@jbrowse/plugin-variants 2.11.0 → 2.11.2

package/dist/ChordVariantDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ChordVariantDisplayF(pluginManager: PluginManager): void;

package/dist/ChordVariantDisplay/index.js

@@ -8,7 +8,7 @@ const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
 // locals
 const configSchema_1 = __importDefault(require("./models/configSchema"));
 const stateModelFactory_1 = __importDefault(require("./models/stateModelFactory"));
-exports.default = (pluginManager) => {
+function ChordVariantDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         const stateModel = (0, stateModelFactory_1.default)(configSchema);
@@ -22,4 +22,5 @@ exports.default = (pluginManager) => {
             ReactComponent: plugin_circular_view_1.BaseChordDisplayComponent,
         });
     });
-};
+}
+exports.default = ChordVariantDisplayF;

package/dist/LinearVariantDisplay/configSchema.d.ts

@@ -24,6 +24,11 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>;
 export type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;

package/dist/LinearVariantDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearVariantDisplayF(pluginManager: PluginManager): void;

package/dist/LinearVariantDisplay/index.js

@@ -7,7 +7,7 @@ const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view"
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const model_1 = __importDefault(require("./model"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function LinearVariantDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
@@ -20,4 +20,5 @@ exports.default = (pluginManager) => {
             ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
         });
     });
-};
+}
+exports.default = LinearVariantDisplayF;

package/dist/LinearVariantDisplay/model.d.ts

@@ -82,32 +82,32 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             type: string;
             defaultValue: number;
             description: string;
-        }; /**
-         * #property
-         */
+        };
         height: {
             type: string;
             defaultValue: number;
             description: string;
-        }; /**
-         * #action
-         */
+        };
         mouseover: {
             type: string;
             description: string;
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">; /**
-     * #property
-     */
+    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>>;
     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: AnyConfigurationSchemaType;
+    jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
 } & {
     /**
      * #property
@@ -229,6 +229,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
+    navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
@@ -242,6 +243,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
     afterAttach(): void;
 } & {
+    readonly activeFilters: any;
     readonly rendererTypeName: any;
     readonly showLabels: any;
     readonly showDescriptions: any;
@@ -254,6 +256,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
+    setJexlFilters(f?: string[] | undefined): void;
     toggleShowLabels(): void;
     toggleShowDescriptions(): void;
     setDisplayMode(val: string): void;
@@ -265,6 +268,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             setSubschema(slotName: string, data: unknown): any;
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+        filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
     };
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {

package/dist/StructuralVariantChordRenderer/Chord.js

@@ -87,7 +87,7 @@ const Chord = (0, mobx_react_1.observer)(function Chord({ feature, blocksForRefs
         const hoverStrokeColor = (0, configuration_1.readConfObject)(config, 'strokeColorHover', {
             feature,
         });
-        return (react_1.default.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), stroke: hovered ? hoverStrokeColor : strokeColor, strokeWidth: hovered ? 3 : 1, onClick: evt => {
+        return (react_1.default.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), ...(0, util_1.getStrokeProps)(hovered ? hoverStrokeColor : strokeColor), strokeWidth: hovered ? 3 : 1, onClick: evt => {
                 if (endBlock && startBlock) {
                     onClick(feature, startBlock.region, endBlock.region, evt);
                 }

package/dist/StructuralVariantChordRenderer/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function StructuralVariantChordRendererF(pluginManager: PluginManager): void;

package/dist/StructuralVariantChordRenderer/index.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 const ReactComponent_1 = __importDefault(require("./ReactComponent"));
-exports.default = (pluginManager) => {
+function StructuralVariantChordRendererF(pluginManager) {
     pluginManager.addRendererType(() => new CircularChordRendererType_1.default({
         name: 'StructuralVariantChordRenderer',
         displayName: 'SV chord renderer',
@@ -14,4 +14,5 @@ exports.default = (pluginManager) => {
         configSchema: configSchema_1.default,
         pluginManager,
     }));
-};
+}
+exports.default = StructuralVariantChordRendererF;

package/dist/VariantFeatureWidget/AnnotGrid.js

@@ -22,24 +22,16 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const x_data_grid_1 = require("@mui/x-data-grid");
 const material_1 = require("@mui/material");
-const ResizeBar_1 = __importDefault(require("@jbrowse/core/ui/ResizeBar"));
 const util_1 = require("@jbrowse/core/util");
-const useResizeBar_1 = require("@jbrowse/core/ui/useResizeBar");
 function VariantAnnotPanel({ rows, columns, }) {
-    const { ref, scrollLeft } = (0, useResizeBar_1.useResizeBar)();
     const [checked, setChecked] = (0, react_1.useState)(false);
-    const [widths, setWidths] = (0, react_1.useState)(columns.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e.field]))));
-    return rows.length ? (react_1.default.createElement("div", { ref: ref },
+    const widths = columns.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e.field])));
+    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", { ref: ref },
-            react_1.default.createElement(ResizeBar_1.default, { widths: widths, setWidths: setWidths, scrollLeft: scrollLeft }),
-            react_1.default.createElement(x_data_grid_1.DataGrid, { rowHeight: 25, rows: rows, columns: columns.map((c, i) => ({ ...c, width: widths[i] })), slots: { toolbar: checked ? x_data_grid_1.GridToolbar : null } })))) : null;
+        react_1.default.createElement(x_data_grid_1.DataGrid, { rowHeight: 25, rows: rows, columns: columns.map((c, i) => ({ ...c, width: widths[i] })), slots: { toolbar: checked ? x_data_grid_1.GridToolbar : null } }))) : null;
 }
 exports.default = VariantAnnotPanel;

package/dist/VariantFeatureWidget/VariantSampleGrid.js

@@ -22,17 +22,12 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const x_data_grid_1 = require("@mui/x-data-grid");
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const util_1 = require("@jbrowse/core/util");
-const ResizeBar_1 = __importDefault(require("@jbrowse/core/ui/ResizeBar"));
-const useResizeBar_1 = require("@jbrowse/core/ui/useResizeBar");
 function SampleFilters({ columns, filter, setFilter, }) {
     return (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"),
@@ -41,7 +36,6 @@ function SampleFilters({ columns, filter, setFilter, }) {
 function VariantSamples(props) {
     var _a;
     const { feature, descriptions = {} } = props;
-    const { ref, scrollLeft } = (0, useResizeBar_1.useResizeBar)();
     const [filter, setFilter] = (0, react_1.useState)({});
     const samples = (feature.samples || {});
     const preFilteredRows = Object.entries(samples);
@@ -74,7 +68,7 @@ function VariantSamples(props) {
     }
     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 widths = keys.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e])));
     const columns = keys.map((field, index) => {
         var _a, _b;
         return ({
@@ -89,10 +83,8 @@ function VariantSamples(props) {
         error ? react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`) : 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") }),
         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(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 } },
-                } }))));
+        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;

package/dist/VariantFeatureWidget/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VariantFeatureWidgetF(pluginManager: PluginManager): void;

package/dist/VariantFeatureWidget/index.js

@@ -30,7 +30,7 @@ const react_1 = require("react");
 const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
 const stateModelFactory_1 = require("./stateModelFactory");
 const configSchema_1 = require("./configSchema");
-exports.default = (pluginManager) => {
+function VariantFeatureWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => new WidgetType_1.default({
         name: 'VariantFeatureWidget',
         heading: 'Feature details',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         stateModel: (0, stateModelFactory_1.stateModelFactory)(pluginManager),
         ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./VariantFeatureWidget')))),
     }));
-};
+}
+exports.default = VariantFeatureWidgetF;

package/dist/VariantFeatureWidget/stateModelFactory.d.ts

@@ -11,6 +11,17 @@ 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>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
     descriptions: import("mobx-state-tree").IType<any, any, any>;
@@ -37,6 +48,17 @@ 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>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "BaseFeatureWidget";
@@ -46,6 +68,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/dist/VariantTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function VariantTrackF(pm: PluginManager): void;

package/dist/VariantTrack/index.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pm) => {
+function VariantTrackF(pm) {
     pm.addTrackType(() => {
         const configSchema = (0, configSchema_1.default)(pm);
         return new TrackType_1.default({
@@ -16,4 +16,5 @@ exports.default = (pm) => {
             stateModel: (0, models_1.createBaseTrackModel)(pm, 'VariantTrack', configSchema),
         });
     });
-};
+}
+exports.default = VariantTrackF;

package/dist/VcfAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VcfAdapterF(pluginManager: PluginManager): void;

package/dist/VcfAdapter/index.js

@@ -28,11 +28,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function VcfAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'VcfAdapter',
         displayName: 'VCF adapter',
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = VcfAdapterF;

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -3,7 +3,7 @@ import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
-export default class extends BaseFeatureDataAdapter {
+export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     private configured?;
     private configurePre;
     protected configure(): Promise<{

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -10,7 +10,7 @@ const tabix_1 = require("@gmod/tabix");
 const vcf_1 = __importDefault(require("@gmod/vcf"));
 // local
 const VcfFeature_1 = __importDefault(require("../VcfFeature"));
-class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
+class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configurePre() {
         const pm = this.pluginManager;
         const vcfGzLocation = this.getConf('vcfGzLocation');
@@ -71,4 +71,4 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     freeResources( /* { region } */) { }
 }
-exports.default = default_1;
+exports.default = VcfTabixAdapter;

package/dist/VcfTabixAdapter/index.d.ts

@@ -1,4 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
 export { default as configSchema } from './configSchema';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VcfTabixAdapterF(pluginManager: PluginManager): void;

package/dist/VcfTabixAdapter/index.js

@@ -31,11 +31,12 @@ const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
 const configSchema_1 = __importDefault(require("./configSchema"));
 var configSchema_2 = require("./configSchema");
 Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_2).default; } });
-exports.default = (pluginManager) => {
+function VcfTabixAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'VcfTabixAdapter',
         displayName: 'VCF tabix adapter',
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfTabixAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = VcfTabixAdapterF;

package/dist/extensionPoints.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ExtensionPointsF(pluginManager: PluginManager): void;

package/dist/extensionPoints.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const tracks_1 = require("@jbrowse/core/util/tracks");
-exports.default = (pluginManager) => {
+function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.vcf\.b?gz$/i;
@@ -47,4 +47,5 @@ exports.default = (pluginManager) => {
             return adapterGuesser(file, index, adapterHint);
         };
     });
-};
+}
+exports.default = ExtensionPointsF;

package/esm/ChordVariantDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ChordVariantDisplayF(pluginManager: PluginManager): void;

package/esm/ChordVariantDisplay/index.js

@@ -3,7 +3,7 @@ import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 // locals
 import configSchemaF from './models/configSchema';
 import stateModelF from './models/stateModelFactory';
-export default (pluginManager) => {
+export default function ChordVariantDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);
         const stateModel = stateModelF(configSchema);
@@ -17,4 +17,4 @@ export default (pluginManager) => {
             ReactComponent: BaseChordDisplayComponent,
         });
     });
-};
+}

package/esm/LinearVariantDisplay/configSchema.d.ts

@@ -24,6 +24,11 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>;
 export type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;

package/esm/LinearVariantDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearVariantDisplayF(pluginManager: PluginManager): void;

package/esm/LinearVariantDisplay/index.js

@@ -2,7 +2,7 @@ import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import stateModelFactory from './model';
 import configSchemaF from './configSchema';
-export default (pluginManager) => {
+export default function LinearVariantDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);
         return new DisplayType({
@@ -15,4 +15,4 @@ export default (pluginManager) => {
             ReactComponent: BaseLinearDisplayComponent,
         });
     });
-};
+}

package/esm/LinearVariantDisplay/model.d.ts

@@ -82,32 +82,32 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             type: string;
             defaultValue: number;
             description: string;
-        }; /**
-         * #property
-         */
+        };
         height: {
             type: string;
             defaultValue: number;
             description: string;
-        }; /**
-         * #action
-         */
+        };
         mouseover: {
             type: string;
             description: string;
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">; /**
-     * #property
-     */
+    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>>;
     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: AnyConfigurationSchemaType;
+    jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
 } & {
     /**
      * #property
@@ -229,6 +229,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
+    navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
@@ -242,6 +243,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
     afterAttach(): void;
 } & {
+    readonly activeFilters: any;
     readonly rendererTypeName: any;
     readonly showLabels: any;
     readonly showDescriptions: any;
@@ -254,6 +256,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
+    setJexlFilters(f?: string[] | undefined): void;
     toggleShowLabels(): void;
     toggleShowDescriptions(): void;
     setDisplayMode(val: string): void;
@@ -265,6 +268,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             setSubschema(slotName: string, data: unknown): any;
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+        filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
     };
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {

package/esm/StructuralVariantChordRenderer/Chord.js

@@ -1,6 +1,6 @@
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
-import { polarToCartesian } from '@jbrowse/core/util';
+import { polarToCartesian, getStrokeProps } from '@jbrowse/core/util';
 import { readConfObject, } from '@jbrowse/core/configuration';
 import { parseBreakend } from '@gmod/vcf';
 function bpToRadians(block, pos) {
@@ -62,7 +62,7 @@ const Chord = observer(function Chord({ feature, blocksForRefs, radius, config,
         const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
             feature,
         });
-        return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), stroke: hovered ? hoverStrokeColor : strokeColor, strokeWidth: hovered ? 3 : 1, onClick: evt => {
+        return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), ...getStrokeProps(hovered ? hoverStrokeColor : strokeColor), strokeWidth: hovered ? 3 : 1, onClick: evt => {
                 if (endBlock && startBlock) {
                     onClick(feature, startBlock.region, endBlock.region, evt);
                 }

package/esm/StructuralVariantChordRenderer/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function StructuralVariantChordRendererF(pluginManager: PluginManager): void;

package/esm/StructuralVariantChordRenderer/index.js

@@ -1,7 +1,7 @@
 import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
 import configSchema from './configSchema';
 import ReactComponent from './ReactComponent';
-export default (pluginManager) => {
+export default function StructuralVariantChordRendererF(pluginManager) {
     pluginManager.addRendererType(() => new ChordRendererType({
         name: 'StructuralVariantChordRenderer',
         displayName: 'SV chord renderer',
@@ -9,4 +9,4 @@ export default (pluginManager) => {
         configSchema,
         pluginManager,
     }));
-};
+}

package/esm/VariantFeatureWidget/AnnotGrid.js

@@ -1,16 +1,11 @@
 import React, { useState } from 'react';
 import { DataGrid, GridToolbar, } from '@mui/x-data-grid';
 import { Checkbox, FormControlLabel, Typography } from '@mui/material';
-import ResizeBar from '@jbrowse/core/ui/ResizeBar';
 import { measureGridWidth } from '@jbrowse/core/util';
-import { useResizeBar } from '@jbrowse/core/ui/useResizeBar';
 export default function VariantAnnotPanel({ rows, columns, }) {
-    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 },
+    const widths = columns.map(e => measureGridWidth(rows.map(r => r[e.field])));
+    return rows.length ? (React.createElement("div", null,
         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;
+        React.createElement(DataGrid, { rowHeight: 25, rows: rows, columns: columns.map((c, i) => ({ ...c, width: widths[i] })), slots: { toolbar: checked ? GridToolbar : null } }))) : null;
 }

package/esm/VariantFeatureWidget/VariantSampleGrid.js

@@ -3,8 +3,6 @@ import { FormControlLabel, Checkbox, TextField, Typography, } from '@mui/materia
 import { DataGrid, GridToolbar } from '@mui/x-data-grid';
 import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import { measureGridWidth } from '@jbrowse/core/util';
-import ResizeBar from '@jbrowse/core/ui/ResizeBar';
-import { useResizeBar } from '@jbrowse/core/ui/useResizeBar';
 function SampleFilters({ columns, filter, setFilter, }) {
     return (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"),
@@ -13,7 +11,6 @@ function SampleFilters({ columns, filter, setFilter, }) {
 export default function VariantSamples(props) {
     var _a;
     const { feature, descriptions = {} } = props;
-    const { ref, scrollLeft } = useResizeBar();
     const [filter, setFilter] = useState({});
     const samples = (feature.samples || {});
     const preFilteredRows = Object.entries(samples);
@@ -46,7 +43,7 @@ export default function VariantSamples(props) {
     }
     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 widths = keys.map(e => measureGridWidth(rows.map(r => r[e])));
     const columns = keys.map((field, index) => {
         var _a, _b;
         return ({
@@ -61,9 +58,7 @@ export default function VariantSamples(props) {
         error ? React.createElement(Typography, { color: "error" }, `${error}`) : null,
         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(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 } },
-                } }))));
+        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 } },
+            } })));
 }

package/esm/VariantFeatureWidget/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VariantFeatureWidgetF(pluginManager: PluginManager): void;

package/esm/VariantFeatureWidget/index.js

@@ -2,7 +2,7 @@ import { lazy } from 'react';
 import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
 import { stateModelFactory } from './stateModelFactory';
 import { configSchema } from './configSchema';
-export default (pluginManager) => {
+export default function VariantFeatureWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => new WidgetType({
         name: 'VariantFeatureWidget',
         heading: 'Feature details',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         stateModel: stateModelFactory(pluginManager),
         ReactComponent: lazy(() => import('./VariantFeatureWidget')),
     }));
-};
+}

package/esm/VariantFeatureWidget/stateModelFactory.d.ts

@@ -11,6 +11,17 @@ 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>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
     descriptions: import("mobx-state-tree").IType<any, any, any>;
@@ -37,6 +48,17 @@ 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>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "BaseFeatureWidget";
@@ -46,6 +68,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/esm/VariantTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function VariantTrackF(pm: PluginManager): void;

package/esm/VariantTrack/index.js

@@ -1,7 +1,7 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 import configSchemaF from './configSchema';
-export default (pm) => {
+export default function VariantTrackF(pm) {
     pm.addTrackType(() => {
         const configSchema = configSchemaF(pm);
         return new TrackType({
@@ -11,4 +11,4 @@ export default (pm) => {
             stateModel: createBaseTrackModel(pm, 'VariantTrack', configSchema),
         });
     });
-};
+}

package/esm/VcfAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VcfAdapterF(pluginManager: PluginManager): void;

package/esm/VcfAdapter/index.js

@@ -1,10 +1,10 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function VcfAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'VcfAdapter',
         displayName: 'VCF adapter',
         configSchema,
         getAdapterClass: () => import('./VcfAdapter').then(r => r.default),
     }));
-};
+}

package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -3,7 +3,7 @@ import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
-export default class extends BaseFeatureDataAdapter {
+export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     private configured?;
     private configurePre;
     protected configure(): Promise<{

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -5,7 +5,7 @@ import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
 // local
 import VcfFeature from '../VcfFeature';
-export default class extends BaseFeatureDataAdapter {
+export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     async configurePre() {
         const pm = this.pluginManager;
         const vcfGzLocation = this.getConf('vcfGzLocation');

package/esm/VcfTabixAdapter/index.d.ts

@@ -1,4 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
 export { default as configSchema } from './configSchema';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VcfTabixAdapterF(pluginManager: PluginManager): void;

package/esm/VcfTabixAdapter/index.js

@@ -1,11 +1,11 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
 export { default as configSchema } from './configSchema';
-export default (pluginManager) => {
+export default function VcfTabixAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'VcfTabixAdapter',
         displayName: 'VCF tabix adapter',
         configSchema,
         getAdapterClass: () => import('./VcfTabixAdapter').then(r => r.default),
     }));
-};
+}

package/esm/extensionPoints.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ExtensionPointsF(pluginManager: PluginManager): void;

package/esm/extensionPoints.js

@@ -1,5 +1,5 @@
 import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
-export default (pluginManager) => {
+export default function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.vcf\.b?gz$/i;
@@ -45,4 +45,4 @@ export default (pluginManager) => {
             return adapterGuesser(file, index, adapterHint);
         };
     });
-};
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.11.0",
+  "version": "2.11.2",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
+  "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
 }