@jbrowse/plugin-variants 2.3.4 → 2.4.0

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Files changed (29) hide show
  1. package/dist/ChordVariantDisplay/index.js +1 -0
  2. package/dist/ChordVariantDisplay/index.js.map +1 -1
  3. package/dist/ChordVariantDisplay/models/stateModelFactory.d.ts +4 -0
  4. package/dist/LinearVariantDisplay/model.d.ts +4 -2
  5. package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts +2 -3
  6. package/dist/StructuralVariantChordRenderer/ReactComponent.js +3 -5
  7. package/dist/StructuralVariantChordRenderer/ReactComponent.js.map +1 -1
  8. package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -1
  9. package/dist/VariantFeatureWidget/VariantSampleGrid.js +11 -7
  10. package/dist/VariantFeatureWidget/VariantSampleGrid.js.map +1 -1
  11. package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -1
  12. package/esm/ChordVariantDisplay/index.js +1 -0
  13. package/esm/ChordVariantDisplay/index.js.map +1 -1
  14. package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts +4 -0
  15. package/esm/LinearVariantDisplay/model.d.ts +4 -2
  16. package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts +2 -3
  17. package/esm/StructuralVariantChordRenderer/ReactComponent.js +3 -5
  18. package/esm/StructuralVariantChordRenderer/ReactComponent.js.map +1 -1
  19. package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -1
  20. package/esm/VariantFeatureWidget/VariantSampleGrid.js +11 -7
  21. package/esm/VariantFeatureWidget/VariantSampleGrid.js.map +1 -1
  22. package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -1
  23. package/package.json +2 -2
  24. package/src/ChordVariantDisplay/index.ts +2 -0
  25. package/src/StructuralVariantChordRenderer/ReactComponent.tsx +14 -15
  26. package/src/VariantFeatureWidget/BreakendOptionDialog.tsx +1 -1
  27. package/src/VariantFeatureWidget/VariantSampleGrid.tsx +48 -33
  28. package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.tsx.snap +8 -8
  29. package/src/VcfTabixAdapter/VcfTabixAdapter.ts +2 -2
package/dist/ChordVariantDisplay/index.js CHANGED
@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  Object.defineProperty(exports, "__esModule", { value: true });
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  const plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
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  const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
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+ // locals
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  const configSchema_1 = __importDefault(require("./models/configSchema"));
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  const stateModelFactory_1 = __importDefault(require("./models/stateModelFactory"));
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  exports.default = (pluginManager) => {
package/dist/ChordVariantDisplay/index.js.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,wEAAyE;AACzE,kGAAyE;AACzE,yEAAiD;AACjD,mFAAoD;AAEpD,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,IAAA,2BAAW,EAAC,YAAY,CAAC,CAAA;QAC5C,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,uBAAuB;YACpC,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,cAAc;YACxB,cAAc,EAAE,gDAAyB;SAC1C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
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+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,wEAAyE;AACzE,kGAAyE;AAEzE,SAAS;AACT,yEAAiD;AACjD,mFAAoD;AAEpD,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,IAAA,2BAAW,EAAC,YAAY,CAAC,CAAA;QAC5C,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,uBAAuB;YACpC,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,cAAc;YACxB,cAAc,EAAE,gDAAyB;SAC1C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
package/dist/ChordVariantDisplay/models/stateModelFactory.d.ts CHANGED
@@ -101,6 +101,10 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
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  setRefNameMap(refNameMap: Record<string, string>): void;
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  } & {
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  afterAttach(): void;
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+ } & {
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+ renderSvg(opts: import("@jbrowse/plugin-circular-view/src/CircularView/models/CircularView").ExportSvgOptions & {
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+ theme: import("@mui/material").ThemeOptions;
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+ }): Promise<JSX.Element>;
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  } & {
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  /**
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  * #getter
package/dist/LinearVariantDisplay/model.d.ts CHANGED
@@ -11,7 +11,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  type: import("mobx-state-tree").ISimpleType<string>;
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  } & {
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- height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
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+ heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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  key: import("mobx-state-tree").ISimpleType<string>;
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  region: import("mobx-state-tree").IModelType<{
@@ -137,6 +137,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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  estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
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  } & {
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+ readonly height: any;
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
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  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
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  } & {
@@ -166,7 +167,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
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  setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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  clearRegionStats(): void;
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- setHeight(displayHeight: number): number;
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+ setHeight(displayHeight: number): any;
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  resizeHeight(distance: number): number;
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  setScrollTop(scrollTop: number): void;
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  updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
@@ -199,6 +200,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  } & {
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  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
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  overrideHeight: number;
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+ theme: import("@mui/material").ThemeOptions;
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  }): Promise<JSX.Element>;
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  } & {
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  readonly rendererTypeName: any;
package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts CHANGED
@@ -2,7 +2,7 @@
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  import { Feature } from '@jbrowse/core/util';
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  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  import { Block, AnyRegion } from './Chord';
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- declare function StructuralVariantChords(props: {
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+ declare const _default: ({ features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, }: {
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  features: Map<string, Feature>;
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  radius: number;
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  config: AnyConfigurationModel;
@@ -13,6 +13,5 @@ declare function StructuralVariantChords(props: {
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  blockDefinitions: Block[];
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  bezierRadius: number;
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  onChordClick: (feature: Feature, reg: AnyRegion, endBlock: AnyRegion, evt: unknown) => void;
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- }): JSX.Element;
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- declare const _default: typeof StructuralVariantChords;
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+ }) => JSX.Element;
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  export default _default;
package/dist/StructuralVariantChordRenderer/ReactComponent.js CHANGED
@@ -30,8 +30,7 @@ const react_1 = __importStar(require("react"));
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  const mobx_react_1 = require("mobx-react");
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  // locals
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  const Chord_1 = __importDefault(require("./Chord"));
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- function StructuralVariantChords(props) {
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- const { features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, } = props;
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+ exports.default = (0, mobx_react_1.observer)(function StructuralVariantChords({ features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, }) {
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  // make a map of refName -> blockDefinition
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  const blocksForRefsMemo = (0, react_1.useMemo)(() => {
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  const blocksForRefs = {};
@@ -47,7 +46,7 @@ function StructuralVariantChords(props) {
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  const selected = String(selectedFeatureId) === String(id);
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  chords.push(react_1.default.createElement(Chord_1.default, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
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  }
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- const trackStyleId = `chords-${displayModel.id}`;
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+ const trackStyleId = `chords-${typeof jest !== 'undefined' ? 'test' : displayModel.id}`;
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  return (react_1.default.createElement("g", { id: trackStyleId, "data-testid": "structuralVariantChordRenderer" },
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  react_1.default.createElement("style", {
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  // eslint-disable-next-line react/no-danger
@@ -60,6 +59,5 @@ function StructuralVariantChords(props) {
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  `,
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  } }),
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  chords));
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- }
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- exports.default = (0, mobx_react_1.observer)(StructuralVariantChords);
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+ });
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  //# sourceMappingURL=ReactComponent.js.map
package/dist/StructuralVariantChordRenderer/ReactComponent.js.map CHANGED
@@ -1 +1 @@
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package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map CHANGED
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package/dist/VariantFeatureWidget/VariantSampleGrid.js CHANGED
@@ -29,12 +29,19 @@ const x_data_grid_1 = require("@mui/x-data-grid");
29
29
  const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
30
30
  const util_1 = require("@jbrowse/core/util");
31
31
  const ResizeBar_1 = __importStar(require("@jbrowse/core/ui/ResizeBar"));
32
+ function SampleFilters({ columns, filter, setFilter, }) {
33
+ const [showFilters, setShowFilters] = (0, react_1.useState)(false);
34
+ return (react_1.default.createElement(react_1.default.Fragment, null,
35
+ react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
36
+ showFilters ? (react_1.default.createElement(react_1.default.Fragment, null,
37
+ react_1.default.createElement(material_1.Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
38
+ columns.map(({ field }) => (react_1.default.createElement(material_1.TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }))))) : null));
39
+ }
32
40
  function VariantSamples(props) {
33
41
  var _a;
34
42
  const { feature, descriptions = {} } = props;
35
43
  const { ref, scrollLeft } = (0, ResizeBar_1.useResizeBar)();
36
44
  const [filter, setFilter] = (0, react_1.useState)({});
37
- const [showFilters, setShowFilters] = (0, react_1.useState)(false);
38
45
  const samples = (feature.samples || {});
39
46
  const preFilteredRows = Object.entries(samples);
40
47
  let error;
@@ -65,7 +72,7 @@ function VariantSamples(props) {
65
72
  }
66
73
  const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
67
74
  const [widths, setWidths] = (0, react_1.useState)(keys.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e]))));
68
- const infoFields = keys.map((field, index) => {
75
+ const columns = keys.map((field, index) => {
69
76
  var _a, _b;
70
77
  return ({
71
78
  field,
@@ -77,14 +84,11 @@ function VariantSamples(props) {
77
84
  // https://github.com/mui-org/material-ui-x/issues/1197
78
85
  return !preFilteredRows.length ? null : (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Samples" },
79
86
  error ? react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`) : null,
80
- react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
81
- showFilters ? (react_1.default.createElement(react_1.default.Fragment, null,
82
- react_1.default.createElement(material_1.Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
83
- infoFields.map(({ field }) => (react_1.default.createElement(material_1.TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }))))) : null,
87
+ react_1.default.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter }),
84
88
  react_1.default.createElement("div", { ref: ref },
85
89
  react_1.default.createElement(ResizeBar_1.default, { widths: widths, setWidths: setWidths, scrollLeft: scrollLeft }),
86
90
  react_1.default.createElement("div", { ref: ref, style: { height: 600, width: '100%', overflow: 'auto' } },
87
- react_1.default.createElement(x_data_grid_1.DataGrid, { rows: rows, columns: infoFields, disableSelectionOnClick: true, rowHeight: 25, headerHeight: 35, disableColumnMenu: true })))));
91
+ react_1.default.createElement(x_data_grid_1.DataGrid, { rows: rows, columns: columns, disableSelectionOnClick: true, rowHeight: 25, headerHeight: 35, disableColumnMenu: true })))));
88
92
  }
89
93
  exports.default = VariantSamples;
90
94
  //# sourceMappingURL=VariantSampleGrid.js.map
package/dist/VariantFeatureWidget/VariantSampleGrid.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map CHANGED
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package/esm/ChordVariantDisplay/index.js CHANGED
@@ -1,5 +1,6 @@
1
1
  import { BaseChordDisplayComponent } from '@jbrowse/plugin-circular-view';
2
2
  import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
3
+ // locals
3
4
  import configSchemaF from './models/configSchema';
4
5
  import stateModelF from './models/stateModelFactory';
5
6
  export default (pluginManager) => {
package/esm/ChordVariantDisplay/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,yBAAyB,EAAE,MAAM,+BAA+B,CAAA;AACzE,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,aAAa,MAAM,uBAAuB,CAAA;AACjD,OAAO,WAAW,MAAM,4BAA4B,CAAA;AAEpD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,WAAW,CAAC,YAAY,CAAC,CAAA;QAC5C,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,uBAAuB;YACpC,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,cAAc;YACxB,cAAc,EAAE,yBAAyB;SAC1C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
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+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,yBAAyB,EAAE,MAAM,+BAA+B,CAAA;AACzE,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,SAAS;AACT,OAAO,aAAa,MAAM,uBAAuB,CAAA;AACjD,OAAO,WAAW,MAAM,4BAA4B,CAAA;AAEpD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,WAAW,CAAC,YAAY,CAAC,CAAA;QAC5C,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,uBAAuB;YACpC,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,cAAc;YACxB,cAAc,EAAE,yBAAyB;SAC1C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts CHANGED
@@ -101,6 +101,10 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
101
101
  setRefNameMap(refNameMap: Record<string, string>): void;
102
102
  } & {
103
103
  afterAttach(): void;
104
+ } & {
105
+ renderSvg(opts: import("@jbrowse/plugin-circular-view/src/CircularView/models/CircularView").ExportSvgOptions & {
106
+ theme: import("@mui/material").ThemeOptions;
107
+ }): Promise<JSX.Element>;
104
108
  } & {
105
109
  /**
106
110
  * #getter
package/esm/LinearVariantDisplay/model.d.ts CHANGED
@@ -11,7 +11,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
11
11
  type: import("mobx-state-tree").ISimpleType<string>;
12
12
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
13
13
  } & {
14
- height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
14
+ heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
15
15
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
16
16
  key: import("mobx-state-tree").ISimpleType<string>;
17
17
  region: import("mobx-state-tree").IModelType<{
@@ -137,6 +137,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
137
137
  estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
138
138
  estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
139
139
  } & {
140
+ readonly height: any;
140
141
  readonly blockType: "dynamicBlocks" | "staticBlocks";
141
142
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
142
143
  } & {
@@ -166,7 +167,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
166
167
  setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
167
168
  setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
168
169
  clearRegionStats(): void;
169
- setHeight(displayHeight: number): number;
170
+ setHeight(displayHeight: number): any;
170
171
  resizeHeight(distance: number): number;
171
172
  setScrollTop(scrollTop: number): void;
172
173
  updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
@@ -199,6 +200,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
199
200
  } & {
200
201
  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
201
202
  overrideHeight: number;
203
+ theme: import("@mui/material").ThemeOptions;
202
204
  }): Promise<JSX.Element>;
203
205
  } & {
204
206
  readonly rendererTypeName: any;
package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts CHANGED
@@ -2,7 +2,7 @@
2
2
  import { Feature } from '@jbrowse/core/util';
3
3
  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
4
4
  import { Block, AnyRegion } from './Chord';
5
- declare function StructuralVariantChords(props: {
5
+ declare const _default: ({ features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, }: {
6
6
  features: Map<string, Feature>;
7
7
  radius: number;
8
8
  config: AnyConfigurationModel;
@@ -13,6 +13,5 @@ declare function StructuralVariantChords(props: {
13
13
  blockDefinitions: Block[];
14
14
  bezierRadius: number;
15
15
  onChordClick: (feature: Feature, reg: AnyRegion, endBlock: AnyRegion, evt: unknown) => void;
16
- }): JSX.Element;
17
- declare const _default: typeof StructuralVariantChords;
16
+ }) => JSX.Element;
18
17
  export default _default;
package/esm/StructuralVariantChordRenderer/ReactComponent.js CHANGED
@@ -2,8 +2,7 @@ import React, { useMemo } from 'react';
2
2
  import { observer } from 'mobx-react';
3
3
  // locals
4
4
  import Chord from './Chord';
5
- function StructuralVariantChords(props) {
6
- const { features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, } = props;
5
+ export default observer(function StructuralVariantChords({ features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, }) {
7
6
  // make a map of refName -> blockDefinition
8
7
  const blocksForRefsMemo = useMemo(() => {
9
8
  const blocksForRefs = {};
@@ -19,7 +18,7 @@ function StructuralVariantChords(props) {
19
18
  const selected = String(selectedFeatureId) === String(id);
20
19
  chords.push(React.createElement(Chord, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
21
20
  }
22
- const trackStyleId = `chords-${displayModel.id}`;
21
+ const trackStyleId = `chords-${typeof jest !== 'undefined' ? 'test' : displayModel.id}`;
23
22
  return (React.createElement("g", { id: trackStyleId, "data-testid": "structuralVariantChordRenderer" },
24
23
  React.createElement("style", {
25
24
  // eslint-disable-next-line react/no-danger
@@ -32,6 +31,5 @@ function StructuralVariantChords(props) {
32
31
  `,
33
32
  } }),
34
33
  chords));
35
- }
36
- export default observer(StructuralVariantChords);
34
+ });
37
35
  //# sourceMappingURL=ReactComponent.js.map
package/esm/StructuralVariantChordRenderer/ReactComponent.js.map CHANGED
@@ -1 +1 @@
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package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map CHANGED
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package/esm/VariantFeatureWidget/VariantSampleGrid.js CHANGED
@@ -4,12 +4,19 @@ import { DataGrid } from '@mui/x-data-grid';
4
4
  import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
5
5
  import { measureGridWidth } from '@jbrowse/core/util';
6
6
  import ResizeBar, { useResizeBar } from '@jbrowse/core/ui/ResizeBar';
7
+ function SampleFilters({ columns, filter, setFilter, }) {
8
+ const [showFilters, setShowFilters] = useState(false);
9
+ return (React.createElement(React.Fragment, null,
10
+ React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
11
+ showFilters ? (React.createElement(React.Fragment, null,
12
+ React.createElement(Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
13
+ columns.map(({ field }) => (React.createElement(TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }))))) : null));
14
+ }
7
15
  export default function VariantSamples(props) {
8
16
  var _a;
9
17
  const { feature, descriptions = {} } = props;
10
18
  const { ref, scrollLeft } = useResizeBar();
11
19
  const [filter, setFilter] = useState({});
12
- const [showFilters, setShowFilters] = useState(false);
13
20
  const samples = (feature.samples || {});
14
21
  const preFilteredRows = Object.entries(samples);
15
22
  let error;
@@ -40,7 +47,7 @@ export default function VariantSamples(props) {
40
47
  }
41
48
  const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
42
49
  const [widths, setWidths] = useState(keys.map(e => measureGridWidth(rows.map(r => r[e]))));
43
- const infoFields = keys.map((field, index) => {
50
+ const columns = keys.map((field, index) => {
44
51
  var _a, _b;
45
52
  return ({
46
53
  field,
@@ -52,13 +59,10 @@ export default function VariantSamples(props) {
52
59
  // https://github.com/mui-org/material-ui-x/issues/1197
53
60
  return !preFilteredRows.length ? null : (React.createElement(BaseCard, { ...props, title: "Samples" },
54
61
  error ? React.createElement(Typography, { color: "error" }, `${error}`) : null,
55
- React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
56
- showFilters ? (React.createElement(React.Fragment, null,
57
- React.createElement(Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
58
- infoFields.map(({ field }) => (React.createElement(TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }))))) : null,
62
+ React.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter }),
59
63
  React.createElement("div", { ref: ref },
60
64
  React.createElement(ResizeBar, { widths: widths, setWidths: setWidths, scrollLeft: scrollLeft }),
61
65
  React.createElement("div", { ref: ref, style: { height: 600, width: '100%', overflow: 'auto' } },
62
- React.createElement(DataGrid, { rows: rows, columns: infoFields, disableSelectionOnClick: true, rowHeight: 25, headerHeight: 35, disableColumnMenu: true })))));
66
+ React.createElement(DataGrid, { rows: rows, columns: columns, disableSelectionOnClick: true, rowHeight: 25, headerHeight: 35, disableColumnMenu: true })))));
63
67
  }
64
68
  //# sourceMappingURL=VariantSampleGrid.js.map
package/esm/VariantFeatureWidget/VariantSampleGrid.js.map CHANGED
@@ -1 +1 @@
1
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+ {"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,SAAS,MAAM,WAAW,CAAA;AAEjC,QAAQ;AACR,OAAO,UAAU,MAAM,eAAe,CAAA;AAEtC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;IAMzC,KAAK,CAAC,YAAY;QACxB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAEtD,MAAM,UAAU,GAAG,YAAY,CAAC,aAAa,EAAE,EAAE,CAAC,CAAA;QAClD,MAAM,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC/B,UAAU;YACV,aAAa,EAAE,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC7D,aAAa,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC9D,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,cAAc,EAAE,UAAU;SAC3B,CAAC,CAAA;QAEF,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,SAAS,EAAE,CAAA;QACpC,OAAO;YACL,GAAG;YACH,MAAM,EAAE,IAAI,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;SAClC,CAAA;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,SAAS,EAAE,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACzC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,GAAG,CAAC,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBACtC,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;wBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;wBAC/B,MAAM;wBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,QAAQ,UAAU,EAAE;qBACnC,CAAC,CACH,CAAA;gBACH,CAAC;gBACD,GAAG,IAAI;aACR,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-variants",
3
- "version": "2.3.4",
3
+ "version": "2.4.0",
4
4
  "description": "JBrowse 2 variant adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -64,5 +64,5 @@
64
64
  "distModule": "esm/index.js",
65
65
  "srcModule": "src/index.ts",
66
66
  "module": "esm/index.js",
67
- "gitHead": "98ae48be91ee2371e1b2768a907b4997995e9915"
67
+ "gitHead": "78707a2bc3ba8489f26a590ef83f62ede945d048"
68
68
  }
package/src/ChordVariantDisplay/index.ts CHANGED
@@ -1,6 +1,8 @@
1
1
  import PluginManager from '@jbrowse/core/PluginManager'
2
2
  import { BaseChordDisplayComponent } from '@jbrowse/plugin-circular-view'
3
3
  import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
4
+
5
+ // locals
4
6
  import configSchemaF from './models/configSchema'
5
7
  import stateModelF from './models/stateModelFactory'
6
8
 
package/src/StructuralVariantChordRenderer/ReactComponent.tsx CHANGED
@@ -6,7 +6,16 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration'
6
6
  // locals
7
7
  import Chord, { Block, AnyRegion } from './Chord'
8
8
 
9
- function StructuralVariantChords(props: {
9
+ export default observer(function StructuralVariantChords({
10
+ features,
11
+ config,
12
+ displayModel,
13
+ blockDefinitions,
14
+ radius,
15
+ bezierRadius,
16
+ displayModel: { selectedFeatureId },
17
+ onChordClick,
18
+ }: {
10
19
  features: Map<string, Feature>
11
20
  radius: number
12
21
  config: AnyConfigurationModel
@@ -20,16 +29,6 @@ function StructuralVariantChords(props: {
20
29
  evt: unknown,
21
30
  ) => void
22
31
  }) {
23
- const {
24
- features,
25
- config,
26
- displayModel,
27
- blockDefinitions,
28
- radius,
29
- bezierRadius,
30
- displayModel: { selectedFeatureId },
31
- onChordClick,
32
- } = props
33
32
  // make a map of refName -> blockDefinition
34
33
  const blocksForRefsMemo = useMemo(() => {
35
34
  const blocksForRefs = {} as { [key: string]: Block }
@@ -57,7 +56,9 @@ function StructuralVariantChords(props: {
57
56
  />,
58
57
  )
59
58
  }
60
- const trackStyleId = `chords-${displayModel.id}`
59
+ const trackStyleId = `chords-${
60
+ typeof jest !== 'undefined' ? 'test' : displayModel.id
61
+ }`
61
62
  return (
62
63
  <g id={trackStyleId} data-testid="structuralVariantChordRenderer">
63
64
  <style
@@ -74,6 +75,4 @@ function StructuralVariantChords(props: {
74
75
  {chords}
75
76
  </g>
76
77
  )
77
- }
78
-
79
- export default observer(StructuralVariantChords)
78
+ })
package/src/VariantFeatureWidget/BreakendOptionDialog.tsx CHANGED
@@ -79,7 +79,7 @@ function BreakendOptionDialog({
79
79
  viewSnapshot.views[0].offsetPx -= view.width / 2 + 100
80
80
  viewSnapshot.views[1].offsetPx -= view.width / 2 + 100
81
81
  viewSnapshot.featureData = feature
82
- const viewTracks = getSnapshot(view.tracks) as any
82
+ const viewTracks = getSnapshot(view.tracks) as unknown[]
83
83
  viewSnapshot.views[0].tracks = remapIds(viewTracks)
84
84
  viewSnapshot.views[1].tracks = remapIds(
85
85
  mirrorTracks ? viewTracks.slice().reverse() : viewTracks,
package/src/VariantFeatureWidget/VariantSampleGrid.tsx CHANGED
@@ -21,6 +21,51 @@ interface Entry {
21
21
  type InfoFields = Record<string, unknown>
22
22
  type Filters = Record<string, string>
23
23
 
24
+ function SampleFilters({
25
+ columns,
26
+ filter,
27
+ setFilter,
28
+ }: {
29
+ columns: { field: string }[]
30
+ filter: Filters
31
+ setFilter: (arg: Filters) => void
32
+ }) {
33
+ const [showFilters, setShowFilters] = useState(false)
34
+ return (
35
+ <>
36
+ <FormControlLabel
37
+ control={
38
+ <Checkbox
39
+ checked={showFilters}
40
+ onChange={() => setShowFilters(f => !f)}
41
+ />
42
+ }
43
+ label="Show sample filters"
44
+ />
45
+ {showFilters ? (
46
+ <>
47
+ <Typography>
48
+ These filters can use a plain text search or regex style query, e.g.
49
+ in the genotype field, entering 1 will query for all genotypes that
50
+ include the first alternate allele e.g. 0|1 or 1|1, entering
51
+ [1-9]\d* will find any non-zero allele e.g. 0|2 or 2/33
52
+ </Typography>
53
+ {columns.map(({ field }) => (
54
+ <TextField
55
+ key={`filter-${field}`}
56
+ placeholder={`Filter ${field}`}
57
+ value={filter[field] || ''}
58
+ onChange={event =>
59
+ setFilter({ ...filter, [field]: event.target.value })
60
+ }
61
+ />
62
+ ))}
63
+ </>
64
+ ) : null}
65
+ </>
66
+ )
67
+ }
68
+
24
69
  export default function VariantSamples(props: {
25
70
  feature: SimpleFeatureSerialized
26
71
  // eslint-disable-next-line @typescript-eslint/no-explicit-any
@@ -29,7 +74,6 @@ export default function VariantSamples(props: {
29
74
  const { feature, descriptions = {} } = props
30
75
  const { ref, scrollLeft } = useResizeBar()
31
76
  const [filter, setFilter] = useState<Filters>({})
32
- const [showFilters, setShowFilters] = useState(false)
33
77
  const samples = (feature.samples || {}) as Record<string, InfoFields>
34
78
  const preFilteredRows = Object.entries(samples)
35
79
 
@@ -69,7 +113,7 @@ export default function VariantSamples(props: {
69
113
  const [widths, setWidths] = useState(
70
114
  keys.map(e => measureGridWidth(rows.map(r => r[e]))),
71
115
  )
72
- const infoFields = keys.map((field, index) => ({
116
+ const columns = keys.map((field, index) => ({
73
117
  field,
74
118
  description: descriptions.FORMAT?.[field]?.Description,
75
119
  width: widths[index],
@@ -80,36 +124,7 @@ export default function VariantSamples(props: {
80
124
  return !preFilteredRows.length ? null : (
81
125
  <BaseCard {...props} title="Samples">
82
126
  {error ? <Typography color="error">{`${error}`}</Typography> : null}
83
-
84
- <FormControlLabel
85
- control={
86
- <Checkbox
87
- checked={showFilters}
88
- onChange={() => setShowFilters(f => !f)}
89
- />
90
- }
91
- label="Show sample filters"
92
- />
93
- {showFilters ? (
94
- <>
95
- <Typography>
96
- These filters can use a plain text search or regex style query, e.g.
97
- in the genotype field, entering 1 will query for all genotypes that
98
- include the first alternate allele e.g. 0|1 or 1|1, entering
99
- [1-9]\d* will find any non-zero allele e.g. 0|2 or 2/33
100
- </Typography>
101
- {infoFields.map(({ field }) => (
102
- <TextField
103
- key={`filter-${field}`}
104
- placeholder={`Filter ${field}`}
105
- value={filter[field] || ''}
106
- onChange={event =>
107
- setFilter({ ...filter, [field]: event.target.value })
108
- }
109
- />
110
- ))}
111
- </>
112
- ) : null}
127
+ <SampleFilters setFilter={setFilter} columns={columns} filter={filter} />
113
128
  <div ref={ref}>
114
129
  <ResizeBar
115
130
  widths={widths}
@@ -119,7 +134,7 @@ export default function VariantSamples(props: {
119
134
  <div ref={ref} style={{ height: 600, width: '100%', overflow: 'auto' }}>
120
135
  <DataGrid
121
136
  rows={rows}
122
- columns={infoFields}
137
+ columns={columns}
123
138
  disableSelectionOnClick
124
139
  rowHeight={25}
125
140
  headerHeight={35}
package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.tsx.snap CHANGED
@@ -29,7 +29,7 @@ exports[`renders with just the required model elements 1`] = `
29
29
  >
30
30
  <svg
31
31
  aria-hidden="true"
32
- class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-125qixp-MuiSvgIcon-root-expandIcon"
32
+ class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-ymsoo8-MuiSvgIcon-root-expandIcon"
33
33
  data-testid="ExpandMoreIcon"
34
34
  focusable="false"
35
35
  viewBox="0 0 24 24"
@@ -66,7 +66,7 @@ exports[`renders with just the required model elements 1`] = `
66
66
  class="css-1m8nxnb-field"
67
67
  >
68
68
  <div
69
- class="css-1y9c7n2-fieldName"
69
+ class="css-1q83rf3-fieldName"
70
70
  >
71
71
  Position
72
72
  </div>
@@ -80,7 +80,7 @@ exports[`renders with just the required model elements 1`] = `
80
80
  class="css-1m8nxnb-field"
81
81
  >
82
82
  <div
83
- class="css-1y9c7n2-fieldName"
83
+ class="css-1q83rf3-fieldName"
84
84
  >
85
85
  Name
86
86
  </div>
@@ -96,7 +96,7 @@ exports[`renders with just the required model elements 1`] = `
96
96
  class="css-1m8nxnb-field"
97
97
  >
98
98
  <div
99
- class="css-1y9c7n2-fieldName"
99
+ class="css-1q83rf3-fieldName"
100
100
  >
101
101
  Length
102
102
  </div>
@@ -121,7 +121,7 @@ exports[`renders with just the required model elements 1`] = `
121
121
  >
122
122
  <div
123
123
  aria-label="reference base(s): Each base must be one of A,C,G,T,N (case insensitive)."
124
- class="css-1qe2j6j-fieldDescription-fieldName"
124
+ class="css-18vnxxj-fieldDescription-fieldName"
125
125
  data-mui-internal-clone-element="true"
126
126
  >
127
127
  REF
@@ -139,7 +139,7 @@ exports[`renders with just the required model elements 1`] = `
139
139
  >
140
140
  <div
141
141
  aria-label="alternate base(s): Comma-separated list of alternate non-reference alleles"
142
- class="css-1qe2j6j-fieldDescription-fieldName"
142
+ class="css-18vnxxj-fieldDescription-fieldName"
143
143
  data-mui-internal-clone-element="true"
144
144
  >
145
145
  ALT
@@ -157,7 +157,7 @@ exports[`renders with just the required model elements 1`] = `
157
157
  >
158
158
  <div
159
159
  aria-label="quality: Phred-scaled quality score for the assertion made in ALT"
160
- class="css-1qe2j6j-fieldDescription-fieldName"
160
+ class="css-18vnxxj-fieldDescription-fieldName"
161
161
  data-mui-internal-clone-element="true"
162
162
  >
163
163
  QUAL
@@ -174,7 +174,7 @@ exports[`renders with just the required model elements 1`] = `
174
174
  class="css-1m8nxnb-field"
175
175
  >
176
176
  <div
177
- class="css-1y9c7n2-fieldName"
177
+ class="css-1q83rf3-fieldName"
178
178
  style="width: 62px;"
179
179
  >
180
180
  INFO.MQ
package/src/VcfTabixAdapter/VcfTabixAdapter.ts CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  BaseFeatureDataAdapter,
3
3
  BaseOptions,
4
4
  } from '@jbrowse/core/data_adapters/BaseAdapter'
5
- import { FileLocation, NoAssemblyRegion } from '@jbrowse/core/util/types'
5
+ import { NoAssemblyRegion } from '@jbrowse/core/util/types'
6
6
  import { openLocation } from '@jbrowse/core/util/io'
7
7
  import { ObservableCreate } from '@jbrowse/core/util/rxjs'
8
8
  import { Feature } from '@jbrowse/core/util'
@@ -24,7 +24,7 @@ export default class extends BaseFeatureDataAdapter {
24
24
  const location = this.getConf(['index', 'location'])
25
25
  const indexType = this.getConf(['index', 'indexType'])
26
26
 
27
- const filehandle = openLocation(vcfGzLocation as FileLocation, pm)
27
+ const filehandle = openLocation(vcfGzLocation, pm)
28
28
  const isCSI = indexType === 'CSI'
29
29
  const vcf = new TabixIndexedFile({
30
30
  filehandle,