@jbrowse/plugin-variants 2.4.2 → 2.6.1

package/esm/LinearVariantDisplay/model.d.ts

@@ -13,6 +13,13 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    /**
+     * #property
+     */
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
@@ -59,17 +66,36 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
     trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
-     * #action
-     */
+    trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
 } & {
     /**
      * #property
@@ -78,10 +104,11 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     /**
      * #property
      */
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
     error: unknown;
+    message: string | undefined;
 } & {
     readonly RenderingComponent: import("react").FC<{
         model: {
@@ -91,6 +118,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -98,6 +126,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
@@ -110,6 +139,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -117,6 +147,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
@@ -126,21 +157,49 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-    regionCannotBeRendered(): undefined;
+    regionCannotBeRendered(): null;
 } & {
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
-    currBpPerPx: number;
     scrollTop: number;
-    message: string;
+} & {
+    readonly height: number;
+} & {
+    setScrollTop(scrollTop: number): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+} & {
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    currStatsBpPerPx: number;
+} & {
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly featureDensityStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    afterAttach(): void;
+} & {
+    setCurrStatsBpPerPx(n: number): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    setFeatureDensityStatsP(arg: any): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    clearFeatureDensityStats(): void;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+} & {
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
-    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -154,49 +213,22 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
-    readonly currentBytesRequested: number;
-    readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
-    readonly maxAllowableBytes: number;
 } & {
-    setMessage(message: string): void;
-} & {
-    afterAttach(): void;
-    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-    setRegionsStatsP(arg: any): void;
-    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionsStats(): void;
-    setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
-    setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
-    setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
-    reload(): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
-} & {
-    readonly regionTooLarge: boolean;
-    readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
 } & {
-    afterAttach(): void;
-} & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
-        overrideHeight: number;
-        theme: import("@mui/material").ThemeOptions;
-    }): Promise<JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    afterAttach(): void;
 } & {
     readonly rendererTypeName: any;
     readonly showLabels: any;

package/esm/StructuralVariantChordRenderer/Chord.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { Feature } from '@jbrowse/core/util';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export interface Region {
@@ -28,5 +28,5 @@ declare const Chord: ({ feature, blocksForRefs, radius, config, bezierRadius, se
     bezierRadius: number;
     selected: boolean;
     onClick: (feature: Feature, reg: AnyRegion, endBlock: AnyRegion, evt: unknown) => void;
-}) => JSX.Element | null;
+}) => React.JSX.Element | null;
 export default Chord;

package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { Feature } from '@jbrowse/core/util';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { Block, AnyRegion } from './Chord';
@@ -13,5 +13,5 @@ declare const _default: ({ features, config, displayModel, blockDefinitions, rad
     blockDefinitions: Block[];
     bezierRadius: number;
     onChordClick: (feature: Feature, reg: AnyRegion, endBlock: AnyRegion, evt: unknown) => void;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;

package/esm/StructuralVariantChordRenderer/configSchema.d.ts

@@ -1,2 +1,30 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    strokeColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    /**
+     * #slot
+     */
+    strokeColorSelected: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    /**
+     * #slot
+     */
+    strokeColorHover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/esm/VariantFeatureWidget/AnnotGrid.d.ts

@@ -1,5 +1,6 @@
-/// <reference types="react" />
+import React from 'react';
+import { GridColDef, GridValidRowModel } from '@mui/x-data-grid';
 export default function VariantAnnotPanel({ rows, columns, }: {
-    rows: any;
-    columns: any[];
-}): JSX.Element | null;
+    rows: GridValidRowModel[];
+    columns: GridColDef[];
+}): React.JSX.Element | null;

package/esm/VariantFeatureWidget/AnnotGrid.js

@@ -1,16 +1,16 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
-import React from 'react';
-import { DataGrid } from '@mui/x-data-grid';
+import React, { useState } from 'react';
+import { DataGrid, GridToolbar, } from '@mui/x-data-grid';
+import { Checkbox, FormControlLabel, Typography } from '@mui/material';
+import ResizeBar, { useResizeBar } from '@jbrowse/core/ui/ResizeBar';
+import { measureGridWidth } from '@jbrowse/core/util';
 export default function VariantAnnotPanel({ rows, columns, }) {
-    const rowHeight = 25;
-    const hideFooter = rows.length < 100;
-    const headerHeight = 80;
-    return rows.length ? (React.createElement("div", { style: {
-            height: Math.min(rows.length, 100) * rowHeight +
-                headerHeight +
-                (hideFooter ? 0 : 50),
-            width: '100%',
-        } },
-        React.createElement(DataGrid, { rowHeight: rowHeight, rows: rows, columns: columns }))) : null;
+    const { ref, scrollLeft } = useResizeBar();
+    const [checked, setChecked] = useState(false);
+    const [widths, setWidths] = useState(columns.map(e => measureGridWidth(rows.map(r => r[e.field]))));
+    return rows.length ? (React.createElement("div", { ref: ref },
+        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: checked, onChange: event => setChecked(event.target.checked) }), label: React.createElement(Typography, { variant: "body2" }, "Show options") }),
+        React.createElement("div", { ref: ref },
+            React.createElement(ResizeBar, { widths: widths, setWidths: setWidths, scrollLeft: scrollLeft }),
+            React.createElement(DataGrid, { rowHeight: 25, rows: rows, columns: columns.map((c, i) => ({ ...c, width: widths[i] })), slots: { toolbar: checked ? GridToolbar : null } })))) : null;
 }
 //# sourceMappingURL=AnnotGrid.js.map

package/esm/VariantFeatureWidget/AnnotGrid.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AnnotGrid.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/AnnotGrid.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EACL,QAAQ,EAER,WAAW,GAEZ,MAAM,kBAAkB,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AACtE,OAAO,SAAS,EAAE,EAAE,YAAY,EAAE,MAAM,4BAA4B,CAAA;AACpE,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAErD,MAAM,CAAC,OAAO,UAAU,iBAAiB,CAAC,EACxC,IAAI,EACJ,OAAO,GAIR;IACC,MAAM,EAAE,GAAG,EAAE,UAAU,EAAE,GAAG,YAAY,EAAE,CAAA;IAC1C,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAClC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,gBAAgB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAC9D,CAAA;IAED,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CACnB,6BAAK,GAAG,EAAE,GAAG;QACX,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,GACnD,EAEJ,KAAK,EAAE,oBAAC,UAAU,IAAC,OAAO,EAAC,OAAO,mBAA0B,GAC5D;QACF,6BAAK,GAAG,EAAE,GAAG;YACX,oBAAC,SAAS,IACR,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,SAAS,EACpB,UAAU,EAAE,UAAU,GACtB;YACF,oBAAC,QAAQ,IACP,SAAS,EAAE,EAAE,EACb,IAAI,EAAE,IAAI,EACV,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAC5D,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,EAAE,GAChD,CACE,CACF,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC"}

package/esm/VariantFeatureWidget/BreakendOptionDialog.d.ts

@@ -1,10 +1,9 @@
-/// <reference types="react" />
+import React from 'react';
 import { Feature } from '@jbrowse/core/util';
-declare function BreakendOptionDialog({ model, handleClose, feature, viewType, }: {
+declare const _default: ({ model, handleClose, feature, viewType, }: {
     model: any;
     handleClose: () => void;
     feature: Feature;
     viewType: any;
-}): JSX.Element;
-declare const _default: typeof BreakendOptionDialog;
+}) => React.JSX.Element;
 export default _default;

package/esm/VariantFeatureWidget/BreakendOptionDialog.js

@@ -12,14 +12,14 @@ const useStyles = makeStyles()({
         display: 'block',
     },
 });
-function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
+export default observer(function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
     const { classes } = useStyles();
     const [copyTracks, setCopyTracks] = useState(true);
     const [mirrorTracks, setMirrorTracks] = useState(true);
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Breakpoint split view options" },
         React.createElement(DialogContent, null,
-            React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: copyTracks, onChange: () => setCopyTracks(val => !val) }), label: "Copy tracks into the new view" }),
-            React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: mirrorTracks, onChange: () => setMirrorTracks(val => !val) }), label: "Mirror tracks vertically in vertically stacked view" })),
+            React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: copyTracks, onChange: event => setCopyTracks(event.target.checked) }), label: "Copy tracks into the new view" }),
+            React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: mirrorTracks, onChange: event => setMirrorTracks(event.target.checked) }), label: "Mirror tracks vertically in vertically stacked view" })),
         React.createElement(DialogActions, null,
             React.createElement(Button, { onClick: () => {
                     const { view } = model;
@@ -48,6 +48,5 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
                     handleClose();
                 }, variant: "contained", color: "primary", autoFocus: true }, "OK"),
             React.createElement(Button, { onClick: () => handleClose(), color: "secondary", variant: "contained" }, "Cancel"))));
-}
-export default observer(BreakendOptionDialog);
+});
 //# sourceMappingURL=BreakendOptionDialog.js.map

package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map

@@ -1 +1 @@
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package/esm/VariantFeatureWidget/BreakendPanel.d.ts

@@ -1,7 +1,7 @@
-/// <reference types="react" />
+import React from 'react';
 import { SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 export default function BreakendPanel(props: {
     locStrings: string[];
     model: any;
     feature: SimpleFeatureSerialized;
-}): JSX.Element;
+}): React.JSX.Element;

package/esm/VariantFeatureWidget/VariantAnnotationTable.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+export default function VariantAnnotationTable({ data, fields, title, }: {
+    data: string[];
+    fields: string[];
+    title: string;
+}): React.JSX.Element | null;

package/esm/VariantFeatureWidget/VariantAnnotationTable.js

@@ -0,0 +1,11 @@
+import React from 'react';
+import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import AnnotGrid from './AnnotGrid';
+export default function VariantAnnotationTable({ data, fields, title, }) {
+    return data.length ? (React.createElement(BaseCard, { title: title },
+        React.createElement(AnnotGrid, { rows: data.map((elt, id) => ({
+                id,
+                ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),
+            })) || [], columns: fields.map(c => ({ field: c })) }))) : null;
+}
+//# sourceMappingURL=VariantAnnotationTable.js.map

package/esm/VariantFeatureWidget/VariantAnnotationTable.js.map

@@ -0,0 +1 @@
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package/esm/VariantFeatureWidget/VariantFeatureWidget.d.ts

@@ -1,4 +1,10 @@
-/// <reference types="react" />
-declare function VariantFeatureDetails(props: any): JSX.Element;
+import React from 'react';
+import { SimpleFeatureSerialized } from '@jbrowse/core/util';
+declare function VariantFeatureDetails(props: {
+    model: {
+        featureData: SimpleFeatureSerialized;
+        descriptions: Record<string, string>;
+    };
+}): React.JSX.Element;
 declare const _default: typeof VariantFeatureDetails;
 export default _default;

package/esm/VariantFeatureWidget/VariantFeatureWidget.js

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
 import React from 'react';
 import { observer } from 'mobx-react';
 import { Divider, Paper } from '@mui/material';
@@ -6,33 +5,46 @@ import { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetai
 import { parseBreakend } from '@gmod/vcf';
 // locals
 import VariantSampleGrid from './VariantSampleGrid';
-import VariantCsqPanel from './VariantCsqPanel';
-import VariantAnnPanel from './VariantAnnPanel';
 import BreakendPanel from './BreakendPanel';
+import VariantAnnotationTable from './VariantAnnotationTable';
+const basicDescriptions = {
+    CHROM: 'chromosome: An identifier from the reference genome',
+    POS: 'position: The reference position, with the 1st base having position 1',
+    ID: 'identifier: Semi-colon separated list of unique identifiers where available',
+    REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
+    ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
+    QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
+    FILTER: 'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
+};
 function VariantFeatureDetails(props) {
     const { model } = props;
     const { featureData, descriptions } = model;
     const feat = JSON.parse(JSON.stringify(featureData));
     const { samples, ...rest } = feat;
-    const basicDescriptions = {
-        CHROM: 'chromosome: An identifier from the reference genome',
-        POS: 'position: The reference position, with the 1st base having position 1',
-        ID: 'identifier: Semi-colon separated list of unique identifiers where available',
-        REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
-        ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
-        QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
-        FILTER: 'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
-    };
     return (React.createElement(Paper, { "data-testid": "variant-side-drawer" },
         React.createElement(FeatureDetails, { feature: rest, descriptions: { ...basicDescriptions, ...descriptions }, ...props }),
         React.createElement(Divider, null),
-        React.createElement(VariantCsqPanel, { feature: rest, descriptions: descriptions }),
+        React.createElement(CsqPanel, { feature: rest, descriptions: descriptions }),
         React.createElement(Divider, null),
-        React.createElement(VariantAnnPanel, { feature: rest, descriptions: descriptions }),
+        React.createElement(AnnPanel, { feature: rest, descriptions: descriptions }),
         React.createElement(Divider, null),
         feat.type === 'breakend' ? (React.createElement(BreakendPanel, { feature: feat, locStrings: feat.ALT.map((alt) => { var _a; return ((_a = parseBreakend(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : null,
         feat.type === 'translocation' ? (React.createElement(BreakendPanel, { feature: feat, model: model, locStrings: [`${feat.INFO.CHR2[0]}:${feat.INFO.END}`] })) : null,
         React.createElement(VariantSampleGrid, { feature: feat, ...props, descriptions: descriptions })));
 }
+function AnnPanel({ descriptions, feature, }) {
+    var _a, _b, _c, _d;
+    const annDesc = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.ANN) === null || _b === void 0 ? void 0 : _b.Description;
+    const annFields = ((_c = annDesc === null || annDesc === void 0 ? void 0 : annDesc.match(/.*Functional annotations:'(.*)'$/)) === null || _c === void 0 ? void 0 : _c[1].split('|')) || [];
+    const ann = ((_d = feature.INFO) === null || _d === void 0 ? void 0 : _d.ANN) || [];
+    return (React.createElement(VariantAnnotationTable, { fields: annFields, data: ann, title: "Variant ANN field" }));
+}
+function CsqPanel({ descriptions, feature, }) {
+    var _a, _b, _c, _d;
+    const csqDescription = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.CSQ) === null || _b === void 0 ? void 0 : _b.Description;
+    const csqFields = ((_c = csqDescription === null || csqDescription === void 0 ? void 0 : csqDescription.match(/.*Format: (.*)/)) === null || _c === void 0 ? void 0 : _c[1].split('|')) || [];
+    const csq = ((_d = feature.INFO) === null || _d === void 0 ? void 0 : _d.CSQ) || [];
+    return (React.createElement(VariantAnnotationTable, { fields: csqFields, data: csq, title: "Variant CSQ field" }));
+}
 export default observer(VariantFeatureDetails);
 //# sourceMappingURL=VariantFeatureWidget.js.map

package/esm/VariantFeatureWidget/VariantFeatureWidget.js.map

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package/esm/VariantFeatureWidget/VariantSampleGrid.d.ts

@@ -1,6 +1,12 @@
-/// <reference types="react" />
+import React from 'react';
 import { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function VariantSamples(props: {
     feature: SimpleFeatureSerialized;
-    descriptions: any;
-}): JSX.Element | null;
+    descriptions: {
+        FORMAT?: {
+            [key: string]: {
+                Description?: string;
+            };
+        };
+    };
+}): React.JSX.Element | null;

package/esm/VariantFeatureWidget/VariantSampleGrid.js

@@ -1,16 +1,13 @@
 import React, { useState } from 'react';
 import { FormControlLabel, Checkbox, TextField, Typography, } from '@mui/material';
-import { DataGrid } from '@mui/x-data-grid';
+import { DataGrid, GridToolbar } from '@mui/x-data-grid';
 import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import { measureGridWidth } from '@jbrowse/core/util';
 import ResizeBar, { useResizeBar } from '@jbrowse/core/ui/ResizeBar';
 function SampleFilters({ columns, filter, setFilter, }) {
-    const [showFilters, setShowFilters] = useState(false);
     return (React.createElement(React.Fragment, null,
-        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
-        showFilters ? (React.createElement(React.Fragment, null,
-            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"),
-            columns.map(({ field }) => (React.createElement(TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }))))) : null));
+        React.createElement(Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
+        columns.map(({ field }) => (React.createElement(TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) })))));
 }
 export default function VariantSamples(props) {
     var _a;
@@ -36,9 +33,10 @@ export default function VariantSamples(props) {
         })
             .filter(row => filters.length
             ? filters.every(key => {
-                const val = row[key];
                 const currFilter = filter[key];
-                return currFilter ? val.match(new RegExp(currFilter, 'i')) : true;
+                return currFilter
+                    ? row[key].match(new RegExp(currFilter, 'i'))
+                    : true;
             })
             : true);
     }
@@ -46,6 +44,7 @@ export default function VariantSamples(props) {
         error = e;
     }
     const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
+    const [checked, setChecked] = useState(false);
     const [widths, setWidths] = useState(keys.map(e => measureGridWidth(rows.map(r => r[e]))));
     const columns = keys.map((field, index) => {
         var _a, _b;
@@ -55,14 +54,16 @@ export default function VariantSamples(props) {
             width: widths[index],
         });
     });
-    // disableSelectionOnClick helps avoid
+    // disableRowSelectionOnClick helps avoid
     // https://github.com/mui-org/material-ui-x/issues/1197
     return !preFilteredRows.length ? null : (React.createElement(BaseCard, { ...props, title: "Samples" },
         error ? React.createElement(Typography, { color: "error" }, `${error}`) : null,
-        React.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter }),
+        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: checked, onChange: event => setChecked(event.target.checked) }), label: React.createElement(Typography, { variant: "body2" }, "Show options") }),
+        checked ? (React.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null,
         React.createElement("div", { ref: ref },
             React.createElement(ResizeBar, { widths: widths, setWidths: setWidths, scrollLeft: scrollLeft }),
-            React.createElement("div", { ref: ref, style: { height: 600, width: '100%', overflow: 'auto' } },
-                React.createElement(DataGrid, { rows: rows, columns: columns, disableSelectionOnClick: true, rowHeight: 25, headerHeight: 35, disableColumnMenu: true })))));
+            React.createElement(DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? GridToolbar : null }, slotProps: {
+                    toolbar: { printOptions: { disableToolbarButton: true } },
+                } }))));
 }
 //# sourceMappingURL=VariantSampleGrid.js.map

package/esm/VariantFeatureWidget/VariantSampleGrid.js.map

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