@jbrowse/plugin-arc 2.17.0 → 3.0.0

package/esm/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>;
     }>;
@@ -131,40 +104,23 @@ 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;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     lastDrawnOffsetPx: number;
     features: Feature[] | undefined;
     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/esm/LinearPairedArcDisplay/model.js

@@ -1,32 +1,13 @@
-import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
-import { getSession, isSessionModelWithWidgets, getContainingView, getContainingTrack, isSelectionContainer, } from '@jbrowse/core/util';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes';
+import { getContainingTrack, getContainingView, getSession, isSelectionContainer, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import { FeatureDensityMixin, TrackHeightMixin, } from '@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)
- */
+import { types } from 'mobx-state-tree';
 export function stateModelFactory(configSchema) {
     return types
         .compose('LinearPairedArcDisplay', BaseDisplay, TrackHeightMixin(), FeatureDensityMixin(), types.model({
-        /**
-         * #property
-         */
         type: types.literal('LinearPairedArcDisplay'),
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
         displayMode: types.maybe(types.string),
     }))
         .volatile(() => ({
@@ -36,18 +17,12 @@ export function stateModelFactory(configSchema) {
         drawn: true,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get displayModeSetting() {
             var _a;
             return (_a = self.displayMode) !== null && _a !== void 0 ? _a : getConf(self, ['renderer', 'displayMode']);
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         selectFeature(feature) {
             const session = getSession(self);
             if (isSessionModelWithWidgets(session)) {
@@ -62,28 +37,18 @@ export 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 {
@@ -96,12 +61,8 @@ export function stateModelFactory(configSchema) {
                 }
             })();
         },
-        /**
-         * #action
-         */
         async renderSvg(opts) {
             const { renderArcSvg } = await import('./renderSvg');
-            // @ts-expect-error
             return renderArcSvg(self, opts);
         },
     }));

package/esm/LinearPairedArcDisplay/renderSvg.d.ts

@@ -1,5 +1,4 @@
-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>;
+}): Promise<import("react/jsx-runtime").JSX.Element>;

package/esm/LinearPairedArcDisplay/renderSvg.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { getContainingView, when } from '@jbrowse/core/util';
 import Arcs from './components/Arcs';
 export async function renderArcSvg(model, _opts) {
@@ -7,10 +7,5 @@ export async function renderArcSvg(model, _opts) {
     const width = view.dynamicBlocks.totalWidthPx;
     const height = model.height;
     const clipid = `arc-${model.id}`;
-    return (React.createElement(React.Fragment, null,
-        React.createElement("defs", null,
-            React.createElement("clipPath", { id: clipid },
-                React.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
-        React.createElement("g", { clipPath: `url(#${clipid})` },
-            React.createElement(Arcs, { model: model, exportSVG: true }))));
+    return (_jsxs(_Fragment, { children: [_jsx("defs", { children: _jsx("clipPath", { id: clipid, children: _jsx("rect", { x: 0, y: 0, width: width, height: height }) }) }), _jsx("g", { clipPath: `url(#${clipid})`, children: _jsx(Arcs, { model: model, exportSVG: true }) })] }));
 }

package/esm/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/esm/LinearPairedArcDisplay/util.js

@@ -1,20 +1,14 @@
-import { toArray } from 'rxjs/operators';
-import { firstValueFrom } from 'rxjs';
-import { addDisposer, isAlive } from 'mobx-state-tree';
 import { autorun } from 'mobx';
-// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
-// BAM does not
+import { addDisposer, isAlive } from 'mobx-state-tree';
+import { firstValueFrom } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 export function getTag(feature, 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
 export 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
 export const orientationTypes = {
     fr: {
         F1R2: 'LR',
@@ -72,8 +66,6 @@ export function getColorWGBS(strand, base) {
     }
     return '#888';
 }
-// fetches region sequence augmenting by +/- 1bp for CpG on either side of
-// requested region
 export async function fetchSequence(region, adapter) {
     var _a;
     const { start, end, originalRefName, refName } = region;
@@ -87,12 +79,9 @@ export async function fetchSequence(region, adapter) {
         .pipe(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
 export 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
 export const modificationColors = {
     m: 'rgb(255,0,0)',
     h: 'rgb(11, 132, 165)',

package/esm/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/esm/index.js

@@ -1,8 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
+import { set1 } from '@jbrowse/core/ui/colors';
+import ArcRendererF from './ArcRenderer';
 import LinearArcDisplayF from './LinearArcDisplay';
 import LinearPairedArcDisplayF from './LinearPairedArcDisplay';
-import ArcRendererF from './ArcRenderer';
-import { set1 } from '@jbrowse/core/ui/colors';
 export default class ArcPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -30,7 +30,7 @@ export default class ArcPlugin extends Plugin {
                 return set1[4];
             }
             else {
-                return set1[6]; // skip 5, yellow
+                return set1[6];
             }
         });
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-arc",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 arc adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -53,5 +53,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }