@jbrowse/plugin-variants 2.4.1 → 2.5.0

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

@@ -1 +1 @@
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+{"version":3,"file":"VariantSampleGrid.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/VariantSampleGrid.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EACL,gBAAgB,EAChB,QAAQ,EACR,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AAEtB,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAA;AACxD,OAAO,EAAE,QAAQ,EAAE,MAAM,mDAAmD,CAAA;AAC5E,OAAO,EAAE,gBAAgB,EAA2B,MAAM,oBAAoB,CAAA;AAC9E,OAAO,SAAS,EAAE,EAAE,YAAY,EAAE,MAAM,4BAA4B,CAAA;AAWpE,SAAS,aAAa,CAAC,EACrB,OAAO,EACP,MAAM,EACN,SAAS,GAKV;IACC,OAAO,CACL;QACE,oBAAC,UAAU,yQAKE;QACZ,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC,CAC1B,oBAAC,SAAS,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,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,KAItC;;IACC,MAAM,EAAE,OAAO,EAAE,YAAY,GAAG,EAAE,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,EAAE,GAAG,EAAE,UAAU,EAAE,GAAG,YAAY,EAAE,CAAA;IAC1C,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAU,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,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAClC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,gBAAgB,CAAC,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,oBAAC,QAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,SAAS;QACjC,KAAK,CAAC,CAAC,CAAC,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,IAAE,GAAG,KAAK,EAAE,CAAc,CAAC,CAAC,CAAC,IAAI;QACnE,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;QACD,OAAO,CAAC,CAAC,CAAC,CACT,oBAAC,aAAa,IACZ,SAAS,EAAE,SAAS,EACpB,OAAO,EAAE,OAAO,EAChB,MAAM,EAAE,MAAM,GACd,CACH,CAAC,CAAC,CAAC,IAAI;QACR,6BAAK,GAAG,EAAE,GAAG;YACX,oBAAC,SAAS,IACR,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,SAAS,EACpB,UAAU,EAAE,UAAU,GACtB;YACF,oBAAC,QAAQ,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,WAAW,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"}

package/esm/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;
 }, {
@@ -33,8 +36,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    id: string;
     type: "BaseFeatureWidget";
+    id: string;
     track: import("mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;

package/esm/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/esm/VcfAdapter/VcfAdapter.js

@@ -25,7 +25,7 @@ const readVcf = (f) => {
 function isGzip(buf) {
     return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
 }
-export default class VcfAdapter extends BaseFeatureDataAdapter {
+class VcfAdapter extends BaseFeatureDataAdapter {
     async getHeader() {
         const { header } = await this.setup();
         return header;
@@ -98,4 +98,5 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     freeResources() { }
 }
 VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
+export default VcfAdapter;
 //# sourceMappingURL=VcfAdapter.js.map

package/esm/VcfAdapter/VcfAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.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;AAC1D,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,GAAG,MAAM,WAAW,CAAA;AAE3B,QAAQ;AACR,OAAO,UAAU,MAAM,eAAe,CAAA;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,sBAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QACtC,MAAM,YAAY,GAAG,EAAqC,CAAA;QAE1D,KAAK,MAAM,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YACvC,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,GAAG,GAAG,CAAC,MAAM,CAAA;YAC9B,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,GAAG,CAAC,CAAA;YACzD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC,EAAE;YACF,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE;gBACtB,YAAY,CAAC,GAAG,CAAC,GAAG,IAAI,YAAY,EAAE,CAAA;aACvC;YACD,YAAY,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;SACpD;QAED,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;gBAClC,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAxFjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA;eADxC,UAAU"}

package/esm/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;

package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -10,7 +10,7 @@ export default class extends BaseFeatureDataAdapter {
         vcf: TabixIndexedFile;
         parser: VcfParser;
     }>;
-    getRefNames(opts?: BaseOptions): Promise<any>;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(): Promise<string>;
     getMetadata(): Promise<any>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;

package/esm/VcfTabixAdapter/configSchema.d.ts

@@ -1,2 +1,33 @@
-declare const VcfTabixAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    vcfGzLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot index.indexType
+         */
+        indexType: {
+            model: import("mobx-state-tree").ISimpleType<string>;
+            type: string;
+            defaultValue: string;
+        };
+        /**
+         * #slot index.location
+         */
+        location: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfTabixAdapter;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.4.1",
+  "version": "2.5.0",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -42,7 +42,7 @@
     "@gmod/tabix": "^1.5.6",
     "@gmod/vcf": "^5.0.9",
     "@mui/icons-material": "^5.0.2",
-    "@mui/x-data-grid": "^5.0.1",
+    "@mui/x-data-grid": "^6.0.1",
     "generic-filehandle": "^3.0.0"
   },
   "peerDependencies": {
@@ -64,5 +64,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
+  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
 }

package/src/LinearVariantDisplay/model.ts

@@ -5,12 +5,12 @@ import {
   getSession,
   getContainingView,
   isSessionModelWithWidgets,
+  Feature,
 } from '@jbrowse/core/util'
 
-import { Feature } from '@jbrowse/core/util/simpleFeature'
 import { linearBasicDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view'
-import { types } from 'mobx-state-tree'
-import { LinearVariantDisplayConfigModel } from './configSchema'
+import { Instance, types } from 'mobx-state-tree'
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 
 /**
  * #stateModel LinearVariantDisplay
@@ -18,7 +18,7 @@ import { LinearVariantDisplayConfigModel } from './configSchema'
  * very similar to basic display, but provides custom widget on feature click
  */
 export default function stateModelFactory(
-  configSchema: LinearVariantDisplayConfigModel,
+  configSchema: AnyConfigurationSchemaType,
 ) {
   return types
     .compose(
@@ -35,6 +35,7 @@ export default function stateModelFactory(
         configuration: ConfigurationReference(configSchema),
       }),
     )
+
     .actions(self => ({
       /**
        * #action
@@ -68,3 +69,8 @@ export default function stateModelFactory(
       },
     }))
 }
+
+export type LinearVariantDisplayStateModel = ReturnType<
+  typeof stateModelFactory
+>
+export type LinearVariantDisplayModel = Instance<LinearVariantDisplayStateModel>

package/src/VariantFeatureWidget/AnnotGrid.tsx

@@ -1,28 +1,52 @@
-/* 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,
+  GridColDef,
+  GridToolbar,
+  GridValidRowModel,
+} from '@mui/x-data-grid'
+import { Checkbox, FormControlLabel, Typography } from '@mui/material'
 
 export default function VariantAnnotPanel({
   rows,
   columns,
 }: {
-  rows: any
-  columns: any[]
+  rows: GridValidRowModel[]
+  columns: GridColDef[]
 }) {
   const rowHeight = 25
-  const hideFooter = rows.length < 100
-  const headerHeight = 80
+  const headerHeight = 100
+  const footerHeight = 50
+  const [checked, setChecked] = useState(false)
+  const height =
+    Math.min(rows.length, 100) * rowHeight +
+    headerHeight +
+    (checked ? 50 : 0) +
+    footerHeight
   return rows.length ? (
-    <div
-      style={{
-        height:
-          Math.min(rows.length, 100) * rowHeight +
-          headerHeight +
-          (hideFooter ? 0 : 50),
-        width: '100%',
-      }}
-    >
-      <DataGrid rowHeight={rowHeight} rows={rows} columns={columns} />
+    <div>
+      <FormControlLabel
+        control={
+          <Checkbox
+            checked={checked}
+            onChange={event => setChecked(event.target.checked)}
+          />
+        }
+        label={<Typography variant="body2">Show options</Typography>}
+      />
+      <div
+        style={{
+          height,
+          width: '100%',
+        }}
+      >
+        <DataGrid
+          rowHeight={rowHeight}
+          rows={rows}
+          columns={columns}
+          slots={{ toolbar: checked ? GridToolbar : null }}
+        />
+      </div>
     </div>
   ) : null
 }

package/src/VariantFeatureWidget/BreakendOptionDialog.tsx

@@ -20,7 +20,7 @@ const useStyles = makeStyles()({
   },
 })
 
-function BreakendOptionDialog({
+export default observer(function BreakendOptionDialog({
   model,
   handleClose,
   feature,
@@ -43,7 +43,7 @@ function BreakendOptionDialog({
           control={
             <Checkbox
               checked={copyTracks}
-              onChange={() => setCopyTracks(val => !val)}
+              onChange={event => setCopyTracks(event.target.checked)}
             />
           }
           label="Copy tracks into the new view"
@@ -54,7 +54,7 @@ function BreakendOptionDialog({
           control={
             <Checkbox
               checked={mirrorTracks}
-              onChange={() => setMirrorTracks(val => !val)}
+              onChange={event => setMirrorTracks(event.target.checked)}
             />
           }
           label="Mirror tracks vertically in vertically stacked view"
@@ -114,5 +114,4 @@ function BreakendOptionDialog({
       </DialogActions>
     </Dialog>
   )
-}
-export default observer(BreakendOptionDialog)
+})

package/src/VariantFeatureWidget/VariantSampleGrid.tsx

@@ -7,7 +7,7 @@ import {
   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, SimpleFeatureSerialized } from '@jbrowse/core/util'
 import ResizeBar, { useResizeBar } from '@jbrowse/core/ui/ResizeBar'
@@ -30,38 +30,24 @@ function SampleFilters({
   filter: Filters
   setFilter: (arg: Filters) => void
 }) {
-  const [showFilters, setShowFilters] = useState(false)
   return (
     <>
-      <FormControlLabel
-        control={
-          <Checkbox
-            checked={showFilters}
-            onChange={() => setShowFilters(f => !f)}
-          />
-        }
-        label="Show sample filters"
-      />
-      {showFilters ? (
-        <>
-          <Typography>
-            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
-          </Typography>
-          {columns.map(({ field }) => (
-            <TextField
-              key={`filter-${field}`}
-              placeholder={`Filter ${field}`}
-              value={filter[field] || ''}
-              onChange={event =>
-                setFilter({ ...filter, [field]: event.target.value })
-              }
-            />
-          ))}
-        </>
-      ) : null}
+      <Typography>
+        These filters can use a plain text search or regex style query, e.g. in
+        the genotype field, entering 1 will query for all genotypes that include
+        the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\d* will find
+        any non-zero allele e.g. 0|2 or 2/33
+      </Typography>
+      {columns.map(({ field }) => (
+        <TextField
+          key={`filter-${field}`}
+          placeholder={`Filter ${field}`}
+          value={filter[field] || ''}
+          onChange={event =>
+            setFilter({ ...filter, [field]: event.target.value })
+          }
+        />
+      ))}
     </>
   )
 }
@@ -98,9 +84,10 @@ 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,
       )
@@ -109,7 +96,7 @@ export default function VariantSamples(props: {
   }
 
   const keys = ['sample', ...Object.keys(preFilteredRows[0]?.[1] || {})]
-
+  const [checked, setChecked] = useState(false)
   const [widths, setWidths] = useState(
     keys.map(e => measureGridWidth(rows.map(r => r[e]))),
   )
@@ -119,28 +106,46 @@ 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 : (
     <BaseCard {...props} title="Samples">
       {error ? <Typography color="error">{`${error}`}</Typography> : null}
-      <SampleFilters setFilter={setFilter} columns={columns} filter={filter} />
+      <FormControlLabel
+        control={
+          <Checkbox
+            checked={checked}
+            onChange={event => setChecked(event.target.checked)}
+          />
+        }
+        label={<Typography variant="body2">Show options</Typography>}
+      />
+      {checked ? (
+        <SampleFilters
+          setFilter={setFilter}
+          columns={columns}
+          filter={filter}
+        />
+      ) : null}
       <div ref={ref}>
         <ResizeBar
           widths={widths}
           setWidths={setWidths}
           scrollLeft={scrollLeft}
         />
-        <div ref={ref} style={{ height: 600, width: '100%', overflow: 'auto' }}>
-          <DataGrid
-            rows={rows}
-            columns={columns}
-            disableSelectionOnClick
-            rowHeight={25}
-            headerHeight={35}
-            disableColumnMenu
-          />
-        </div>
+        <DataGrid
+          rows={rows}
+          hideFooter={rows.length < 100}
+          columns={columns}
+          disableRowSelectionOnClick
+          rowHeight={25}
+          columnHeaderHeight={35}
+          disableColumnMenu
+          slots={{ toolbar: checked ? GridToolbar : null }}
+          slotProps={{
+            toolbar: { printOptions: { disableToolbarButton: true } },
+          }}
+        />
       </div>
     </BaseCard>
   )

package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.tsx.snap

@@ -188,7 +188,7 @@ exports[`renders with just the required model elements 1`] = `
                 </div>
               </div>
               <div
-                class="css-1upvn7b-container2"
+                class="css-1lttu3w-container"
               >
                 <button
                   class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium css-sghohy-MuiButtonBase-root-MuiButton-root"
@@ -224,7 +224,6 @@ exports[`renders with just the required model elements 1`] = `
                     />
                   </button>
                 </div>
-                <br />
               </div>
             </div>
           </div>