@jbrowse/plugin-linear-genome-view 3.6.5 → 4.0.0

package/dist/LinearGenomeView/model.js

@@ -1,1109 +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 });
-exports.renderToSvg = exports.SearchBox = exports.RefNameAutocomplete = exports.ReactComponent = exports.LinearGenomeView = void 0;
-exports.stateModelFactory = stateModelFactory;
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-const ui_1 = require("@jbrowse/core/ui");
-const Icons_1 = require("@jbrowse/core/ui/Icons");
-const util_1 = require("@jbrowse/core/util");
-const Base1DUtils_1 = require("@jbrowse/core/util/Base1DUtils");
-const Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DViewModel"));
-const calculateDynamicBlocks_1 = __importDefault(require("@jbrowse/core/util/calculateDynamicBlocks"));
-const calculateStaticBlocks_1 = __importDefault(require("@jbrowse/core/util/calculateStaticBlocks"));
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const mst_1 = require("@jbrowse/core/util/types/mst");
-const product_core_1 = require("@jbrowse/product-core");
-const FolderOpen_1 = __importDefault(require("@mui/icons-material/FolderOpen"));
-const Label_1 = __importDefault(require("@mui/icons-material/Label"));
-const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
-const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
-const PhotoCamera_1 = __importDefault(require("@mui/icons-material/PhotoCamera"));
-const Search_1 = __importDefault(require("@mui/icons-material/Search"));
-const SyncAlt_1 = __importDefault(require("@mui/icons-material/SyncAlt"));
-const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
-const ZoomIn_1 = __importDefault(require("@mui/icons-material/ZoomIn"));
-const file_saver_1 = require("file-saver");
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const Header_1 = __importDefault(require("./components/Header"));
-const util_2 = require("./util");
-const searchUtils_1 = require("../searchUtils");
-const MiniControls_1 = __importDefault(require("./components/MiniControls"));
-const consts_1 = require("./consts");
-const ReturnToImportFormDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ReturnToImportFormDialog'))));
-const SequenceSearchDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SequenceSearchDialog'))));
-const ExportSvgDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ExportSvgDialog'))));
-const GetSequenceDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/GetSequenceDialog'))));
-const SearchResultsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SearchResultsDialog'))));
-function stateModelFactory(pluginManager) {
-    return mobx_state_tree_1.types
-        .compose('LinearGenomeView', models_1.BaseViewModel, mobx_state_tree_1.types.model({
-        id: mst_1.ElementId,
-        type: mobx_state_tree_1.types.literal('LinearGenomeView'),
-        offsetPx: 0,
-        bpPerPx: 1,
-        displayedRegions: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), []),
-        tracks: mobx_state_tree_1.types.array(pluginManager.pluggableMstType('track', 'stateModel')),
-        hideHeader: false,
-        hideHeaderOverview: false,
-        hideNoTracksActive: false,
-        trackSelectorType: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.enumeration(['hierarchical']), 'hierarchical'),
-        showCenterLine: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => (0, util_1.localStorageGetBoolean)('lgv-showCenterLine', false)),
-        showCytobandsSetting: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => (0, util_1.localStorageGetBoolean)('lgv-showCytobands', true)),
-        trackLabels: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, () => (0, util_1.localStorageGetItem)('lgv-trackLabels') || ''),
-        showGridlines: true,
-        highlight: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.array(mobx_state_tree_1.types.frozen()), []),
-        colorByCDS: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => (0, util_1.localStorageGetBoolean)('lgv-colorByCDS', false)),
-        showTrackOutlines: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => (0, util_1.localStorageGetBoolean)('lgv-showTrackOutlines', true)),
-        init: mobx_state_tree_1.types.frozen(),
-    }))
-        .volatile(() => ({
-        volatileWidth: undefined,
-        minimumBlockWidth: 3,
-        draggingTrackId: undefined,
-        volatileError: undefined,
-        afterDisplayedRegionsSetCallbacks: [],
-        scaleFactor: 1,
-        trackRefs: {},
-        coarseDynamicBlocks: [],
-        coarseTotalBp: 0,
-        leftOffset: undefined,
-        rightOffset: undefined,
-    }))
-        .views(self => ({
-        get pinnedTracks() {
-            return self.tracks.filter(t => t.pinned);
-        },
-        get unpinnedTracks() {
-            return self.tracks.filter(t => !t.pinned);
-        },
-        get trackLabelsSetting() {
-            const sessionSetting = (0, configuration_1.getConf)((0, util_1.getSession)(self), [
-                'LinearGenomeViewPlugin',
-                'trackLabels',
-            ]);
-            return self.trackLabels || sessionSetting;
-        },
-        get width() {
-            if (self.volatileWidth === undefined) {
-                throw new Error('width undefined, make sure to check for model.initialized');
-            }
-            return self.volatileWidth;
-        },
-        get interRegionPaddingWidth() {
-            return consts_1.INTER_REGION_PADDING_WIDTH;
-        },
-        get assemblyNames() {
-            return [
-                ...new Set(self.displayedRegions.map(region => region.assemblyName)),
-            ];
-        },
-        get assemblyDisplayNames() {
-            const { assemblyManager } = (0, util_1.getSession)(self);
-            return this.assemblyNames.map(assemblyName => {
-                var _a;
-                const assembly = assemblyManager.get(assemblyName);
-                return (_a = assembly === null || assembly === void 0 ? void 0 : assembly.displayName) !== null && _a !== void 0 ? _a : assemblyName;
-            });
-        },
-        get isTopLevelView() {
-            const session = (0, util_1.getSession)(self);
-            return session.views.some(r => r.id === self.id);
-        },
-        get stickyViewHeaders() {
-            const session = (0, util_1.getSession)(self);
-            return (0, product_core_1.isSessionWithMultipleViews)(session)
-                ? this.isTopLevelView && session.stickyViewHeaders
-                : false;
-        },
-        get rubberbandTop() {
-            let pinnedTracksTop = 0;
-            if (this.stickyViewHeaders) {
-                pinnedTracksTop = ui_1.VIEW_HEADER_HEIGHT;
-                if (!self.hideHeader) {
-                    pinnedTracksTop += consts_1.HEADER_BAR_HEIGHT;
-                    if (!self.hideHeaderOverview) {
-                        pinnedTracksTop += consts_1.HEADER_OVERVIEW_HEIGHT;
-                    }
-                }
-            }
-            return pinnedTracksTop;
-        },
-        get pinnedTracksTop() {
-            return this.rubberbandTop + consts_1.SCALE_BAR_HEIGHT;
-        },
-    }))
-        .views(self => ({
-        scaleBarDisplayPrefix() {
-            return (0, mobx_state_tree_1.getParent)(self, 2).type === 'LinearSyntenyView'
-                ? self.assemblyDisplayNames[0]
-                : '';
-        },
-        MiniControlsComponent() {
-            return MiniControls_1.default;
-        },
-        HeaderComponent() {
-            return Header_1.default;
-        },
-        get assembliesNotFound() {
-            const { assemblyManager } = (0, util_1.getSession)(self);
-            const r0 = self.assemblyNames
-                .map(a => (!assemblyManager.get(a) ? a : undefined))
-                .filter(f => !!f)
-                .join(',');
-            return r0 ? `Assemblies ${r0} not found` : undefined;
-        },
-        get assemblyErrors() {
-            const { assemblyManager } = (0, util_1.getSession)(self);
-            return self.assemblyNames
-                .map(a => { var _a; return (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.error; })
-                .filter(f => !!f)
-                .join(', ');
-        },
-        get assembliesInitialized() {
-            const { assemblyManager } = (0, util_1.getSession)(self);
-            return self.assemblyNames.every(a => { var _a; return (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.initialized; });
-        },
-        get initialized() {
-            return self.volatileWidth !== undefined && this.assembliesInitialized;
-        },
-        get hasDisplayedRegions() {
-            return self.displayedRegions.length > 0;
-        },
-        get scaleBarHeight() {
-            return consts_1.SCALE_BAR_HEIGHT + consts_1.RESIZE_HANDLE_HEIGHT;
-        },
-        get headerHeight() {
-            if (self.hideHeader) {
-                return 0;
-            }
-            else if (self.hideHeaderOverview) {
-                return consts_1.HEADER_BAR_HEIGHT;
-            }
-            else {
-                return consts_1.HEADER_BAR_HEIGHT + consts_1.HEADER_OVERVIEW_HEIGHT;
-            }
-        },
-        get trackHeights() {
-            return (0, util_1.sum)(self.tracks.map(t => t.displays[0].height));
-        },
-        get trackHeightsWithResizeHandles() {
-            return this.trackHeights + self.tracks.length * consts_1.RESIZE_HANDLE_HEIGHT;
-        },
-        get height() {
-            return (this.trackHeightsWithResizeHandles +
-                this.headerHeight +
-                this.scaleBarHeight);
-        },
-        get totalBp() {
-            return (0, util_1.sum)(self.displayedRegions.map(r => r.end - r.start));
-        },
-        get maxBpPerPx() {
-            return this.totalBp / (self.width * 0.9);
-        },
-        get minBpPerPx() {
-            return 1 / 50;
-        },
-        get error() {
-            return (self.volatileError || this.assemblyErrors || this.assembliesNotFound);
-        },
-        get maxOffset() {
-            const leftPadding = 10;
-            return this.displayedRegionsTotalPx - leftPadding;
-        },
-        get minOffset() {
-            const rightPadding = 30;
-            return -self.width + rightPadding;
-        },
-        get displayedRegionsTotalPx() {
-            return this.totalBp / self.bpPerPx;
-        },
-        renderProps() {
-            return {
-                ...(0, tracks_1.getParentRenderProps)(self),
-                bpPerPx: self.bpPerPx,
-                colorByCDS: self.colorByCDS,
-            };
-        },
-        searchScope(assemblyName) {
-            return {
-                assemblyName,
-                includeAggregateIndexes: true,
-                tracks: self.tracks,
-            };
-        },
-        getTrack(id) {
-            return self.tracks.find(t => t.configuration.trackId === id);
-        },
-        rankSearchResults(results) {
-            return results;
-        },
-        rewriteOnClicks(trackType, viewMenuActions) {
-            for (const action of viewMenuActions) {
-                if ('subMenu' in action) {
-                    this.rewriteOnClicks(trackType, action.subMenu);
-                }
-                if ('onClick' in action) {
-                    const holdOnClick = action.onClick;
-                    action.onClick = (...args) => {
-                        for (const track of self.tracks) {
-                            if (track.type === trackType) {
-                                holdOnClick.apply(track, [track, ...args]);
-                            }
-                        }
-                    };
-                }
-            }
-        },
-        get trackTypeActions() {
-            const allActions = new Map();
-            for (const track of self.tracks) {
-                const trackInMap = allActions.get(track.type);
-                if (!trackInMap) {
-                    const viewMenuActions = structuredClone(track.viewMenuActions);
-                    this.rewriteOnClicks(track.type, viewMenuActions);
-                    allActions.set(track.type, viewMenuActions);
-                }
-            }
-            return allActions;
-        },
-    }))
-        .actions(self => ({
-        setShowTrackOutlines(arg) {
-            self.showTrackOutlines = arg;
-        },
-        setColorByCDS(flag) {
-            self.colorByCDS = flag;
-        },
-        setShowCytobands(flag) {
-            self.showCytobandsSetting = flag;
-        },
-        setWidth(newWidth) {
-            self.volatileWidth = newWidth;
-        },
-        setError(error) {
-            self.volatileError = error;
-        },
-        setHideHeader(b) {
-            self.hideHeader = b;
-        },
-        setHideHeaderOverview(b) {
-            self.hideHeaderOverview = b;
-        },
-        setHideNoTracksActive(b) {
-            self.hideNoTracksActive = b;
-        },
-        setShowGridlines(b) {
-            self.showGridlines = b;
-        },
-        addToHighlights(highlight) {
-            self.highlight.push(highlight);
-        },
-        setHighlight(highlight) {
-            self.highlight = (0, mobx_state_tree_1.cast)(highlight);
-        },
-        removeHighlight(highlight) {
-            self.highlight.remove(highlight);
-        },
-        scrollTo(offsetPx) {
-            const newOffsetPx = (0, util_1.clamp)(offsetPx, self.minOffset, self.maxOffset);
-            self.offsetPx = newOffsetPx;
-            return newOffsetPx;
-        },
-        zoomTo(bpPerPx, offset = self.width / 2, centerAtOffset = false) {
-            const newBpPerPx = (0, util_1.clamp)(bpPerPx, self.minBpPerPx, self.maxBpPerPx);
-            if (newBpPerPx === self.bpPerPx) {
-                return newBpPerPx;
-            }
-            const oldBpPerPx = self.bpPerPx;
-            if (Math.abs(oldBpPerPx - newBpPerPx) < 0.000001) {
-                console.warn('zoomTo bpPerPx rounding error');
-                return oldBpPerPx;
-            }
-            self.bpPerPx = newBpPerPx;
-            this.scrollTo(Math.round(((self.offsetPx + offset) * oldBpPerPx) / newBpPerPx -
-                (centerAtOffset ? self.width / 2 : offset)));
-            return newBpPerPx;
-        },
-        setOffsets(left, right) {
-            self.leftOffset = left;
-            self.rightOffset = right;
-        },
-        setSearchResults(searchResults, searchQuery, assemblyName) {
-            (0, util_1.getSession)(self).queueDialog(handleClose => [
-                SearchResultsDialog,
-                {
-                    model: self,
-                    searchResults,
-                    searchQuery,
-                    handleClose,
-                    assemblyName,
-                },
-            ]);
-        },
-        setNewView(bpPerPx, offsetPx) {
-            this.zoomTo(bpPerPx);
-            this.scrollTo(offsetPx);
-        },
-        horizontallyFlip() {
-            self.displayedRegions = (0, mobx_state_tree_1.cast)([...self.displayedRegions]
-                .reverse()
-                .map(region => ({ ...region, reversed: !region.reversed })));
-            this.scrollTo(self.totalBp / self.bpPerPx - self.offsetPx - self.width);
-        },
-        showTrack(trackId, initialSnapshot = {}, displayInitialSnapshot = {}) {
-            const schema = pluginManager.pluggableConfigSchemaType('track');
-            const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
-            if (!conf) {
-                throw new Error(`Could not resolve identifier "${trackId}"`);
-            }
-            const trackType = pluginManager.getTrackType(conf === null || conf === void 0 ? void 0 : conf.type);
-            if (!trackType) {
-                throw new Error(`Unknown track type ${conf.type}`);
-            }
-            const viewType = pluginManager.getViewType(self.type);
-            const supportedDisplays = new Set(viewType.displayTypes.map(d => d.name));
-            const displayConf = conf.displays.find((d) => supportedDisplays.has(d.type));
-            if (!displayConf) {
-                throw new Error(`Could not find a compatible display for view type ${self.type}`);
-            }
-            const t = self.tracks.filter(t => t.configuration === conf);
-            if (t.length === 0) {
-                const track = trackType.stateModel.create({
-                    ...initialSnapshot,
-                    type: conf.type,
-                    configuration: conf,
-                    displays: [
-                        {
-                            type: displayConf.type,
-                            configuration: displayConf,
-                            ...displayInitialSnapshot,
-                        },
-                    ],
-                });
-                self.tracks.push(track);
-                return track;
-            }
-            return t[0];
-        },
-        hideTrack(trackId) {
-            const schema = pluginManager.pluggableConfigSchemaType('track');
-            const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
-            const tracks = self.tracks.filter(t => t.configuration === conf);
-            (0, mobx_1.transaction)(() => {
-                for (const track of tracks) {
-                    self.tracks.remove(track);
-                }
-            });
-            return tracks.length;
-        },
-    }))
-        .actions(self => ({
-        moveTrackDown(id) {
-            const idx = self.tracks.findIndex(v => v.id === id);
-            if (idx === -1) {
-                return;
-            }
-            if (idx !== -1 && idx < self.tracks.length - 1) {
-                self.tracks.splice(idx, 2, self.tracks[idx + 1], self.tracks[idx]);
-            }
-        },
-        moveTrackUp(id) {
-            const idx = self.tracks.findIndex(track => track.id === id);
-            if (idx > 0) {
-                self.tracks.splice(idx - 1, 2, self.tracks[idx], self.tracks[idx - 1]);
-            }
-        },
-        moveTrackToTop(id) {
-            const idx = self.tracks.findIndex(track => track.id === id);
-            self.tracks = (0, mobx_state_tree_1.cast)([
-                self.tracks[idx],
-                ...self.tracks.filter(track => track.id !== id),
-            ]);
-        },
-        moveTrackToBottom(id) {
-            const idx = self.tracks.findIndex(track => track.id === id);
-            self.tracks = (0, mobx_state_tree_1.cast)([
-                ...self.tracks.filter(track => track.id !== id),
-                self.tracks[idx],
-            ]);
-        },
-        moveTrack(movingId, targetId) {
-            const oldIndex = self.tracks.findIndex(track => track.id === movingId);
-            if (oldIndex === -1) {
-                throw new Error(`Track ID ${movingId} not found`);
-            }
-            const newIndex = self.tracks.findIndex(track => track.id === targetId);
-            if (newIndex === -1) {
-                throw new Error(`Track ID ${targetId} not found`);
-            }
-            const tracks = self.tracks.filter((_, idx) => idx !== oldIndex);
-            tracks.splice(newIndex, 0, self.tracks[oldIndex]);
-            self.tracks = (0, mobx_state_tree_1.cast)(tracks);
-        },
-        toggleTrack(trackId) {
-            const hiddenCount = self.hideTrack(trackId);
-            if (!hiddenCount) {
-                self.showTrack(trackId);
-                return true;
-            }
-            return false;
-        },
-        setTrackLabels(setting) {
-            localStorage.setItem('lgv-trackLabels', setting);
-            self.trackLabels = setting;
-        },
-        setShowCenterLine(b) {
-            self.showCenterLine = b;
-        },
-        setDisplayedRegions(regions) {
-            self.displayedRegions = (0, mobx_state_tree_1.cast)(regions);
-            self.zoomTo(self.bpPerPx);
-        },
-        activateTrackSelector() {
-            if (self.trackSelectorType === 'hierarchical') {
-                const session = (0, util_1.getSession)(self);
-                if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                    const selector = session.addWidget('HierarchicalTrackSelectorWidget', 'hierarchicalTrackSelector', { view: self });
-                    session.showWidget(selector);
-                    return selector;
-                }
-            }
-            throw new Error(`invalid track selector type ${self.trackSelectorType}`);
-        },
-        getSelectedRegions(leftOffset, rightOffset) {
-            const snap = (0, mobx_state_tree_1.getSnapshot)(self);
-            const simView = Base1DViewModel_1.default.create({
-                ...snap,
-                interRegionPaddingWidth: self.interRegionPaddingWidth,
-            });
-            simView.setVolatileWidth(self.width);
-            simView.moveTo(leftOffset, rightOffset);
-            return simView.dynamicBlocks.contentBlocks.map(region => ({
-                ...region,
-                start: Math.floor(region.start),
-                end: Math.ceil(region.end),
-            }));
-        },
-        afterDisplayedRegionsSet(cb) {
-            self.afterDisplayedRegionsSetCallbacks.push(cb);
-        },
-        horizontalScroll(distance) {
-            const oldOffsetPx = self.offsetPx;
-            const newOffsetPx = self.scrollTo(self.offsetPx + distance);
-            return newOffsetPx - oldOffsetPx;
-        },
-        center() {
-            const centerBp = self.totalBp / 2;
-            const centerPx = centerBp / self.bpPerPx;
-            self.scrollTo(Math.round(centerPx - self.width / 2));
-        },
-        showAllRegions() {
-            self.zoomTo(self.maxBpPerPx);
-            this.center();
-        },
-        showAllRegionsInAssembly(assemblyName) {
-            const session = (0, util_1.getSession)(self);
-            const { assemblyManager } = session;
-            if (!assemblyName) {
-                const names = new Set(self.displayedRegions.map(r => r.assemblyName));
-                if (names.size > 1) {
-                    session.notify(`Can't perform operation with multiple assemblies currently`);
-                    return;
-                }
-                ;
-                [assemblyName] = [...names];
-            }
-            const assembly = assemblyManager.get(assemblyName);
-            if (assembly) {
-                const { regions } = assembly;
-                if (regions) {
-                    this.setDisplayedRegions(regions);
-                    self.zoomTo(self.maxBpPerPx);
-                    this.center();
-                }
-            }
-        },
-        setDraggingTrackId(idx) {
-            self.draggingTrackId = idx;
-        },
-        setScaleFactor(factor) {
-            self.scaleFactor = factor;
-        },
-        clearView() {
-            this.setDisplayedRegions([]);
-            self.tracks.clear();
-            self.scrollTo(0);
-            self.zoomTo(10);
-        },
-        setInit(arg) {
-            self.init = arg;
-        },
-        async exportSvg(opts = {}) {
-            const { renderToSvg } = await Promise.resolve().then(() => __importStar(require('./svgcomponents/SVGLinearGenomeView')));
-            const html = await renderToSvg(self, opts);
-            const blob = new Blob([html], { type: 'image/svg+xml' });
-            (0, file_saver_1.saveAs)(blob, opts.filename || 'image.svg');
-        },
-    }))
-        .actions(self => {
-        let cancelLastAnimation = () => { };
-        function slide(viewWidths) {
-            const [animate, cancelAnimation] = (0, util_1.springAnimate)(self.offsetPx, self.offsetPx + self.width * viewWidths, self.scrollTo, undefined, undefined, 200);
-            cancelLastAnimation();
-            cancelLastAnimation = cancelAnimation;
-            animate();
-        }
-        return { slide };
-    })
-        .actions(self => {
-        let cancelLastAnimation = () => { };
-        function zoom(targetBpPerPx) {
-            self.zoomTo(self.bpPerPx);
-            if ((targetBpPerPx < self.bpPerPx && self.bpPerPx === self.minBpPerPx) ||
-                (targetBpPerPx > self.bpPerPx && self.bpPerPx === self.maxBpPerPx)) {
-                return;
-            }
-            const factor = self.bpPerPx / targetBpPerPx;
-            const [animate, cancelAnimation] = (0, util_1.springAnimate)(1, factor, self.setScaleFactor, () => {
-                self.zoomTo(targetBpPerPx);
-                self.setScaleFactor(1);
-            });
-            cancelLastAnimation();
-            cancelLastAnimation = cancelAnimation;
-            animate();
-        }
-        return { zoom };
-    })
-        .views(self => ({
-        get canShowCytobands() {
-            return self.displayedRegions.length === 1 && this.anyCytobandsExist;
-        },
-        get showCytobands() {
-            return this.canShowCytobands && self.showCytobandsSetting;
-        },
-        get anyCytobandsExist() {
-            const { assemblyManager } = (0, util_1.getSession)(self);
-            return self.assemblyNames.some(a => { var _a, _b; return (_b = (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.cytobands) === null || _b === void 0 ? void 0 : _b.length; });
-        },
-        get cytobandOffset() {
-            var _a;
-            return this.showCytobands
-                ? (0, util_1.measureText)(((_a = self.displayedRegions[0]) === null || _a === void 0 ? void 0 : _a.refName) || '', 12) + 15
-                : 0;
-        },
-    }))
-        .views(self => ({
-        menuItems() {
-            const { canShowCytobands, showCytobands } = self;
-            const session = (0, util_1.getSession)(self);
-            const menuItems = [
-                {
-                    label: 'Return to import form',
-                    onClick: () => {
-                        (0, util_1.getSession)(self).queueDialog(handleClose => [
-                            ReturnToImportFormDialog,
-                            { model: self, handleClose },
-                        ]);
-                    },
-                    icon: FolderOpen_1.default,
-                },
-                ...((0, util_1.isSessionWithAddTracks)(session)
-                    ? [
-                        {
-                            label: 'Sequence search',
-                            icon: Search_1.default,
-                            onClick: () => {
-                                (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                    SequenceSearchDialog,
-                                    {
-                                        model: self,
-                                        handleClose,
-                                    },
-                                ]);
-                            },
-                        },
-                    ]
-                    : []),
-                {
-                    label: 'Export SVG',
-                    icon: PhotoCamera_1.default,
-                    onClick: () => {
-                        (0, util_1.getSession)(self).queueDialog(handleClose => [
-                            ExportSvgDialog,
-                            {
-                                model: self,
-                                handleClose,
-                            },
-                        ]);
-                    },
-                },
-                {
-                    label: 'Open track selector',
-                    onClick: self.activateTrackSelector,
-                    icon: Icons_1.TrackSelector,
-                },
-                {
-                    label: 'Horizontally flip',
-                    icon: SyncAlt_1.default,
-                    onClick: self.horizontallyFlip,
-                },
-                {
-                    label: 'Color by CDS',
-                    type: 'checkbox',
-                    checked: self.colorByCDS,
-                    icon: Palette_1.default,
-                    onClick: () => {
-                        self.setColorByCDS(!self.colorByCDS);
-                    },
-                },
-                {
-                    label: 'Show...',
-                    icon: Visibility_1.default,
-                    subMenu: [
-                        {
-                            label: 'Show all regions in assembly',
-                            onClick: self.showAllRegionsInAssembly,
-                        },
-                        {
-                            label: 'Show center line',
-                            type: 'checkbox',
-                            checked: self.showCenterLine,
-                            onClick: () => {
-                                self.setShowCenterLine(!self.showCenterLine);
-                            },
-                        },
-                        {
-                            label: 'Show header',
-                            type: 'checkbox',
-                            checked: !self.hideHeader,
-                            onClick: () => {
-                                self.setHideHeader(!self.hideHeader);
-                            },
-                        },
-                        {
-                            label: 'Show track outlines',
-                            type: 'checkbox',
-                            checked: self.showTrackOutlines,
-                            onClick: () => {
-                                self.setShowTrackOutlines(!self.showTrackOutlines);
-                            },
-                        },
-                        {
-                            label: 'Show header overview',
-                            type: 'checkbox',
-                            checked: !self.hideHeaderOverview,
-                            onClick: () => {
-                                self.setHideHeaderOverview(!self.hideHeaderOverview);
-                            },
-                            disabled: self.hideHeader,
-                        },
-                        {
-                            label: 'Show no tracks active button',
-                            type: 'checkbox',
-                            checked: !self.hideNoTracksActive,
-                            onClick: () => {
-                                self.setHideNoTracksActive(!self.hideNoTracksActive);
-                            },
-                        },
-                        {
-                            label: 'Show guidelines',
-                            type: 'checkbox',
-                            checked: self.showGridlines,
-                            onClick: () => {
-                                self.setShowGridlines(!self.showGridlines);
-                            },
-                        },
-                        ...(canShowCytobands
-                            ? [
-                                {
-                                    label: 'Show ideogram',
-                                    type: 'checkbox',
-                                    checked: self.showCytobands,
-                                    onClick: () => {
-                                        self.setShowCytobands(!showCytobands);
-                                    },
-                                },
-                            ]
-                            : []),
-                    ],
-                },
-                {
-                    label: 'Track labels',
-                    icon: Label_1.default,
-                    subMenu: [
-                        {
-                            label: 'Overlapping',
-                            icon: Visibility_1.default,
-                            type: 'radio',
-                            checked: self.trackLabelsSetting === 'overlapping',
-                            onClick: () => {
-                                self.setTrackLabels('overlapping');
-                            },
-                        },
-                        {
-                            label: 'Offset',
-                            icon: Visibility_1.default,
-                            type: 'radio',
-                            checked: self.trackLabelsSetting === 'offset',
-                            onClick: () => {
-                                self.setTrackLabels('offset');
-                            },
-                        },
-                        {
-                            label: 'Hidden',
-                            icon: Visibility_1.default,
-                            type: 'radio',
-                            checked: self.trackLabelsSetting === 'hidden',
-                            onClick: () => {
-                                self.setTrackLabels('hidden');
-                            },
-                        },
-                    ],
-                },
-            ];
-            for (const [key, value] of self.trackTypeActions.entries()) {
-                if (value.length) {
-                    menuItems.push({ type: 'divider' }, { type: 'subHeader', label: key });
-                    for (const action of value) {
-                        menuItems.push(action);
-                    }
-                }
-            }
-            return menuItems;
-        },
-    }))
-        .views(self => {
-        let currentlyCalculatedStaticBlocks;
-        let stringifiedCurrentlyCalculatedStaticBlocks = '';
-        return {
-            get staticBlocks() {
-                const ret = (0, calculateStaticBlocks_1.default)(self);
-                const sret = JSON.stringify(ret);
-                if (stringifiedCurrentlyCalculatedStaticBlocks !== sret) {
-                    currentlyCalculatedStaticBlocks = ret;
-                    stringifiedCurrentlyCalculatedStaticBlocks = sret;
-                }
-                return currentlyCalculatedStaticBlocks;
-            },
-            get dynamicBlocks() {
-                return (0, calculateDynamicBlocks_1.default)(self);
-            },
-            get roundedDynamicBlocks() {
-                return this.dynamicBlocks.contentBlocks.map(block => ({
-                    ...block,
-                    start: Math.floor(block.start),
-                    end: Math.ceil(block.end),
-                }));
-            },
-            get visibleLocStrings() {
-                return (0, util_2.calculateVisibleLocStrings)(this.dynamicBlocks.contentBlocks);
-            },
-            get coarseVisibleLocStrings() {
-                return (0, util_2.calculateVisibleLocStrings)(self.coarseDynamicBlocks);
-            },
-        };
-    })
-        .actions(self => ({
-        setCoarseDynamicBlocks(blocks) {
-            self.coarseDynamicBlocks = blocks.contentBlocks;
-            self.coarseTotalBp = blocks.totalBp;
-        },
-    }))
-        .actions(self => ({
-        moveTo(start, end) {
-            (0, Base1DUtils_1.moveTo)(self, start, end);
-        },
-        async navToLocString(input, optAssemblyName, grow) {
-            const { assemblyNames } = self;
-            const { assemblyManager } = (0, util_1.getSession)(self);
-            const assemblyName = optAssemblyName || assemblyNames[0];
-            if (assemblyName) {
-                await assemblyManager.waitForAssembly(assemblyName);
-            }
-            return this.navToLocations((0, util_2.parseLocStrings)(input, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName, grow);
-        },
-        async navToSearchString({ input, assembly, }) {
-            await (0, searchUtils_1.handleSelectedRegion)({
-                input,
-                assembly,
-                model: self,
-            });
-        },
-        async navToLocation(parsedLocString, assemblyName, grow) {
-            return this.navToLocations([parsedLocString], assemblyName, grow);
-        },
-        async navToLocations(regions, assemblyName, grow) {
-            const { assemblyManager } = (0, util_1.getSession)(self);
-            await (0, mobx_1.when)(() => self.volatileWidth !== undefined);
-            const locations = await (0, util_2.generateLocations)({
-                regions,
-                assemblyManager,
-                assemblyName,
-                grow,
-            });
-            if (locations.length === 1) {
-                const location = locations[0];
-                const { reversed, parentRegion, start, end } = location;
-                self.setDisplayedRegions([
-                    {
-                        reversed,
-                        ...parentRegion,
-                    },
-                ]);
-                this.navTo({
-                    ...location,
-                    start: (0, util_1.clamp)(start !== null && start !== void 0 ? start : 0, 0, parentRegion.end),
-                    end: (0, util_1.clamp)(end !== null && end !== void 0 ? end : parentRegion.end, 0, parentRegion.end),
-                });
-            }
-            else {
-                self.setDisplayedRegions(locations.map(location => {
-                    const { start, end } = location;
-                    return start === undefined || end === undefined
-                        ? location.parentRegion
-                        : {
-                            ...location,
-                            start,
-                            end,
-                        };
-                }));
-                self.showAllRegions();
-            }
-        },
-        navTo(query) {
-            this.navToMultiple([query]);
-        },
-        navToMultiple(locations) {
-            if (locations.some(l => l.start !== undefined && l.end !== undefined && l.start > l.end)) {
-                throw new Error('found start greater than end');
-            }
-            const firstLocation = locations.at(0);
-            const lastLocation = locations.at(-1);
-            if (!firstLocation || !lastLocation) {
-                return;
-            }
-            const defaultAssemblyName = self.assemblyNames[0];
-            const { assemblyManager } = (0, util_1.getSession)(self);
-            const firstAssembly = assemblyManager.get(firstLocation.assemblyName || defaultAssemblyName);
-            const firstRefName = (firstAssembly === null || firstAssembly === void 0 ? void 0 : firstAssembly.getCanonicalRefName(firstLocation.refName)) ||
-                firstLocation.refName;
-            const firstRegion = self.displayedRegions.find(r => r.refName === firstRefName);
-            const lastAssembly = assemblyManager.get(lastLocation.assemblyName || defaultAssemblyName);
-            const lastRefName = (lastAssembly === null || lastAssembly === void 0 ? void 0 : lastAssembly.getCanonicalRefName(lastLocation.refName)) ||
-                lastLocation.refName;
-            const lastRegion = (0, util_1.findLast)(self.displayedRegions, r => r.refName === lastRefName);
-            if (!firstRegion) {
-                throw new Error(`could not find a region with refName "${firstRefName}"`);
-            }
-            if (!lastRegion) {
-                throw new Error(`could not find a region with refName "${lastRefName}"`);
-            }
-            const firstStart = firstLocation.start === undefined
-                ? firstRegion.start
-                : firstLocation.start;
-            const firstEnd = firstLocation.end === undefined ? firstRegion.end : firstLocation.end;
-            const lastStart = lastLocation.start === undefined
-                ? lastRegion.start
-                : lastLocation.start;
-            const lastEnd = lastLocation.end === undefined ? lastRegion.end : lastLocation.end;
-            const firstIndex = self.displayedRegions.findIndex(r => firstRefName === r.refName &&
-                firstStart >= r.start &&
-                firstStart <= r.end &&
-                firstEnd <= r.end &&
-                firstEnd >= r.start);
-            const lastIndex = self.displayedRegions.findIndex(r => lastRefName === r.refName &&
-                lastStart >= r.start &&
-                lastStart <= r.end &&
-                lastEnd <= r.end &&
-                lastEnd >= r.start);
-            if (firstIndex === -1 || lastIndex === -1) {
-                throw new Error(`could not find a region that contained "${locations.map(l => (0, util_1.assembleLocString)(l))}"`);
-            }
-            const startDisplayedRegion = self.displayedRegions[firstIndex];
-            const endDisplayedRegion = self.displayedRegions[lastIndex];
-            const startOffset = startDisplayedRegion.reversed
-                ? startDisplayedRegion.end - firstEnd
-                : firstStart - startDisplayedRegion.start;
-            const endOffset = endDisplayedRegion.reversed
-                ? endDisplayedRegion.end - lastStart
-                : lastEnd - endDisplayedRegion.start;
-            this.moveTo({
-                index: firstIndex,
-                offset: startOffset,
-            }, {
-                index: lastIndex,
-                offset: endOffset,
-            });
-        },
-    }))
-        .views(self => ({
-        rubberBandMenuItems() {
-            return [
-                {
-                    label: 'Zoom to region',
-                    icon: ZoomIn_1.default,
-                    onClick: () => {
-                        self.moveTo(self.leftOffset, self.rightOffset);
-                    },
-                },
-                {
-                    label: 'Get sequence',
-                    icon: MenuOpen_1.default,
-                    onClick: () => {
-                        (0, util_1.getSession)(self).queueDialog(handleClose => [
-                            GetSequenceDialog,
-                            { model: self, handleClose },
-                        ]);
-                    },
-                },
-            ];
-        },
-        bpToPx({ refName, coord, regionNumber, }) {
-            return (0, Base1DUtils_1.bpToPx)({ refName, coord, regionNumber, self });
-        },
-        centerAt(coord, refName, regionNumber) {
-            const centerPx = this.bpToPx({
-                refName,
-                coord,
-                regionNumber,
-            });
-            if (centerPx !== undefined) {
-                self.scrollTo(Math.round(centerPx.offsetPx - self.width / 2));
-            }
-        },
-        pxToBp(px) {
-            return (0, Base1DUtils_1.pxToBp)(self, px);
-        },
-        get centerLineInfo() {
-            return self.displayedRegions.length > 0
-                ? this.pxToBp(self.width / 2)
-                : undefined;
-        },
-    }))
-        .actions(self => ({
-        afterCreate() {
-            function handler(e) {
-                const session = (0, util_1.getSession)(self);
-                if (session.focusedViewId === self.id && (e.ctrlKey || e.metaKey)) {
-                    if (e.code === 'ArrowLeft') {
-                        e.preventDefault();
-                        self.slide(-0.9);
-                    }
-                    else if (e.code === 'ArrowRight') {
-                        e.preventDefault();
-                        self.slide(0.9);
-                    }
-                    else if (e.code === 'ArrowUp' && self.scaleFactor === 1) {
-                        e.preventDefault();
-                        self.zoom(self.bpPerPx / 2);
-                    }
-                    else if (e.code === 'ArrowDown' && self.scaleFactor === 1) {
-                        e.preventDefault();
-                        self.zoom(self.bpPerPx * 2);
-                    }
-                }
-            }
-            document.addEventListener('keydown', handler);
-            (0, mobx_state_tree_1.addDisposer)(self, () => {
-                document.removeEventListener('keydown', handler);
-            });
-        },
-        afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                var _a;
-                const { init } = self;
-                if (init) {
-                    self
-                        .navToLocString(init.loc, init.assembly)
-                        .catch((e) => {
-                        console.error(init, e);
-                        (0, util_1.getSession)(self).notifyError(`${e}`, e);
-                    });
-                    (_a = init.tracks) === null || _a === void 0 ? void 0 : _a.map(t => self.showTrack(t));
-                    self.setInit(undefined);
-                }
-            }));
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                if (self.initialized) {
-                    self.setCoarseDynamicBlocks(self.dynamicBlocks);
-                }
-            }, { delay: 150 }));
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                const s = (s) => JSON.stringify(s);
-                const { showCytobandsSetting, showCenterLine, colorByCDS } = self;
-                (0, util_1.localStorageSetItem)('lgv-showCytobands', s(showCytobandsSetting));
-                (0, util_1.localStorageSetItem)('lgv-showCenterLine', s(showCenterLine));
-                (0, util_1.localStorageSetItem)('lgv-colorByCDS', s(colorByCDS));
-            }));
-        },
-    }))
-        .preProcessSnapshot(snap => {
-        if (!snap) {
-            return snap;
-        }
-        const { highlight, ...rest } = snap;
-        return {
-            highlight: Array.isArray(highlight) || highlight === undefined
-                ? highlight
-                : [highlight],
-            ...rest,
-        };
-    })
-        .postProcessSnapshot(snap => {
-        if (!snap) {
-            return snap;
-        }
-        else {
-            const { init, ...rest } = snap;
-            return rest;
-        }
-    });
-}
-var LinearGenomeView_1 = require("./components/LinearGenomeView");
-Object.defineProperty(exports, "LinearGenomeView", { enumerable: true, get: function () { return __importDefault(LinearGenomeView_1).default; } });
-Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(LinearGenomeView_1).default; } });
-var RefNameAutocomplete_1 = require("./components/RefNameAutocomplete");
-Object.defineProperty(exports, "RefNameAutocomplete", { enumerable: true, get: function () { return __importDefault(RefNameAutocomplete_1).default; } });
-var SearchBox_1 = require("./components/SearchBox");
-Object.defineProperty(exports, "SearchBox", { enumerable: true, get: function () { return __importDefault(SearchBox_1).default; } });
-var SVGLinearGenomeView_1 = require("./svgcomponents/SVGLinearGenomeView");
-Object.defineProperty(exports, "renderToSvg", { enumerable: true, get: function () { return SVGLinearGenomeView_1.renderToSvg; } });