@jbrowse/plugin-variants 2.11.1 → 2.12.0

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/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/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/stateModelFactory.d.ts

@@ -12,13 +12,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
@@ -49,13 +62,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;

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/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/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/stateModelFactory.d.ts

@@ -12,13 +12,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
@@ -49,13 +62,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.11.1",
+  "version": "2.12.0",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -46,7 +46,6 @@
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
-    "@jbrowse/plugin-alignments": "^2.0.0",
     "@jbrowse/plugin-circular-view": "^2.0.0",
     "@jbrowse/plugin-linear-genome-view": "^2.0.0",
     "@mui/material": "^5.0.0",
@@ -63,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
+  "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
 }