@jbrowse/plugin-wiggle 2.4.2 → 2.6.1

package/dist/LinearWiggleDisplay/models/model.js

@@ -26,17 +26,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_1 = require("mobx");
 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 Tooltip_1 = __importDefault(require("../components/Tooltip"));
-const YScaleBar_1 = __importDefault(require("../../shared/YScaleBar"));
-const SetMinMaxDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../../shared/SetMinMaxDialog'))));
+const modelShared_1 = __importDefault(require("../../shared/modelShared"));
+// lazies
 const SetColorDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../components/SetColorDialog'))));
 // using a map because it preserves order
 const rendererTypes = new Map([
@@ -46,212 +45,15 @@ const rendererTypes = new Map([
 ]);
 /**
  * #stateModel LinearWiggleDisplay
- * Extends `BaseLinearDisplay`
+ * extends `SharedWiggleMixin`
  */
 function stateModelFactory(pluginManager, configSchema) {
     return mobx_state_tree_1.types
-        .compose('LinearWiggleDisplay', plugin_linear_genome_view_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
+        .compose('LinearWiggleDisplay', (0, modelShared_1.default)(configSchema), mobx_state_tree_1.types.model({
         /**
          * #property
          */
         type: mobx_state_tree_1.types.literal('LinearWiggleDisplay'),
-        /**
-         * #property
-         */
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        /**
-         * #property
-         */
-        selectedRendering: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, ''),
-        /**
-         * #property
-         */
-        resolution: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1),
-        /**
-         * #property
-         */
-        fill: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
-        minSize: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        /**
-         * #property
-         */
-        color: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
-        posColor: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
-        negColor: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
-        summaryScoreMode: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
-        rendererTypeNameState: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
-        scale: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
-        autoscale: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
-        displayCrossHatches: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
-        constraints: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.model({
-            max: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-            min: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        }), {}),
-    }))
-        .volatile(() => ({
-        message: undefined,
-        stats: undefined,
-        statsFetchInProgress: undefined,
-    }))
-        .actions(self => ({
-        /**
-         * #action
-         */
-        updateStats(stats) {
-            const { scoreMin, scoreMax } = stats;
-            const EPSILON = 0.000001;
-            if (!self.stats) {
-                self.stats = { scoreMin, scoreMax };
-            }
-            else if (Math.abs(self.stats.scoreMax - scoreMax) > EPSILON ||
-                Math.abs(self.stats.scoreMin - scoreMin) > EPSILON) {
-                self.stats = { scoreMin, scoreMax };
-            }
-        },
-        /**
-         * #action
-         */
-        setColor(color) {
-            self.color = color;
-        },
-        /**
-         * #action
-         */
-        setPosColor(color) {
-            self.posColor = color;
-        },
-        /**
-         * #action
-         */
-        setNegColor(color) {
-            self.negColor = color;
-        },
-        /**
-         * #action
-         */
-        setLoading(aborter) {
-            const { statsFetchInProgress: statsFetch } = self;
-            if (statsFetch !== undefined && !statsFetch.signal.aborted) {
-                statsFetch.abort();
-            }
-            self.statsFetchInProgress = aborter;
-        },
-        /**
-         * #action
-         * this overrides the BaseLinearDisplayModel to avoid popping up a
-         * feature detail display, but still sets the feature selection on the
-         * model so listeners can detect a click
-         */
-        selectFeature(feature) {
-            const session = (0, util_1.getSession)(self);
-            if ((0, util_1.isSelectionContainer)(session)) {
-                session.setSelection(feature);
-            }
-        },
-        /**
-         * #action
-         */
-        setResolution(res) {
-            self.resolution = res;
-        },
-        /**
-         * #action
-         */
-        setFill(fill) {
-            if (fill === 0) {
-                self.fill = true;
-                self.minSize = 0;
-            }
-            else if (fill === 1) {
-                self.fill = false;
-                self.minSize = 1;
-            }
-            else if (fill === 2) {
-                self.fill = false;
-                self.minSize = 2;
-            }
-        },
-        /**
-         * #action
-         */
-        toggleLogScale() {
-            self.scale = self.scale === 'log' ? 'linear' : 'log';
-        },
-        /**
-         * #action
-         */
-        setScaleType(scale) {
-            self.scale = scale;
-        },
-        /**
-         * #action
-         */
-        setSummaryScoreMode(val) {
-            self.summaryScoreMode = val;
-        },
-        /**
-         * #action
-         */
-        setAutoscale(val) {
-            self.autoscale = val;
-        },
-        /**
-         * #action
-         */
-        setMaxScore(val) {
-            self.constraints.max = val;
-        },
-        /**
-         * #action
-         */
-        setRendererType(val) {
-            self.rendererTypeNameState = val;
-        },
-        /**
-         * #action
-         */
-        setMinScore(val) {
-            self.constraints.min = val;
-        },
-        /**
-         * #action
-         */
-        toggleCrossHatches() {
-            self.displayCrossHatches = !self.displayCrossHatches;
-        },
-        /**
-         * #action
-         */
-        setCrossHatches(cross) {
-            self.displayCrossHatches = cross;
-        },
     }))
         .views(self => ({
         /**
@@ -260,160 +62,18 @@ function stateModelFactory(pluginManager, configSchema) {
         get TooltipComponent() {
             return Tooltip_1.default;
         },
-        /**
-         * #getter
-         */
-        get adapterTypeName() {
-            return self.adapterConfig.type;
-        },
-        /**
-         * #getter
-         */
-        get rendererTypeNameSimple() {
-            return self.rendererTypeNameState || (0, configuration_1.getConf)(self, 'defaultRendering');
-        },
         /**
          * #getter
          */
         get rendererTypeName() {
-            const name = this.rendererTypeNameSimple;
+            const name = self.rendererTypeNameSimple;
             const rendererType = rendererTypes.get(name);
             if (!rendererType) {
                 throw new Error(`unknown renderer ${name}`);
             }
             return rendererType;
         },
-        /**
-         * #getter
-         * subclasses can define these, as snpcoverage track does
-         */
-        get filters() {
-            return undefined;
-        },
-        /**
-         * #getter
-         */
-        get scaleType() {
-            return self.scale || (0, configuration_1.getConf)(self, 'scaleType');
-        },
-        /**
-         * #getter
-         */
-        get maxScore() {
-            var _a;
-            return (_a = self.constraints.max) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'maxScore');
-        },
-        /**
-         * #getter
-         */
-        get minScore() {
-            var _a;
-            return (_a = self.constraints.min) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'minScore');
-        },
     }))
-        .views(self => ({
-        /**
-         * #getter
-         */
-        get rendererConfig() {
-            const configBlob = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
-            const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, } = self;
-            return self.rendererType.configSchema.create({
-                ...configBlob,
-                ...(scaleType ? { scaleType } : {}),
-                ...(fill !== undefined ? { filled: fill } : {}),
-                ...(displayCrossHatches !== undefined
-                    ? { displayCrossHatches }
-                    : {}),
-                ...(summaryScoreMode !== undefined ? { summaryScoreMode } : {}),
-                ...(color !== undefined ? { color } : {}),
-                ...(negColor !== undefined ? { negColor } : {}),
-                ...(posColor !== undefined ? { posColor } : {}),
-                ...(minSize !== undefined ? { minSize } : {}),
-            }, (0, util_1.getEnv)(self));
-        },
-    }))
-        .views(self => {
-        let oldDomain = [0, 0];
-        return {
-            /**
-             * #getter
-             */
-            get filled() {
-                const { fill, rendererConfig: conf } = self;
-                return fill !== null && fill !== void 0 ? fill : (0, configuration_1.readConfObject)(conf, 'filled');
-            },
-            /**
-             * #getter
-             */
-            get summaryScoreModeSetting() {
-                const { summaryScoreMode, rendererConfig: conf } = self;
-                return summaryScoreMode !== null && summaryScoreMode !== void 0 ? summaryScoreMode : (0, configuration_1.readConfObject)(conf, 'summaryScoreMode');
-            },
-            /**
-             * #getter
-             */
-            get domain() {
-                const { stats, scaleType, minScore, maxScore } = self;
-                if (!stats) {
-                    return undefined;
-                }
-                const ret = (0, util_2.getNiceDomain)({
-                    domain: [stats.scoreMin, stats.scoreMax],
-                    bounds: [minScore, maxScore],
-                    scaleType,
-                });
-                // avoid weird scalebar if log value and empty region displayed
-                if (scaleType === 'log' && ret[1] === Number.MIN_VALUE) {
-                    return [0, Number.MIN_VALUE];
-                }
-                // avoid returning a new object if it matches the old value
-                if (JSON.stringify(oldDomain) !== JSON.stringify(ret)) {
-                    oldDomain = ret;
-                }
-                return oldDomain;
-            },
-            /**
-             * #getter
-             */
-            get needsScalebar() {
-                return (self.rendererTypeName === 'XYPlotRenderer' ||
-                    self.rendererTypeName === 'LinePlotRenderer');
-            },
-            /**
-             * #getter
-             */
-            get scaleOpts() {
-                return {
-                    domain: this.domain,
-                    stats: self.stats,
-                    autoscaleType: this.autoscaleType,
-                    scaleType: self.scaleType,
-                    inverted: (0, configuration_1.getConf)(self, 'inverted'),
-                };
-            },
-            /**
-             * #getter
-             */
-            get canHaveFill() {
-                return self.rendererTypeName === 'XYPlotRenderer';
-            },
-            /**
-             * #getter
-             */
-            get autoscaleType() {
-                var _a;
-                return (_a = self.autoscale) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'autoscale');
-            },
-            /**
-             * #getter
-             */
-            get displayCrossHatchesSetting() {
-                const { displayCrossHatches: hatches, rendererConfig: conf } = self;
-                return hatches !== null && hatches !== void 0 ? hatches : (0, configuration_1.readConfObject)(conf, 'displayCrossHatches');
-            },
-        };
-    })
         .views(self => ({
         /**
          * #getter
@@ -437,13 +97,6 @@ function stateModelFactory(pluginManager, configSchema) {
                 ? { ...ticks, values: domain }
                 : ticks;
         },
-        /**
-         * #getter
-         */
-        get adapterCapabilities() {
-            const type = self.adapterTypeName;
-            return pluginManager.getAdapterType(type).adapterCapabilities;
-        },
     }))
         .views(self => {
         const { renderProps: superRenderProps } = self;
@@ -471,14 +124,9 @@ function stateModelFactory(pluginManager, configSchema) {
             /**
              * #getter
              */
-            get hasResolution() {
-                return self.adapterCapabilities.includes('hasResolution');
-            },
-            /**
-             * #getter
-             */
-            get hasGlobalStats() {
-                return self.adapterCapabilities.includes('hasGlobalStats');
+            get needsScalebar() {
+                const { rendererTypeName: type } = self;
+                return type === 'XYPlotRenderer' || type === 'LinePlotRenderer';
             },
             /**
              * #getter
@@ -506,32 +154,10 @@ function stateModelFactory(pluginManager, configSchema) {
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
-                    ...(self.hasResolution
-                        ? [
-                            {
-                                label: 'Resolution',
-                                subMenu: [
-                                    {
-                                        label: 'Finer resolution',
-                                        onClick: () => self.setResolution(self.resolution * 5),
-                                    },
-                                    {
-                                        label: 'Coarser resolution',
-                                        onClick: () => self.setResolution(self.resolution / 5),
-                                    },
-                                ],
-                            },
-                            {
-                                label: 'Summary score mode',
-                                subMenu: ['min', 'max', 'avg', 'whiskers'].map(elt => ({
-                                    label: elt,
-                                    type: 'radio',
-                                    checked: self.summaryScoreModeSetting === elt,
-                                    onClick: () => self.setSummaryScoreMode(elt),
-                                })),
-                            },
-                        ]
-                        : []),
+                    {
+                        label: 'Score',
+                        subMenu: self.scoreTrackMenuItems(),
+                    },
                     ...(self.canHaveFill
                         ? [
                             {
@@ -545,10 +171,6 @@ function stateModelFactory(pluginManager, configSchema) {
                             },
                         ]
                         : []),
-                    {
-                        label: self.scaleType === 'log' ? 'Set linear scale' : 'Set log scale',
-                        onClick: () => self.toggleLogScale(),
-                    },
                     ...(self.needsScalebar
                         ? [
                             {
@@ -572,33 +194,6 @@ function stateModelFactory(pluginManager, configSchema) {
                             },
                         ]
                         : []),
-                    {
-                        label: 'Autoscale type',
-                        subMenu: [
-                            ['local', 'Local'],
-                            ...(self.hasGlobalStats
-                                ? [
-                                    ['global', 'Global'],
-                                    ['globalsd', 'Global ± 3σ'],
-                                ]
-                                : []),
-                            ['localsd', 'Local ± 3σ'],
-                        ].map(([val, label]) => ({
-                            label,
-                            type: 'radio',
-                            checked: self.autoscaleType === val,
-                            onClick: () => self.setAutoscale(val),
-                        })),
-                    },
-                    {
-                        label: 'Set min/max score',
-                        onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                SetMinMaxDlg,
-                                { model: self, handleClose },
-                            ]);
-                        },
-                    },
                     {
                         label: 'Set color',
                         onClick: () => {
@@ -613,44 +208,17 @@ function stateModelFactory(pluginManager, configSchema) {
         };
     })
         .actions(self => {
-        const { reload: superReload, renderSvg: superRenderSvg } = self;
+        const { renderSvg: superRenderSvg } = self;
         return {
-            /**
-             * #action
-             * re-runs stats and refresh whole display on reload
-             */
-            async reload() {
-                self.setError();
-                const aborter = new AbortController();
-                self.setLoading(aborter);
-                try {
-                    const 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);
-                }
-            },
             afterAttach() {
-                (0, util_2.statsAutorun)(self);
+                (0, util_2.quantitativeStatsAutorun)(self);
             },
             /**
              * #action
              */
             async renderSvg(opts) {
-                await (0, mobx_1.when)(() => !!self.stats && !!self.regionCannotBeRenderedText);
-                const { needsScalebar, stats } = self;
-                const { offsetPx } = (0, util_1.getContainingView)(self);
-                return (react_1.default.createElement(react_1.default.Fragment, null,
-                    react_1.default.createElement("g", { id: "snpcov" }, await superRenderSvg(opts)),
-                    needsScalebar && stats ? (react_1.default.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
-                        react_1.default.createElement(YScaleBar_1.default, { model: self, orientation: "left" }))) : null));
+                const { renderSvg } = await Promise.resolve().then(() => __importStar(require('./renderSvg')));
+                return renderSvg(self, opts, superRenderSvg);
             },
         };
     });

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

@@ -1 +1 @@
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package/dist/LinearWiggleDisplay/models/renderSvg.d.ts

@@ -0,0 +1,4 @@
+import React from 'react';
+import { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
+import { WiggleDisplayModel } from './model';
+export declare function renderSvg(self: WiggleDisplayModel, opts: ExportSvgDisplayOptions, superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>): Promise<React.JSX.Element>;

package/dist/LinearWiggleDisplay/models/renderSvg.js

@@ -0,0 +1,21 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderSvg = void 0;
+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"));
+async function renderSvg(self, opts, superRenderSvg) {
+    await (0, mobx_1.when)(() => !!self.stats && !!self.regionCannotBeRenderedText);
+    const { needsScalebar, stats } = self;
+    const { offsetPx } = (0, util_1.getContainingView)(self);
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement("g", { id: "snpcov" }, await superRenderSvg(opts)),
+        needsScalebar && stats ? (react_1.default.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
+            react_1.default.createElement(YScaleBar_1.default, { model: self, orientation: "left" }))) : null));
+}
+exports.renderSvg = renderSvg;
+//# sourceMappingURL=renderSvg.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../../src/LinearWiggleDisplay/models/renderSvg.tsx"],"names":[],"mappings":";;;;;;AAAA,kDAAyB;AACzB,6CAAsD;AACtD,+BAA2B;AAC3B,uEAA8C;AAOvC,KAAK,UAAU,SAAS,CAC7B,IAAwB,EACxB,IAA6B,EAC7B,cAA2E;IAE3E,MAAM,IAAA,WAAI,EAAC,GAAG,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,CAAC,0BAA0B,CAAC,CAAA;IACnE,MAAM,EAAE,aAAa,EAAE,KAAK,EAAE,GAAG,IAAI,CAAA;IACrC,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAA0B,CAAA;IACrE,OAAO,CACL;QACE,qCAAG,EAAE,EAAC,QAAQ,IAAE,MAAM,cAAc,CAAC,IAAI,CAAC,CAAK;QAC9C,aAAa,IAAI,KAAK,CAAC,CAAC,CAAC,CACxB,qCAAG,SAAS,EAAE,aAAa,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,GAAG;YAClD,8BAAC,mBAAS,IAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAC,MAAM,GAAG,CAC3C,CACL,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC;AAlBD,8BAkBC"}

package/dist/MultiDensityRenderer/MultiDensityRenderer.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const util_1 = require("../util");
+const util_1 = require("@jbrowse/core/util");
 const WiggleBaseRenderer_1 = __importDefault(require("../WiggleBaseRenderer"));
 const drawxy_1 = require("../drawxy");
 class MultiXYPlotRenderer extends WiggleBaseRenderer_1.default {

package/dist/MultiDensityRenderer/MultiDensityRenderer.js.map

@@ -1 +1 @@
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