@jbrowse/plugin-linear-genome-view 2.11.1 → 2.11.2

package/dist/LinearGenomeView/components/Gridlines.js

@@ -4,7 +4,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const blockTypes_1 = require("@jbrowse/core/util/blockTypes");
 const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
 const Block_1 = require("../../BaseLinearDisplay/components/Block");
@@ -50,13 +49,13 @@ const RenderedVerticalGuides = (0, mobx_react_1.observer)(({ model }) => {
     const { staticBlocks, bpPerPx } = model;
     return (react_1.default.createElement(react_1.default.Fragment, null, staticBlocks.map((block, index) => {
         const k = `${block.key}-${index}`;
-        if (block instanceof blockTypes_1.ContentBlock) {
+        if (block.type === 'ContentBlock') {
             return react_1.default.createElement(RenderedBlockLines, { key: k, block: block, bpPerPx: bpPerPx });
         }
-        else if (block instanceof blockTypes_1.ElidedBlock) {
+        else if (block.type === 'ElidedBlock') {
             return react_1.default.createElement(Block_1.ElidedBlock, { key: k, width: block.widthPx });
         }
-        else if (block instanceof blockTypes_1.InterRegionPaddingBlock) {
+        else if (block.type === 'InterRegionPaddingBlock') {
             return (react_1.default.createElement(Block_1.InterRegionPaddingBlock, { key: k, width: block.widthPx, boundary: block.variant === 'boundary' }));
         }
         return null;

package/dist/LinearGenomeView/components/Highlight.js

@@ -61,26 +61,6 @@ const Highlight = (0, mobx_react_1.observer)(function Highlight({ model, highlig
     const dismissHighlight = () => {
         model.removeHighlight(highlight);
     };
-    const menuItems = [
-        {
-            label: 'Dismiss highlight',
-            icon: Close_1.default,
-            onClick: () => dismissHighlight(),
-        },
-        {
-            label: 'Bookmark highlighted region',
-            icon: Bookmark_1.default,
-            onClick: () => {
-                let bookmarkWidget = session.widgets.get('GridBookmark');
-                if (!bookmarkWidget) {
-                    bookmarkWidget = session.addWidget('GridBookmarkWidget', 'GridBookmark');
-                }
-                // @ts-ignore
-                bookmarkWidget.addBookmark(highlight);
-                dismissHighlight();
-            },
-        },
-    ];
     function handleClose() {
         setOpen(false);
     }
@@ -118,7 +98,26 @@ const Highlight = (0, mobx_react_1.observer)(function Highlight({ model, highlig
         react_1.default.createElement(ui_1.Menu, { anchorEl: anchorEl.current, onMenuItemClick: (_event, callback) => {
                 callback(session);
                 handleClose();
-            }, open: open, onClose: handleClose, menuItems: menuItems }))) : null;
+            }, open: open, onClose: handleClose, menuItems: [
+                {
+                    label: 'Dismiss highlight',
+                    icon: Close_1.default,
+                    onClick: () => dismissHighlight(),
+                },
+                {
+                    label: 'Bookmark highlighted region',
+                    icon: Bookmark_1.default,
+                    onClick: () => {
+                        let bookmarkWidget = session.widgets.get('GridBookmark');
+                        if (!bookmarkWidget) {
+                            bookmarkWidget = session.addWidget('GridBookmarkWidget', 'GridBookmark');
+                        }
+                        // @ts-ignore
+                        bookmarkWidget.addBookmark(highlight);
+                        dismissHighlight();
+                    },
+                },
+            ] }))) : null;
 });
 const HighlightGroup = (0, mobx_react_1.observer)(function HighlightGroup({ model, }) {
     return model.highlight.map((highlight, idx) => (react_1.default.createElement(Highlight, { key: JSON.stringify(highlight) + '-' + idx, model: model, highlight: highlight })));

package/dist/LinearGenomeView/components/OverviewScalebar.js

@@ -33,7 +33,6 @@ const mobx_react_1 = require("mobx-react");
 // core
 const Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DViewModel"));
 const util_1 = require("@jbrowse/core/util");
-const blockTypes_1 = require("@jbrowse/core/util/blockTypes");
 // locals
 const __1 = require("..");
 const util_2 = require("../util");
@@ -176,7 +175,7 @@ const Scalebar = (0, mobx_react_1.observer)(function ({ model, scale, overview,
                 borderColor: color,
             } }),
         overviewVisibleRegions.map((block, idx) => {
-            return !(block instanceof blockTypes_1.ContentBlock) ? (react_1.default.createElement("div", { key: `${JSON.stringify(block)}-${idx}`, className: classes.scalebarContig, style: {
+            return !(block.type === 'ContentBlock') ? (react_1.default.createElement("div", { key: `${JSON.stringify(block)}-${idx}`, className: classes.scalebarContig, style: {
                     width: block.widthPx,
                     left: block.offsetPx,
                     backgroundColor: '#999',

package/dist/LinearGenomeView/components/Scalebar.js

@@ -5,7 +5,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
-const blockTypes_1 = require("@jbrowse/core/util/blockTypes");
 const mobx_react_1 = require("mobx-react");
 const react_1 = __importDefault(require("react"));
 const Block_1 = require("../../BaseLinearDisplay/components/Block");
@@ -61,7 +60,7 @@ const RenderedRefNameLabels = (0, mobx_react_1.observer)(({ model }) => {
         }
     });
     return (react_1.default.createElement(react_1.default.Fragment, null, model.staticBlocks.map((block, index) => {
-        return block instanceof blockTypes_1.ContentBlock &&
+        return block.type === 'ContentBlock' &&
             (block.isLeftEndOfDisplayedRegion || index === lastLeftBlock) ? (react_1.default.createElement(material_1.Typography, { key: `refLabel-${block.key}-${index}`, style: {
                 left: index === lastLeftBlock
                     ? Math.max(0, -model.offsetPx)
@@ -88,13 +87,13 @@ const RenderedScalebarLabels = (0, mobx_react_1.observer)(({ model }) => {
     return (react_1.default.createElement(react_1.default.Fragment, null, staticBlocks.map((block, idx) => {
         const { key, widthPx } = block;
         const k = `${key}-${idx}`;
-        if (block instanceof blockTypes_1.ContentBlock) {
+        if (block.type === 'ContentBlock') {
             return react_1.default.createElement(RenderedBlockTicks, { key: k, block: block, bpPerPx: bpPerPx });
         }
-        else if (block instanceof blockTypes_1.ElidedBlock) {
+        else if (block.type === 'ElidedBlock') {
             return react_1.default.createElement(Block_1.ElidedBlock, { key: k, width: widthPx });
         }
-        else if (block instanceof blockTypes_1.InterRegionPaddingBlock) {
+        else if (block.type === 'InterRegionPaddingBlock') {
             return (react_1.default.createElement(Block_1.InterRegionPaddingBlock, { key: k, width: widthPx, style: { background: 'none' }, boundary: block.variant === 'boundary' }));
         }
         return null;

package/dist/LinearGenomeView/model.d.ts

@@ -364,6 +364,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
         start: number;
         end: number;
+        type: string;
         regionNumber?: number | undefined;
         reversed?: boolean | undefined;
         refName: string;

package/dist/index.d.ts

@@ -143,6 +143,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         defaultValue: string;
                         contextVariable: string[];
                     };
+                    jexlFilters: {
+                        type: string;
+                        description: string;
+                        defaultValue: never[];
+                    };
                 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 rendererTypeName: string;
@@ -258,6 +263,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
                 deleteBlock(key: string): void;
                 selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+                navToFeature(feature: import("@jbrowse/core/util").Feature): void;
                 clearFeatureSelection(): void;
                 setFeatureIdUnderMouse(feature?: string | undefined): void;
                 setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
@@ -355,6 +361,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         defaultValue: string;
                         contextVariable: string[];
                     };
+                    jexlFilters: {
+                        type: string;
+                        description: string;
+                        defaultValue: never[];
+                    };
                 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             }, {
                 rendererTypeName: string;
@@ -470,6 +481,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
                 deleteBlock(key: string): void;
                 selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+                navToFeature(feature: import("@jbrowse/core/util").Feature): void;
                 clearFeatureSelection(): void;
                 setFeatureIdUnderMouse(feature?: string | undefined): void;
                 setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
@@ -567,6 +579,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         defaultValue: string;
                         contextVariable: string[];
                     };
+                    jexlFilters: {
+                        type: string;
+                        description: string;
+                        defaultValue: never[];
+                    };
                 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             }>>, {
                 type: string;
@@ -664,6 +681,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     defaultValue: string;
                     contextVariable: string[];
                 };
+                jexlFilters: {
+                    type: string;
+                    description: string;
+                    defaultValue: never[];
+                };
             }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
         }, {
             rendererTypeName: string;
@@ -779,6 +801,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
             deleteBlock(key: string): void;
             selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+            navToFeature(feature: import("@jbrowse/core/util").Feature): void;
             clearFeatureSelection(): void;
             setFeatureIdUnderMouse(feature?: string | undefined): void;
             setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
@@ -876,6 +899,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     defaultValue: string;
                     contextVariable: string[];
                 };
+                jexlFilters: {
+                    type: string;
+                    description: string;
+                    defaultValue: never[];
+                };
             }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
         }>>, {
             type: string;
@@ -908,6 +936,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 defaultValue: string;
                 contextVariable: string[];
             };
+            jexlFilters: {
+                type: string;
+                description: string;
+                defaultValue: never[];
+            };
         }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
         SearchBox: ({ model, showHelp, }: {
             showHelp?: boolean | undefined;
@@ -1039,6 +1072,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;
@@ -1368,6 +1402,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;
@@ -1737,6 +1772,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;
@@ -2066,6 +2102,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;
@@ -2435,6 +2472,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;
@@ -2764,6 +2802,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
                     start: number;
                     end: number;
+                    type: string;
                     regionNumber?: number | undefined;
                     reversed?: boolean | undefined;
                     refName: string;

package/esm/BaseLinearDisplay/components/LinearBlocks.js

@@ -2,7 +2,6 @@ import React from 'react';
 import { makeStyles } from 'tss-react/mui';
 import { getContainingView } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-import { ContentBlock, ElidedBlock, InterRegionPaddingBlock, } from '@jbrowse/core/util/blockTypes';
 import { ContentBlock as ContentBlockComponent, ElidedBlock as ElidedBlockComponent, InterRegionPaddingBlock as InterRegionPaddingBlockComponent, } from './Block';
 const useStyles = makeStyles()({
     linearBlocks: {
@@ -29,9 +28,10 @@ const RenderedBlocks = observer(function ({ model, }) {
     const { classes } = useStyles();
     const { blockDefinitions, blockState } = model;
     return (React.createElement(React.Fragment, null, blockDefinitions.map(block => {
-        if (block instanceof ContentBlock) {
+        const key = `${model.id}-${block.key}`;
+        if (block.type === 'ContentBlock') {
             const state = blockState.get(block.key);
-            return (React.createElement(ContentBlockComponent, { block: block, key: `${model.id}-${block.key}` },
+            return (React.createElement(ContentBlockComponent, { block: block, key: key },
                 (state === null || state === void 0 ? void 0 : state.ReactComponent) ? (React.createElement(state.ReactComponent, { model: state })) : null,
                 (state === null || state === void 0 ? void 0 : state.maxHeightReached) ? (React.createElement("div", { className: classes.heightOverflowed, style: {
                         top: state.layout.getTotalHeight() - 16,
@@ -39,11 +39,11 @@ const RenderedBlocks = observer(function ({ model, }) {
                         height: 16,
                     } }, "Max height reached")) : null));
         }
-        if (block instanceof ElidedBlock) {
-            return (React.createElement(ElidedBlockComponent, { key: `${model.id}-${block.key}`, width: block.widthPx }));
+        else if (block.type === 'ElidedBlock') {
+            return React.createElement(ElidedBlockComponent, { key: key, width: block.widthPx });
         }
-        if (block instanceof InterRegionPaddingBlock) {
-            return (React.createElement(InterRegionPaddingBlockComponent, { key: block.key, width: block.widthPx, style: { background: 'none' }, boundary: block.variant === 'boundary' }));
+        else if (block.type === 'InterRegionPaddingBlock') {
+            return (React.createElement(InterRegionPaddingBlockComponent, { key: key, width: block.widthPx, style: { background: 'none' }, boundary: block.variant === 'boundary' }));
         }
         throw new Error(`invalid block type ${JSON.stringify(block)}`);
     })));

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -110,6 +110,11 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }, {
     rendererTypeName: string;
@@ -200,7 +205,9 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features"; /**
+     * #action
+     */
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
 } & {
     featureIdUnderMouse: string | undefined;
@@ -273,6 +280,10 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
      * #action
      */
     selectFeature(feature: Feature): void;
+    /**
+     * #action
+     */
+    navToFeature(feature: Feature): void;
     /**
      * #action
      */
@@ -401,6 +412,11 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>>, {
     type: string;

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -7,6 +7,7 @@ import { autorun } from 'mobx';
 import { addDisposer, isAlive, types } from 'mobx-state-tree';
 // icons
 import MenuOpenIcon from '@mui/icons-material/MenuOpen';
+import CenterFocusStrongIcon from '@mui/icons-material/CenterFocusStrong';
 import { Tooltip } from '../components/BaseLinearDisplay';
 import BlockState from './serverSideRenderedBlock';
 import configSchema from './configSchema';
@@ -182,6 +183,17 @@ function stateModelFactory() {
                 session.setSelection(feature);
             }
         },
+        /**
+         * #action
+         */
+        navToFeature(feature) {
+            const view = getContainingView(self);
+            view.navTo({
+                refName: feature.get('refName'),
+                start: feature.get('start'),
+                end: feature.get('end'),
+            });
+        },
         /**
          * #action
          */
@@ -239,6 +251,15 @@ function stateModelFactory() {
                                 }
                             },
                         },
+                        {
+                            label: 'Zoom to feature',
+                            icon: CenterFocusStrongIcon,
+                            onClick: () => {
+                                if (self.contextMenuFeature) {
+                                    self.navToFeature(self.contextMenuFeature);
+                                }
+                            },
+                        },
                     ]
                     : []),
             ];

package/esm/BaseLinearDisplay/models/configSchema.d.ts

@@ -32,5 +32,15 @@ declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration
         defaultValue: string;
         contextVariable: string[];
     };
+    /**
+     * #slot
+     * config jexlFilters are deferred evaluated so they are prepended with
+     * jexl at runtime rather than being stored with jexl in the config
+     */
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 export default baseLinearDisplayConfigSchema;

package/esm/BaseLinearDisplay/models/configSchema.js

@@ -2,9 +2,11 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
 /**
  * #config BaseLinearDisplay
  * #category display
- * `BaseLinearDisplay` is a "base" config that is extended by classes like
- * `LinearBasicDisplay` (used for feature tracks, etc) and `LinearBareDisplay`
- * (more stripped down than even the basic display, not commonly used)
+ *
+ * `BaseLinearDisplay` is a "base" config that is extended by other configs including
+ * - `LinearBasicDisplay` (used for feature tracks, etc)
+ * - `LinearBareDisplay` (more stripped down than even the basic display, not
+ *   commonly used)
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const baseLinearDisplayConfigSchema = ConfigurationSchema('BaseLinearDisplay', {
@@ -41,6 +43,16 @@ const baseLinearDisplayConfigSchema = ConfigurationSchema('BaseLinearDisplay', {
         defaultValue: `jexl:get(feature,'name')`,
         contextVariable: ['feature'],
     },
+    /**
+     * #slot
+     * config jexlFilters are deferred evaluated so they are prepended with
+     * jexl at runtime rather than being stored with jexl in the config
+     */
+    jexlFilters: {
+        type: 'stringArray',
+        description: 'default set of jexl filters to apply to a track. note: these do not use the jexl prefix because they have a deferred evaluation system',
+        defaultValue: [],
+    },
 }, {
     /**
      * #identifier

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js

@@ -96,6 +96,7 @@ const blockState = types
             renderInProgress = undefined;
         },
         setError(error) {
+            console.error(error);
             if (renderInProgress && !renderInProgress.signal.aborted) {
                 renderInProgress.abort();
             }

package/esm/LinearBareDisplay/configSchema.d.ts

@@ -30,5 +30,10 @@ declare function configSchemaFactory(pluginManager: PluginManager): import("@jbr
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
 export { configSchemaFactory };

package/esm/LinearBareDisplay/model.d.ts

@@ -77,7 +77,9 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         };
         fetchSizeLimit: {
             type: string;
-            defaultValue: number;
+            defaultValue: number; /**
+             * #method
+             */
             description: string;
         };
         height: {
@@ -91,6 +93,11 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     /**
@@ -215,6 +222,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
@@ -309,7 +317,9 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         };
         fetchSizeLimit: {
             type: string;
-            defaultValue: number;
+            defaultValue: number; /**
+             * #method
+             */
             description: string;
         };
         height: {
@@ -323,6 +333,11 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;

package/esm/LinearBasicDisplay/components/AddFiltersDialog.d.ts

@@ -0,0 +1,10 @@
+import React from 'react';
+declare const AddFiltersDialog: ({ model, handleClose, }: {
+    model: {
+        jexlFilters?: string[];
+        activeFilters: string[];
+        setJexlFilters: (arg?: string[]) => void;
+    };
+    handleClose: () => void;
+}) => React.JSX.Element;
+export default AddFiltersDialog;

package/esm/LinearBasicDisplay/components/AddFiltersDialog.js

@@ -0,0 +1,69 @@
+import React, { useEffect, useState } from 'react';
+import { observer } from 'mobx-react';
+import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, TextField } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { stringToJexlExpression } from '@jbrowse/core/util/jexlStrings';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+    error: {
+        color: 'red',
+        fontSize: '0.8em',
+    },
+});
+function checkJexl(code) {
+    stringToJexlExpression(code);
+}
+const AddFiltersDialog = observer(function ({ model, handleClose, }) {
+    const { classes } = useStyles();
+    const { activeFilters } = model;
+    const [data, setData] = useState(activeFilters.join('\n'));
+    const [error, setError] = useState();
+    useEffect(() => {
+        try {
+            data
+                .split('\n')
+                .map(line => line.trim())
+                .filter(line => !!line)
+                .map(line => checkJexl(line.trim()));
+            setError(undefined);
+        }
+        catch (e) {
+            console.error(e);
+            setError(e);
+        }
+    }, [data]);
+    return (React.createElement(Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Add track filters" },
+        React.createElement(DialogContent, null,
+            React.createElement("div", null,
+                "Add filters, in jexl format, one per line, starting with the string jexl:. Examples:",
+                ' ',
+                React.createElement("ul", null,
+                    React.createElement("li", null,
+                        React.createElement("code", null, "jexl:get(feature,'name')=='BRCA1'"),
+                        " - show only feature where the name attribute is BRCA1"),
+                    React.createElement("li", null,
+                        React.createElement("code", null, "jexl:get(feature,'type')=='gene'"),
+                        " - show only gene type features in a GFF that has many other feature types"),
+                    React.createElement("li", null,
+                        React.createElement("code", null, "jexl:get(feature,'score') > 400"),
+                        " - show only features that have a score greater than 400"))),
+            error ? React.createElement("p", { className: classes.error }, `${error}`) : null,
+            React.createElement(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => setData(event.target.value), InputProps: {
+                    classes: {
+                        input: classes.textAreaFont,
+                    },
+                } })),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, disabled: !!error, onClick: () => {
+                    model.setJexlFilters(data.split('\n'));
+                    handleClose();
+                } }, "Submit"),
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"))));
+});
+export default AddFiltersDialog;

package/esm/LinearBasicDisplay/components/{SetMaxHeight.js → SetMaxHeightDialog.js}

@@ -15,12 +15,12 @@ const SetMaxHeightDialog = observer(function ({ model, handleClose, }) {
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set max height" },
         React.createElement(DialogContent, { className: classes.root },
             React.createElement(Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
-            React.createElement(TextField, { value: max, onChange: event => setMax(event.target.value), placeholder: "Enter max score" }),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
-                        model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
-                        handleClose();
-                    } }, "Submit"),
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
+            React.createElement(TextField, { value: max, onChange: event => setMax(event.target.value), placeholder: "Enter max score" })),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
+                    model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
+                    handleClose();
+                } }, "Submit"),
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"))));
 });
 export default SetMaxHeightDialog;

package/esm/LinearBasicDisplay/configSchema.d.ts

@@ -30,5 +30,10 @@ declare function configSchemaFactory(pluginManager: PluginManager): import("@jbr
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
 export default configSchemaFactory;