@jbrowse/plugin-arc 2.16.1 → 2.18.0

package/dist/LinearPairedArcDisplay/fetchChains.js

@@ -3,11 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.fetchChains = fetchChains;
 const util_1 = require("@jbrowse/core/util");
 async function fetchChains(self) {
-    // @ts-expect-error
     const { rpcSessionId: sessionId } = (0, util_1.getContainingTrack)(self);
     const { rpcManager } = (0, util_1.getSession)(self);
     const view = (0, util_1.getContainingView)(self);
-    if (!view.initialized || self.error || self.regionTooLarge) {
+    if (!view.initialized || self.error || !self.statsReadyAndRegionNotTooLarge) {
         return;
     }
     self.setLoading(true);

package/dist/LinearPairedArcDisplay/index.d.ts

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

package/dist/LinearPairedArcDisplay/index.js

@@ -24,10 +24,10 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LinearPairedArcDisplayF;
+const react_1 = require("react");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const configSchema_1 = require("./configSchema");
 const model_1 = require("./model");
-const react_1 = require("react");
 function LinearPairedArcDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.configSchemaFactory)();

package/dist/LinearPairedArcDisplay/model.d.ts

@@ -1,17 +1,7 @@
-import React from 'react';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { Instance } from 'mobx-state-tree';
-import { Feature } from '@jbrowse/core/util';
-/**
- * #stateModel LinearPairedArcDisplay
- * this is a non-block-based track type, and can connect arcs across multiple
- * displayedRegions
- *
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [TrackHeightMixin](../trackheightmixin)
- * - [FeatureDensityMixin](../featuredensitymixin)
- */
+import type React from 'react';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
+import type { Instance } from 'mobx-state-tree';
 export 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>;
@@ -22,17 +12,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"LinearPairedArcDisplay">;
-    /**
-     * #property
-     */
     configuration: AnyConfigurationSchemaType;
-    /**
-     * #property
-     */
     displayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 }, {
     rendererTypeName: string;
@@ -49,22 +30,14 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree" /**
-             * #property
-             */).ISimpleType<string>, [undefined]>;
+            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(
-            /**
-             * #getter
-             */
-            "mobx-state-tree").ISimpleType<string>>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree" /**
-         * #action
-         */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
@@ -131,6 +104,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     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;
 } & {
@@ -139,32 +113,14 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     loading: boolean;
     drawn: boolean;
 } & {
-    /**
-     * #getter
-     */
     readonly displayModeSetting: any;
 } & {
-    /**
-     * #action
-     */
     selectFeature(feature: Feature): void;
-    /**
-     * #action
-     */
     setLoading(flag: boolean): void;
-    /**
-     * #action
-     */
     setFeatures(f: Feature[]): void;
-    /**
-     * #action
-     */
     setDisplayMode(flag: string): void;
 } & {
     afterAttach(): void;
-    /**
-     * #action
-     */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<React.ReactNode>;

package/dist/LinearPairedArcDisplay/model.js

@@ -25,34 +25,15 @@ var __importStar = (this && this.__importStar) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = stateModelFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-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");
-/**
- * #stateModel LinearPairedArcDisplay
- * this is a non-block-based track type, and can connect arcs across multiple
- * displayedRegions
- *
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [TrackHeightMixin](../trackheightmixin)
- * - [FeatureDensityMixin](../featuredensitymixin)
- */
+const mobx_state_tree_1 = require("mobx-state-tree");
 function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearPairedArcDisplay', 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('LinearPairedArcDisplay'),
-        /**
-         * #property
-         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        /**
-         * #property
-         */
         displayMode: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
     }))
         .volatile(() => ({
@@ -62,18 +43,12 @@ function stateModelFactory(configSchema) {
         drawn: true,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get displayModeSetting() {
             var _a;
             return (_a = self.displayMode) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, ['renderer', 'displayMode']);
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         selectFeature(feature) {
             const session = (0, util_1.getSession)(self);
             if ((0, util_1.isSessionModelWithWidgets)(session)) {
@@ -88,28 +63,18 @@ function stateModelFactory(configSchema) {
                 session.setSelection(feature);
             }
         },
-        /**
-         * #action
-         */
         setLoading(flag) {
             self.loading = flag;
         },
-        /**
-         * #action
-         */
         setFeatures(f) {
             self.features = f;
         },
-        /**
-         * #action
-         */
         setDisplayMode(flag) {
             self.displayMode = flag;
         },
     }))
         .actions(self => ({
         afterAttach() {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             ;
             (async () => {
                 try {
@@ -122,12 +87,8 @@ function stateModelFactory(configSchema) {
                 }
             })();
         },
-        /**
-         * #action
-         */
         async renderSvg(opts) {
             const { renderArcSvg } = await Promise.resolve().then(() => __importStar(require('./renderSvg')));
-            // @ts-expect-error
             return renderArcSvg(self, opts);
         },
     }));

package/dist/LinearPairedArcDisplay/renderSvg.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { LinearArcDisplayModel } from './model';
+import type { LinearArcDisplayModel } from './model';
 export declare function renderArcSvg(model: LinearArcDisplayModel, _opts: {
     rasterizeLayers?: boolean;
 }): Promise<React.JSX.Element>;

package/dist/LinearPairedArcDisplay/util.d.ts

@@ -1,7 +1,7 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, AugmentedRegion } from '@jbrowse/core/util';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { IAutorunOptions } from 'mobx';
+import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { AugmentedRegion, Feature } from '@jbrowse/core/util';
+import type { IAutorunOptions } from 'mobx';
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function getTag(feature: Feature, tag: string): any;
 export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
 export declare const orientationTypes: {

package/dist/LinearPairedArcDisplay/util.js

@@ -8,24 +8,17 @@ exports.fetchSequence = fetchSequence;
 exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
 exports.createAutorun = createAutorun;
 exports.randomColor = randomColor;
-const operators_1 = require("rxjs/operators");
-const rxjs_1 = require("rxjs");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const mobx_1 = require("mobx");
-// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
-// BAM does not
+const mobx_state_tree_1 = require("mobx-state-tree");
+const rxjs_1 = require("rxjs");
+const operators_1 = require("rxjs/operators");
 function getTag(feature, tag) {
-    const tags = feature.get('tags');
-    return tags !== undefined ? tags[tag] : feature.get(tag);
+    return feature.get('tags')[tag];
 }
-// use fallback alt tag, used in situations where upper case/lower case tags
-// exist e.g. Mm/MM for base modifications
 function getTagAlt(feature, tag, alt) {
     var _a;
     return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
 }
-// orientation definitions from igv.js, see also
-// https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
 exports.orientationTypes = {
     fr: {
         F1R2: 'LR',
@@ -83,8 +76,6 @@ function getColorWGBS(strand, base) {
     }
     return '#888';
 }
-// fetches region sequence augmenting by +/- 1bp for CpG on either side of
-// requested region
 async function fetchSequence(region, adapter) {
     var _a;
     const { start, end, originalRefName, refName } = region;
@@ -98,12 +89,9 @@ async function fetchSequence(region, adapter) {
         .pipe((0, operators_1.toArray)()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
 }
-// has to check underlying C-G (aka CpG) on the reference sequence
 function shouldFetchReferenceSequence(type) {
     return type === 'methylation';
 }
-// adapted from IGV
-// https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27
 exports.modificationColors = {
     m: 'rgb(255,0,0)',
     h: 'rgb(11, 132, 165)',

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class ArcPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const colors_1 = require("@jbrowse/core/ui/colors");
+const ArcRenderer_1 = __importDefault(require("./ArcRenderer"));
 const LinearArcDisplay_1 = __importDefault(require("./LinearArcDisplay"));
 const LinearPairedArcDisplay_1 = __importDefault(require("./LinearPairedArcDisplay"));
-const ArcRenderer_1 = __importDefault(require("./ArcRenderer"));
-const colors_1 = require("@jbrowse/core/ui/colors");
 class ArcPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -35,7 +35,7 @@ class ArcPlugin extends Plugin_1.default {
                 return colors_1.set1[4];
             }
             else {
-                return colors_1.set1[6]; // skip 5, yellow
+                return colors_1.set1[6];
             }
         });
     }

package/esm/ArcRenderer/ArcRendering.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Feature, Region } from '@jbrowse/core/util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature, Region } from '@jbrowse/core/util';
 declare const ArcRendering: ({ features, config, regions, bpPerPx, height, exportSVG, displayModel, onFeatureClick, }: {
     features: Map<string, Feature>;
     config: AnyConfigurationModel;

package/esm/ArcRenderer/ArcRendering.js

@@ -1,8 +1,7 @@
-import React, { lazy, Suspense, useState } from 'react';
-import { readConfObject, } from '@jbrowse/core/configuration';
+import React, { Suspense, lazy, useState } from 'react';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { bpSpanPx, getStrokeProps } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-// locals
 const ArcTooltip = lazy(() => import('../ArcTooltip'));
 function Arc({ selectedFeatureId, region, bpPerPx, config, height: displayHeight, feature, onFeatureClick, }) {
     const [isMouseOvered, setIsMouseOvered] = useState(false);
@@ -16,7 +15,6 @@ function Arc({ selectedFeatureId, region, bpPerPx, config, height: displayHeight
     const strokeWidth = readConfObject(config, 'thickness', { feature }) || 2;
     const height = Math.min(readConfObject(config, 'height', { feature }) || 100, displayHeight);
     const ref = React.createRef();
-    // formula: https://en.wikipedia.org/wiki/B%C3%A9zier_curve#Cubic_B%C3%A9zier_curves
     const t = 0.5;
     const t1 = 1 - t;
     const textYCoord = 3 * (t1 * t1) * (t * height) + 3 * t1 * (t * t) * height;

package/esm/ArcRenderer/configSchema.d.ts

@@ -1,52 +1,34 @@
 declare const ArcRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     color: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     thickness: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     label: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     height: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     caption: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     displayMode: {
         type: string;
         defaultValue: string;

package/esm/ArcRenderer/configSchema.js

@@ -1,58 +1,37 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-/**
- * #config ArcRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const ArcRenderer = ConfigurationSchema('ArcRenderer', {
-    /**
-     * #slot
-     */
     color: {
         type: 'color',
         description: 'the color of the arcs',
         defaultValue: 'darkblue',
         contextVariable: ['feature'],
     },
-    /**
-     * #slot
-     */
     thickness: {
         type: 'number',
         description: 'the thickness of the arcs',
         defaultValue: `jexl:logThickness(feature,'score')`,
         contextVariable: ['feature'],
     },
-    /**
-     * #slot
-     */
     label: {
         type: 'string',
         description: 'the label to appear at the apex of the arcs',
         defaultValue: `jexl:get(feature,'score')`,
         contextVariable: ['feature'],
     },
-    /**
-     * #slot
-     */
     height: {
         type: 'number',
         description: 'the height of the arcs',
         defaultValue: `jexl:log10(get(feature,'end')-get(feature,'start'))*50`,
         contextVariable: ['feature'],
     },
-    /**
-     * #slot
-     */
     caption: {
         type: 'string',
         description: 'the caption to appear when hovering over any point on the arcs',
         defaultValue: `jexl:get(feature,'name')`,
         contextVariable: ['feature'],
     },
-    /**
-     * #slot
-     */
     displayMode: {
         type: 'enum',
         defaultValue: 'arcs',

package/esm/ArcRenderer/index.d.ts

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

package/esm/ArcRenderer/index.js

@@ -1,6 +1,6 @@
+import ArcRenderer from './ArcRenderer';
 import ReactComponent from './ArcRendering';
 import configSchema from './configSchema';
-import ArcRenderer from './ArcRenderer';
 export default function ArcRendererF(pluginManager) {
     pluginManager.addRendererType(() => new ArcRenderer({
         name: 'ArcRenderer',

package/esm/ArcTooltip.js

@@ -1,7 +1,7 @@
 import React, { Suspense } from 'react';
 import { SanitizedHTML } from '@jbrowse/core/ui';
-import { observer } from 'mobx-react';
 import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
+import { observer } from 'mobx-react';
 const TooltipContents = React.forwardRef(function TooltipContents2({ message }, ref) {
     return (React.createElement("div", { ref: ref }, React.isValidElement(message) ? (message) : message ? (React.createElement(SanitizedHTML, { html: String(message) })) : null));
 });

package/esm/LinearArcDisplay/configSchema.d.ts

@@ -1,11 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LinearArcDisplay
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
 export declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     renderer: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IAnyModelType, [undefined]>;
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {

package/esm/LinearArcDisplay/configSchema.js

@@ -1,19 +1,10 @@
-import { types } from 'mobx-state-tree';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
-/**
- * #config LinearArcDisplay
- */
+import { types } from 'mobx-state-tree';
 export function configSchemaFactory(pluginManager) {
     return ConfigurationSchema('LinearArcDisplay', {
-        /**
-         * #slot
-         */
         renderer: types.optional(pluginManager.pluggableConfigSchemaType('renderer'), { type: 'ArcRenderer' }),
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });

package/esm/LinearArcDisplay/index.d.ts

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