@jbrowse/plugin-alignments 2.16.1 → 2.18.0

package/dist/LinearAlignmentsDisplay/{models/configSchema.d.ts → configSchema.d.ts}

@@ -1,21 +1,7 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LinearAlignmentsDisplay
- * has a "pileup" sub-display, where you can see individual reads and a
- * quantitative "snpcoverage" sub-display track showing SNP frequencies
- */
-export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function configModelFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     pileupDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    /**
-     * #slot
-     */
     snpCoverageDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    /**
-     * #slot
-     */
     height: {
         type: string;
         defaultValue: number;

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

@@ -3,33 +3,16 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = configModelFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-/**
- * #config LinearAlignmentsDisplay
- * has a "pileup" sub-display, where you can see individual reads and a
- * quantitative "snpcoverage" sub-display track showing SNP frequencies
- */
-function configModelFactory(pm) {
+function configModelFactory(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LinearAlignmentsDisplay', {
-        /**
-         * #slot
-         */
-        pileupDisplay: pm.getDisplayType('LinearPileupDisplay').configSchema,
-        /**
-         * #slot
-         */
-        snpCoverageDisplay: pm.getDisplayType('LinearSNPCoverageDisplay')
+        pileupDisplay: pluginManager.getDisplayType('LinearPileupDisplay')
             .configSchema,
-        /**
-         * #slot
-         */
+        snpCoverageDisplay: pluginManager.getDisplayType('LinearSNPCoverageDisplay').configSchema,
         height: {
             type: 'number',
             defaultValue: 250,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });

package/dist/LinearAlignmentsDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function LinearAlignmentsDisplayF(pluginManager: PluginManager): void;

package/dist/LinearAlignmentsDisplay/index.js

@@ -5,10 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LinearAlignmentsDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-// locals
-const configSchema_1 = __importDefault(require("./models/configSchema"));
-const model_1 = __importDefault(require("./models/model"));
 const AlignmentsDisplay_1 = __importDefault(require("./components/AlignmentsDisplay"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+const model_1 = __importDefault(require("./model"));
 function LinearAlignmentsDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);

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

@@ -1,16 +1,10 @@
 import React from 'react';
-import { Instance, IStateTreeNode } from 'mobx-state-tree';
-import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { MenuItem } from '@jbrowse/core/ui';
-import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { IFilter } from '../../shared';
-/**
- * #stateModel LinearAlignmentsDisplay
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [LinearAlignmentsDisplayMixin](../linearalignmentsdisplaymixin)
- */
+import type { FilterBy } from '../shared/types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { MenuItem } from '@jbrowse/core/ui';
+import type { Instance } from 'mobx-state-tree';
 declare function stateModelFactory(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): 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>;
@@ -85,93 +79,33 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     scrollTop: number;
 } & {
-    /**
-     * #action
-     */
     setScrollTop(scrollTop: number): void;
-    /**
-     * #action
-     */
     setSNPCoverageHeight(n: number): void;
 } & {
-    /**
-     * #getter
-     */
     readonly height: any;
-    /**
-     * #getter
-     */
     readonly featureIdUnderMouse: any;
 } & {
-    /**
-     * #getter
-     */
     readonly pileupConf: any;
-    /**
-     * #method
-     */
     getFeatureByID(blockKey: string, id: string): any;
-    /**
-     * #method
-     */
     searchFeatureByID(id: string): any;
-    /**
-     * #getter
-     */
     readonly features: any;
-    /**
-     * #getteralignmentsdisplaymodel
-     */
     readonly DisplayBlurb: any;
-    /**
-     * #getter
-     */
     readonly sortedBy: any;
-    /**
-     * #getter
-     */
     readonly coverageConf: any;
 } & {
-    /**
-     * #action
-     */
     setSNPCoverageDisplay(configuration: AnyConfigurationModel): void;
-    /**
-     * #action
-     */
     setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;
-    /**
-     * #action
-     */
     setPileupDisplay(configuration: AnyConfigurationModel): void;
-    /**
-     * #action
-     */
     setHeight(n: number): number;
-    /**
-     * #action
-     */
-    setFilterBy(filter: IFilter): void;
-    /**
-     * #action
-     */
+    setFilterBy(filter: FilterBy): void;
     setLowerPanelType(type: string): void;
-    /**
-     * #action
-     */
     resizeHeight(distance: number): number;
 } & {
     afterAttach(): void;
-    /**
-     * #action
-     */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<React.JSX.Element>;
 } & {
-    /**
-     * #method
-     */
     trackMenuItems(): MenuItem[];
 }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;

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

@@ -4,19 +4,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
-// jbrowse
 const configuration_1 = require("@jbrowse/core/configuration");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-// locals
+const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const alignmentsModel_1 = require("./alignmentsModel");
 const util_1 = require("./util");
 const minDisplayHeight = 20;
-function deepSnap(x1, x2) {
-    return (0, fast_deep_equal_1.default)(x1 ? (0, mobx_state_tree_1.getSnapshot)(x1) : undefined, x2 ? (0, mobx_state_tree_1.getSnapshot)(x2) : undefined);
-}
 function preCheck(self) {
     const { PileupDisplay, SNPCoverageDisplay } = self;
     return (PileupDisplay ||
@@ -29,8 +24,10 @@ function propagateColorBy(self) {
     if (!preCheck(self) || !PileupDisplay.colorBy) {
         return;
     }
-    if (!deepSnap(PileupDisplay.colorBy, SNPCoverageDisplay.colorBy)) {
-        SNPCoverageDisplay.setColorBy((0, mobx_state_tree_1.getSnapshot)(PileupDisplay.colorBy));
+    if (!(0, fast_deep_equal_1.default)(PileupDisplay.colorBy, SNPCoverageDisplay.colorBy)) {
+        SNPCoverageDisplay.setColorScheme({
+            ...PileupDisplay.colorBy,
+        });
     }
 }
 function propagateFilterBy(self) {
@@ -38,16 +35,12 @@ function propagateFilterBy(self) {
     if (!preCheck(self) || !PileupDisplay.filterBy) {
         return;
     }
-    if (!deepSnap(PileupDisplay.filterBy, SNPCoverageDisplay.filterBy)) {
-        SNPCoverageDisplay.setFilterBy((0, mobx_state_tree_1.getSnapshot)(PileupDisplay.filterBy));
+    if (!(0, fast_deep_equal_1.default)(PileupDisplay.filterBy, SNPCoverageDisplay.filterBy)) {
+        SNPCoverageDisplay.setFilterBy({
+            ...PileupDisplay.filterBy,
+        });
     }
 }
-/**
- * #stateModel LinearAlignmentsDisplay
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [LinearAlignmentsDisplayMixin](../linearalignmentsdisplaymixin)
- */
 function stateModelFactory(pluginManager, configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearAlignmentsDisplay', models_1.BaseDisplay, (0, alignmentsModel_1.LinearAlignmentsDisplayMixin)(pluginManager, configSchema))
@@ -55,94 +48,58 @@ function stateModelFactory(pluginManager, configSchema) {
         scrollTop: 0,
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setScrollTop(scrollTop) {
             self.scrollTop = scrollTop;
         },
-        /**
-         * #action
-         */
         setSNPCoverageHeight(n) {
             self.snpCovHeight = n;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get height() {
             var _a;
             return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'height');
         },
-        /**
-         * #getter
-         */
         get featureIdUnderMouse() {
             return (self.PileupDisplay.featureIdUnderMouse ||
                 self.SNPCoverageDisplay.featureIdUnderMouse);
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get pileupConf() {
             const conf = (0, configuration_1.getConf)(self, 'pileupDisplay');
             return {
                 ...conf,
                 type: self.lowerPanelType,
-                displayId: `${self.configuration.displayId}_${self.lowerPanelType}_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
+                displayId: `${self.configuration.displayId}_${self.lowerPanelType}_xyz`,
             };
         },
-        /**
-         * #method
-         */
         getFeatureByID(blockKey, id) {
             return self.PileupDisplay.getFeatureByID(blockKey, id);
         },
-        /**
-         * #method
-         */
         searchFeatureByID(id) {
             var _a, _b;
             return (_b = (_a = self.PileupDisplay).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, id);
         },
-        /**
-         * #getter
-         */
         get features() {
             return self.PileupDisplay.features;
         },
-        /**
-         * #getteralignmentsdisplaymodel
-         */
         get DisplayBlurb() {
             var _a;
             return (_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.DisplayBlurb;
         },
-        /**
-         * #getter
-         */
         get sortedBy() {
             return self.PileupDisplay.sortedBy;
         },
-        /**
-         * #getter
-         */
         get coverageConf() {
             const conf = (0, configuration_1.getConf)(self, 'snpCoverageDisplay');
             return {
                 ...conf,
-                displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
+                displayId: `${self.configuration.displayId}_snpcoverage_xyz`,
             };
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setSNPCoverageDisplay(configuration) {
             self.SNPCoverageDisplay = {
                 type: 'LinearSNPCoverageDisplay',
@@ -150,45 +107,27 @@ function stateModelFactory(pluginManager, configSchema) {
                 height: self.snpCovHeight,
             };
         },
-        /**
-         * #action
-         */
         setFeatureDensityStatsLimit(stats) {
             self.PileupDisplay.setFeatureDensityStatsLimit(stats);
             self.SNPCoverageDisplay.setFeatureDensityStatsLimit(stats);
         },
-        /**
-         * #action
-         */
         setPileupDisplay(configuration) {
             self.PileupDisplay = {
                 type: configuration.type || 'LinearPileupDisplay',
                 configuration,
             };
         },
-        /**
-         * #action
-         */
         setHeight(n) {
             self.heightPreConfig = Math.max(n, minDisplayHeight);
             return self.heightPreConfig;
         },
-        /**
-         * #action
-         */
         setFilterBy(filter) {
             self.PileupDisplay.setFilterBy(filter);
             self.SNPCoverageDisplay.setFilterBy(filter);
         },
-        /**
-         * #action
-         */
         setLowerPanelType(type) {
             self.lowerPanelType = type;
         },
-        /**
-         * #action
-         */
         resizeHeight(distance) {
             const oldHeight = self.height;
             const newHeight = this.setHeight(self.height + distance);
@@ -222,9 +161,6 @@ function stateModelFactory(pluginManager, configSchema) {
                 self.PileupDisplay.setHeight(self.height - self.SNPCoverageDisplay.height);
             }));
         },
-        /**
-         * #action
-         */
         async renderSvg(opts) {
             const pileupHeight = self.height - self.SNPCoverageDisplay.height;
             await (0, mobx_1.when)(() => !self.PileupDisplay.renderProps().notReady &&
@@ -240,9 +176,6 @@ function stateModelFactory(pluginManager, configSchema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
         return {
-            /**
-             * #method
-             */
             trackMenuItems() {
                 if (!self.PileupDisplay) {
                     return [];
@@ -277,11 +210,9 @@ function stateModelFactory(pluginManager, configSchema) {
         };
     })
         .preProcessSnapshot(snap => {
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!snap) {
             return snap;
         }
-        // @ts-expect-error
         const { height, ...rest } = snap;
         return { heightPreConfig: height, ...rest };
     });

package/dist/LinearAlignmentsDisplay/{models/util.d.ts → util.d.ts}

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export declare function getLowerPanelDisplays(pluginManager: PluginManager): import("@jbrowse/core/pluggableElementTypes").DisplayType[];