@jbrowse/plugin-linear-genome-view 2.0.0 → 2.1.2

package/dist/LinearGenomeView/components/util.js

@@ -1,98 +1,25 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
-var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
-    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
-        if (ar || !(i in from)) {
-            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
-            ar[i] = from[i];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.fetchResults = exports.dedupe = void 0;
-var BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
-function dedupe(results, cb) {
-    if (results === void 0) { results = []; }
-    return results.filter(function (elt, idx, self) { return idx === self.findIndex(function (t) { return cb(t) === cb(elt); }); });
+const BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
+function dedupe(results = [], cb) {
+    return results.filter((elt, idx, self) => idx === self.findIndex(t => cb(t) === cb(elt)));
 }
 exports.dedupe = dedupe;
-function fetchResults(_a) {
-    var _b;
-    var queryString = _a.queryString, searchType = _a.searchType, searchScope = _a.searchScope, rankSearchResults = _a.rankSearchResults, textSearchManager = _a.textSearchManager, assembly = _a.assembly;
-    return __awaiter(this, void 0, void 0, function () {
-        var textSearchResults, refNameResults;
-        return __generator(this, function (_c) {
-            switch (_c.label) {
-                case 0:
-                    if (!textSearchManager) {
-                        console.warn('No text search manager');
-                    }
-                    return [4 /*yield*/, (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
-                            queryString: queryString,
-                            searchType: searchType,
-                        }, searchScope, rankSearchResults))];
-                case 1:
-                    textSearchResults = _c.sent();
-                    refNameResults = (_b = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _b === void 0 ? void 0 : _b.filter(function (ref) { return ref.toLowerCase().startsWith(queryString.toLowerCase()); }).slice(0, 10).map(function (r) { return new BaseResults_1.default({ label: r }); });
-                    return [2 /*return*/, dedupe(__spreadArray(__spreadArray([], __read((refNameResults || [])), false), __read((textSearchResults || [])), false), function (elt) { return elt.getId(); })];
-            }
-        });
-    });
+async function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }) {
+    var _a;
+    if (!textSearchManager) {
+        console.warn('No text search manager');
+    }
+    const textSearchResults = await (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
+        queryString,
+        searchType,
+    }, searchScope, rankSearchResults));
+    const refNameResults = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _a === void 0 ? void 0 : _a.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase())).slice(0, 10).map(r => new BaseResults_1.default({ label: r }));
+    return dedupe([...(refNameResults || []), ...(textSearchResults || [])], elt => elt.getId());
 }
 exports.fetchResults = fetchResults;
 //# sourceMappingURL=util.js.map

package/dist/LinearGenomeView/components/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/util.ts"],"names":[],"mappings":";;;;;;AAEA,uFAA6D;AAI7D,SAAgB,MAAM,CACpB,UAAwB,EAAE,EAC1B,EAAkC;IAElC,OAAO,OAAO,CAAC,MAAM,CACnB,CAAC,GAAG,EAAE,GAAG,EAAE,IAAI,EAAE,EAAE,CAAC,GAAG,KAAK,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,CAAC,CACnE,CAAA;AACH,CAAC;AAPD,wBAOC;AAEM,KAAK,UAAU,YAAY,CAAC,EACjC,WAAW,EACX,UAAU,EACV,WAAW,EACX,iBAAiB,EACjB,iBAAiB,EACjB,QAAQ,GAQT;;IACC,IAAI,CAAC,iBAAiB,EAAE;QACtB,OAAO,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAA;KACvC;IAED,MAAM,iBAAiB,GAAG,MAAM,CAAA,iBAAiB,aAAjB,iBAAiB,uBAAjB,iBAAiB,CAAE,MAAM,CACvD;QACE,WAAW;QACX,UAAU;KACX,EACD,WAAW,EACX,iBAAiB,CAClB,CAAA,CAAA;IAED,MAAM,cAAc,GAAG,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,0CACxC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,EACtE,KAAK,CAAC,CAAC,EAAE,EAAE,EACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,qBAAU,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAEzC,OAAO,MAAM,CACX,CAAC,GAAG,CAAC,cAAc,IAAI,EAAE,CAAC,EAAE,GAAG,CAAC,iBAAiB,IAAI,EAAE,CAAC,CAAC,EACzD,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,KAAK,EAAE,CACnB,CAAA;AACH,CAAC;AArCD,oCAqCC"}

package/dist/LinearGenomeView/index.d.ts

@@ -61,6 +61,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     width: number;
 } & {
@@ -113,45 +114,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         includeAggregateIndexes: boolean;
         tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
     };
-    bpToPx({ refName, coord, regionNumber, }: {
-        refName: string;
-        coord: number;
-        regionNumber?: number | undefined;
-    }): {
-        index: number;
-        offsetPx: number;
-    } | undefined;
-    /**
-     *
-     * @param px - px in the view area, return value is the displayed regions
-     * @returns BpOffset of the displayed region that it lands in
-     */
-    pxToBp(px: number): {
-        oob: boolean;
-        coord: number;
-        offset: number;
-        index: number;
-        start: number;
-        end: number;
-        reversed: boolean;
-        refName: string;
-        assemblyName: string;
-    };
     getTrack(id: string): any;
     rankSearchResults(results: BaseResult[]): BaseResult[];
     rewriteOnClicks(trackType: string, viewMenuActions: MenuItem[]): void;
     readonly trackTypeActions: Map<string, MenuItem[]>;
-    readonly centerLineInfo: {
-        oob: boolean;
-        coord: number;
-        offset: number;
-        index: number;
-        start: number;
-        end: number;
-        reversed: boolean;
-        refName: string;
-        assemblyName: string;
-    } | undefined;
 } & {
     setShowCytobands(flag: boolean): void;
     setWidth(newWidth: number): void;
@@ -159,11 +125,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     toggleHeader(): void;
     toggleHeaderOverview(): void;
     toggleNoTracksActive(): void;
+    toggleShowGridlines(): void;
     scrollTo(offsetPx: number): number;
     zoomTo(bpPerPx: number): number;
-    setOffsets(left: undefined | BpOffset, right: undefined | BpOffset): void;
-    setSearchResults(results: BaseResult[] | undefined, query: string | undefined): void;
-    setSequenceDialogOpen(open: boolean): void;
+    setOffsets(left?: BpOffset, right?: BpOffset): void;
+    setSearchResults(results?: BaseResult[], query?: string): void;
+    setGetSequenceDialogOpen(open: boolean): void;
     setNewView(bpPerPx: number, offsetPx: number): void;
     horizontallyFlip(): void;
     showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
@@ -176,30 +143,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     toggleCenterLine(): void;
     setDisplayedRegions(regions: Region[]): void;
     activateTrackSelector(): import("@jbrowse/core/util").Widget;
-    navToLocString(locString: string, optAssemblyName?: string): void;
-    /**
-     * Navigate to a location based on its refName and optionally start, end,
-     * and assemblyName. Can handle if there are multiple displayedRegions
-     * from same refName. Only navigates to a location if it is entirely
-     * within a displayedRegion. Navigates to the first matching location
-     * encountered.
-     *
-     * Throws an error if navigation was unsuccessful
-     *
-     * @param location - a proposed location to navigate to
-     */
-    navTo(query: NavLocation): void;
-    navToMultiple(locations: NavLocation[]): void;
-    /**
-     * Navigate to a location based on user clicking and dragging on the
-     * overview scale bar to select a region to zoom into.
-     * Can handle if there are multiple displayedRegions from same refName.
-     * Only navigates to a location if it is entirely within a displayedRegion.
-     *
-     * @param leftPx- `object as {start, end, index, offset}`, offset = start of user drag
-     * @param rightPx- `object as {start, end, index, offset}`, offset = end of user drag
-     */
-    zoomToDisplayedRegions(leftPx: BpOffset, rightPx: BpOffset): void;
     /**
      * Helper method for the fetchSequence.
      * Retrieves the corresponding regions that were selected by the rubberband
@@ -208,7 +151,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * @param rightOffset - `object as {start, end, index, offset}`, offset = end of user drag
      * @returns array of Region[]
      */
-    getSelectedRegions(leftOffset: BpOffset | undefined, rightOffset: BpOffset | undefined): {
+    getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
         start: number;
         end: number;
         regionNumber?: number | undefined;
@@ -222,23 +165,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         isLeftEndOfDisplayedRegion?: boolean | undefined;
     }[];
     afterDisplayedRegionsSet(cb: Function): void;
-    /**
-     * offset is the base-pair-offset in the displayed region, index is the index of the
-     * displayed region in the linear genome view
-     *
-     * @param start - object as `{start, end, offset, index}`
-     * @param end - object as `{start, end, offset, index}`
-     */
-    moveTo(start: BpOffset, end: BpOffset): void;
     horizontalScroll(distance: number): number;
-    /**
-     * scrolls the view to center on the given bp. if that is not in any
-     * of the displayed regions, does nothing
-     * @param bp - basepair at which you want to center the view
-     * @param refName - refName of the displayedRegion you are centering at
-     * @param regionIndex - index of the displayedRegion
-     */
-    centerAt(bp: number, refName: string, regionIndex: number): void;
     center(): void;
     showAllRegions(): void;
     showAllRegionsInAssembly(assemblyName?: string): void;
@@ -279,8 +206,68 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     afterAttach(): void;
 } & {
     exportSvg(opts?: ExportSvgOptions): Promise<void>;
+    /**
+     * offset is the base-pair-offset in the displayed region, index is the index of the
+     * displayed region in the linear genome view
+     *
+     * @param start - object as `{start, end, offset, index}`
+     * @param end - object as `{start, end, offset, index}`
+     */
+    moveTo(start?: BpOffset, end?: BpOffset): void;
+    navToLocString(locString: string, optAssemblyName?: string): void;
+    /**
+     * Navigate to a location based on its refName and optionally start, end,
+     * and assemblyName. Can handle if there are multiple displayedRegions
+     * from same refName. Only navigates to a location if it is entirely
+     * within a displayedRegion. Navigates to the first matching location
+     * encountered.
+     *
+     * Throws an error if navigation was unsuccessful
+     *
+     * @param location - a proposed location to navigate to
+     */
+    navTo(query: NavLocation): void;
+    navToMultiple(locations: NavLocation[]): void;
 } & {
     rubberBandMenuItems(): MenuItem[];
+    bpToPx({ refName, coord, regionNumber, }: {
+        refName: string;
+        coord: number;
+        regionNumber?: number | undefined;
+    }): {
+        index: number;
+        offsetPx: number;
+    } | undefined;
+    /**
+     * scrolls the view to center on the given bp. if that is not in any
+     * of the displayed regions, does nothing
+     * @param coord - basepair at which you want to center the view
+     * @param refName - refName of the displayedRegion you are centering at
+     * @param regionNumber - index of the displayedRegion
+     */
+    centerAt(coord: number, refName: string, regionNumber: number): void;
+    pxToBp(px: number): {
+        coord: number;
+        index: number;
+        refName: string;
+        oob: boolean;
+        assemblyName: string;
+        offset: number;
+        start: number;
+        end: number;
+        reversed: boolean;
+    };
+    readonly centerLineInfo: {
+        coord: number;
+        index: number;
+        refName: string;
+        oob: boolean;
+        assemblyName: string;
+        offset: number;
+        start: number;
+        end: number;
+        reversed: boolean;
+    } | undefined;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export { renderToSvg, RefNameAutocomplete, SearchBox };
 export declare type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;