@jbrowse/plugin-wiggle 2.11.1 → 2.12.0

package/dist/LinePlotRenderer/LinePlotRenderer.d.ts

@@ -1,6 +1,7 @@
+import { Feature } from '@jbrowse/core/util';
 import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
 export default class LinePlotRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<{
-        reducedFeatures: import("@jbrowse/core/util").Feature[];
+        reducedFeatures: Feature[];
     }>;
 }

package/dist/LinePlotRenderer/LinePlotRenderer.js

@@ -3,15 +3,20 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
 const WiggleBaseRenderer_1 = __importDefault(require("../WiggleBaseRenderer"));
 const util_1 = require("../util");
 const drawLine_1 = require("../drawLine");
 class LinePlotRenderer extends WiggleBaseRenderer_1.default {
     async draw(ctx, props) {
+        const { config } = props;
+        const c = (0, configuration_1.readConfObject)(config, 'color');
         return (0, drawLine_1.drawLine)(ctx, {
             ...props,
             offset: util_1.YSCALEBAR_LABEL_OFFSET,
-            colorCallback: () => 'grey',
+            colorCallback: c === '#f0f'
+                ? () => 'grey'
+                : (feature) => (0, configuration_1.readConfObject)(config, 'color', { feature }),
         });
     }
 }

package/dist/LinearWiggleDisplay/components/SetColorDialog.js

@@ -33,8 +33,8 @@ const SetColorDialog = (0, mobx_react_1.observer)(function SetColorDialog({ mode
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set color" },
         react_1.default.createElement(material_1.DialogContent, null,
             react_1.default.createElement(material_1.Typography, null, "Select either an overall color, or the positive/negative colors. Note that density renderers only work properly with positive/negative colors"),
-            react_1.default.createElement(material_1.FormControlLabel, { checked: !posneg, onClick: () => setPosNeg(false), control: react_1.default.createElement(material_1.Radio, null), label: 'Overall color' }),
-            react_1.default.createElement(material_1.FormControlLabel, { checked: posneg, onClick: () => setPosNeg(true), control: react_1.default.createElement(material_1.Radio, null), label: 'Positive/negative color' }),
+            react_1.default.createElement(material_1.FormControlLabel, { checked: !posneg, onClick: () => setPosNeg(false), control: react_1.default.createElement(material_1.Radio, null), label: "Overall color" }),
+            react_1.default.createElement(material_1.FormControlLabel, { checked: posneg, onClick: () => setPosNeg(true), control: react_1.default.createElement(material_1.Radio, null), label: "Positive/negative color" }),
             posneg ? (react_1.default.createElement(react_1.default.Fragment, null,
                 react_1.default.createElement(material_1.Typography, null, "Positive color"),
                 react_1.default.createElement(ColorPicker_1.ColorPicker, { color: model.posColor || 'black', onChange: event => {

package/dist/LinearWiggleDisplay/models/configSchema.d.ts

@@ -69,7 +69,9 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         type: string;
         defaultValue: number;
         description: string;
-    };
+    }; /**
+     * #slot
+     */
     height: {
         type: string;
         defaultValue: number;
@@ -81,4 +83,9 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;

package/dist/LinearWiggleDisplay/models/model.d.ts

@@ -95,6 +95,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -235,6 +240,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     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;

package/dist/MultiLinearWiggleDisplay/components/DraggableDialog.js

@@ -1,9 +1,32 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __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 = __importDefault(require("react"));
+const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
@@ -18,18 +41,19 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         color: theme.palette.grey[500],
     },
 }));
-// draggable dialog demo https://mui.com/material-ui/react-dialog/#draggable-dialog
 function PaperComponent(props) {
-    return (react_1.default.createElement(react_draggable_1.default, { handle: "#draggable-dialog-title", cancel: '[class*="MuiDialogContent-root"]' },
-        react_1.default.createElement(material_1.Paper, { ...props })));
+    const ref = (0, react_1.useRef)(null);
+    return (react_1.default.createElement(react_draggable_1.default, { nodeRef: ref, cancel: '[class*="MuiDialogContent-root"]', 
+        // @ts-expect-error
+        onStart: arg => { var _a, _b; return (_b = (_a = arg.target) === null || _a === void 0 ? void 0 : _a.className) === null || _b === void 0 ? void 0 : _b.includes('MuiDialogTitle'); } },
+        react_1.default.createElement(material_1.Paper, { ref: ref, ...props })));
 }
 const DraggableDialog = (0, mobx_react_1.observer)(function DraggableDialog(props) {
     const { classes } = useStyles();
     const { title, children, onClose } = props;
-    return (react_1.default.createElement(material_1.Dialog, { ...props, PaperComponent: PaperComponent, "aria-labelledby": "draggable-dialog-title" // this area is important for the draggable functionality
-     },
+    return (react_1.default.createElement(material_1.Dialog, { ...props, PaperComponent: PaperComponent },
         react_1.default.createElement(material_1.ScopedCssBaseline, null,
-            react_1.default.createElement(material_1.DialogTitle, { style: { cursor: 'move' }, id: "draggable-dialog-title" },
+            react_1.default.createElement(material_1.DialogTitle, { style: { cursor: 'move' } },
                 title,
                 onClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => {
                         // @ts-expect-error

package/dist/MultiLinearWiggleDisplay/components/SourcesGrid.js

@@ -31,15 +31,15 @@ const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
 const x_data_grid_1 = require("@mui/x-data-grid");
 const mui_1 = require("tss-react/mui");
-// locals
 const ColorPicker_1 = __importStar(require("@jbrowse/core/ui/ColorPicker"));
+const ui_1 = require("@jbrowse/core/ui");
+// locals
 const util_2 = require("./util");
 // icons
 const KeyboardDoubleArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardDoubleArrowUp"));
 const KeyboardDoubleArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardDoubleArrowDown"));
 const KeyboardArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardArrowDown"));
 const KeyboardArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardArrowUp"));
-const ui_1 = require("@jbrowse/core/ui");
 const useStyles = (0, mui_1.makeStyles)()({
     cell: {
         whiteSpace: 'nowrap',
@@ -51,7 +51,6 @@ function SourcesGrid({ rows, onChange, showTips, }) {
     const { classes } = useStyles();
     const [anchorEl, setAnchorEl] = (0, react_1.useState)(null);
     const [selected, setSelected] = (0, react_1.useState)([]);
-    // @ts-expect-error
     const { name: _name, color: _color, baseUri: _baseUri, ...rest } = rows[0];
     const [widgetColor, setWidgetColor] = (0, react_1.useState)('blue');
     const [currSort, setCurrSort] = (0, react_1.useState)({
@@ -100,33 +99,29 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                     },
                     {
                         field: 'name',
-                        sortingOrder: [null],
                         headerName: 'Name',
                         width: (0, util_1.measureGridWidth)(rows.map(r => r.name)),
                     },
                     ...Object.keys(rest).map(val => ({
                         field: val,
-                        sortingOrder: [null],
-                        renderCell: (params) => {
-                            const { value } = params;
-                            return (react_1.default.createElement("div", { className: classes.cell },
-                                react_1.default.createElement(ui_1.SanitizedHTML, { html: (0, util_1.getStr)(value) })));
-                        },
-                        // @ts-ignore
-                        width: (0, util_1.measureGridWidth)(rows.map(r => r[val])),
+                        renderCell: ({ value }) => (react_1.default.createElement("div", { className: classes.cell },
+                            react_1.default.createElement(ui_1.SanitizedHTML, { html: (0, util_1.getStr)(value) }))),
+                        width: (0, util_1.measureGridWidth)(rows.map(r => `${r[val]}`)),
                     })),
                 ], sortModel: [
                 /* we control the sort as a controlled component using onSortModelChange */
                 ], onSortModelChange: args => {
                     const sort = args[0];
+                    // this idx%2 flip flops the sorting order, we could inspect args
+                    // for sort direction asc or desc but this is just a simplified
+                    // thing since we are controlling sort instead of the default data
+                    // grid sort anyways
                     const idx = (currSort.idx + 1) % 2;
                     const field = (sort === null || sort === void 0 ? void 0 : sort.field) || currSort.field;
                     setCurrSort({ idx, field });
                     onChange(field
                         ? [...rows].sort((a, b) => {
-                            // @ts-expect-error
                             const aa = (0, util_1.getStr)(a[field]);
-                            // @ts-expect-error
                             const bb = (0, util_1.getStr)(b[field]);
                             return idx === 1
                                 ? aa.localeCompare(bb)

package/dist/MultiLinearWiggleDisplay/models/configSchema.d.ts

@@ -78,11 +78,18 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         type: string;
         defaultValue: number;
         description: string;
-    };
+    }; /**
+     * #slot
+     */
     mouseover: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;

package/dist/MultiLinearWiggleDisplay/models/model.d.ts

@@ -101,7 +101,14 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
             defaultValue: string;
             contextVariable: string[];
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>; /**
+     * #action
+     */
 } & {
     selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -249,6 +256,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     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;

package/dist/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js

@@ -80,7 +80,10 @@ function MultiWiggleWidget({ model }) {
                     bigWigs = JSON.parse(val);
                 }
                 catch (e) {
-                    bigWigs = val.split(/\n|\r\n|\r/);
+                    bigWigs = val
+                        .split(/\n|\r\n|\r/)
+                        .map(f => f.trim())
+                        .filter(f => !!f);
                 }
                 const obj = typeof bigWigs[0] === 'string'
                     ? { bigWigs }

package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts

@@ -16,5 +16,5 @@ export declare class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType
         headers?: Record<string, string>;
         regions: Region[];
         bpPerPx: number;
-    }, rpcDriverClassName: string): Promise<import("@jbrowse/core/util/stats").QuantitativeStats>;
+    }, rpcDriverClassName: string): Promise<any>;
 }

package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js

@@ -8,7 +8,6 @@ const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementT
 const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const util_1 = require("@jbrowse/core/util");
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType_1.default {
     constructor() {
         super(...arguments);
@@ -44,10 +43,8 @@ class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType_1.default {
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
         const { regions, adapterConfig, sessionId } = deserializedArgs;
         const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
-        if (dataAdapter instanceof BaseAdapter_1.BaseFeatureDataAdapter) {
-            return dataAdapter.getMultiRegionQuantitativeStats(regions, deserializedArgs);
-        }
-        throw new Error('Data adapter not found');
+        // @ts-expect-error
+        return dataAdapter.getMultiRegionQuantitativeStats(regions, deserializedArgs);
     }
 }
 exports.WiggleGetMultiRegionQuantitativeStats = WiggleGetMultiRegionQuantitativeStats;

package/dist/index.d.ts

@@ -148,6 +148,11 @@ export default class WigglePlugin extends Plugin {
                         defaultValue: string;
                         contextVariable: string[];
                     };
+                    jexlFilters: {
+                        type: string;
+                        description: string;
+                        defaultValue: never[];
+                    };
                 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">> & import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
                 selectedRendering: string;
                 resolution: number;
@@ -280,6 +285,7 @@ export default class WigglePlugin 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;
@@ -525,6 +531,11 @@ export default class WigglePlugin extends Plugin {
                         defaultValue: string;
                         contextVariable: string[];
                     };
+                    jexlFilters: {
+                        type: string;
+                        description: string;
+                        defaultValue: never[];
+                    };
                 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             } & {
                 selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -658,6 +669,7 @@ export default class WigglePlugin 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;

package/dist/shared/configShared.d.ts

@@ -71,7 +71,9 @@ export default function sharedWiggleConfigFactory(): import("@jbrowse/core/confi
     fetchSizeLimit: {
         type: string;
         defaultValue: number;
-        description: string;
+        description: string; /**
+         * #slot
+         */
     };
     height: {
         type: string;
@@ -84,4 +86,9 @@ export default function sharedWiggleConfigFactory(): import("@jbrowse/core/confi
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/dist/shared/modelShared.d.ts

@@ -76,7 +76,9 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         fetchSizeLimit: {
             type: string;
             defaultValue: number;
-            description: string;
+            description: string; /**
+             * #property
+             */
         };
         height: {
             type: string;
@@ -89,6 +91,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     /**
@@ -268,13 +275,15 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     readonly featureUnderMouse: Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    /**
+     * #action
+     */
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void; /**
-     * #getter
-     */
+    selectFeature(feature: Feature): void;
+    navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
@@ -283,12 +292,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
 } & {
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    renderProps(): any; /**
-     * #getter
-     */
+    renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>; /**
-     * #getter
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    /**
+     * #method
      */
     afterAttach(): void;
 } & {
@@ -563,7 +571,9 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         fetchSizeLimit: {
             type: string;
             defaultValue: number;
-            description: string;
+            description: string; /**
+             * #property
+             */
         };
         height: {
             type: string;
@@ -576,6 +586,11 @@ export default function SharedWiggleMixin(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/dist/util.d.ts

@@ -9,6 +9,7 @@ export interface ScaleOpts {
     inverted?: boolean;
 }
 export interface Source {
+    baseUri?: string;
     name: string;
     color?: string;
     group?: string;

package/esm/LinePlotRenderer/LinePlotRenderer.d.ts

@@ -1,6 +1,7 @@
+import { Feature } from '@jbrowse/core/util';
 import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
 export default class LinePlotRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<{
-        reducedFeatures: import("@jbrowse/core/util").Feature[];
+        reducedFeatures: Feature[];
     }>;
 }

package/esm/LinePlotRenderer/LinePlotRenderer.js

@@ -1,12 +1,17 @@
+import { readConfObject } from '@jbrowse/core/configuration';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
 import { YSCALEBAR_LABEL_OFFSET } from '../util';
 import { drawLine } from '../drawLine';
 export default class LinePlotRenderer extends WiggleBaseRenderer {
     async draw(ctx, props) {
+        const { config } = props;
+        const c = readConfObject(config, 'color');
         return drawLine(ctx, {
             ...props,
             offset: YSCALEBAR_LABEL_OFFSET,
-            colorCallback: () => 'grey',
+            colorCallback: c === '#f0f'
+                ? () => 'grey'
+                : (feature) => readConfObject(config, 'color', { feature }),
         });
     }
 }

package/esm/LinearWiggleDisplay/components/SetColorDialog.js

@@ -8,8 +8,8 @@ const SetColorDialog = observer(function SetColorDialog({ model, handleClose, })
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set color" },
         React.createElement(DialogContent, null,
             React.createElement(Typography, null, "Select either an overall color, or the positive/negative colors. Note that density renderers only work properly with positive/negative colors"),
-            React.createElement(FormControlLabel, { checked: !posneg, onClick: () => setPosNeg(false), control: React.createElement(Radio, null), label: 'Overall color' }),
-            React.createElement(FormControlLabel, { checked: posneg, onClick: () => setPosNeg(true), control: React.createElement(Radio, null), label: 'Positive/negative color' }),
+            React.createElement(FormControlLabel, { checked: !posneg, onClick: () => setPosNeg(false), control: React.createElement(Radio, null), label: "Overall color" }),
+            React.createElement(FormControlLabel, { checked: posneg, onClick: () => setPosNeg(true), control: React.createElement(Radio, null), label: "Positive/negative color" }),
             posneg ? (React.createElement(React.Fragment, null,
                 React.createElement(Typography, null, "Positive color"),
                 React.createElement(ColorPicker, { color: model.posColor || 'black', onChange: event => {

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

@@ -69,7 +69,9 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         type: string;
         defaultValue: number;
         description: string;
-    };
+    }; /**
+     * #slot
+     */
     height: {
         type: string;
         defaultValue: number;
@@ -81,4 +83,9 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;

package/esm/LinearWiggleDisplay/models/model.d.ts

@@ -95,6 +95,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -235,6 +240,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     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;

package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import React, { useRef } from 'react';
 import { Dialog, DialogTitle, IconButton, Divider, Paper, ScopedCssBaseline, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
@@ -13,18 +13,19 @@ const useStyles = makeStyles()(theme => ({
         color: theme.palette.grey[500],
     },
 }));
-// draggable dialog demo https://mui.com/material-ui/react-dialog/#draggable-dialog
 function PaperComponent(props) {
-    return (React.createElement(Draggable, { handle: "#draggable-dialog-title", cancel: '[class*="MuiDialogContent-root"]' },
-        React.createElement(Paper, { ...props })));
+    const ref = useRef(null);
+    return (React.createElement(Draggable, { nodeRef: ref, cancel: '[class*="MuiDialogContent-root"]', 
+        // @ts-expect-error
+        onStart: arg => { var _a, _b; return (_b = (_a = arg.target) === null || _a === void 0 ? void 0 : _a.className) === null || _b === void 0 ? void 0 : _b.includes('MuiDialogTitle'); } },
+        React.createElement(Paper, { ref: ref, ...props })));
 }
 const DraggableDialog = observer(function DraggableDialog(props) {
     const { classes } = useStyles();
     const { title, children, onClose } = props;
-    return (React.createElement(Dialog, { ...props, PaperComponent: PaperComponent, "aria-labelledby": "draggable-dialog-title" // this area is important for the draggable functionality
-     },
+    return (React.createElement(Dialog, { ...props, PaperComponent: PaperComponent },
         React.createElement(ScopedCssBaseline, null,
-            React.createElement(DialogTitle, { style: { cursor: 'move' }, id: "draggable-dialog-title" },
+            React.createElement(DialogTitle, { style: { cursor: 'move' } },
                 title,
                 onClose ? (React.createElement(IconButton, { className: classes.closeButton, onClick: () => {
                         // @ts-expect-error

package/esm/MultiLinearWiggleDisplay/components/SourcesGrid.js

@@ -3,15 +3,15 @@ import { Button } from '@mui/material';
 import { getStr, measureGridWidth } from '@jbrowse/core/util';
 import { DataGrid } from '@mui/x-data-grid';
 import { makeStyles } from 'tss-react/mui';
-// locals
 import ColorPicker, { ColorPopover } from '@jbrowse/core/ui/ColorPicker';
+import { SanitizedHTML } from '@jbrowse/core/ui';
+// locals
 import { moveUp, moveDown } from './util';
 // icons
 import KeyboardDoubleArrowUpIcon from '@mui/icons-material/KeyboardDoubleArrowUp';
 import KeyboardDoubleArrowDownIcon from '@mui/icons-material/KeyboardDoubleArrowDown';
 import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown';
 import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp';
-import { SanitizedHTML } from '@jbrowse/core/ui';
 const useStyles = makeStyles()({
     cell: {
         whiteSpace: 'nowrap',
@@ -23,7 +23,6 @@ function SourcesGrid({ rows, onChange, showTips, }) {
     const { classes } = useStyles();
     const [anchorEl, setAnchorEl] = useState(null);
     const [selected, setSelected] = useState([]);
-    // @ts-expect-error
     const { name: _name, color: _color, baseUri: _baseUri, ...rest } = rows[0];
     const [widgetColor, setWidgetColor] = useState('blue');
     const [currSort, setCurrSort] = useState({
@@ -72,33 +71,29 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                     },
                     {
                         field: 'name',
-                        sortingOrder: [null],
                         headerName: 'Name',
                         width: measureGridWidth(rows.map(r => r.name)),
                     },
                     ...Object.keys(rest).map(val => ({
                         field: val,
-                        sortingOrder: [null],
-                        renderCell: (params) => {
-                            const { value } = params;
-                            return (React.createElement("div", { className: classes.cell },
-                                React.createElement(SanitizedHTML, { html: getStr(value) })));
-                        },
-                        // @ts-ignore
-                        width: measureGridWidth(rows.map(r => r[val])),
+                        renderCell: ({ value }) => (React.createElement("div", { className: classes.cell },
+                            React.createElement(SanitizedHTML, { html: getStr(value) }))),
+                        width: measureGridWidth(rows.map(r => `${r[val]}`)),
                     })),
                 ], sortModel: [
                 /* we control the sort as a controlled component using onSortModelChange */
                 ], onSortModelChange: args => {
                     const sort = args[0];
+                    // this idx%2 flip flops the sorting order, we could inspect args
+                    // for sort direction asc or desc but this is just a simplified
+                    // thing since we are controlling sort instead of the default data
+                    // grid sort anyways
                     const idx = (currSort.idx + 1) % 2;
                     const field = (sort === null || sort === void 0 ? void 0 : sort.field) || currSort.field;
                     setCurrSort({ idx, field });
                     onChange(field
                         ? [...rows].sort((a, b) => {
-                            // @ts-expect-error
                             const aa = getStr(a[field]);
-                            // @ts-expect-error
                             const bb = getStr(b[field]);
                             return idx === 1
                                 ? aa.localeCompare(bb)

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

@@ -78,11 +78,18 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         type: string;
         defaultValue: number;
         description: string;
-    };
+    }; /**
+     * #slot
+     */
     mouseover: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;

package/esm/MultiLinearWiggleDisplay/models/model.d.ts

@@ -101,7 +101,14 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
             defaultValue: string;
             contextVariable: string[];
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>; /**
+     * #action
+     */
 } & {
     selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -249,6 +256,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     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;

package/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js

@@ -55,7 +55,10 @@ export default function MultiWiggleWidget({ model }) {
                     bigWigs = JSON.parse(val);
                 }
                 catch (e) {
-                    bigWigs = val.split(/\n|\r\n|\r/);
+                    bigWigs = val
+                        .split(/\n|\r\n|\r/)
+                        .map(f => f.trim())
+                        .filter(f => !!f);
                 }
                 const obj = typeof bigWigs[0] === 'string'
                     ? { bigWigs }

package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts

@@ -16,5 +16,5 @@ export declare class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType
         headers?: Record<string, string>;
         regions: Region[];
         bpPerPx: number;
-    }, rpcDriverClassName: string): Promise<import("@jbrowse/core/util/stats").QuantitativeStats>;
+    }, rpcDriverClassName: string): Promise<any>;
 }

package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js

@@ -2,7 +2,6 @@ import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { renameRegionsIfNeeded } from '@jbrowse/core/util';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 export class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType {
     constructor() {
         super(...arguments);
@@ -38,9 +37,7 @@ export class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType {
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
         const { regions, adapterConfig, sessionId } = deserializedArgs;
         const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
-        if (dataAdapter instanceof BaseFeatureDataAdapter) {
-            return dataAdapter.getMultiRegionQuantitativeStats(regions, deserializedArgs);
-        }
-        throw new Error('Data adapter not found');
+        // @ts-expect-error
+        return dataAdapter.getMultiRegionQuantitativeStats(regions, deserializedArgs);
     }
 }

package/esm/index.d.ts

@@ -148,6 +148,11 @@ export default class WigglePlugin extends Plugin {
                         defaultValue: string;
                         contextVariable: string[];
                     };
+                    jexlFilters: {
+                        type: string;
+                        description: string;
+                        defaultValue: never[];
+                    };
                 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">> & import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
                 selectedRendering: string;
                 resolution: number;
@@ -280,6 +285,7 @@ export default class WigglePlugin 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;
@@ -525,6 +531,11 @@ export default class WigglePlugin extends Plugin {
                         defaultValue: string;
                         contextVariable: string[];
                     };
+                    jexlFilters: {
+                        type: string;
+                        description: string;
+                        defaultValue: never[];
+                    };
                 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             } & {
                 selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -658,6 +669,7 @@ export default class WigglePlugin 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;

package/esm/shared/configShared.d.ts

@@ -71,7 +71,9 @@ export default function sharedWiggleConfigFactory(): import("@jbrowse/core/confi
     fetchSizeLimit: {
         type: string;
         defaultValue: number;
-        description: string;
+        description: string; /**
+         * #slot
+         */
     };
     height: {
         type: string;
@@ -84,4 +86,9 @@ export default function sharedWiggleConfigFactory(): import("@jbrowse/core/confi
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/esm/shared/modelShared.d.ts

@@ -76,7 +76,9 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         fetchSizeLimit: {
             type: string;
             defaultValue: number;
-            description: string;
+            description: string; /**
+             * #property
+             */
         };
         height: {
             type: string;
@@ -89,6 +91,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     /**
@@ -268,13 +275,15 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     readonly featureUnderMouse: Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    /**
+     * #action
+     */
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void; /**
-     * #getter
-     */
+    selectFeature(feature: Feature): void;
+    navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
@@ -283,12 +292,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
 } & {
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    renderProps(): any; /**
-     * #getter
-     */
+    renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>; /**
-     * #getter
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    /**
+     * #method
      */
     afterAttach(): void;
 } & {
@@ -563,7 +571,9 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         fetchSizeLimit: {
             type: string;
             defaultValue: number;
-            description: string;
+            description: string; /**
+             * #property
+             */
         };
         height: {
             type: string;
@@ -576,6 +586,11 @@ export default function SharedWiggleMixin(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/util.d.ts

@@ -9,6 +9,7 @@ export interface ScaleOpts {
     inverted?: boolean;
 }
 export interface Source {
+    baseUri?: string;
     name: string;
     color?: string;
     group?: string;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "2.11.1",
+  "version": "2.12.0",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -39,6 +39,7 @@
     "@floating-ui/react": "^0.26.3",
     "@gmod/bbi": "^4.0.0",
     "@mui/icons-material": "^5.0.2",
+    "@mui/x-data-grid": "^7.0.0",
     "clone": "^2.1.2",
     "d3-color": "^3.0.2",
     "d3-scale": "^3.0.2",
@@ -52,7 +53,6 @@
     "@jbrowse/plugin-data-management": "^2.0.0",
     "@jbrowse/plugin-linear-genome-view": "^2.0.0",
     "@mui/material": "^5.0.0",
-    "@mui/x-data-grid": "^7.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -66,5 +66,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
+  "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
 }