wuepgg3-track 5.0.0 → 5.0.2

package/dist/{BufferResource-ChgmE3N0.mjs → BufferResource-RmJVWkXV.mjs}

@@ -1,4 +1,4 @@
-import { w as U, g, h as c, u as S, i as _, j as m, k as I, l as p } from "./index-Dky1S9zX.mjs";
+import { w as U, g, h as c, u as S, i as _, j as m, k as I, l as p } from "./index-CF0QNcGP.mjs";
 const x = {
   name: "local-uniform-bit",
   vertex: {

package/dist/{CanvasRenderer-DhKd7knL.mjs → CanvasRenderer-CqXi5K_I.mjs}

@@ -1,5 +1,5 @@
-import { D as O, C as ee, m as D, n as Re, o as ce, M as F, E as R, p as Xe, w as $e, c as He, q as ze, s as Je, r as Ke, F as Qe, t as Ze, v as et, A as tt, R as nt, f as he } from "./index-Dky1S9zX.mjs";
-import { R as at, S as st, B as ot, a as rt, b as it, c as ct, A as lt, C as ht } from "./RenderTargetSystem-CSn-OARB.mjs";
+import { D as O, C as ee, m as D, n as Re, o as ce, M as F, E as R, p as Xe, w as $e, c as He, q as ze, s as Je, r as Ke, F as Qe, t as Ze, v as et, A as tt, R as nt, f as he } from "./index-CF0QNcGP.mjs";
+import { R as at, S as st, B as ot, a as rt, b as it, c as ct, A as lt, C as ht } from "./RenderTargetSystem-DZg7wxxc.mjs";
 let Z;
 function Ae(o) {
   const e = O.get().createCanvas(6, 1), t = e.getContext("2d");

package/dist/{Filter-Cmf7BYhk.mjs → Filter-hBKIgKG1.mjs}

@@ -1,4 +1,4 @@
-import { S as n, a as u, G as o, b as f } from "./index-Dky1S9zX.mjs";
+import { S as n, a as u, G as o, b as f } from "./index-CF0QNcGP.mjs";
 const s = class i extends n {
   /**
    * @param options - The optional parameters of this filter.

package/dist/{RenderTargetSystem-CSn-OARB.mjs → RenderTargetSystem-DZg7wxxc.mjs}

@@ -1,5 +1,5 @@
-import { Z as Ve, U as oe, M as m, G as Ne, b as je, a as $e, _ as le, E as l, f as W, $ as w, a0 as qe, e as z, T, R as V, a1 as de, a2 as Ke, c as f, h as g, N as D, a3 as ue, w as ce, a4 as ee, a5 as he, a6 as pe, a7 as fe, a8 as me, H as P, a9 as Ye, C as E, D as N, O as v, aa as B, ab as Je, P as Xe, ac as Ze, B as Qe, x as te, ad as re, ae as p, l as et, v as O, af as tt, ag as rt, ah as st, ai as nt } from "./index-Dky1S9zX.mjs";
-import { F as at } from "./Filter-Cmf7BYhk.mjs";
+import { Z as Ve, U as oe, M as m, G as Ne, b as je, a as $e, _ as le, E as l, f as W, $ as w, a0 as qe, e as z, T, R as V, a1 as de, a2 as Ke, c as f, h as g, N as D, a3 as ue, w as ce, a4 as ee, a5 as he, a6 as pe, a7 as fe, a8 as me, H as P, a9 as Ye, C as E, D as N, O as v, aa as B, ab as Je, P as Xe, ac as Ze, B as Qe, x as te, ad as re, ae as p, l as et, v as O, af as tt, ag as rt, ah as st, ai as nt } from "./index-CF0QNcGP.mjs";
+import { F as at } from "./Filter-hBKIgKG1.mjs";
 var it = `in vec2 vMaskCoord;
 in vec2 vTextureCoord;
 

package/dist/{WebGLRenderer-DOtXnBSh.mjs → WebGLRenderer-CyKbwsab.mjs}

@@ -1,6 +1,6 @@
-import { D as R, a as F, E as d, J as O, j as B, w as p, g as z, b as ye, S as P, c as S, d as Ne, O as q, aj as Ce, h as g, aa as V, v as y, N, U as M, M as Z, ak as J, al as De, am as Q, an as Ie, ao as Ge, A as Ue, R as Fe, f as A } from "./index-Dky1S9zX.mjs";
-import { e as Oe, G as Pe, c as Me, b as Le, U as we, B as ee, d as C, f as te, g as He } from "./BufferResource-ChgmE3N0.mjs";
-import { R as Ve, S as Xe, d as ke } from "./RenderTargetSystem-CSn-OARB.mjs";
+import { D as R, a as F, E as d, J as O, j as B, w as p, g as z, b as ye, S as P, c as S, d as Ne, O as q, aj as Ce, h as g, aa as V, v as y, N, U as M, M as Z, ak as J, al as De, am as Q, an as Ie, ao as Ge, A as Ue, R as Fe, f as A } from "./index-CF0QNcGP.mjs";
+import { e as Oe, G as Pe, c as Me, b as Le, U as we, B as ee, d as C, f as te, g as He } from "./BufferResource-RmJVWkXV.mjs";
+import { R as Ve, S as Xe, d as ke } from "./RenderTargetSystem-DZg7wxxc.mjs";
 function We() {
   const { userAgent: t } = R.get().getNavigator();
   return /^((?!chrome|android).)*safari/i.test(t);

package/dist/{WebGPURenderer-BBVV8q01.mjs → WebGPURenderer-CxkXXhfW.mjs}

@@ -1,6 +1,6 @@
-import { I as L, a as A, E as l, J as D, l as ce, K as de, D as B, h as C, j as T, i as he, B as k, L as w, w as v, N as y, v as pe, O as le, U as z, Q as M, M as F, V as O, W as fe, X as I, Y as ge, S as W, c as R, A as me, R as _e, f as S } from "./index-Dky1S9zX.mjs";
-import { c as be, u as ye, U as xe, B as Ge, G as Pe, e as Be, l as Se, a as Te, t as Ce } from "./BufferResource-ChgmE3N0.mjs";
-import { R as ve, S as Ue, d as we } from "./RenderTargetSystem-CSn-OARB.mjs";
+import { I as L, a as A, E as l, J as D, l as ce, K as de, D as B, h as C, j as T, i as he, B as k, L as w, w as v, N as y, v as pe, O as le, U as z, Q as M, M as F, V as O, W as fe, X as I, Y as ge, S as W, c as R, A as me, R as _e, f as S } from "./index-CF0QNcGP.mjs";
+import { c as be, u as ye, U as xe, B as Ge, G as Pe, e as Be, l as Se, a as Te, t as Ce } from "./BufferResource-RmJVWkXV.mjs";
+import { R as ve, S as Ue, d as we } from "./RenderTargetSystem-DZg7wxxc.mjs";
 const G = A.for2d();
 class H {
   start(e, t, r) {

package/dist/{browserAll-BF2mDjKn.mjs → browserAll-BhOrSw39.mjs}

@@ -1,5 +1,5 @@
-import { x as O, y as Z, P as _, z as Q, E as P, k as ee, w as y, f as D, H as V } from "./index-Dky1S9zX.mjs";
-import "./init-BuN8b-s9.mjs";
+import { x as O, y as Z, P as _, z as Q, E as P, k as ee, w as y, f as D, H as V } from "./index-CF0QNcGP.mjs";
+import "./init-DBpfulRP.mjs";
 class te {
   constructor(e) {
     this._lastTransform = "", this._observer = null, this._tickerAttached = !1, this.updateTranslation = () => {

package/dist/components/GenomeView/TrackComponents/GroupedTrackManager.d.ts

@@ -1,6 +1,9 @@
 import { default as TrackModel } from '../../../models/TrackModel';
 import { NumericalAggregator } from './commonComponents/numerical/NumericalAggregator';
 import { default as OpenInterval } from '../../../models/OpenInterval';
+import { FeaturePlacementResult } from '../../../models/FeatureArranger';
+import { default as DisplayedRegionModel } from '../../../models/DisplayedRegionModel';
+import { Fiber } from '../../../models/Feature';
 export declare const numericalTracks: {
     bigwig: string;
     bedgraph: string;
@@ -33,18 +36,17 @@ export declare class GroupedTrackManager {
      * @returns list of groups found in the track list, their data, and their original indicies
      */
     aggregator: NumericalAggregator;
-    dynseqAggregator: (data: any[], viewRegion: any, width: number, aggregatorId: string) => any;
     aggregateRecords: (data: any[], viewRegion: any, width: number) => any;
-    aggregateFeaturesMatplot: (data: any, viewRegion: any, width: any, aggregatorId: any) => any;
-    constructor();
-    getGroupScale(tracks: TrackModel[], trackData: any, width: number, viewWindow: OpenInterval, dataIdx: number, trackFetchedDataCache: any): {
-        [groupId: number]: {
-            scale: TrackModel;
-            min: {};
-            max: {};
-        };
+    aggregateFibers: (data: Fiber[], viewRegion: DisplayedRegionModel, width: number) => {
+        xToFibers: Array<{
+            on: number;
+            off: number;
+            count: number;
+        }>;
+        placements: FeaturePlacementResult["placements"];
     };
-    getGroupScaleWithXvalues(tracks: TrackModel[], trackData: any, viewWindow: OpenInterval): {
+    constructor();
+    getGroupScale(trackData: any, width: number, viewWindow: OpenInterval, dataIdx: number, trackManagerState: any): {
         [groupId: number]: {
             scale: TrackModel;
             min: {};

package/dist/components/GenomeView/TrackComponents/commonComponents/ErrorBoundary.d.ts

@@ -0,0 +1,24 @@
+import { default as React } from 'react';
+type Props = {
+    children: React.ReactNode;
+    fallbackRender?: (error: Error | null) => React.ReactNode;
+    errorDrawData?: {
+        [key: string]: any;
+    } | null;
+};
+type State = {
+    hasError: boolean;
+    error?: Error | null;
+    fallbackElement?: React.ReactNode | null;
+};
+declare class ErrorBoundary extends React.Component<Props, State> {
+    constructor(props: Props);
+    static getDerivedStateFromError(error: Error): {
+        hasError: boolean;
+        error: Error;
+    };
+    componentDidCatch(error: Error, info: any): void;
+    reset: () => any;
+    render(): any;
+}
+export default ErrorBoundary;

package/dist/components/GenomeView/TrackComponents/commonComponents/VerticalDivider.d.ts

@@ -0,0 +1,12 @@
+import { default as React } from 'react';
+interface VerticalDividerProps {
+    visData: {
+        visRegion: any;
+        viewWindowRegion: any;
+        viewWindow: {
+            getLength: () => number;
+        };
+    };
+}
+declare const VerticalDivider: React.FC<VerticalDividerProps>;
+export default VerticalDivider;

package/dist/components/GenomeView/TrackComponents/displayModeComponentMap.d.ts

@@ -21,6 +21,6 @@ export declare function getDisplayModeFunction(drawData: {
     [key: string]: any;
 }): any;
 export declare const twoDataTypeTracks: {};
-export declare function formatDataByType(genesArr: any[], type: string, initialLoad: boolean, regionLoci: Array<any>): any[] | {
+export declare function formatDataByType(genesArr: any[], type: string, initialLoad?: boolean, regionLoci?: Array<any>): any[] | {
     error: any;
 };

package/dist/components/GenomeView/genomeNavigator/DragAcrossDiv.d.ts

@@ -4,68 +4,17 @@ export interface CoordinateDiff {
     dx: number;
     dy: number;
 }
-interface DragAcrossDivProps {
-    mouseButton: MouseButton | undefined;
-    style?: object;
-    children: React.ReactNode;
-    /**
-     * Callback for when dragging starts.
-     *
-     * @param {React.MouseEvent} event - the event that triggered this callback
-     */
-    onDragStart?(event: React.MouseEvent): void;
-    /**
-     * Callback for each little bit of movement during a drag.
-     *
-     * @param {React.MouseEvent} event - the event that triggered this callback
-     * @param {CoordinateDiff} coordinateDiff - how far the mouse has moved since the drag started
-     */
-    onDrag?(event: React.MouseEvent, coordinateDiff: CoordinateDiff): void;
-    /**
-     * Callback for when the user lets go of the mouse and stops dragging.
-     *
-     * @param {React.MouseEvent} event - the event that triggered this callback
-     * @param {CoordinateDiff} coordinateDiff - how far the mouse has moved since the drag started
-     */
-    onDragEnd?(event: React.MouseEvent, coordinateDiff: CoordinateDiff): void;
+interface DragAcrossDivProps extends React.HTMLAttributes<HTMLDivElement> {
+    mouseButton?: MouseButton;
+    onDragStart?(event: React.PointerEvent<HTMLDivElement>): void;
+    onDrag?(event: React.PointerEvent<HTMLDivElement>, coordinateDiff: CoordinateDiff): void;
+    onDragEnd?(event: React.PointerEvent<HTMLDivElement>, coordinateDiff: CoordinateDiff): void;
 }
-declare function doNothing(): void;
 /**
  * A <div> that listens for drag-across events, where a user drags the cursor inside the div.  The drag callbacks will
  * fire even for short clicks; be sure to take this possibility into account when working with this component!
  *
- * @author Silas Hsu
+ * Implemented as a function component using hooks.
  */
-export declare class DragAcrossDiv extends React.Component<DragAcrossDivProps> {
-    static defaultProps: {
-        onDragStart: typeof doNothing;
-        onDrag: typeof doNothing;
-        onDragEnd: typeof doNothing;
-    };
-    private originEvent;
-    constructor(props: DragAcrossDivProps);
-    /**
-     * Callback for mousedown events on the <div>.
-     *
-     * @param {React.MouseEvent} event - mouse event that triggered this callback
-     */
-    mousedown(event: React.MouseEvent): void;
-    /**
-     * Callback for mousemove events on the <div>.
-     *
-     * @param {React.MouseEvent} event - mouse event that triggered this callback
-     */
-    mousemove(event: React.MouseEvent): void;
-    /**
-     * Callback for mouseup events on the <div>.
-     *
-     * @param {React.MouseEvent} event - mouse event that triggered this callback
-     */
-    mouseup(event: React.MouseEvent): void;
-    /**
-     * @return {JSX.Element} a div that listens to drag events
-     * @override
-     */
-    render(): any;
-}
+export declare function DragAcrossDiv(props: DragAcrossDivProps): any;
 export {};

package/dist/components/GenomeView/genomeNavigator/GeneSearchBox.d.ts

@@ -1,9 +1,10 @@
 import { FC } from 'react';
 import { default as NavigationContext } from '../../../models/NavigationContext';
 import { default as Genome } from '../../../models/Genome';
+import { GenomeCoordinate } from '../../../types';
 interface GeneSearchBoxProps {
     navContext: NavigationContext;
-    onRegionSelected: (newStart: number, newEnd: number, toolTitle: number | string, highlightSearch: boolean) => void;
+    onRegionSelected: (query: string | GenomeCoordinate, highlightSearch: boolean) => void;
     handleCloseModal: () => void;
     onNewHighlight?: (newStart: number, newEnd: number, geneName: string) => void;
     doHighlight: boolean;

package/dist/components/GenomeView/genomeNavigator/RegionsPanel.d.ts

@@ -0,0 +1,17 @@
+import { default as React } from 'react';
+import { default as Genome } from '../../../models/Genome';
+import { default as DisplayedRegionModel } from '../../../models/DisplayedRegionModel';
+import { GenomeCoordinate } from '../../../types/track-container';
+interface RegionsPanelProps {
+    selectedRegion: DisplayedRegionModel;
+    onRegionSelected: (query: string | GenomeCoordinate, highlightSearch: boolean) => void;
+    contentColorSetup: {
+        color: string;
+        background: string;
+    };
+    virusBrowserMode?: boolean;
+    genomeConfig: Genome;
+    onClose: () => void;
+}
+declare const RegionsPanel: React.FC<RegionsPanelProps>;
+export default RegionsPanel;

package/dist/components/GenomeView/genomeNavigator/SnpSearchBox.d.ts

@@ -1,14 +1,16 @@
 import { default as React } from 'react';
 import { default as NavigationContext } from '../../../models/NavigationContext';
+import { GenomeCoordinate } from '../../../types';
 interface SnpSearchBoxProps {
     genomeConfig: any;
     navContext: NavigationContext;
-    onRegionSelected: (newStart: number, newEnd: number, toolTitle: number | string, highlightSearch: boolean) => void;
+    onRegionSelected: (query: string | GenomeCoordinate, highlightSearch: boolean) => void;
     handleCloseModal: () => void;
     onNewHighlight?: (start: number, end: number, text: string) => void;
     doHighlight: boolean;
     color?: string;
     background?: string;
+    customButton?: React.ElementType;
 }
 declare const SnpSearchBox: React.FC<SnpSearchBoxProps>;
 export default SnpSearchBox;

package/dist/components/GenomeView/genomeNavigator/TrackRegionButton.d.ts

@@ -0,0 +1,8 @@
+import { default as React } from 'react';
+interface TrackRegionButtonProps {
+    coordinates: string;
+    onClick: () => void;
+    style?: React.CSSProperties;
+}
+declare const TrackRegionButton: React.FC<TrackRegionButtonProps>;
+export default TrackRegionButton;

package/dist/components/GenomeView/genomeNavigator/TrackRegionController.d.ts

@@ -1,9 +1,10 @@
 import { FC } from 'react';
 import { default as DisplayedRegionModel } from '../../../models/DisplayedRegionModel';
 import { default as Genome } from '../../../models/Genome';
+import { GenomeCoordinate } from '../../../types/track-container';
 interface TrackRegionControllerProps {
     selectedRegion: DisplayedRegionModel;
-    onRegionSelected: (newStart: number, newEnd: number, toolTitle: number | string, highlightSearch: boolean) => void;
+    onRegionSelected: (query: string | GenomeCoordinate, highlightSearch: boolean) => void;
     contentColorSetup: {
         color: string;
         background: string;
@@ -13,7 +14,6 @@ interface TrackRegionControllerProps {
     genomeArr: any[];
     genomeIdx: number;
     addGlobalState: any;
-    trackManagerState: any;
     windowWidth?: number;
     fontSize?: number;
     padding?: number;

package/dist/genome-hub/GenomeHubManager.d.ts

@@ -12,4 +12,5 @@ export default class GenomeHubManager {
     getGenomeFromCache(id: string): IGenome | undefined;
     putGenome(genome: IGenome): Promise<void>;
     deleteAllGenomes(): Promise<void>;
+    deleteGenome(id: string): Promise<void>;
 }

package/dist/genome-hub/LocalGenomeRepository.d.ts

@@ -10,6 +10,7 @@ export default class LocalGenomeRepository implements IGenomeHubSource {
     getGenomeById(id: uuid): Promise<IGenome>;
     putGenome(genome: IGenome): Promise<uuid>;
     deleteAllGenomes(): Promise<void>;
+    deleteGenome(id: uuid): Promise<void>;
 }
 type uuid = string;
 export {};

package/dist/getLocalData/LocalBigSourceGmod.d.ts

@@ -1,17 +1,14 @@
 import { BigWig } from '@gmod/bbi';
-/**
- * Reads and gets data from bigwig or bigbed files hosted remotely using @gmod/bbi library
- *
- * @author Daofeng Li
- */
 declare class LocalBigSourceGmod {
     blob: any;
     bw: BigWig;
+    private chromNamingCache;
     /**
      *
      * @param {string} url - the URL from which to fetch data
      */
     constructor(blob: any);
+    detectChromosomeNaming(): Promise<boolean | null>;
     /**
      * Gets BigWig or BigBed features inside the requested locations.
      *

package/dist/getRemoteData/BigSourceWorkerGmod.d.ts

@@ -1,33 +1,19 @@
 import { BigWig } from '@gmod/bbi';
+/**
+ * Reads and gets data from bigwig or bigbed files hosted remotely using @gmod/bbi library
+ *
+ * @author Daofeng Li
+ */
 declare class BigSourceWorkerGmod {
-    url: any;
-    private chromNamingCache;
+    url: string;
     bw: BigWig;
-    useEnsemblStyle: null | boolean;
+    private chromNamingCache;
     /**
      *
      * @param {string} url - the URL from which to fetch data
      */
     constructor(url: any);
-    /**
-     * Clears browser disk cache
-     */
-    private clearDiskCache;
-    /**
-     * Recreates the BigWig instance to clear any cached data
-     */
-    private recreateBigWigInstance;
-    /**
-     * Detects if the BigWig file uses Ensembl
-     * @return {Promise<boolean>} True if Ensembl naming (1, 2, 3...), false if UCSC naming (chr1, chr2, chr3...)
-     */
     detectChromosomeNaming(): Promise<boolean | null>;
-    /**
-     * Fetches features from BigWig/BigBed file for the given loci
-     * @param {ChromosomeInterval[]} loci - locations for which to fetch data
-     * @return {Promise<DASFeature[]>} a Promise for the data
-     */
-    private fetchSource;
     /**
      * Gets BigWig or BigBed features inside the requested locations.
      *
@@ -36,6 +22,6 @@ declare class BigSourceWorkerGmod {
      * @return {Promise<DASFeature[]>} a Promise for the data
      * @override
      */
-    getData: (loci: any, basesPerPixel: any, options: any) => Promise<any[]>;
+    getData(loci: any, basesPerPixel: any, options: any): Promise<any[]>;
 }
 export default BigSourceWorkerGmod;

package/dist/getRemoteData/VcfSource.d.ts

@@ -5,7 +5,9 @@ declare class VcfSource {
     parser: any;
     url: any;
     indexUrl: any;
+    private chromNamingCache;
     constructor(url: any, indexUrl?: null);
+    private detectChromosomeNaming;
     /**
      * Fetches data from VCF file for the given regions
      * @param {ChromosomeInterval[]} region - locations for which to fetch data
@@ -14,6 +16,6 @@ declare class VcfSource {
      */
     private fetchSource;
     getData(region: any, basesPerPixel: any, options: any): Promise<any[]>;
-    _getDataInLocus(locus: any, options: any): Promise<any>;
+    _getDataInLocus(locus: any, isEnsembl: any): Promise<any>;
 }
 export default VcfSource;

package/dist/getRemoteData/tabixSource.d.ts

@@ -1,4 +1,3 @@
-import { TabixIndexedFile } from '@gmod/tabix';
 /**
  * A DataSource that gets BedRecords from remote bed files.  Designed to run in webworker context.  Only indexed bed
  * files supported.
@@ -6,35 +5,14 @@ import { TabixIndexedFile } from '@gmod/tabix';
  * @author Daofeng Li based on Silas's version
  */
 declare class TabixSource {
-    url: any;
-    indexUrl?: any;
-    dataLimit: number;
-    tabix: TabixIndexedFile;
-    private chromNamingCache;
-    useEnsemblStyle: null | boolean;
     /**
      * Prepares to fetch data from a bed file located at the input url.  Assumes the index is located at the same url,
      * plus a file extension of ".tbi".  This method will request and store the tabix index from this url immediately.
      *
      * @param {string} url - the url of the bed-like file to fetch.
      */
-    constructor(url: any, indexUrl?: null, dataLimit?: number);
-    /**
-     * Recreates the Tabix instance to clear any cached data
-     */
-    private recreateTabixInstance;
-    /**
-     * Detects if the Tabix file uses Ensembl
-     * @return {Promise<boolean>} True if Ensembl naming (1, 2, 3...), false if UCSC naming (chr1, chr2, chr3...)
-     */
-    detectChromosomeNaming(): Promise<boolean | null>;
-    /**
-     * Fetches data from Tabix file for the given loci
-     * @param {ChromosomeInterval[]} loci - locations for which to fetch data
-     * @param {any} options - fetch options including ensemblStyle
-     * @return {Promise<BedRecord[]>} a Promise for the data
-     */
-    private fetchSource;
+    constructor(url: any, indexUrl: any, dataLimit?: number);
+    detectChromosomeNaming(): Promise<any>;
     /**
      * Gets data for a list of chromosome intervals.
      *