from 'react';
3
2
  import { createJBrowseTheme } from '@jbrowse/core/ui';
4
3
  import { observer } from 'mobx-react';
@@ -48,6 +47,7 @@ function DNA(props) {
48
47
  const len = feature.get('end') - feature.get('start');
49
48
  const w = Math.max((rightPx - leftPx) / len, 0.8);
50
49
  return (React.createElement(React.Fragment, null, seq.split('').map((letter, index) => {
50
+ // @ts-expect-error
51
51
  const color = theme.palette.bases[letter.toUpperCase()];
52
52
  const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
53
53
  return (React.createElement(React.Fragment, { key: index },
@@ -55,7 +55,7 @@ function DNA(props) {
55
55
  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));
56
56
  })));
57
57
  }
58
- const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) => {
58
+ function SequenceSVG({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) {
59
59
  const [region] = regions;
60
60
  const theme = createJBrowseTheme(configTheme);
61
61
  const codonTable = generateCodonTable(defaultCodonTable);
@@ -80,16 +80,16 @@ const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showRe
80
80
  showTranslation && (region.reversed ? showForward : showReverse)
81
81
  ? [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 })))
82
82
  : null));
83
- };
84
- const Wrapper = ({ exportSVG, width, totalHeight, children, }) => {
83
+ }
84
+ function Wrapper({ exportSVG, width, totalHeight, children, }) {
85
85
  return exportSVG ? (React.createElement(React.Fragment, null, children)) : (React.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: { width, height: totalHeight } }, children));
86
- };
87
- function Sequence(props) {
86
+ }
87
+ const DivSequenceRendering = observer(function (props) {
88
88
  const { regions, bpPerPx } = props;
89
89
  const [region] = regions;
90
90
  const width = (region.end - region.start) / bpPerPx;
91
91
  const totalHeight = 200;
92
92
  return (React.createElement(Wrapper, { ...props, totalHeight: totalHeight, width: width },
93
93
  React.createElement(SequenceSVG, { ...props })));
94
- }
95
- export default observer(Sequence);
94
+ });
95
+ export default DivSequenceRendering;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-sequence",
3
- "version": "2.6.2",
3
+ "version": "2.7.0",
4
4
  "description": "JBrowse 2 sequence adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -46,7 +46,7 @@
46
46
  "@jbrowse/plugin-wiggle": "^2.0.0",
47
47
  "@mui/material": "^5.0.0",
48
48
  "mobx": "^6.0.0",
49
- "mobx-react": "^7.0.0",
49
+ "mobx-react": "^9.0.0",
50
50
  "mobx-state-tree": "^5.0.0",
51
51
  "react": ">=16.8.0",
52
52
  "rxjs": "^7.0.0"
@@ -57,5 +57,5 @@
57
57
  "distModule": "esm/index.js",
58
58
  "srcModule": "src/index.ts",
59
59
  "module": "esm/index.js",
60
- "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
60
+ "gitHead": "dbe7fb1af01fc89f833d2744635eb44a17365b41"
61
61
  }