@jbrowse/plugin-wiggle 2.4.2 → 2.5.0

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

@@ -19,9 +19,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>; /**
-             * #property
-             */
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
@@ -45,9 +43,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         }) => any;
         renderProps: any;
     } & {
-        doReload(): void; /**
-         * #property
-         */
+        doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
@@ -57,7 +53,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
-            renderProps: any;
+            renderProps: any; /**
+             * #action
+             */
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
@@ -67,6 +65,29 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
      */
     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">>;
 } & {
     /**
      * #property
@@ -75,7 +96,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #property
      */
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     /**
      * #property
      */
@@ -161,13 +182,15 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
-            error: unknown;
+            error: unknown; /**
+             * #property
+             */
         } & 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>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
              * #property
              */
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
@@ -189,14 +212,15 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     reload(): void;
 } & {
     currBpPerPx: number;
-    scrollTop: number; /**
-     * #property
-     */
+    scrollTop: number;
     message: string;
     featureIdUnderMouse: string | undefined;
+    /**
+     * #property
+     */
     contextMenuFeature: Feature | undefined;
-    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionsStats: 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";
@@ -215,36 +239,37 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
+    readonly featureDensityStatsReady: boolean; /**
+     * #getter
+     */
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
 } & {
     afterAttach(): void;
-    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-    setRegionsStatsP(arg: any): void;
-    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionsStats(): 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 | undefined): 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;
-    /**
-     * #getter
-     */
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
 } & {
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
-    reload(): Promise<void>;
+    reload(): Promise<void>; /**
+     * #method
+     */
 } & {
     afterAttach(): void;
 } & {
@@ -269,7 +294,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #action
      */
-    updateStats(stats: {
+    updateQuantitativeStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
@@ -506,9 +531,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>; /**
-             * #property
-             */
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
@@ -532,9 +555,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         }) => any;
         renderProps: any;
     } & {
-        doReload(): void; /**
-         * #property
-         */
+        doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
@@ -544,7 +565,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
-            renderProps: any;
+            renderProps: any; /**
+             * #action
+             */
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
@@ -554,9 +577,33 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
      */
     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/esm/LinearWiggleDisplay/models/model.js

@@ -3,9 +3,9 @@ import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/
 import { getEnv, getSession, getContainingView, isSelectionContainer, } from '@jbrowse/core/util';
 import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
 import { when } from 'mobx';
-import { isAlive, types } from 'mobx-state-tree';
+import { types } from 'mobx-state-tree';
 import { axisPropsFromTickScale } from 'react-d3-axis-mod';
-import { getNiceDomain, getScale, getStats, statsAutorun, YSCALEBAR_LABEL_OFFSET, } from '../../util';
+import { getNiceDomain, getScale, quantitativeStatsAutorun, YSCALEBAR_LABEL_OFFSET, } from '../../util';
 import Tooltip from '../components/Tooltip';
 import YScaleBar from '../../shared/YScaleBar';
 const SetMinMaxDlg = lazy(() => import('../../shared/SetMinMaxDialog'));
@@ -96,7 +96,7 @@ function stateModelFactory(pluginManager, configSchema) {
         /**
          * #action
          */
-        updateStats(stats) {
+        updateQuantitativeStats(stats) {
             const { scoreMin, scoreMax } = stats;
             const EPSILON = 0.000001;
             if (!self.stats) {
@@ -288,8 +288,8 @@ function stateModelFactory(pluginManager, configSchema) {
          * #getter
          */
         get rendererConfig() {
-            const configBlob = getConf(self, ['renderers', self.rendererTypeName]) || {};
-            const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, } = self;
+            const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, rendererTypeName, } = self;
+            const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};
             return self.rendererType.configSchema.create({
                 ...configBlob,
                 ...(scaleType ? { scaleType } : {}),
@@ -312,15 +312,13 @@ function stateModelFactory(pluginManager, configSchema) {
              * #getter
              */
             get filled() {
-                const { fill, rendererConfig: conf } = self;
-                return fill !== null && fill !== void 0 ? fill : readConfObject(conf, 'filled');
+                return readConfObject(self.rendererConfig, 'filled');
             },
             /**
              * #getter
              */
             get summaryScoreModeSetting() {
-                const { summaryScoreMode, rendererConfig: conf } = self;
-                return summaryScoreMode !== null && summaryScoreMode !== void 0 ? summaryScoreMode : readConfObject(conf, 'summaryScoreMode');
+                return readConfObject(self.rendererConfig, 'summaryScoreMode');
             },
             /**
              * #getter
@@ -381,8 +379,7 @@ function stateModelFactory(pluginManager, configSchema) {
              * #getter
              */
             get displayCrossHatchesSetting() {
-                const { displayCrossHatches: hatches, rendererConfig: conf } = self;
-                return hatches !== null && hatches !== void 0 ? hatches : readConfObject(conf, 'displayCrossHatches');
+                return readConfObject(self.rendererConfig, 'displayCrossHatches');
             },
         };
     })
@@ -593,24 +590,10 @@ function stateModelFactory(pluginManager, configSchema) {
              */
             async reload() {
                 self.setError();
-                const aborter = new AbortController();
-                self.setLoading(aborter);
-                try {
-                    const stats = await getStats(self, {
-                        signal: aborter.signal,
-                        ...self.renderProps(),
-                    });
-                    if (isAlive(self)) {
-                        self.updateStats(stats);
-                        superReload();
-                    }
-                }
-                catch (e) {
-                    self.setError(e);
-                }
+                superReload();
             },
             afterAttach() {
-                statsAutorun(self);
+                quantitativeStatsAutorun(self);
             },
             /**
              * #action

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

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

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

package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js

@@ -58,43 +58,11 @@ function SourcesGrid({ rows, onChange, showTips, }) {
     const [selected, setSelected] = 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.createElement(ColorPicker, { 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: measureGridWidth(rows.map(r => r.name)),
-        },
-        ...Object.keys(rest).map(val => ({
-            field: val,
-            sortingOrder: [null],
-            renderCell: (params) => {
-                const { value } = params;
-                return isUriLocation(value) ? React.createElement(UriLink, { value: value }) : getStr(value);
-            },
-            // @ts-expect-error
-            width: 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] = useState('blue');
-    const [currSort, setCurrSort] = useState({ idx: 0, field: null });
+    const [currSort, setCurrSort] = useState({
+        idx: 0,
+        field: null,
+    });
     return (React.createElement("div", null,
         React.createElement(Button, { disabled: !selected.length, onClick: event => setAnchorEl(event.currentTarget) }, "Change color of selected items"),
         React.createElement(Button, { onClick: () => onChange(moveUp([...rows], selected)), disabled: !selected.length },
@@ -120,7 +88,38 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                 onChange([...rows]);
             }, onClose: () => setAnchorEl(null) }),
         React.createElement("div", { style: { height: 400, width: '100%' } },
-            React.createElement(DataGrid, { getRowId: row => row.name, checkboxSelection: true, disableSelectionOnClick: true, onSelectionModelChange: arg => setSelected(arg), rows: rows, rowHeight: 25, headerHeight: 33, columns: columns, sortModel: [
+            React.createElement(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.createElement(ColorPicker, { 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: measureGridWidth(rows.map(r => r.name)),
+                    },
+                    ...Object.keys(rest).map(val => ({
+                        field: val,
+                        sortingOrder: [null],
+                        renderCell: (params) => {
+                            const { value } = params;
+                            return isUriLocation(value) ? (React.createElement(UriLink, { value: value })) : (getStr(value));
+                        },
+                        // @ts-ignore
+                        width: measureGridWidth(rows.map(r => r[val])),
+                    })),
+                ], sortModel: [
                 /* we control the sort as a controlled component using onSortModelChange */
                 ], onSortModelChange: args => {
                     const sort = args[0];

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

@@ -1 +1 @@
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package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts

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