@jbrowse/plugin-variants 3.4.0 → 3.5.1

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Files changed (19) hide show
  1. package/dist/LinearVariantDisplay/model.d.ts +2 -1
  2. package/dist/MultiLinearVariantDisplay/model.d.ts +2 -1
  3. package/dist/MultiLinearVariantMatrixDisplay/model.d.ts +2 -1
  4. package/dist/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js +18 -52
  5. package/dist/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.d.ts +5 -0
  6. package/dist/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.js +46 -0
  7. package/dist/shared/MultiVariantBaseModel.d.ts +2 -1
  8. package/dist/shared/SharedVariantMixin.d.ts +2 -1
  9. package/dist/shared/components/SourcesDataGrid.js +1 -1
  10. package/esm/LinearVariantDisplay/model.d.ts +2 -1
  11. package/esm/MultiLinearVariantDisplay/model.d.ts +2 -1
  12. package/esm/MultiLinearVariantMatrixDisplay/model.d.ts +2 -1
  13. package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js +19 -53
  14. package/esm/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.d.ts +5 -0
  15. package/esm/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.js +43 -0
  16. package/esm/shared/MultiVariantBaseModel.d.ts +2 -1
  17. package/esm/shared/SharedVariantMixin.d.ts +2 -1
  18. package/esm/shared/components/SourcesDataGrid.js +1 -1
  19. package/package.json +7 -7
package/dist/LinearVariantDisplay/model.d.ts CHANGED
@@ -191,6 +191,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
191
191
  readonly renderDelay: number;
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  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
193
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  readonly selectedFeatureId: string | undefined;
194
+ copyInfoToClipboard(feature: Feature): void;
194
195
  } & {
195
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  readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
196
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  readonly featureUnderMouse: Feature | undefined;
@@ -200,7 +201,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
200
201
  } & {
201
202
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
202
203
  deleteBlock(key: string): void;
203
- selectFeature(feature: Feature): Promise<void>;
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+ selectFeature(feature: Feature): void;
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205
  navToFeature(feature: Feature): void;
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206
  clearFeatureSelection(): void;
206
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  setFeatureIdUnderMouse(feature?: string): void;
package/dist/MultiLinearVariantDisplay/model.d.ts CHANGED
@@ -199,6 +199,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
199
199
  readonly renderDelay: number;
200
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  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
201
201
  readonly selectedFeatureId: string | undefined;
202
+ copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
202
203
  } & {
203
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  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
204
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  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -208,7 +209,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
208
209
  } & {
209
210
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
210
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  deleteBlock(key: string): void;
211
- selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
212
+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
212
213
  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
213
214
  clearFeatureSelection(): void;
214
215
  setFeatureIdUnderMouse(feature?: string): void;
package/dist/MultiLinearVariantMatrixDisplay/model.d.ts CHANGED
@@ -199,6 +199,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
199
199
  readonly renderDelay: number;
200
200
  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
201
201
  readonly selectedFeatureId: string | undefined;
202
+ copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
202
203
  } & {
203
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  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
204
205
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -208,7 +209,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
208
209
  } & {
209
210
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
210
211
  deleteBlock(key: string): void;
211
- selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
212
+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
212
213
  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
213
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  clearFeatureSelection(): void;
214
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  setFeatureIdUnderMouse(feature?: string): void;
package/dist/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js CHANGED
@@ -16,57 +16,19 @@ const x_data_grid_1 = require("@mui/x-data-grid");
16
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  const Checkbox2_1 = __importDefault(require("../Checkbox2"));
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  const VariantGenotypeFrequencyTable_1 = __importDefault(require("./VariantGenotypeFrequencyTable"));
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  const VariantSampleFilters_1 = __importDefault(require("./VariantSampleFilters"));
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- const util_2 = require("./util");
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- const util_3 = require("../../VcfFeature/util");
19
+ const getSampleGridRows_1 = require("./getSampleGridRows");
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  function VariantSampleGrid(props) {
22
- var _a;
23
21
  const { feature, descriptions = {} } = props;
24
22
  const [filter, setFilter] = (0, react_1.useState)({});
25
- const [showOnlyGenotypeColumns, setShowOnlyGenotypeColumns] = (0, react_1.useState)(true);
23
+ const [columnDisplayMode, setColumnDisplayMode] = (0, react_1.useState)('all');
26
24
  const [showFilters, setShowFilters] = (0, react_1.useState)(false);
27
25
  const samples = (feature.samples || {});
28
26
  const ALT = feature.ALT;
29
27
  const REF = feature.REF;
30
- const preFilteredRows = Object.entries(samples).map(([key, val]) => {
31
- var _a, _b;
32
- return [
33
- key,
34
- {
35
- ...val,
36
- GT: `${(_a = val.GT) === null || _a === void 0 ? void 0 : _a[0]}`,
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- genotype: (0, util_3.makeSimpleAltString)(`${(_b = val.GT) === null || _b === void 0 ? void 0 : _b[0]}`, REF, ALT),
38
- },
39
- ];
40
- });
41
- let error;
42
- let rows = [];
43
- const filters = Object.keys(filter);
44
- try {
45
- rows = preFilteredRows
46
- .map(([key, val]) => {
47
- return {
48
- ...Object.fromEntries(Object.entries(val).map(([formatField, formatValue]) => [
49
- formatField,
50
- formatValue,
51
- ])),
52
- sample: key,
53
- id: key,
54
- };
55
- })
56
- .filter(row => filters.length
57
- ? filters.every(key => {
58
- const currFilter = filter[key];
59
- return currFilter
60
- ? new RegExp(currFilter, 'i').exec(row[key])
61
- : true;
62
- })
63
- : true);
64
- }
65
- catch (e) {
66
- console.error(e);
67
- error = e;
68
- }
69
- const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
28
+ const { rows, error } = (0, getSampleGridRows_1.getSampleGridRows)(samples, REF, ALT, filter);
29
+ const colKeySet = new Set(['sample', ...Object.keys(rows[0] || {})]);
30
+ colKeySet.delete('id');
31
+ const keys = [...colKeySet];
70
32
  const widths = keys.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e])));
71
33
  const columns = keys.map((field, index) => {
72
34
  var _a, _b;
@@ -76,13 +38,17 @@ function VariantSampleGrid(props) {
76
38
  width: widths[index],
77
39
  });
78
40
  });
79
- const s1 = new Set(['sample', 'GT', 'genotype']);
80
- const s2 = new Set(keys);
81
- return !preFilteredRows.length ? null : ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(BaseCard_1.default, { ...props, title: "Genotype frequencies", children: (0, jsx_runtime_1.jsx)(ErrorBoundary_1.ErrorBoundary, { FallbackComponent: ui_1.ErrorMessage, children: (0, jsx_runtime_1.jsx)(VariantGenotypeFrequencyTable_1.default, { rows: rows }) }) }), (0, jsx_runtime_1.jsxs)(BaseCard_1.default, { ...props, title: "Samples", children: [error ? (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: `${error}` }) : null, (0, jsx_runtime_1.jsx)(Checkbox2_1.default, { label: "Show filters", checked: showFilters, onChange: event => {
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- setShowFilters(event.target.checked);
83
- } }), (0, util_2.areSetsEqual)(s1, s2) ? null : ((0, jsx_runtime_1.jsx)(Checkbox2_1.default, { label: "Show only genotype columns", checked: showOnlyGenotypeColumns, onChange: event => {
84
- setShowOnlyGenotypeColumns(event.target.checked);
85
- } })), showFilters ? ((0, jsx_runtime_1.jsx)(VariantSampleFilters_1.default, { setFilter: setFilter, columns: columns, filter: filter })) : null, (0, jsx_runtime_1.jsx)(DataGridFlexContainer_1.default, { children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: showOnlyGenotypeColumns
41
+ const s1 = new Set(['sample', 'GT']);
42
+ const s2 = new Set(['sample', 'GT', 'genotype']);
43
+ return !rows.length ? null : ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(BaseCard_1.default, { ...props, title: "Genotype frequencies", children: (0, jsx_runtime_1.jsx)(ErrorBoundary_1.ErrorBoundary, { FallbackComponent: ui_1.ErrorMessage, children: (0, jsx_runtime_1.jsx)(VariantGenotypeFrequencyTable_1.default, { rows: rows }) }) }), (0, jsx_runtime_1.jsxs)(BaseCard_1.default, { ...props, title: "Samples", children: [error ? (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: `${error}` }) : null, (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(Checkbox2_1.default, { label: "Show filters", checked: showFilters, onChange: event => {
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+ setShowFilters(event.target.checked);
45
+ } }), (0, jsx_runtime_1.jsxs)(material_1.ToggleButtonGroup, { value: columnDisplayMode, exclusive: true, size: "small", onChange: (_, newValue) => {
46
+ if (newValue !== null) {
47
+ setColumnDisplayMode(newValue);
48
+ }
49
+ }, children: [(0, jsx_runtime_1.jsx)(material_1.ToggleButton, { value: "all", children: "All" }), (0, jsx_runtime_1.jsx)(material_1.ToggleButton, { value: "gtOnly", children: "GT only" }), (0, jsx_runtime_1.jsx)(material_1.ToggleButton, { value: "genotypeOnly", children: "GT+resolved genotype" })] })] }), showFilters ? ((0, jsx_runtime_1.jsx)(VariantSampleFilters_1.default, { setFilter: setFilter, columns: columns, filter: filter })) : null, (0, jsx_runtime_1.jsx)(DataGridFlexContainer_1.default, { children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columnDisplayMode === 'gtOnly'
86
50
  ? columns.filter(f => s1.has(f.field))
87
- : columns, rowHeight: 25, columnHeaderHeight: 35, showToolbar: true }) })] })] }));
51
+ : columnDisplayMode === 'genotypeOnly'
52
+ ? columns.filter(f => s2.has(f.field))
53
+ : columns, rowHeight: 25, columnHeaderHeight: 35, showToolbar: true }) })] })] }));
88
54
  }
package/dist/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.d.ts ADDED
@@ -0,0 +1,5 @@
1
+ import type { Filters, InfoFields, VariantSampleGridRow } from './types';
2
+ export declare function getSampleGridRows(samples: Record<string, InfoFields>, REF: string, ALT: string[], filter: Filters): {
3
+ rows: VariantSampleGridRow[];
4
+ error: unknown;
5
+ };
package/dist/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.js ADDED
@@ -0,0 +1,46 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.getSampleGridRows = getSampleGridRows;
4
+ const util_1 = require("../../VcfFeature/util");
5
+ function getSampleGridRows(samples, REF, ALT, filter) {
6
+ const preFilteredRows = Object.entries(samples).map(([key, val]) => {
7
+ var _a, _b;
8
+ return [
9
+ key,
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+ {
11
+ ...val,
12
+ GT: `${(_a = val.GT) === null || _a === void 0 ? void 0 : _a[0]}`,
13
+ genotype: (0, util_1.makeSimpleAltString)(`${(_b = val.GT) === null || _b === void 0 ? void 0 : _b[0]}`, REF, ALT),
14
+ },
15
+ ];
16
+ });
17
+ let error;
18
+ let rows = [];
19
+ const filters = Object.keys(filter);
20
+ try {
21
+ rows = preFilteredRows
22
+ .map(([key, val]) => {
23
+ return {
24
+ ...Object.fromEntries(Object.entries(val).map(([formatField, formatValue]) => [
25
+ formatField,
26
+ formatValue,
27
+ ])),
28
+ sample: key,
29
+ id: key,
30
+ };
31
+ })
32
+ .filter(row => filters.length
33
+ ? filters.every(key => {
34
+ const currFilter = filter[key];
35
+ return currFilter
36
+ ? new RegExp(currFilter, 'i').exec(row[key])
37
+ : true;
38
+ })
39
+ : true);
40
+ }
41
+ catch (e) {
42
+ console.error(e);
43
+ error = e;
44
+ }
45
+ return { rows, error };
46
+ }
package/dist/shared/MultiVariantBaseModel.d.ts CHANGED
@@ -196,6 +196,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
196
196
  readonly renderDelay: number;
197
197
  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
198
198
  readonly selectedFeatureId: string | undefined;
199
+ copyInfoToClipboard(feature: Feature): void;
199
200
  } & {
200
201
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
201
202
  readonly featureUnderMouse: Feature | undefined;
@@ -205,7 +206,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
205
206
  } & {
206
207
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
207
208
  deleteBlock(key: string): void;
208
- selectFeature(feature: Feature): Promise<void>;
209
+ selectFeature(feature: Feature): void;
209
210
  navToFeature(feature: Feature): void;
210
211
  clearFeatureSelection(): void;
211
212
  setFeatureIdUnderMouse(feature?: string): void;
package/dist/shared/SharedVariantMixin.d.ts CHANGED
@@ -184,6 +184,7 @@ export default function SharedVariantMixin(configSchema: AnyConfigurationSchemaT
184
184
  readonly renderDelay: number;
185
185
  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
186
186
  readonly selectedFeatureId: string | undefined;
187
+ copyInfoToClipboard(feature: Feature): void;
187
188
  } & {
188
189
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
189
190
  readonly featureUnderMouse: Feature | undefined;
@@ -193,7 +194,7 @@ export default function SharedVariantMixin(configSchema: AnyConfigurationSchemaT
193
194
  } & {
194
195
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
195
196
  deleteBlock(key: string): void;
196
- selectFeature(feature: Feature): Promise<void>;
197
+ selectFeature(feature: Feature): void;
197
198
  navToFeature(feature: Feature): void;
198
199
  clearFeatureSelection(): void;
199
200
  setFeatureIdUnderMouse(feature?: string): void;
package/dist/shared/components/SourcesDataGrid.js CHANGED
@@ -25,7 +25,7 @@ function SourcesDataGrid({ rows, onChange, setSelected, }) {
25
25
  idx: 0,
26
26
  field: null,
27
27
  });
28
- return ((0, jsx_runtime_1.jsx)("div", { style: { height: 400, width: '100%' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { checkboxSelection: true, onRowSelectionModelChange: arg => {
28
+ return ((0, jsx_runtime_1.jsx)("div", { style: { height: 400, width: '100%' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { checkboxSelection: true, disableRowSelectionOnClick: true, onRowSelectionModelChange: arg => {
29
29
  setSelected([...arg.ids]);
30
30
  }, rows: rows, rowHeight: 25, columnHeaderHeight: 33, columns: [
31
31
  {
package/esm/LinearVariantDisplay/model.d.ts CHANGED
@@ -191,6 +191,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
191
191
  readonly renderDelay: number;
192
192
  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
193
193
  readonly selectedFeatureId: string | undefined;
194
+ copyInfoToClipboard(feature: Feature): void;
194
195
  } & {
195
196
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
196
197
  readonly featureUnderMouse: Feature | undefined;
@@ -200,7 +201,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
200
201
  } & {
201
202
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
202
203
  deleteBlock(key: string): void;
203
- selectFeature(feature: Feature): Promise<void>;
204
+ selectFeature(feature: Feature): void;
204
205
  navToFeature(feature: Feature): void;
205
206
  clearFeatureSelection(): void;
206
207
  setFeatureIdUnderMouse(feature?: string): void;
package/esm/MultiLinearVariantDisplay/model.d.ts CHANGED
@@ -199,6 +199,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
199
199
  readonly renderDelay: number;
200
200
  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
201
201
  readonly selectedFeatureId: string | undefined;
202
+ copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
202
203
  } & {
203
204
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
204
205
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -208,7 +209,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
208
209
  } & {
209
210
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
210
211
  deleteBlock(key: string): void;
211
- selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
212
+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
212
213
  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
213
214
  clearFeatureSelection(): void;
214
215
  setFeatureIdUnderMouse(feature?: string): void;
package/esm/MultiLinearVariantMatrixDisplay/model.d.ts CHANGED
@@ -199,6 +199,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
199
199
  readonly renderDelay: number;
200
200
  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
201
201
  readonly selectedFeatureId: string | undefined;
202
+ copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
202
203
  } & {
203
204
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
204
205
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -208,7 +209,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
208
209
  } & {
209
210
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
210
211
  deleteBlock(key: string): void;
211
- selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
212
+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
212
213
  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
213
214
  clearFeatureSelection(): void;
214
215
  setFeatureIdUnderMouse(feature?: string): void;
package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js CHANGED
@@ -5,62 +5,24 @@ import { ErrorMessage } from '@jbrowse/core/ui';
5
5
  import DataGridFlexContainer from '@jbrowse/core/ui/DataGridFlexContainer';
6
6
  import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary';
7
7
  import { measureGridWidth } from '@jbrowse/core/util';
8
- import { Typography } from '@mui/material';
8
+ import { ToggleButton, ToggleButtonGroup, Typography } from '@mui/material';
9
9
  import { DataGrid } from '@mui/x-data-grid';
10
10
  import Checkbox2 from '../Checkbox2';
11
11
  import VariantGenotypeFrequencyTable from './VariantGenotypeFrequencyTable';
12
12
  import SampleFilters from './VariantSampleFilters';
13
- import { areSetsEqual } from './util';
14
- import { makeSimpleAltString } from '../../VcfFeature/util';
13
+ import { getSampleGridRows } from './getSampleGridRows';
15
14
  export default function VariantSampleGrid(props) {
16
- var _a;
17
15
  const { feature, descriptions = {} } = props;
18
16
  const [filter, setFilter] = useState({});
19
- const [showOnlyGenotypeColumns, setShowOnlyGenotypeColumns] = useState(true);
17
+ const [columnDisplayMode, setColumnDisplayMode] = useState('all');
20
18
  const [showFilters, setShowFilters] = useState(false);
21
19
  const samples = (feature.samples || {});
22
20
  const ALT = feature.ALT;
23
21
  const REF = feature.REF;
24
- const preFilteredRows = Object.entries(samples).map(([key, val]) => {
25
- var _a, _b;
26
- return [
27
- key,
28
- {
29
- ...val,
30
- GT: `${(_a = val.GT) === null || _a === void 0 ? void 0 : _a[0]}`,
31
- genotype: makeSimpleAltString(`${(_b = val.GT) === null || _b === void 0 ? void 0 : _b[0]}`, REF, ALT),
32
- },
33
- ];
34
- });
35
- let error;
36
- let rows = [];
37
- const filters = Object.keys(filter);
38
- try {
39
- rows = preFilteredRows
40
- .map(([key, val]) => {
41
- return {
42
- ...Object.fromEntries(Object.entries(val).map(([formatField, formatValue]) => [
43
- formatField,
44
- formatValue,
45
- ])),
46
- sample: key,
47
- id: key,
48
- };
49
- })
50
- .filter(row => filters.length
51
- ? filters.every(key => {
52
- const currFilter = filter[key];
53
- return currFilter
54
- ? new RegExp(currFilter, 'i').exec(row[key])
55
- : true;
56
- })
57
- : true);
58
- }
59
- catch (e) {
60
- console.error(e);
61
- error = e;
62
- }
63
- const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
22
+ const { rows, error } = getSampleGridRows(samples, REF, ALT, filter);
23
+ const colKeySet = new Set(['sample', ...Object.keys(rows[0] || {})]);
24
+ colKeySet.delete('id');
25
+ const keys = [...colKeySet];
64
26
  const widths = keys.map(e => measureGridWidth(rows.map(r => r[e])));
65
27
  const columns = keys.map((field, index) => {
66
28
  var _a, _b;
@@ -70,13 +32,17 @@ export default function VariantSampleGrid(props) {
70
32
  width: widths[index],
71
33
  });
72
34
  });
73
- const s1 = new Set(['sample', 'GT', 'genotype']);
74
- const s2 = new Set(keys);
75
- return !preFilteredRows.length ? null : (_jsxs(_Fragment, { children: [_jsx(BaseCard, { ...props, title: "Genotype frequencies", children: _jsx(ErrorBoundary, { FallbackComponent: ErrorMessage, children: _jsx(VariantGenotypeFrequencyTable, { rows: rows }) }) }), _jsxs(BaseCard, { ...props, title: "Samples", children: [error ? _jsx(Typography, { color: "error", children: `${error}` }) : null, _jsx(Checkbox2, { label: "Show filters", checked: showFilters, onChange: event => {
76
- setShowFilters(event.target.checked);
77
- } }), areSetsEqual(s1, s2) ? null : (_jsx(Checkbox2, { label: "Show only genotype columns", checked: showOnlyGenotypeColumns, onChange: event => {
78
- setShowOnlyGenotypeColumns(event.target.checked);
79
- } })), showFilters ? (_jsx(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null, _jsx(DataGridFlexContainer, { children: _jsx(DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: showOnlyGenotypeColumns
35
+ const s1 = new Set(['sample', 'GT']);
36
+ const s2 = new Set(['sample', 'GT', 'genotype']);
37
+ return !rows.length ? null : (_jsxs(_Fragment, { children: [_jsx(BaseCard, { ...props, title: "Genotype frequencies", children: _jsx(ErrorBoundary, { FallbackComponent: ErrorMessage, children: _jsx(VariantGenotypeFrequencyTable, { rows: rows }) }) }), _jsxs(BaseCard, { ...props, title: "Samples", children: [error ? _jsx(Typography, { color: "error", children: `${error}` }) : null, _jsxs("div", { children: [_jsx(Checkbox2, { label: "Show filters", checked: showFilters, onChange: event => {
38
+ setShowFilters(event.target.checked);
39
+ } }), _jsxs(ToggleButtonGroup, { value: columnDisplayMode, exclusive: true, size: "small", onChange: (_, newValue) => {
40
+ if (newValue !== null) {
41
+ setColumnDisplayMode(newValue);
42
+ }
43
+ }, children: [_jsx(ToggleButton, { value: "all", children: "All" }), _jsx(ToggleButton, { value: "gtOnly", children: "GT only" }), _jsx(ToggleButton, { value: "genotypeOnly", children: "GT+resolved genotype" })] })] }), showFilters ? (_jsx(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null, _jsx(DataGridFlexContainer, { children: _jsx(DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columnDisplayMode === 'gtOnly'
80
44
  ? columns.filter(f => s1.has(f.field))
81
- : columns, rowHeight: 25, columnHeaderHeight: 35, showToolbar: true }) })] })] }));
45
+ : columnDisplayMode === 'genotypeOnly'
46
+ ? columns.filter(f => s2.has(f.field))
47
+ : columns, rowHeight: 25, columnHeaderHeight: 35, showToolbar: true }) })] })] }));
82
48
  }
package/esm/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.d.ts ADDED
@@ -0,0 +1,5 @@
1
+ import type { Filters, InfoFields, VariantSampleGridRow } from './types';
2
+ export declare function getSampleGridRows(samples: Record<string, InfoFields>, REF: string, ALT: string[], filter: Filters): {
3
+ rows: VariantSampleGridRow[];
4
+ error: unknown;
5
+ };
package/esm/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.js ADDED
@@ -0,0 +1,43 @@
1
+ import { makeSimpleAltString } from '../../VcfFeature/util';
2
+ export function getSampleGridRows(samples, REF, ALT, filter) {
3
+ const preFilteredRows = Object.entries(samples).map(([key, val]) => {
4
+ var _a, _b;
5
+ return [
6
+ key,
7
+ {
8
+ ...val,
9
+ GT: `${(_a = val.GT) === null || _a === void 0 ? void 0 : _a[0]}`,
10
+ genotype: makeSimpleAltString(`${(_b = val.GT) === null || _b === void 0 ? void 0 : _b[0]}`, REF, ALT),
11
+ },
12
+ ];
13
+ });
14
+ let error;
15
+ let rows = [];
16
+ const filters = Object.keys(filter);
17
+ try {
18
+ rows = preFilteredRows
19
+ .map(([key, val]) => {
20
+ return {
21
+ ...Object.fromEntries(Object.entries(val).map(([formatField, formatValue]) => [
22
+ formatField,
23
+ formatValue,
24
+ ])),
25
+ sample: key,
26
+ id: key,
27
+ };
28
+ })
29
+ .filter(row => filters.length
30
+ ? filters.every(key => {
31
+ const currFilter = filter[key];
32
+ return currFilter
33
+ ? new RegExp(currFilter, 'i').exec(row[key])
34
+ : true;
35
+ })
36
+ : true);
37
+ }
38
+ catch (e) {
39
+ console.error(e);
40
+ error = e;
41
+ }
42
+ return { rows, error };
43
+ }
package/esm/shared/MultiVariantBaseModel.d.ts CHANGED
@@ -196,6 +196,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
196
196
  readonly renderDelay: number;
197
197
  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
198
198
  readonly selectedFeatureId: string | undefined;
199
+ copyInfoToClipboard(feature: Feature): void;
199
200
  } & {
200
201
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
201
202
  readonly featureUnderMouse: Feature | undefined;
@@ -205,7 +206,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
205
206
  } & {
206
207
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
207
208
  deleteBlock(key: string): void;
208
- selectFeature(feature: Feature): Promise<void>;
209
+ selectFeature(feature: Feature): void;
209
210
  navToFeature(feature: Feature): void;
210
211
  clearFeatureSelection(): void;
211
212
  setFeatureIdUnderMouse(feature?: string): void;
package/esm/shared/SharedVariantMixin.d.ts CHANGED
@@ -184,6 +184,7 @@ export default function SharedVariantMixin(configSchema: AnyConfigurationSchemaT
184
184
  readonly renderDelay: number;
185
185
  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
186
186
  readonly selectedFeatureId: string | undefined;
187
+ copyInfoToClipboard(feature: Feature): void;
187
188
  } & {
188
189
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
189
190
  readonly featureUnderMouse: Feature | undefined;
@@ -193,7 +194,7 @@ export default function SharedVariantMixin(configSchema: AnyConfigurationSchemaT
193
194
  } & {
194
195
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
195
196
  deleteBlock(key: string): void;
196
- selectFeature(feature: Feature): Promise<void>;
197
+ selectFeature(feature: Feature): void;
197
198
  navToFeature(feature: Feature): void;
198
199
  clearFeatureSelection(): void;
199
200
  setFeatureIdUnderMouse(feature?: string): void;
package/esm/shared/components/SourcesDataGrid.js CHANGED
@@ -19,7 +19,7 @@ export default function SourcesDataGrid({ rows, onChange, setSelected, }) {
19
19
  idx: 0,
20
20
  field: null,
21
21
  });
22
- return (_jsx("div", { style: { height: 400, width: '100%' }, children: _jsx(DataGrid, { checkboxSelection: true, onRowSelectionModelChange: arg => {
22
+ return (_jsx("div", { style: { height: 400, width: '100%' }, children: _jsx(DataGrid, { checkboxSelection: true, disableRowSelectionOnClick: true, onRowSelectionModelChange: arg => {
23
23
  setSelected([...arg.ids]);
24
24
  }, rows: rows, rowHeight: 25, columnHeaderHeight: 33, columns: [
25
25
  {
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-variants",
3
- "version": "3.4.0",
3
+ "version": "3.5.1",
4
4
  "description": "JBrowse 2 variant adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -37,13 +37,13 @@
37
37
  },
38
38
  "dependencies": {
39
39
  "@flatten-js/interval-tree": "^1.0.15",
40
- "@gmod/bgzf-filehandle": "^3.0.2",
40
+ "@gmod/bgzf-filehandle": "^4.0.0",
41
41
  "@gmod/tabix": "^3.0.1",
42
42
  "@gmod/vcf": "^6.0.8",
43
- "@jbrowse/core": "^3.4.0",
44
- "@jbrowse/plugin-circular-view": "^3.4.0",
45
- "@jbrowse/plugin-linear-genome-view": "^3.4.0",
46
- "@jbrowse/sv-core": "^3.4.0",
43
+ "@jbrowse/core": "^3.5.1",
44
+ "@jbrowse/plugin-circular-view": "^3.5.1",
45
+ "@jbrowse/plugin-linear-genome-view": "^3.5.1",
46
+ "@jbrowse/sv-core": "^3.5.1",
47
47
  "@mui/icons-material": "^7.0.0",
48
48
  "@mui/material": "^7.0.0",
49
49
  "@mui/x-data-grid": "^8.0.0",
@@ -63,5 +63,5 @@
63
63
  "distModule": "esm/index.js",
64
64
  "srcModule": "src/index.ts",
65
65
  "module": "esm/index.js",
66
- "gitHead": "a9f1ac35fc2dd810bae92cdaf1fc19995bee4413"
66
+ "gitHead": "cb8859da9d838ad2594964777c5c54f385d98f5e"
67
67
  }