@jbrowse/plugin-variants 2.4.2 → 2.5.0

package/dist/ChordVariantDisplay/models/configSchema.d.ts

@@ -1,3 +1,15 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    renderer: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IAnyModelType, [undefined]>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    onChordClick: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
 export default stateModelFactory;

package/dist/ChordVariantDisplay/models/stateModelFactory.d.ts

@@ -12,6 +12,14 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
 } & {
     bezierRadiusRatio: import("mobx-state-tree").IType<number | undefined, number, number>;
     assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        onChordClick: {
+            type: string;
+            description: string;
+            defaultValue: boolean;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     /**
      * #property
@@ -20,7 +28,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     /**
      * #property
      */
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
     error: unknown; /**

package/dist/LinearVariantDisplay/configSchema.d.ts

@@ -1,5 +1,29 @@
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderer: import("mobx-state-tree").IAnyModelType;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<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">>, undefined>>, undefined>>;
 export type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>;
 export type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;

package/dist/LinearVariantDisplay/model.d.ts

@@ -61,6 +61,35 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }, 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; /**
+             * #property
+             */
+        }; /**
+         * #property
+         */
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string; /**
+             * #action
+             */
+        };
+        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>>;
@@ -69,7 +98,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
      */
     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
@@ -78,7 +107,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     /**
      * #property
      */
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -137,8 +166,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     message: string;
     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;
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
 } & {
     readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -157,26 +186,26 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
+    readonly featureDensityStatsReady: 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;
+    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;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | 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;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
 } & {

package/dist/StructuralVariantChordRenderer/Chord.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Feature } from '@jbrowse/core/util';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export interface Region {

package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Feature } from '@jbrowse/core/util';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { Block, AnyRegion } from './Chord';

package/dist/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/dist/VariantFeatureWidget/AnnotGrid.d.ts

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

package/dist/VariantFeatureWidget/AnnotGrid.js

@@ -1,22 +1,47 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable @typescript-eslint/no-explicit-any */
-const react_1 = __importDefault(require("react"));
+const react_1 = __importStar(require("react"));
 const x_data_grid_1 = require("@mui/x-data-grid");
+const material_1 = require("@mui/material");
 function VariantAnnotPanel({ rows, columns, }) {
     const rowHeight = 25;
-    const hideFooter = rows.length < 100;
-    const headerHeight = 80;
-    return rows.length ? (react_1.default.createElement("div", { style: {
-            height: Math.min(rows.length, 100) * rowHeight +
-                headerHeight +
-                (hideFooter ? 0 : 50),
-            width: '100%',
-        } },
-        react_1.default.createElement(x_data_grid_1.DataGrid, { rowHeight: rowHeight, rows: rows, columns: columns }))) : null;
+    const headerHeight = 100;
+    const footerHeight = 50;
+    const [checked, setChecked] = (0, react_1.useState)(false);
+    const height = Math.min(rows.length, 100) * rowHeight +
+        headerHeight +
+        (checked ? 50 : 0) +
+        footerHeight;
+    return rows.length ? (react_1.default.createElement("div", null,
+        react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: checked, onChange: event => setChecked(event.target.checked) }), label: react_1.default.createElement(material_1.Typography, { variant: "body2" }, "Show options") }),
+        react_1.default.createElement("div", { style: {
+                height,
+                width: '100%',
+            } },
+            react_1.default.createElement(x_data_grid_1.DataGrid, { rowHeight: rowHeight, rows: rows, columns: columns, slots: { toolbar: checked ? x_data_grid_1.GridToolbar : null } })))) : null;
 }
 exports.default = VariantAnnotPanel;
 //# sourceMappingURL=AnnotGrid.js.map

package/dist/VariantFeatureWidget/AnnotGrid.js.map

@@ -1 +1 @@
-{"version":3,"file":"AnnotGrid.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/AnnotGrid.tsx"],"names":[],"mappings":";;;;;AAAA,uDAAuD;AACvD,kDAAyB;AACzB,kDAA2C;AAE3C,SAAwB,iBAAiB,CAAC,EACxC,IAAI,EACJ,OAAO,GAIR;IACC,MAAM,SAAS,GAAG,EAAE,CAAA;IACpB,MAAM,UAAU,GAAG,IAAI,CAAC,MAAM,GAAG,GAAG,CAAA;IACpC,MAAM,YAAY,GAAG,EAAE,CAAA;IACvB,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CACnB,uCACE,KAAK,EAAE;YACL,MAAM,EACJ,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,CAAC,GAAG,SAAS;gBACtC,YAAY;gBACZ,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YACvB,KAAK,EAAE,MAAM;SACd;QAED,8BAAC,sBAAQ,IAAC,SAAS,EAAE,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,OAAO,EAAE,OAAO,GAAI,CAC5D,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AAvBD,oCAuBC"}
+{"version":3,"file":"AnnotGrid.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/AnnotGrid.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,kDAKyB;AACzB,4CAAsE;AAEtE,SAAwB,iBAAiB,CAAC,EACxC,IAAI,EACJ,OAAO,GAIR;IACC,MAAM,SAAS,GAAG,EAAE,CAAA;IACpB,MAAM,YAAY,GAAG,GAAG,CAAA;IACxB,MAAM,YAAY,GAAG,EAAE,CAAA;IACvB,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,MAAM,GACV,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,CAAC,GAAG,SAAS;QACtC,YAAY;QACZ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;QAClB,YAAY,CAAA;IACd,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CACnB;QACE,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,GACnD,EAEJ,KAAK,EAAE,8BAAC,qBAAU,IAAC,OAAO,EAAC,OAAO,mBAA0B,GAC5D;QACF,uCACE,KAAK,EAAE;gBACL,MAAM;gBACN,KAAK,EAAE,MAAM;aACd;YAED,8BAAC,sBAAQ,IACP,SAAS,EAAE,SAAS,EACpB,IAAI,EAAE,IAAI,EACV,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC,yBAAW,CAAC,CAAC,CAAC,IAAI,EAAE,GAChD,CACE,CACF,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AA1CD,oCA0CC"}

package/dist/VariantFeatureWidget/BreakendOptionDialog.d.ts

@@ -1,10 +1,8 @@
-/// <reference types="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;
+}) => JSX.Element;
 export default _default;

package/dist/VariantFeatureWidget/BreakendOptionDialog.js

@@ -37,14 +37,14 @@ const useStyles = (0, mui_1.makeStyles)()({
         display: 'block',
     },
 });
-function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
+exports.default = (0, mobx_react_1.observer)(function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
     const { classes } = useStyles();
     const [copyTracks, setCopyTracks] = (0, react_1.useState)(true);
     const [mirrorTracks, setMirrorTracks] = (0, react_1.useState)(true);
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Breakpoint split view options" },
         react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: copyTracks, onChange: () => setCopyTracks(val => !val) }), label: "Copy tracks into the new view" }),
-            react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: mirrorTracks, onChange: () => setMirrorTracks(val => !val) }), label: "Mirror tracks vertically in vertically stacked view" })),
+            react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: copyTracks, onChange: event => setCopyTracks(event.target.checked) }), label: "Copy tracks into the new view" }),
+            react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: mirrorTracks, onChange: event => setMirrorTracks(event.target.checked) }), label: "Mirror tracks vertically in vertically stacked view" })),
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { onClick: () => {
                     const { view } = model;
@@ -73,6 +73,5 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
                     handleClose();
                 }, variant: "contained", color: "primary", autoFocus: true }, "OK"),
             react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), color: "secondary", variant: "contained" }, "Cancel"))));
-}
-exports.default = (0, mobx_react_1.observer)(BreakendOptionDialog);
+});
 //# sourceMappingURL=BreakendOptionDialog.js.map

package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 export default function BreakendPanel(props: {
     locStrings: string[];

package/dist/VariantFeatureWidget/VariantAnnPanel.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 export default function VariantAnnPanel({ feature, descriptions, }: {
     feature: any;
     descriptions: any;

package/dist/VariantFeatureWidget/VariantCsqPanel.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 export default function VariantCsqPanel({ feature, descriptions, }: {
     feature: any;
     descriptions: any;

package/dist/VariantFeatureWidget/VariantFeatureWidget.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function VariantFeatureDetails(props: any): JSX.Element;
 declare const _default: typeof VariantFeatureDetails;
 export default _default;

package/dist/VariantFeatureWidget/VariantSampleGrid.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function VariantSamples(props: {
     feature: SimpleFeatureSerialized;

package/dist/VariantFeatureWidget/VariantSampleGrid.js

@@ -30,12 +30,9 @@ const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeature
 const util_1 = require("@jbrowse/core/util");
 const ResizeBar_1 = __importStar(require("@jbrowse/core/ui/ResizeBar"));
 function SampleFilters({ columns, filter, setFilter, }) {
-    const [showFilters, setShowFilters] = (0, react_1.useState)(false);
     return (react_1.default.createElement(react_1.default.Fragment, null,
-        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" }),
-        showFilters ? (react_1.default.createElement(react_1.default.Fragment, null,
-            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"),
-            columns.map(({ field }) => (react_1.default.createElement(material_1.TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }))))) : null));
+        react_1.default.createElement(material_1.Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
+        columns.map(({ field }) => (react_1.default.createElement(material_1.TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) })))));
 }
 function VariantSamples(props) {
     var _a;
@@ -61,9 +58,10 @@ function VariantSamples(props) {
         })
             .filter(row => filters.length
             ? filters.every(key => {
-                const val = row[key];
                 const currFilter = filter[key];
-                return currFilter ? val.match(new RegExp(currFilter, 'i')) : true;
+                return currFilter
+                    ? row[key].match(new RegExp(currFilter, 'i'))
+                    : true;
             })
             : true);
     }
@@ -71,6 +69,7 @@ function VariantSamples(props) {
         error = e;
     }
     const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
+    const [checked, setChecked] = (0, react_1.useState)(false);
     const [widths, setWidths] = (0, react_1.useState)(keys.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e]))));
     const columns = keys.map((field, index) => {
         var _a, _b;
@@ -80,15 +79,17 @@ function VariantSamples(props) {
             width: widths[index],
         });
     });
-    // disableSelectionOnClick helps avoid
+    // disableRowSelectionOnClick helps avoid
     // https://github.com/mui-org/material-ui-x/issues/1197
     return !preFilteredRows.length ? null : (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Samples" },
         error ? react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`) : null,
-        react_1.default.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter }),
+        react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: checked, onChange: event => setChecked(event.target.checked) }), label: react_1.default.createElement(material_1.Typography, { variant: "body2" }, "Show options") }),
+        checked ? (react_1.default.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null,
         react_1.default.createElement("div", { ref: ref },
             react_1.default.createElement(ResizeBar_1.default, { widths: widths, setWidths: setWidths, scrollLeft: scrollLeft }),
-            react_1.default.createElement("div", { ref: ref, style: { height: 600, width: '100%', overflow: 'auto' } },
-                react_1.default.createElement(x_data_grid_1.DataGrid, { rows: rows, columns: columns, disableSelectionOnClick: true, rowHeight: 25, headerHeight: 35, disableColumnMenu: true })))));
+            react_1.default.createElement(x_data_grid_1.DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? x_data_grid_1.GridToolbar : null }, slotProps: {
+                    toolbar: { printOptions: { disableToolbarButton: true } },
+                } }))));
 }
 exports.default = VariantSamples;
 //# sourceMappingURL=VariantSampleGrid.js.map

package/dist/VariantFeatureWidget/VariantSampleGrid.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VariantSampleGrid.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/VariantSampleGrid.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AAEvC,4CAKsB;AAEtB,kDAAwD;AACxD,yFAA4E;AAC5E,6CAA8E;AAC9E,wEAAoE;AAWpE,SAAS,aAAa,CAAC,EACrB,OAAO,EACP,MAAM,EACN,SAAS,GAKV;IACC,OAAO,CACL;QACE,8BAAC,qBAAU,yQAKE;QACZ,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC,CAC1B,8BAAC,oBAAS,IACR,GAAG,EAAE,UAAU,KAAK,EAAE,EACtB,WAAW,EAAE,UAAU,KAAK,EAAE,EAC9B,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,EAAE,EAC1B,QAAQ,EAAE,KAAK,CAAC,EAAE,CAChB,SAAS,CAAC,EAAE,GAAG,MAAM,EAAE,CAAC,KAAK,CAAC,EAAE,KAAK,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,GAEvD,CACH,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAwB,cAAc,CAAC,KAItC;;IACC,MAAM,EAAE,OAAO,EAAE,YAAY,GAAG,EAAE,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,EAAE,GAAG,EAAE,UAAU,EAAE,GAAG,IAAA,wBAAY,GAAE,CAAA;IAC1C,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAU,EAAE,CAAC,CAAA;IACjD,MAAM,OAAO,GAAG,CAAC,OAAO,CAAC,OAAO,IAAI,EAAE,CAA+B,CAAA;IACrE,MAAM,eAAe,GAAG,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAA;IAE/C,IAAI,KAAK,CAAA;IACT,IAAI,IAAI,GAAG,EAAa,CAAA;IACxB,MAAM,OAAO,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IAEnC,qCAAqC;IACrC,wEAAwE;IACxE,4BAA4B;IAC5B,IAAI;QACF,IAAI,GAAG,eAAe;aACnB,GAAG,CAAC,GAAG,CAAC,EAAE;YACT,OAAO;gBACL,GAAG,MAAM,CAAC,WAAW,CACnB,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CACnD;gBACD,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC;gBACd,EAAE,EAAE,GAAG,CAAC,CAAC,CAAC;aACF,CAAA;QACZ,CAAC,CAAC;aACD,MAAM,CAAC,GAAG,CAAC,EAAE,CACZ,OAAO,CAAC,MAAM;YACZ,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE;gBAClB,MAAM,UAAU,GAAG,MAAM,CAAC,GAAG,CAAC,CAAA;gBAC9B,OAAO,UAAU;oBACf,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,MAAM,CAAC,UAAU,EAAE,GAAG,CAAC,CAAC;oBAC7C,CAAC,CAAC,IAAI,CAAA;YACV,CAAC,CAAC;YACJ,CAAC,CAAC,IAAI,CACT,CAAA;KACJ;IAAC,OAAO,CAAC,EAAE;QACV,KAAK,GAAG,CAAC,CAAA;KACV;IAED,MAAM,IAAI,GAAG,CAAC,QAAQ,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA,MAAA,eAAe,CAAC,CAAC,CAAC,0CAAG,CAAC,CAAC,KAAI,EAAE,CAAC,CAAC,CAAA;IACtE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAClC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAA,uBAAgB,EAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACrD,CAAA;IACD,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE;;QAAC,OAAA,CAAC;YAC1C,KAAK;YACL,WAAW,EAAE,MAAA,MAAA,YAAY,CAAC,MAAM,0CAAG,KAAK,CAAC,0CAAE,WAAW;YACtD,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC;SACrB,CAAC,CAAA;KAAA,CAAC,CAAA;IAEH,yCAAyC;IACzC,uDAAuD;IACvD,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACtC,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,SAAS;QACjC,KAAK,CAAC,CAAC,CAAC,8BAAC,qBAAU,IAAC,KAAK,EAAC,OAAO,IAAE,GAAG,KAAK,EAAE,CAAc,CAAC,CAAC,CAAC,IAAI;QACnE,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,GACnD,EAEJ,KAAK,EAAE,8BAAC,qBAAU,IAAC,OAAO,EAAC,OAAO,mBAA0B,GAC5D;QACD,OAAO,CAAC,CAAC,CAAC,CACT,8BAAC,aAAa,IACZ,SAAS,EAAE,SAAS,EACpB,OAAO,EAAE,OAAO,EAChB,MAAM,EAAE,MAAM,GACd,CACH,CAAC,CAAC,CAAC,IAAI;QACR,uCAAK,GAAG,EAAE,GAAG;YACX,8BAAC,mBAAS,IACR,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,SAAS,EACpB,UAAU,EAAE,UAAU,GACtB;YACF,8BAAC,sBAAQ,IACP,IAAI,EAAE,IAAI,EACV,UAAU,EAAE,IAAI,CAAC,MAAM,GAAG,GAAG,EAC7B,OAAO,EAAE,OAAO,EAChB,0BAA0B,QAC1B,SAAS,EAAE,EAAE,EACb,kBAAkB,EAAE,EAAE,EACtB,iBAAiB,QACjB,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC,yBAAW,CAAC,CAAC,CAAC,IAAI,EAAE,EAChD,SAAS,EAAE;oBACT,OAAO,EAAE,EAAE,YAAY,EAAE,EAAE,oBAAoB,EAAE,IAAI,EAAE,EAAE;iBAC1D,GACD,CACE,CACG,CACZ,CAAA;AACH,CAAC;AAjGD,iCAiGC"}

package/dist/VariantFeatureWidget/index.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
@@ -14,10 +14,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
     descriptions: import("mobx-state-tree").IType<any, any, any>;
 }, {
+    error: unknown;
+} & {
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
     setExtra(type?: string | undefined, trackId?: string | undefined): void;
+    setError(e: unknown): void;
 } & {
     afterCreate(): void;
 }, {

package/dist/VariantTrack/configSchema.d.ts

@@ -1,3 +1,75 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
 export default configSchema;

package/dist/VcfAdapter/VcfAdapter.js

@@ -102,6 +102,6 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     freeResources() { }
 }
-exports.default = VcfAdapter;
 VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
+exports.default = VcfAdapter;
 //# sourceMappingURL=VcfAdapter.js.map

package/dist/VcfAdapter/VcfAdapter.js.map

@@ -1 +1 @@
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package/dist/VcfAdapter/configSchema.d.ts

@@ -1,2 +1,13 @@
-declare const VcfAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const VcfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    vcfLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfAdapter;