@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/dist/LinearReadArcsDisplay/model.d.ts

@@ -1,17 +1,8 @@
-import React from 'react';
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { ColorBy, FilterBy } from '../shared/types';
-import { ChainData } from '../shared/fetchChains';
-/**
- * #stateModel LinearReadArcsDisplay
- * the arc display is a non-block-based track, so draws to a single canvas and
- * can connect multiple regions
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [TrackHeightMixin](../trackheightmixin)
- * - [FeatureDensityMixin](../featuredensitymixin)
- */
+import type React from 'react';
+import type { ChainData } from '../shared/fetchChains';
+import type { ColorBy, FilterBy } from '../shared/types';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Instance } from 'mobx-state-tree';
 declare function stateModelFactory(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>;
@@ -24,10 +15,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearReadArcsDisplay">;
     configuration: AnyConfigurationSchemaType;
-    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<FilterBy, FilterBy, FilterBy>, [undefined]>;
     lineWidth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     jitter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    colorBy: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
+    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
     drawInter: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawLongRange: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
@@ -54,17 +45,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: () => void;
-        blockState? /**
-         * #property
-         */: Record<string, any>;
+        blockState?: Record<string, any>;
     }>;
-    readonly DisplayBlurb: React.
-    /**
-     * #property
-     */
-    FC /**
-     * #property
-     */<{
+    readonly DisplayBlurb: React.FC<{
         model: {
             id: string;
             type: string;
@@ -75,9 +58,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             message: string | undefined;
         } & 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" /**
-             * #action
-             */).ISimpleType<string>;
+            type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
@@ -89,10 +70,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: undefined | React.FC /**
-     * #action
-     * thin, bold, extrabold, etc
-     */<any>;
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
@@ -132,8 +110,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     loading: boolean;
     chainData: ChainData | undefined;
@@ -141,83 +120,29 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     lastDrawnBpPerPx: number;
     ref: HTMLCanvasElement | null;
 } & {
-    /**
-     * #action
-     */
+    readonly colorBy: any;
+    readonly filterBy: any;
+} & {
     setLastDrawnOffsetPx(n: number): void;
-    /**
-     * #action
-     */
     setLastDrawnBpPerPx(n: number): void;
-    /**
-     * #action
-     */
     setLoading(f: boolean): void;
-    /**
-     * #action
-     */
     reload(): void;
-    /**
-     * #action
-     * internal, a reference to a HTMLCanvas because we use a autorun to draw
-     * the canvas
-     */
     setRef(ref: HTMLCanvasElement | null): void;
-    /**
-     * #action
-     */
     setColorScheme(colorBy: {
         type: string;
     }): void;
-    /**
-     * #action
-     */
     setChainData(args: ChainData): void;
-    /**
-     * #action
-     */
     setDrawInter(f: boolean): void;
-    /**
-     * #action
-     */
     setDrawLongRange(f: boolean): void;
-    /**
-     * #action
-     */
     setFilterBy(filter: FilterBy): void;
-    /**
-     * #action
-     * thin, bold, extrabold, etc
-     */
     setLineWidth(n: number): void;
-    /**
-     * #action
-     * jitter val, helpful to jitter the x direction so you see better
-     * evidence when e.g. 100 long reads map to same x position
-     */
     setJitter(n: number): void;
 } & {
-    /**
-     * #getter
-     */
     readonly drawn: boolean;
-    /**
-     * #getter
-     */
     readonly lineWidthSetting: any;
-    /**
-     * #getter
-     */
     readonly jitterVal: number;
 } & {
-    /**
-     * #method
-     * only used to tell system it's ready for export
-     */
     renderProps(): any;
-    /**
-     * #method
-     */
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -260,9 +185,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         checked?: undefined;
     })[];
 } & {
-    /**
-     * #method
-     */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<React.ReactNode>;

package/dist/LinearReadArcsDisplay/model.js

@@ -15,72 +15,46 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = require("react");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
+const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-// icons
-const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
 const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
-const util_2 = require("../shared/util");
-// lazies
+const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
+const mobx_state_tree_1 = require("mobx-state-tree");
 const FilterByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/components/FilterByTagDialog'))));
-/**
- * #stateModel LinearReadArcsDisplay
- * the arc display is a non-block-based track, so draws to a single canvas and
- * can connect multiple regions
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [TrackHeightMixin](../trackheightmixin)
- * - [FeatureDensityMixin](../featuredensitymixin)
- */
 function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearReadArcsDisplay', pluggableElementTypes_1.BaseDisplay, (0, plugin_linear_genome_view_1.TrackHeightMixin)(), (0, plugin_linear_genome_view_1.FeatureDensityMixin)(), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LinearReadArcsDisplay'),
-        /**
-         * #property
-         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        /**
-         * #property
-         */
-        filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), util_2.defaultFilterFlags),
-        /**
-         * #property
-         */
         lineWidth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        /**
-         * #property
-         */
         jitter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        /**
-         * #property
-         */
-        colorBy: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
+        colorBySetting: mobx_state_tree_1.types.frozen(),
+        filterBySetting: mobx_state_tree_1.types.frozen(),
         drawInter: true,
-        /**
-         * #property
-         */
         drawLongRange: true,
     }))
         .volatile(() => ({
@@ -89,107 +63,67 @@ function stateModelFactory(configSchema) {
         lastDrawnOffsetPx: undefined,
         lastDrawnBpPerPx: 0,
         ref: null,
+    }))
+        .views(self => ({
+        get colorBy() {
+            var _a;
+            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
+        },
+        get filterBy() {
+            var _a;
+            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
+        },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setLastDrawnOffsetPx(n) {
             self.lastDrawnOffsetPx = n;
         },
-        /**
-         * #action
-         */
         setLastDrawnBpPerPx(n) {
             self.lastDrawnBpPerPx = n;
         },
-        /**
-         * #action
-         */
         setLoading(f) {
             self.loading = f;
         },
-        /**
-         * #action
-         */
         reload() {
             self.error = undefined;
         },
-        /**
-         * #action
-         * internal, a reference to a HTMLCanvas because we use a autorun to draw
-         * the canvas
-         */
         setRef(ref) {
             self.ref = ref;
         },
-        /**
-         * #action
-         */
         setColorScheme(colorBy) {
-            self.colorBy = {
+            self.colorBySetting = {
                 ...colorBy,
             };
         },
-        /**
-         * #action
-         */
         setChainData(args) {
             self.chainData = args;
         },
-        /**
-         * #action
-         */
         setDrawInter(f) {
             self.drawInter = f;
         },
-        /**
-         * #action
-         */
         setDrawLongRange(f) {
             self.drawLongRange = f;
         },
-        /**
-         * #action
-         */
         setFilterBy(filter) {
-            self.filterBy = {
+            self.filterBySetting = {
                 ...filter,
             };
         },
-        /**
-         * #action
-         * thin, bold, extrabold, etc
-         */
         setLineWidth(n) {
             self.lineWidth = n;
         },
-        /**
-         * #action
-         * jitter val, helpful to jitter the x direction so you see better
-         * evidence when e.g. 100 long reads map to same x position
-         */
         setJitter(n) {
             self.jitter = n;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get drawn() {
             return self.lastDrawnOffsetPx !== undefined;
         },
-        /**
-         * #getter
-         */
         get lineWidthSetting() {
             var _a;
             return (_a = self.lineWidth) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'lineWidth');
         },
-        /**
-         * #getter
-         */
         get jitterVal() {
             var _a;
             return (_a = self.jitter) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'jitter');
@@ -198,19 +132,12 @@ function stateModelFactory(configSchema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
         return {
-            /**
-             * #method
-             * only used to tell system it's ready for export
-             */
             renderProps() {
                 return {
                     ...superRenderProps(),
                     notReady: !self.chainData,
                 };
             },
-            /**
-             * #method
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -327,9 +254,6 @@ function stateModelFactory(configSchema) {
         };
     })
         .views(self => ({
-        /**
-         * #method
-         */
         async renderSvg(opts) {
             const { renderSvg } = await Promise.resolve().then(() => __importStar(require('../shared/renderSvgUtil')));
             const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeats')));
@@ -338,7 +262,6 @@ function stateModelFactory(configSchema) {
     }))
         .actions(self => ({
         afterAttach() {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             ;
             (async () => {
                 try {

package/dist/LinearReadArcsDisplay/util.d.ts

@@ -1,2 +1,2 @@
-import { ChainData } from '../shared/fetchChains';
+import type { ChainData } from '../shared/fetchChains';
 export declare function hasPairedReads(features: ChainData): boolean;

package/dist/LinearReadCloudDisplay/components/ReactComponent.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
-import { LinearReadCloudDisplayModel } from '../model';
+import type { LinearReadCloudDisplayModel } from '../model';
 declare const LinearReadCloudReactComponent: ({ model, }: {
     model: LinearReadCloudDisplayModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default LinearReadCloudReactComponent;

package/dist/LinearReadCloudDisplay/components/ReactComponent.js

@@ -1,50 +1,23 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 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 mobx_react_1 = require("mobx-react");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
 const BaseDisplayComponent_1 = __importDefault(require("../../shared/components/BaseDisplayComponent"));
 const Cloud = (0, mobx_react_1.observer)(function ({ model, }) {
     const view = (0, util_1.getContainingView)(model);
     const width = Math.round(view.dynamicBlocks.totalWidthPx);
     const height = model.height;
-    // biome-ignore lint/correctness/useExhaustiveDependencies:
     const cb = (0, react_1.useCallback)((ref) => {
         model.setRef(ref);
-    }, 
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-    [model, width, height]);
-    // note: the position absolute below avoids scrollbar from appearing on track
-    return (react_1.default.createElement("canvas", { "data-testid": "cloud-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
+    }, [model, width, height]);
+    return ((0, jsx_runtime_1.jsx)("canvas", { "data-testid": "cloud-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
 });
 const LinearReadCloudReactComponent = (0, mobx_react_1.observer)(function ({ model, }) {
-    return (react_1.default.createElement(BaseDisplayComponent_1.default, { model: model },
-        react_1.default.createElement(Cloud, { model: model })));
+    return ((0, jsx_runtime_1.jsx)(BaseDisplayComponent_1.default, { model: model, children: (0, jsx_runtime_1.jsx)(Cloud, { model: model }) }));
 });
 exports.default = LinearReadCloudReactComponent;

package/dist/LinearReadCloudDisplay/configSchema.d.ts

@@ -1,31 +1,19 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LinearReadCloudDisplay
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     maxFeatureScreenDensity: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     featureHeight: {
         type: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
-    colorScheme: {
+    colorBy: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-        defaultValue: string;
+        defaultValue: {
+            type: string;
+        };
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     renderer: import("mobx-state-tree").IAnyModelType;

package/dist/LinearReadCloudDisplay/configSchema.js

@@ -2,47 +2,22 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_state_tree_1 = require("mobx-state-tree");
-/**
- * #config LinearReadCloudDisplay
- */
 function configSchemaF(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LinearReadCloudDisplay', {
-        /**
-         * #slot
-         */
         maxFeatureScreenDensity: {
             type: 'number',
             description: 'maximum features per pixel that is displayed in the view',
             defaultValue: 5,
         },
-        /**
-         * #slot
-         */
         featureHeight: {
             type: 'number',
             defaultValue: 7,
         },
-        /**
-         * #slot
-         */
-        colorScheme: {
-            type: 'stringEnum',
-            model: mobx_state_tree_1.types.enumeration('colorScheme', [
-                'strand',
-                'normal',
-                'insertSize',
-                'insertSizeAndOrientation',
-                'mappingQuality',
-                'tag',
-            ]),
-            description: 'color scheme to use',
-            defaultValue: 'normal',
+        colorBy: {
+            type: 'frozen',
+            defaultValue: { type: 'insertSizeAndOrientation' },
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager),
         explicitlyTyped: true,
     });

package/dist/LinearReadCloudDisplay/drawFeats.d.ts

@@ -1,2 +1,2 @@
-import { LinearReadCloudDisplayModel } from './model';
+import type { LinearReadCloudDisplayModel } from './model';
 export declare function drawFeats(self: LinearReadCloudDisplayModel, ctx: CanvasRenderingContext2D): void;

package/dist/LinearReadCloudDisplay/drawFeats.js

@@ -2,9 +2,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.drawFeats = drawFeats;
 const util_1 = require("@jbrowse/core/util");
-const util_2 = require("../shared/util");
-const drawPairChains_1 = require("./drawPairChains");
 const drawLongReadChains_1 = require("./drawLongReadChains");
+const drawPairChains_1 = require("./drawPairChains");
+const util_2 = require("../shared/util");
 function drawFeats(self, ctx) {
     const { chainData } = self;
     if (!chainData) {

package/dist/LinearReadCloudDisplay/drawLongReadChains.d.ts

@@ -1,7 +1,7 @@
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import { ChainData } from '../shared/fetchChains';
-import { LinearReadCloudDisplayModel } from './model';
+import type { LinearReadCloudDisplayModel } from './model';
+import type { ChainData } from '../shared/fetchChains';
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function drawLongReadChains({ ctx, self, chainData, view, asm, }: {
     ctx: CanvasRenderingContext2D;
     self: LinearReadCloudDisplayModel;

package/dist/LinearReadCloudDisplay/drawLongReadChains.js

@@ -3,8 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.drawLongReadChains = drawLongReadChains;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
-const color_1 = require("../shared/color");
 const util_2 = require("./util");
+const color_1 = require("../shared/color");
 function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     var _a, _b, _c, _d, _e;
     const distances = [];
@@ -12,8 +12,6 @@ function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     const { chains } = chainData;
     const { height } = self;
     const featureHeight = (0, configuration_1.getConf)(self, 'featureHeight');
-    // get bounds on the 'distances' (pixel span that a particular split long
-    // read 'chain' would have in view)
     for (const chain of chains) {
         let minX = Number.MAX_VALUE;
         let maxX = Number.MIN_VALUE;
@@ -34,7 +32,6 @@ function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     const minD = Math.max(Math.log((0, util_1.min)(distances)) - 1, 0);
     const scaler = (height - 20) / (maxD - minD);
     const halfHeight = featureHeight / 2 - 0.5;
-    // draw split long read 'chains' as connected entities
     for (let i = 0; i < chains.length; i++) {
         const chain = chains[i];
         const w = distances[i];

package/dist/LinearReadCloudDisplay/drawPairChains.d.ts

@@ -1,7 +1,7 @@
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains';
-import { LinearReadCloudDisplayModel } from './model';
+import type { LinearReadCloudDisplayModel } from './model';
+import type { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains';
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function drawPairChains({ ctx, self, chainData, view, asm, }: {
     ctx: CanvasRenderingContext2D;
     self: LinearReadCloudDisplayModel;