@jbrowse/plugin-linear-genome-view 2.11.0 → 2.11.2

package/dist/LinearBasicDisplay/model.d.ts

@@ -2,6 +2,7 @@
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { MenuItem } from '@jbrowse/core/ui';
 import { Instance } from 'mobx-state-tree';
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 /**
  * #stateModel LinearBasicDisplay
  * #category display
@@ -50,11 +51,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             model: {
                 error?: unknown;
                 reload: () => void;
-                message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined; /**
-                 * #getter
+                message: import("react").ReactNode; /**
+                 * #property
                  */
+                filled?: boolean | undefined;
+                status?: string | undefined;
                 reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
             };
         }) => import("react").JSX.Element | undefined;
@@ -63,7 +64,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(abortController: AbortController): void; /**
+         * #getter
+         */
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
@@ -94,10 +97,17 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         };
         mouseover: {
             type: string;
-            description: string;
+            description: string; /**
+             * #property
+             */
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     /**
@@ -124,6 +134,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      * #property
      */
     configuration: AnyConfigurationSchemaType;
+    /**
+     * #property
+     */
+    jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -140,7 +154,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
+            type: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             */
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
@@ -166,11 +182,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined; /**
-             * #action
-             */
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }> | null;
+    }> | null; /**
+     * #getter
+     */
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
@@ -208,13 +224,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setCurrStatsBpPerPx(n: number): void;
     setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    setFeatureDensityStatsP(arg: any): void; /**
-     * #method
-     */
+    setFeatureDensityStatsP(arg: any): void;
     setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     clearFeatureDensityStats(): void;
 } & {
-    readonly regionTooLarge: boolean;
+    readonly regionTooLarge: boolean; /**
+     * #method
+     */
     readonly regionTooLargeReason: string;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
@@ -240,6 +256,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     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;
@@ -253,6 +270,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     renderSvg(opts: import("../BaseLinearDisplay").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
     afterAttach(): void;
 } & {
+    /**
+     * #getter
+     */
+    readonly activeFilters: any;
     /**
      * #getter
      */
@@ -283,6 +304,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
+    /**
+     * #action
+     */
+    setJexlFilters(f?: string[]): void;
     /**
      * #action
      */
@@ -309,6 +334,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             setSubschema(slotName: string, data: unknown): any;
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+        filters: SerializableFilterChain;
     };
     /**
      * #method
@@ -355,11 +381,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             model: {
                 error?: unknown;
                 reload: () => void;
-                message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined; /**
-                 * #getter
+                message: import("react").ReactNode; /**
+                 * #property
                  */
+                filled?: boolean | undefined;
+                status?: string | undefined;
                 reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
             };
         }) => import("react").JSX.Element | undefined;
@@ -368,7 +394,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(abortController: AbortController): void; /**
+         * #getter
+         */
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
@@ -399,10 +427,17 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         };
         mouseover: {
             type: string;
-            description: string;
+            description: string; /**
+             * #property
+             */
             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/dist/LinearBasicDisplay/model.js

@@ -34,7 +34,9 @@ const mobx_state_tree_1 = require("mobx-state-tree");
 const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
 // locals
 const BaseLinearDisplay_1 = require("../BaseLinearDisplay");
-const SetMaxHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetMaxHeight'))));
+const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
+const SetMaxHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetMaxHeightDialog'))));
+const AddFiltersDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/AddFiltersDialog'))));
 /**
  * #stateModel LinearBasicDisplay
  * #category display
@@ -71,8 +73,21 @@ function stateModelFactory(configSchema) {
          * #property
          */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
+        /**
+         * #property
+         */
+        jexlFilters: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string)),
     }))
         .views(self => ({
+        /**
+         * #getter
+         */
+        get activeFilters() {
+            var _a;
+            // config jexlFilters are deferred evaluated so they are prepended with
+            // jexl at runtime rather than being stored with jexl in the config
+            return ((_a = self.jexlFilters) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'jexlFilters').map((r) => `jexl:${r}`));
+        },
         /**
          * #getter
          */
@@ -125,6 +140,12 @@ function stateModelFactory(configSchema) {
         },
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
+        setJexlFilters(f) {
+            self.jexlFilters = (0, mobx_state_tree_1.cast)(f);
+        },
         /**
          * #action
          */
@@ -157,12 +178,13 @@ function stateModelFactory(configSchema) {
              * #method
              */
             renderProps() {
-                const config = self.rendererConfig;
                 const superProps = superRenderProps();
-                const superPropsOmit = superProps;
                 return {
-                    ...superPropsOmit,
-                    config,
+                    ...superProps,
+                    config: self.rendererConfig,
+                    filters: new serializableFilterChain_1.default({
+                        filters: self.activeFilters,
+                    }),
                 };
             },
             /**
@@ -207,6 +229,15 @@ function stateModelFactory(configSchema) {
                             ]);
                         },
                     },
+                    {
+                        label: 'Edit filters',
+                        onClick: () => {
+                            (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                AddFiltersDialog,
+                                { model: self, handleClose },
+                            ]);
+                        },
+                    },
                 ];
             },
         };

package/dist/LinearGenomeView/components/Cytobands.js

@@ -8,6 +8,7 @@ const mobx_react_1 = require("mobx-react");
 // locals
 const __1 = require("..");
 const util_1 = require("./util");
+const util_2 = require("@jbrowse/core/util");
 // rounded rect from https://stackoverflow.com/a/45889603/2129219
 // prettier-ignore
 function rightRoundedRect(x, y, width, height, radius) {
@@ -68,28 +69,26 @@ const Cytobands = (0, mobx_react_1.observer)(function ({ overview, block, assemb
         const e = overview.bpToPx({ refName, coord: end }) || 0;
         const l = Math.min(s, e);
         const w = Math.abs(e - s);
-        const c = colorMap[type];
+        const c = colorMap[type] || 'black';
         if (type === 'acen' && !centromereSeen) {
             centromereSeen = true; // the next acen entry is drawn with different right triangle
-            const tri = reversed
-                ? rightTriangle(s - w, 0, w, h)
-                : leftTriangle(s, 0, w, h);
-            return react_1.default.createElement("polygon", { key: k, points: tri, fill: c });
+            return (react_1.default.createElement("polygon", { key: k, points: reversed
+                    ? rightTriangle(s - w, 0, w, h)
+                    : leftTriangle(s, 0, w, h), ...(0, util_2.getFillProps)(c) }));
         }
         else if (type === 'acen' && centromereSeen) {
-            const tri = reversed
-                ? leftTriangle(s - w, 0, w, h)
-                : rightTriangle(s, 0, w, h);
-            return react_1.default.createElement("polygon", { key: k, points: tri, fill: c });
+            return (react_1.default.createElement("polygon", { key: k, points: reversed
+                    ? leftTriangle(s - w, 0, w, h)
+                    : rightTriangle(s, 0, w, h), ...(0, util_2.getFillProps)(c) }));
         }
         else if (lcap === index) {
-            return react_1.default.createElement("path", { key: k, d: leftRoundedRect(l, 0, w, h, 8), fill: c });
+            return (react_1.default.createElement("path", { key: k, d: leftRoundedRect(l, 0, w, h, 8), ...(0, util_2.getFillProps)(c) }));
         }
         else if (rcap === index) {
-            return react_1.default.createElement("path", { key: k, d: rightRoundedRect(l, 0, w, h, 8), fill: c });
+            return (react_1.default.createElement("path", { key: k, d: rightRoundedRect(l, 0, w, h, 8), ...(0, util_2.getFillProps)(c) }));
         }
         else {
-            return react_1.default.createElement("rect", { key: k, x: l, y: 0, width: w, height: h, fill: c });
+            return (react_1.default.createElement("rect", { key: k, x: l, y: 0, width: w, height: h, ...(0, util_2.getFillProps)(c) }));
         }
     })));
 });

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/OverviewScalebarPolygon.js

@@ -8,6 +8,7 @@ const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 // locals
 const __1 = require("..");
+const util_1 = require("@jbrowse/core/util");
 const OverviewScalebarPolygon = (0, mobx_react_1.observer)(function ({ model, overview, useOffset = true, }) {
     const theme = (0, material_1.useTheme)();
     const multiplier = Number(useOffset);
@@ -41,6 +42,6 @@ const OverviewScalebarPolygon = (0, mobx_react_1.observer)(function ({ model, ov
         [topRight, 0],
         [topLeft, 0],
     ];
-    return (react_1.default.createElement("polygon", { points: points.toString(), fill: (0, material_1.alpha)(polygonColor, 0.3), stroke: (0, material_1.alpha)(polygonColor, 0.8) }));
+    return (react_1.default.createElement("polygon", { points: points.toString(), ...(0, util_1.getFillProps)((0, material_1.alpha)(polygonColor, 0.3)), ...(0, util_1.getStrokeProps)((0, material_1.alpha)(polygonColor, 0.8)) }));
 });
 exports.default = OverviewScalebarPolygon;

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/LinearGenomeView/svgcomponents/SVGHeader.js

@@ -47,7 +47,7 @@ function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }) {
         react_1.default.createElement("text", { x: 0, y: 0, dominantBaseline: "hanging", fontSize: fontSize, fill: c }, assemblyName),
         showCytobands ? (react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight})` },
             react_1.default.createElement(Cytobands_1.default, { overview: overview, assembly: assembly, block: block }),
-            react_1.default.createElement("rect", { stroke: "red", fill: "rgb(255,0,0,0.1)", width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: __1.HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
+            react_1.default.createElement("rect", { stroke: "red", fill: "rgb(255,0,0)", fillOpacity: 0.1, width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: __1.HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
             react_1.default.createElement("g", { transform: `translate(0,${__1.HEADER_OVERVIEW_HEIGHT})` },
                 react_1.default.createElement(OverviewScalebarPolygon_1.default, { overview: overview, model: model, useOffset: false })))) : null,
         react_1.default.createElement("g", { transform: `translate(0 ${fontSize + y})` },

package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.js

@@ -8,7 +8,7 @@ const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
 function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }) {
     const theme = (0, material_1.useTheme)();
-    const fill = theme.palette.text.primary;
+    const fill = (0, util_1.stripAlpha)(theme.palette.text.primary);
     const xoff = trackLabels === 'overlay' ? 5 : 0;
     const yoff = trackLabels === 'offset' ? 5 : 0;
     const name = (0, util_1.coarseStripHTML)(trackName);

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;