@jbrowse/plugin-wiggle 2.16.1 → 2.17.0

package/dist/LinearWiggleDisplay/components/Tooltip.js

@@ -11,7 +11,7 @@ const Tooltip_1 = __importDefault(require("../../Tooltip"));
 const util_1 = require("../../util");
 const en = (n) => n.toLocaleString('en-US');
 const TooltipContents = react_1.default.forwardRef(function TooltipContents2({ feature }, ref) {
-    const start = feature.get('start');
+    const start = feature.get('start') + 1;
     const end = feature.get('end');
     const refName = feature.get('refName');
     const name = feature.get('name');

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { WiggleDisplayModel } from '../models/model';
+import { WiggleDisplayModel } from '../model';
 declare const LinearWiggleDisplay: (props: {
     model: WiggleDisplayModel;
 }) => React.JSX.Element;

package/dist/LinearWiggleDisplay/{models/configSchema.js → configSchema.js}

@@ -7,7 +7,7 @@ exports.default = WiggleConfigFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
 // locals
-const configShared_1 = __importDefault(require("../../shared/configShared"));
+const SharedWiggleConfigSchema_1 = __importDefault(require("../shared/SharedWiggleConfigSchema"));
 /**
  * #config LinearWiggleDisplay
  * extends
@@ -38,7 +38,7 @@ function WiggleConfigFactory(pluginManager) {
         /**
          * #baseConfiguration
          */
-        baseConfiguration: (0, configShared_1.default)(),
+        baseConfiguration: (0, SharedWiggleConfigSchema_1.default)(),
         explicitlyTyped: true,
     });
 }

package/dist/LinearWiggleDisplay/index.d.ts

@@ -2,4 +2,4 @@ import PluginManager from '@jbrowse/core/PluginManager';
 export default function LinearWiggleDisplayF(pluginManager: PluginManager): void;
 export { default as Tooltip } from './components/Tooltip';
 export { default as ReactComponent } from './components/WiggleDisplayComponent';
-export { default as modelFactory } from './models/model';
+export { default as modelFactory } from './model';

package/dist/LinearWiggleDisplay/index.js

@@ -29,8 +29,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.modelFactory = exports.ReactComponent = exports.Tooltip = void 0;
 exports.default = LinearWiggleDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const configSchema_1 = __importDefault(require("./models/configSchema"));
-const model_1 = __importDefault(require("./models/model"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+const model_1 = __importDefault(require("./model"));
 const react_1 = require("react");
 function LinearWiggleDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
@@ -51,5 +51,5 @@ var Tooltip_1 = require("./components/Tooltip");
 Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return __importDefault(Tooltip_1).default; } });
 var WiggleDisplayComponent_1 = require("./components/WiggleDisplayComponent");
 Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(WiggleDisplayComponent_1).default; } });
-var model_2 = require("./models/model");
+var model_2 = require("./model");
 Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return __importDefault(model_2).default; } });

package/{esm/LinearWiggleDisplay/models → dist/LinearWiggleDisplay}/model.d.ts

@@ -49,7 +49,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
                 reload: () => void;
                 message: React.ReactNode;
                 filled?: boolean;
-                status?: string;
+                status? /**
+                 * #getter
+                 */: string;
                 reactElement?: React.ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
@@ -145,9 +147,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll? /**
-         * #getter
-         */: () => void;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{
@@ -252,19 +252,21 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     message: undefined | string;
     stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     } | undefined;
     statsFetchInProgress: undefined | AbortController;
 } & {
     updateQuantitativeStats(stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     }): void;
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setLoading(aborter: AbortController): void;
+    setStatsLoading(aborter: AbortController): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -306,6 +308,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly scaleOpts: {
         domain: number[] | undefined;
         stats: {
+            currStatsBpPerPx: number;
             scoreMin: number;
             scoreMax: number;
         } | undefined;
@@ -350,7 +353,16 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
      * #getter
      */
     readonly rendererTypeName: string;
+    /**
+     * #getter
+     * unused currently
+     */
+    readonly quantitativeStatsRelevantToCurrentZoom: boolean;
 } & {
+    /**
+     * #method
+     */
+    adapterProps(): any;
     /**
      * #getter
      */
@@ -372,7 +384,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #getter
      */
-    readonly fillSetting: 2 | 0 | 1;
+    readonly fillSetting: 2 | 1 | 0;
+    /**
+     * #getter
+     */
+    readonly quantitativeStatsReady: boolean;
 } & {
     /**
      * #method

package/dist/LinearWiggleDisplay/{models/model.js → model.js}

@@ -32,11 +32,11 @@ const util_1 = require("@jbrowse/core/util");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const react_d3_axis_mod_1 = require("react-d3-axis-mod");
 // locals
-const util_2 = require("../../util");
-const modelShared_1 = __importDefault(require("../../shared/modelShared"));
+const util_2 = require("../util");
+const SharedWiggleMixin_1 = __importDefault(require("../shared/SharedWiggleMixin"));
 // lazies
-const Tooltip = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../components/Tooltip'))));
-const SetColorDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../components/SetColorDialog'))));
+const Tooltip = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/Tooltip'))));
+const SetColorDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetColorDialog'))));
 // using a map because it preserves order
 const rendererTypes = new Map([
     ['xyplot', 'XYPlotRenderer'],
@@ -50,7 +50,7 @@ const rendererTypes = new Map([
  */
 function stateModelFactory(pluginManager, configSchema) {
     return mobx_state_tree_1.types
-        .compose('LinearWiggleDisplay', (0, modelShared_1.default)(configSchema), mobx_state_tree_1.types.model({
+        .compose('LinearWiggleDisplay', (0, SharedWiggleMixin_1.default)(configSchema), mobx_state_tree_1.types.model({
         /**
          * #property
          */
@@ -74,29 +74,14 @@ function stateModelFactory(pluginManager, configSchema) {
             }
             return rendererType;
         },
-    }))
-        .views(self => ({
         /**
          * #getter
+         * unused currently
          */
-        get ticks() {
-            const { scaleType, domain, height } = self;
-            const minimalTicks = (0, configuration_1.getConf)(self, 'minimalTicks');
-            const inverted = (0, configuration_1.getConf)(self, 'inverted');
-            const range = [height - util_2.YSCALEBAR_LABEL_OFFSET, util_2.YSCALEBAR_LABEL_OFFSET];
-            if (!domain) {
-                return undefined;
-            }
-            const scale = (0, util_2.getScale)({
-                scaleType,
-                domain,
-                range,
-                inverted,
-            });
-            const ticks = (0, react_d3_axis_mod_1.axisPropsFromTickScale)(scale, 4);
-            return height < 100 || minimalTicks
-                ? { ...ticks, values: domain }
-                : ticks;
+        get quantitativeStatsRelevantToCurrentZoom() {
+            var _a;
+            const view = (0, util_1.getContainingView)(self);
+            return ((_a = self.stats) === null || _a === void 0 ? void 0 : _a.currStatsBpPerPx) === view.bpPerPx;
         },
     }))
         .views(self => {
@@ -105,46 +90,93 @@ function stateModelFactory(pluginManager, configSchema) {
             /**
              * #method
              */
-            renderProps() {
+            adapterProps() {
                 const superProps = superRenderProps();
-                const { filters, ticks, height, resolution, scaleOpts } = self;
+                const { filters, resolution, scaleOpts } = self;
                 return {
                     ...superProps,
-                    notReady: superProps.notReady || !self.stats,
                     rpcDriverName: self.rpcDriverName,
                     displayModel: self,
                     config: self.rendererConfig,
                     displayCrossHatches: self.displayCrossHatchesSetting,
                     scaleOpts,
                     resolution,
-                    height,
-                    ticks,
                     filters,
                 };
             },
             /**
              * #getter
              */
-            get needsScalebar() {
-                const { rendererTypeName: type } = self;
-                return type === 'XYPlotRenderer' || type === 'LinePlotRenderer';
-            },
-            /**
-             * #getter
-             */
-            get fillSetting() {
-                if (self.filled) {
-                    return 0;
-                }
-                else if (self.minSize === 1) {
-                    return 1;
+            get ticks() {
+                const { scaleType, domain, height } = self;
+                const minimalTicks = (0, configuration_1.getConf)(self, 'minimalTicks');
+                const inverted = (0, configuration_1.getConf)(self, 'inverted');
+                if (domain) {
+                    const ticks = (0, react_d3_axis_mod_1.axisPropsFromTickScale)((0, util_2.getScale)({
+                        scaleType,
+                        domain,
+                        range: [
+                            height - util_2.YSCALEBAR_LABEL_OFFSET,
+                            util_2.YSCALEBAR_LABEL_OFFSET,
+                        ],
+                        inverted,
+                    }), 4);
+                    return height < 100 || minimalTicks
+                        ? { ...ticks, values: domain }
+                        : ticks;
                 }
                 else {
-                    return 2;
+                    return undefined;
                 }
             },
         };
     })
+        .views(self => ({
+        /**
+         * #method
+         */
+        renderProps() {
+            const { ticks, height } = self;
+            const superProps = self.adapterProps();
+            return {
+                ...self.adapterProps(),
+                notReady: superProps.notReady || !self.stats,
+                height,
+                ticks,
+            };
+        },
+        /**
+         * #getter
+         */
+        get needsScalebar() {
+            return (self.rendererTypeName === 'XYPlotRenderer' ||
+                self.rendererTypeName === 'LinePlotRenderer');
+        },
+        /**
+         * #getter
+         */
+        get fillSetting() {
+            if (self.filled) {
+                return 0;
+            }
+            else if (self.minSize === 1) {
+                return 1;
+            }
+            else {
+                return 2;
+            }
+        },
+        /**
+         * #getter
+         */
+        get quantitativeStatsReady() {
+            const view = (0, util_1.getContainingView)(self);
+            return (view.initialized &&
+                self.featureDensityStatsReady &&
+                !self.regionTooLarge &&
+                !self.error);
+        },
+    }))
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
         const hasRenderings = (0, configuration_1.getConf)(self, 'defaultRendering');
@@ -206,7 +238,10 @@ function stateModelFactory(pluginManager, configSchema) {
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(handleClose => [
                                 SetColorDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },
@@ -221,8 +256,8 @@ function stateModelFactory(pluginManager, configSchema) {
                 // eslint-disable-next-line @typescript-eslint/no-floating-promises
                 ;
                 (async () => {
-                    const { quantitativeStatsAutorun } = await Promise.resolve().then(() => __importStar(require('../../util')));
-                    quantitativeStatsAutorun(self);
+                    const { getQuantitativeStatsAutorun } = await Promise.resolve().then(() => __importStar(require('../getQuantitativeStatsAutorun')));
+                    getQuantitativeStatsAutorun(self);
                 })();
             },
             /**

package/dist/LinearWiggleDisplay/{models/renderSvg.js → renderSvg.js}

@@ -7,7 +7,8 @@ exports.renderSvg = renderSvg;
 const react_1 = __importDefault(require("react"));
 const util_1 = require("@jbrowse/core/util");
 const mobx_1 = require("mobx");
-const YScaleBar_1 = __importDefault(require("../../shared/YScaleBar"));
+// locals
+const YScaleBar_1 = __importDefault(require("../shared/YScaleBar"));
 async function renderSvg(self, opts, superRenderSvg) {
     await (0, mobx_1.when)(() => !!self.stats && !!self.regionCannotBeRenderedText);
     const { needsScalebar, stats } = self;

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { WiggleDisplayModel } from '../models/model';
+import { WiggleDisplayModel } from '../model';
 declare const ColorLegend: ({ model, rowHeight, labelWidth, exportSVG, }: {
     model: WiggleDisplayModel;
     rowHeight: number;

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { WiggleDisplayModel } from '../models/model';
+import { WiggleDisplayModel } from '../model';
 declare const ScoreLegend: ({ model }: {
     model: WiggleDisplayModel;
 }) => React.JSX.Element;

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { WiggleDisplayModel } from '../models/model';
+import { WiggleDisplayModel } from '../model';
 declare const MultiLinearWiggleDisplayComponent: (props: {
     model: WiggleDisplayModel;
 }) => React.JSX.Element;

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { WiggleDisplayModel } from '../models/model';
+import { WiggleDisplayModel } from '../model';
 export declare const YScaleBars: (props: {
     model: WiggleDisplayModel;
     orientation?: string;

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

@@ -1,4 +1,4 @@
-import { WiggleDisplayModel } from '../models/model';
+import { WiggleDisplayModel } from '../model';
 export declare function moveUp(arr: {
     name: string;
 }[], sel: string[], by?: number): {

package/dist/MultiLinearWiggleDisplay/{models/configSchema.js → configSchema.js}

@@ -7,7 +7,7 @@ exports.default = WiggleConfigFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
 // locals
-const configShared_1 = __importDefault(require("../../shared/configShared"));
+const SharedWiggleConfigSchema_1 = __importDefault(require("../shared/SharedWiggleConfigSchema"));
 /**
  * #config MultiLinearWiggleDisplay
  * extends
@@ -56,7 +56,7 @@ function WiggleConfigFactory(pluginManager) {
         /**
          * #baseConfiguration
          */
-        baseConfiguration: (0, configShared_1.default)(),
+        baseConfiguration: (0, SharedWiggleConfigSchema_1.default)(),
         explicitlyTyped: true,
     });
 }

package/dist/MultiLinearWiggleDisplay/index.js

@@ -28,8 +28,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = MultiLinearWiggleDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const configSchema_1 = __importDefault(require("./models/configSchema"));
-const model_1 = __importDefault(require("./models/model"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+const model_1 = __importDefault(require("./model"));
 const react_1 = require("react");
 function MultiLinearWiggleDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {

package/dist/MultiLinearWiggleDisplay/{models/model.d.ts → model.d.ts}

@@ -3,11 +3,7 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature, AnyReactComponentType } from '@jbrowse/core/util';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
-interface Source {
-    name: string;
-    color?: string;
-    group?: string;
-}
+import { Source } from '../util';
 /**
  * #stateModel MultiLinearWiggleDisplay
  * extends
@@ -166,12 +162,12 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        } & import("mobx-state-tree" /**
-         * #action
-         */).IStateTreeNode<import("mobx-state-tree").IModelType<{
+        } & 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>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+            rpcDriverName: import("mobx-state-tree" /**
+             * #getter
+             */).IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
@@ -261,19 +257,21 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
 } & {
     message: undefined | string;
     stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     } | undefined;
     statsFetchInProgress: undefined | AbortController;
 } & {
     updateQuantitativeStats(stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     }): void;
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setLoading(aborter: AbortController): void;
+    setStatsLoading(aborter: AbortController): void;
     selectFeature(feature: Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -303,7 +301,9 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
                 [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree/dist/internal" /**
+             * #property
+             */).NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
     readonly autoscaleType: any;
@@ -315,6 +315,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     readonly scaleOpts: {
         domain: number[] | undefined;
         stats: {
+            currStatsBpPerPx: number;
             scoreMin: number;
             scoreMax: number;
         } | undefined;
@@ -402,6 +403,9 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
      * implemented like this yet but flag can be used for this
      */
     readonly needsCustomLegend: boolean;
+    /**
+     * #getter
+     */
     readonly canHaveFill: boolean;
     /**
      * #getter
@@ -421,9 +425,14 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
      */
     readonly sources: {
         color: string;
+        baseUri?: string;
         name: string;
         group?: string;
     }[] | undefined;
+    /**
+     * #getter
+     */
+    readonly quantitativeStatsReady: boolean;
 } & {
     /**
      * #getter
@@ -438,6 +447,10 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
      */
     readonly useMinimalTicks: any;
 } & {
+    /**
+     * #method
+     */
+    adapterProps(): any;
     /**
      * #getter
      */
@@ -451,6 +464,11 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
      * #getter
      */
     readonly colors: string[];
+    /**
+     * #getter
+     * unused currently
+     */
+    readonly quantitativeStatsRelevantToCurrentZoom: boolean;
 } & {
     /**
      * #method
@@ -467,7 +485,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     /**
      * #getter
      */
-    readonly fillSetting: 2 | 0 | 1;
+    readonly fillSetting: 2 | 1 | 0;
 } & {
     /**
      * #method