@jbrowse/plugin-wiggle 2.4.1 → 2.5.0

package/dist/LinearWiggleDisplay/models/model.js.map

@@ -1 +1 @@
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package/dist/MultiDensityRenderer/configSchema.d.ts

@@ -1,2 +1,34 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/dist/MultiLineRenderer/configSchema.d.ts

@@ -1,2 +1,52 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    displayCrossHatches: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    summaryScoreMode: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/dist/MultiLinearWiggleDisplay/components/DraggableDialog.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { DialogProps } from '@mui/material';
 declare function DraggableDialog(props: DialogProps & {
     title: string;

package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Source } from '../../util';
 export default function SetColorDialog({ model, handleClose, }: {
     model: {

package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js

@@ -87,43 +87,11 @@ function SourcesGrid({ rows, onChange, showTips, }) {
     const [selected, setSelected] = (0, react_1.useState)([]);
     // @ts-expect-error
     const { name: _name, color: _color, baseUri: _baseUri, ...rest } = rows[0];
-    // similar to BaseFeatureDetail data-grid for auto-measuring columns
-    const columns = [
-        {
-            field: 'color',
-            headerName: 'Color',
-            renderCell: (params) => {
-                const { value, id } = params;
-                return (react_1.default.createElement(ColorPicker_1.default, { color: value || 'blue', onChange: c => {
-                        const elt = rows.find(f => f.name === id);
-                        if (elt) {
-                            elt.color = c;
-                        }
-                        onChange([...rows]);
-                    } }));
-            },
-        },
-        {
-            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 (0, util_1.isUriLocation)(value) ? react_1.default.createElement(BaseFeatureDetail_1.UriLink, { value: value }) : (0, util_1.getStr)(value);
-            },
-            // @ts-expect-error
-            width: (0, util_1.measureGridWidth)(rows.map(r => r[val])),
-        })),
-    ];
-    // this helps keep track of the selection, even though it is not used
-    // anywhere except inside the picker
     const [widgetColor, setWidgetColor] = (0, react_1.useState)('blue');
-    const [currSort, setCurrSort] = (0, react_1.useState)({ idx: 0, field: null });
+    const [currSort, setCurrSort] = (0, react_1.useState)({
+        idx: 0,
+        field: null,
+    });
     return (react_1.default.createElement("div", null,
         react_1.default.createElement(material_1.Button, { disabled: !selected.length, onClick: event => setAnchorEl(event.currentTarget) }, "Change color of selected items"),
         react_1.default.createElement(material_1.Button, { onClick: () => onChange((0, util_2.moveUp)([...rows], selected)), disabled: !selected.length },
@@ -149,7 +117,38 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                 onChange([...rows]);
             }, onClose: () => setAnchorEl(null) }),
         react_1.default.createElement("div", { style: { height: 400, width: '100%' } },
-            react_1.default.createElement(x_data_grid_1.DataGrid, { getRowId: row => row.name, checkboxSelection: true, disableSelectionOnClick: true, onSelectionModelChange: arg => setSelected(arg), rows: rows, rowHeight: 25, headerHeight: 33, columns: columns, sortModel: [
+            react_1.default.createElement(x_data_grid_1.DataGrid, { getRowId: row => row.name, checkboxSelection: true, disableRowSelectionOnClick: true, onRowSelectionModelChange: arg => setSelected(arg), rows: rows, rowHeight: 25, columnHeaderHeight: 33, columns: [
+                    {
+                        field: 'color',
+                        headerName: 'Color',
+                        renderCell: params => {
+                            const { value, id } = params;
+                            return (react_1.default.createElement(ColorPicker_1.default, { color: value || 'blue', onChange: c => {
+                                    const elt = rows.find(f => f.name === id);
+                                    if (elt) {
+                                        elt.color = c;
+                                    }
+                                    onChange([...rows]);
+                                } }));
+                        },
+                    },
+                    {
+                        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 (0, util_1.isUriLocation)(value) ? (react_1.default.createElement(BaseFeatureDetail_1.UriLink, { value: value })) : ((0, util_1.getStr)(value));
+                        },
+                        // @ts-ignore
+                        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];

package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js.map

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package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { WiggleDisplayModel } from '../models/model';
 export declare const StatBars: (props: {
     model: WiggleDisplayModel;

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

@@ -1,2 +1,108 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    autoscale: {
+        type: string;
+        defaultValue: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    minimalTicks: {
+        type: string;
+        defaultValue: boolean;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    minScore: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    maxScore: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    numStdDev: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    scaleType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    inverted: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    defaultRendering: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        MultiXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        MultiDensityRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        MultiRowXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        MultiLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        MultiRowLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        defaultValue: number;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

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

@@ -62,9 +62,32 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"MultiLinearWiggleDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     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]>;
     fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
@@ -140,8 +163,8 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
-    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
 } & {
     readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -154,35 +177,32 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
+    readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
+} & {
     afterAttach(): void;
-    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-        headers?: Record<string, string> | undefined;
-        signal?: AbortSignal | undefined;
-        filters?: string[] | undefined;
-    }): Promise<{}>;
-    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionStats(): void;
+    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    setFeatureDensityStatsP(arg: any): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    clearFeatureDensityStats(): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
 } & {
@@ -190,18 +210,13 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
+} & {
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    contextMenuItems(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -221,7 +236,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
 } & {
     setLayout(layout: Source[]): void;
     clearLayout(): void;
-    updateStats(stats: {
+    updateQuantitativeStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
@@ -387,9 +402,33 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;
     id: string;
+    configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
     rpcDriverName: string | undefined;
     heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;

package/dist/MultiLinearWiggleDisplay/models/model.js

@@ -90,7 +90,7 @@ const stateModelFactory = (pluginManager, configSchema) => mobx_state_tree_1.typ
     clearLayout() {
         self.layout = [];
     },
-    updateStats(stats) {
+    updateQuantitativeStats(stats) {
         const { scoreMin, scoreMax } = stats;
         const EPSILON = 0.000001;
         if (!self.stats) {
@@ -550,28 +550,12 @@ const stateModelFactory = (pluginManager, configSchema) => mobx_state_tree_1.typ
     .actions(self => {
     const { reload: superReload, renderSvg: superRenderSvg } = self;
     return {
-        // re-runs stats and refresh whole display on reload
         async reload() {
             self.setError();
-            const aborter = new AbortController();
-            let stats;
-            try {
-                self.setLoading(aborter);
-                stats = await (0, util_2.getStats)(self, {
-                    signal: aborter.signal,
-                    ...self.renderProps(),
-                });
-                if ((0, mobx_state_tree_1.isAlive)(self)) {
-                    self.updateStats(stats);
-                    superReload();
-                }
-            }
-            catch (e) {
-                self.setError(e);
-            }
+            superReload();
         },
         afterAttach() {
-            (0, util_2.statsAutorun)(self);
+            (0, util_2.quantitativeStatsAutorun)(self);
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
                 const { rpcManager } = (0, util_1.getSession)(self);
                 const { adapterConfig } = self;