@jbrowse/plugin-alignments 3.7.0 → 4.0.1

package/esm/shared/primaryStrand.js

@@ -1,20 +1,22 @@
 export function getPrimaryStrand(feat) {
-    var _a, _b;
-    if (!(feat.flags & 2048)) {
-        return feat.strand;
+    const flags = feat.get('flags');
+    if (!(flags & 2048)) {
+        return feat.get('strand');
     }
     else {
-        const res = (_b = (_a = feat.SA) === null || _a === void 0 ? void 0 : _a.split(';')[0]) === null || _b === void 0 ? void 0 : _b.split(',')[2];
+        const SA = feat.get('tags')?.SA;
+        const res = SA?.split(';')[0]?.split(',')[2];
         return res === '-' ? -1 : 1;
     }
 }
 export function getPrimaryStrandFromFlags(feat) {
-    var _a, _b;
-    if (!(feat.flags & 2048)) {
-        return feat.flags & 16 ? -1 : 1;
+    const flags = feat.get('flags');
+    if (!(flags & 2048)) {
+        return flags & 16 ? -1 : 1;
     }
     else {
-        const res = (_b = (_a = feat.SA) === null || _a === void 0 ? void 0 : _a.split(';')[0]) === null || _b === void 0 ? void 0 : _b.split(',')[2];
+        const SA = feat.get('tags')?.SA;
+        const res = SA?.split(';')[0]?.split(',')[2];
         return res === '-' ? -1 : 1;
     }
 }

package/esm/shared/samFlags.d.ts

@@ -0,0 +1,12 @@
+export declare const SAM_FLAG_PAIRED = 1;
+export declare const SAM_FLAG_PROPER_PAIR = 2;
+export declare const SAM_FLAG_UNMAPPED = 4;
+export declare const SAM_FLAG_MATE_UNMAPPED = 8;
+export declare const SAM_FLAG_REVERSE = 16;
+export declare const SAM_FLAG_MATE_REVERSE = 32;
+export declare const SAM_FLAG_FIRST_IN_PAIR = 64;
+export declare const SAM_FLAG_SECOND_IN_PAIR = 128;
+export declare const SAM_FLAG_SECONDARY = 256;
+export declare const SAM_FLAG_FAILS_QC = 512;
+export declare const SAM_FLAG_DUPLICATE = 1024;
+export declare const SAM_FLAG_SUPPLEMENTARY = 2048;

package/esm/shared/samFlags.js

@@ -0,0 +1,12 @@
+export const SAM_FLAG_PAIRED = 1;
+export const SAM_FLAG_PROPER_PAIR = 2;
+export const SAM_FLAG_UNMAPPED = 4;
+export const SAM_FLAG_MATE_UNMAPPED = 8;
+export const SAM_FLAG_REVERSE = 16;
+export const SAM_FLAG_MATE_REVERSE = 32;
+export const SAM_FLAG_FIRST_IN_PAIR = 64;
+export const SAM_FLAG_SECOND_IN_PAIR = 128;
+export const SAM_FLAG_SECONDARY = 256;
+export const SAM_FLAG_FAILS_QC = 512;
+export const SAM_FLAG_DUPLICATE = 1024;
+export const SAM_FLAG_SUPPLEMENTARY = 2048;

package/esm/shared/setupModificationsAutorun.d.ts

@@ -0,0 +1,11 @@
+import type { ModificationType } from './types.ts';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export interface ModificationsAutorunModel {
+    adapterConfig: AnyConfigurationModel;
+    updateVisibleModifications: (arg: ModificationType[]) => void;
+    setSimplexModifications: (arg: string[]) => void;
+    setModificationsReady: (arg: boolean) => void;
+    setStatusMessage: (arg: string) => void;
+    effectiveRpcDriverName?: string;
+}
+export declare function setupModificationsAutorun(model: ModificationsAutorunModel, isReady: () => boolean): void;

package/esm/shared/setupModificationsAutorun.js

@@ -0,0 +1,27 @@
+import { getContainingView } from '@jbrowse/core/util';
+import { isAlive } from '@jbrowse/mobx-state-tree';
+import { getUniqueModifications } from "./getUniqueModifications.js";
+import { createAutorun } from "../util.js";
+export function setupModificationsAutorun(model, isReady) {
+    createAutorun(model, async () => {
+        if (!isReady()) {
+            return;
+        }
+        const view = getContainingView(model);
+        const { adapterConfig } = model;
+        const { staticBlocks } = view;
+        const { modifications, simplexModifications } = await getUniqueModifications({
+            model,
+            adapterConfig,
+            blocks: staticBlocks,
+        });
+        if (isAlive(model)) {
+            model.updateVisibleModifications(modifications);
+            model.setSimplexModifications(simplexModifications);
+            model.setModificationsReady(true);
+        }
+    }, {
+        delay: 1000,
+        name: 'GetModInfo',
+    });
+}

package/esm/shared/types.d.ts

@@ -1,3 +1,5 @@
+import type { MismatchCallback } from './forEachMismatchTypes.ts';
+import type { Feature } from '@jbrowse/core/util';
 export type SkipMap = Record<string, {
     score: number;
     feature: unknown;
@@ -12,6 +14,10 @@ export interface BinEntry {
     '0': number;
     '1': number;
     avgProbability?: number;
+    avgLength?: number;
+    minLength?: number;
+    maxLength?: number;
+    topSequence?: string;
 }
 type BinType = Record<string, BinEntry>;
 export interface BaseCoverageBin {
@@ -30,7 +36,18 @@ export interface PreBinEntry {
     '-1': number;
     '0': number;
     '1': number;
-    probabilities: number[];
+    probabilityTotal: number;
+    probabilityCount: number;
+    lengthTotal: number;
+    lengthCount: number;
+    lengthMin: number;
+    lengthMax: number;
+    sequenceCounts?: Map<string, number>;
+    avgProbability?: number;
+    avgLength?: number;
+    minLength?: number;
+    maxLength?: number;
+    topSequence?: string;
 }
 type PreBinType = Record<string, PreBinEntry>;
 export interface PreBaseCoverageBin extends PreBaseCoverageBinSubtypes {
@@ -82,15 +99,59 @@ export interface SortedBy {
     assemblyName: string;
     tag?: string;
 }
-export interface Mismatch {
-    qual?: number;
+interface BaseMismatch {
     start: number;
     length: number;
-    insertedBases?: string;
-    type: string;
+}
+export interface SNPMismatch extends BaseMismatch {
+    type: 'mismatch';
     base: string;
+    qual?: number;
     altbase?: string;
-    seq?: string;
-    cliplen?: number;
+}
+export interface InsertionMismatch extends BaseMismatch {
+    type: 'insertion';
+    insertlen: number;
+    insertedBases?: string;
+}
+export interface DeletionMismatch extends BaseMismatch {
+    type: 'deletion';
+}
+export interface SkipMismatch extends BaseMismatch {
+    type: 'skip';
+}
+export interface ClipMismatch extends BaseMismatch {
+    type: 'softclip' | 'hardclip';
+    cliplen: number;
+}
+export type Mismatch = SNPMismatch | InsertionMismatch | DeletionMismatch | SkipMismatch | ClipMismatch;
+export interface ReducedFeature {
+    name: string;
+    strand: number;
+    refName: string;
+    start: number;
+    end: number;
+    id: string;
+    flags: number;
+    tlen: number;
+    pair_orientation: string;
+    next_ref?: string;
+    next_pos?: number;
+    clipLengthAtStartOfRead: number;
+    SA?: string;
+}
+export interface ChainStats {
+    max: number;
+    min: number;
+    upper: number;
+    lower: number;
+}
+export interface ChainData {
+    stats?: ChainStats;
+    chains: Feature[][];
+}
+export type MismatchType = 'mismatch' | 'insertion' | 'deletion' | 'skip' | 'softclip' | 'hardclip';
+export interface FeatureWithMismatchIterator extends Feature {
+    forEachMismatch(callback: MismatchCallback): void;
 }
 export {};

package/esm/shared/util.d.ts

@@ -1,10 +1,18 @@
-import type { ChainData } from './fetchChains';
+import type { ChainData } from './types.ts';
+import type { Feature } from '@jbrowse/core/util';
+import type { Theme } from '@mui/material';
 export declare function hasPairedReads(features: ChainData): boolean;
 export declare function alphaColor(baseColor: string, p: number): string;
 export declare const defaultFilterFlags: {
     flagInclude: number;
     flagExclude: number;
 };
+export declare function isDefaultFilterFlags(filterBy: {
+    flagInclude?: number;
+    flagExclude?: number;
+    readName?: string;
+    tagFilter?: unknown;
+} | undefined): boolean;
 export declare const negFlags: {
     flagInclude: number;
     flagExclude: number;
@@ -20,3 +28,46 @@ export declare function filterReadFlag(flags: number, flagInclude: number, flagE
 export declare function filterTagValue(readVal: unknown, filterVal?: string): boolean;
 export declare function shouldRenderChevrons(bpPerPx: number, featureHeight: number): boolean;
 export declare const CHEVRON_WIDTH = 5;
+interface SamHeaderLine {
+    tag: string;
+    data: {
+        tag: string;
+        value: string;
+    }[];
+}
+export interface ParsedSamHeader {
+    idToName: string[];
+    nameToId: Record<string, number>;
+    readGroups: string[];
+}
+export declare function parseSamHeader(samHeader: SamHeaderLine[]): ParsedSamHeader;
+export declare function getColorBaseMap(theme: Theme): {
+    A: string;
+    C: string;
+    G: string;
+    T: string;
+    deletion: string;
+    insertion: string;
+    hardclip: string;
+    softclip: string;
+    skip: string;
+};
+export declare function getContrastBaseMap(theme: Theme): {
+    [k: string]: string;
+};
+export declare function shouldDrawSNPsMuted(type?: string): boolean;
+export declare function shouldDrawIndels(): boolean;
+export interface LayoutFeature {
+    heightPx: number;
+    topPx: number;
+    feature: Feature;
+}
+export declare function setAlignmentFont(ctx: CanvasRenderingContext2D): void;
+export declare function getCharWidthHeight(): {
+    charWidth: number;
+    charHeight: number;
+};
+export declare function measureTextSmallNumber(n: number, fontSize?: number): number;
+export declare function convertTagsToPlainArrays(tags: Record<string, unknown>): Record<string, unknown>;
+export declare function buildMismatchMap(feature: Feature, featureStart: number): Map<number, string>;
+export {};

package/esm/shared/util.js

@@ -1,7 +1,10 @@
+import { measureText } from '@jbrowse/core/util';
 import { colord } from '@jbrowse/core/util/colord';
+import { MISMATCH_TYPE } from "./forEachMismatchTypes.js";
+import { SAM_FLAG_PAIRED } from "./samFlags.js";
 export function hasPairedReads(features) {
     for (const f of features.chains.values()) {
-        if (f[0].flags & 1) {
+        if (f[0].get('flags') & SAM_FLAG_PAIRED) {
             return true;
         }
     }
@@ -18,6 +21,15 @@ export const defaultFilterFlags = {
     flagInclude: 0,
     flagExclude: 1540,
 };
+export function isDefaultFilterFlags(filterBy) {
+    if (!filterBy) {
+        return true;
+    }
+    return (filterBy.flagInclude === 0 &&
+        filterBy.flagExclude === 1540 &&
+        !filterBy.readName &&
+        !filterBy.tagFilter);
+}
 export const negFlags = {
     flagInclude: 16,
     flagExclude: 1540,
@@ -57,3 +69,108 @@ export function shouldRenderChevrons(bpPerPx, featureHeight) {
     return bpPerPx < 50 && featureHeight >= 3;
 }
 export const CHEVRON_WIDTH = 5;
+export function parseSamHeader(samHeader) {
+    const idToName = [];
+    const nameToId = {};
+    const readGroups = [];
+    let refId = 0;
+    let rgId = 0;
+    for (const element of samHeader) {
+        const line = element;
+        if (line.tag === 'SQ') {
+            const data = line.data;
+            for (const datum of data) {
+                const item = datum;
+                if (item.tag === 'SN') {
+                    const refName = item.value;
+                    nameToId[refName] = refId;
+                    idToName[refId] = refName;
+                    break;
+                }
+            }
+            refId++;
+        }
+        else if (line.tag === 'RG') {
+            const data = line.data;
+            for (const datum of data) {
+                const item = datum;
+                if (item.tag === 'ID') {
+                    readGroups[rgId] = item.value;
+                    break;
+                }
+            }
+            rgId++;
+        }
+    }
+    return { idToName, nameToId, readGroups };
+}
+export function getColorBaseMap(theme) {
+    const { skip, deletion, insertion, hardclip, softclip, bases } = theme.palette;
+    return {
+        A: bases.A.main,
+        C: bases.C.main,
+        G: bases.G.main,
+        T: bases.T.main,
+        deletion,
+        insertion,
+        hardclip,
+        softclip,
+        skip,
+    };
+}
+export function getContrastBaseMap(theme) {
+    return Object.fromEntries(Object.entries(getColorBaseMap(theme)).map(([key, value]) => [
+        key,
+        theme.palette.getContrastText(value),
+    ]));
+}
+export function shouldDrawSNPsMuted(type) {
+    return ['methylation', 'modifications'].includes(type || '');
+}
+export function shouldDrawIndels() {
+    return true;
+}
+export function setAlignmentFont(ctx) {
+    ctx.font = 'bold 10px Courier New,monospace';
+}
+export function getCharWidthHeight() {
+    const charWidth = measureText('A');
+    const charHeight = measureText('M') - 2;
+    return { charWidth, charHeight };
+}
+const smallNumberWidthCache10 = new Map();
+const smallNumberWidthCache = new Map();
+export function measureTextSmallNumber(n, fontSize) {
+    const cache = fontSize === 10 ? smallNumberWidthCache10 : smallNumberWidthCache;
+    if (n >= 0 && n < 100) {
+        let width = cache.get(n);
+        if (width === undefined) {
+            width = measureText(String(n), fontSize);
+            cache.set(n, width);
+        }
+        return width;
+    }
+    return measureText(String(n), fontSize);
+}
+function isTypedArray(val) {
+    return ArrayBuffer.isView(val) && !(val instanceof DataView);
+}
+export function convertTagsToPlainArrays(tags) {
+    const result = {};
+    for (const [key, value] of Object.entries(tags)) {
+        result[key] = isTypedArray(value) ? [...value] : value;
+    }
+    return result;
+}
+export function buildMismatchMap(feature, featureStart) {
+    const mismatchMap = new Map();
+    if ('forEachMismatch' in feature) {
+        const feat = feature;
+        feat.forEachMismatch((type, mismatchStart, _len, base) => {
+            if (type === MISMATCH_TYPE) {
+                mismatchMap.set(featureStart + mismatchStart, base);
+            }
+        });
+    }
+    return mismatchMap;
+}

package/esm/svgExportUtil.d.ts

@@ -0,0 +1,9 @@
+export declare function isReadyOrHasError(display: {
+    renderProps(): {
+        notReady?: boolean;
+    };
+    error?: unknown;
+}): boolean;
+export declare function hasAnySubDisplayError(displays: {
+    error?: unknown;
+}[]): boolean;

package/esm/svgExportUtil.js

@@ -0,0 +1,6 @@
+export function isReadyOrHasError(display) {
+    return !display.renderProps().notReady || !!display.error;
+}
+export function hasAnySubDisplayError(displays) {
+    return displays.some(d => !!d.error);
+}

package/esm/util.d.ts

@@ -1,7 +1,7 @@
 import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { AugmentedRegion, Feature } from '@jbrowse/core/util';
+import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree';
 import type { IAutorunOptions } from 'mobx';
-import type { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
 export declare const orientationTypes: {
     fr: Record<string, string>;
@@ -17,9 +17,9 @@ export declare const pairMap: {
 export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
 export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
 type DisplayModel = IAnyStateTreeNode & {
-    setError: (arg: unknown) => void;
+    setError?: (arg: unknown) => void;
 };
 export declare function createAutorun(self: DisplayModel, cb: () => Promise<void>, opts?: IAutorunOptions): void;
 export declare function randomColor(str: string): string;
 export declare function getColorForModification(str: string): string;
-export { modificationData } from './shared/modificationData';
+export { modificationData } from './shared/modificationData.ts';

package/esm/util.js

@@ -1,12 +1,11 @@
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
-import { addDisposer, isAlive } from 'mobx-state-tree';
 import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
-import { modificationData } from './shared/modificationData';
+import { modificationData } from "./shared/modificationData.js";
 export function getTagAlt(feature, tag, alt) {
-    var _a;
     const tags = feature.get('tags');
-    return (_a = tags[tag]) !== null && _a !== void 0 ? _a : tags[alt];
+    return tags[tag] ?? tags[alt];
 }
 export const orientationTypes = {
     fr: {
@@ -66,7 +65,6 @@ export function getColorWGBS(strand, base) {
     return '#888';
 }
 export async function fetchSequence(region, adapter) {
-    var _a;
     const { start, end, originalRefName, refName } = region;
     const feats = await firstValueFrom(adapter
         .getFeatures({
@@ -76,16 +74,16 @@ export async function fetchSequence(region, adapter) {
         start,
     })
         .pipe(toArray()));
-    return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
+    return feats[0]?.get('seq');
 }
 export function createAutorun(self, cb, opts) {
-    addDisposer(self, autorun(async () => {
+    addDisposer(self, autorun(async function sharedAlignmentsAutorun() {
         try {
             await cb();
         }
         catch (e) {
             if (isAlive(self)) {
-                self.setError(e);
+                self.setError?.(e);
             }
         }
     }, opts));
@@ -98,7 +96,6 @@ export function randomColor(str) {
     return `hsl(${sum * 10}, 20%, 50%)`;
 }
 export function getColorForModification(str) {
-    var _a;
-    return ((_a = modificationData[str]) === null || _a === void 0 ? void 0 : _a.color) || randomColor(str);
+    return modificationData[str]?.color || randomColor(str);
 }
-export { modificationData } from './shared/modificationData';
+export { modificationData } from "./shared/modificationData.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "3.7.0",
+  "version": "4.0.1",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -15,44 +15,28 @@
     "directory": "plugins/alignments"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/alignments",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@gmod/bam": "^6.0.1",
-    "@gmod/cram": "^5.0.4",
-    "@jbrowse/core": "^3.7.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.7.0",
-    "@jbrowse/plugin-wiggle": "^3.7.0",
-    "@jbrowse/sv-core": "^3.7.0",
-    "@mui/icons-material": "^7.0.0",
-    "@mui/material": "^7.0.0",
+    "@gmod/bam": "^7.1.15",
+    "@gmod/cram": "^7.0.3",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/icons-material": "^7.3.6",
+    "@mui/material": "^7.3.6",
+    "@mui/x-charts-vendor": "^8.23.0",
     "canvas2svg": "^1.0.16",
-    "copy-to-clipboard": "^3.3.1",
+    "copy-to-clipboard": "^3.3.3",
     "fast-deep-equal": "^3.1.3",
-    "generic-filehandle2": "^2.0.1",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0",
-    "tss-react": "^4.0.0"
+    "generic-filehandle2": "^2.0.18",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "rxjs": "^7.8.2",
+    "@jbrowse/core": "^4.0.1",
+    "@jbrowse/plugin-linear-genome-view": "^4.0.1",
+    "@jbrowse/plugin-wiggle": "^4.0.1",
+    "@jbrowse/sv-core": "^4.0.1"
   },
   "peerDependencies": {
     "react": ">=18.0.0"
@@ -60,8 +44,19 @@
   "publishConfig": {
     "access": "public"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/alignments",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,5 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-declare const AlignmentsFeatureDetails: (props: {
-    model: AlignmentFeatureWidgetModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default AlignmentsFeatureDetails;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -1,63 +0,0 @@
-"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 () {
-    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 jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const Flags_1 = __importDefault(require("./Flags"));
-const Formatter_1 = __importDefault(require("./Formatter"));
-const PairLink_1 = __importDefault(require("./PairLink"));
-const tagInfo_1 = require("./tagInfo");
-const util_1 = require("./util");
-const SupplementaryAlignments = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SupplementaryAlignments'))));
-const LinkedPairedAlignments = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LinkedPairedAlignments'))));
-const FeatDefined = (0, mobx_react_1.observer)(function (props) {
-    const { model, feat } = props;
-    const flags = feat.flags;
-    const SA = (0, util_1.getTag)('SA', feat);
-    return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { "data-testid": "alignment-side-drawer", children: [(0, jsx_runtime_1.jsx)(FeatureDetails_1.default, { ...props, descriptions: { tags: tagInfo_1.tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? ((0, jsx_runtime_1.jsx)(PairLink_1.default, { model: model, locString: value })) : ((0, jsx_runtime_1.jsx)(Formatter_1.default, { value: value })) }), SA !== undefined ? ((0, jsx_runtime_1.jsx)(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null, flags != null ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [flags & 1 ? ((0, jsx_runtime_1.jsx)(LinkedPairedAlignments, { model: model, feature: feat })) : null, (0, jsx_runtime_1.jsx)(Flags_1.default, { flags: flags, ...props })] })) : null] }));
-});
-const AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
-    const { model } = props;
-    const { featureData } = model;
-    const feat = structuredClone(featureData);
-    return feat ? ((0, jsx_runtime_1.jsx)(FeatDefined, { feat: feat, ...props })) : ((0, jsx_runtime_1.jsx)("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" }));
-});
-exports.default = AlignmentsFeatureDetails;

package/dist/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.d.ts

@@ -1 +0,0 @@
-export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';

package/dist/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js

@@ -1,5 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = void 0;
-var sv_core_1 = require("@jbrowse/sv-core");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendMultiLevelOptionDialog; } });