@jbrowse/plugin-linear-genome-view 1.7.11 → 2.0.0

package/esm/LinearGenomeView/index.js

@@ -0,0 +1,1124 @@
+import { getConf } from '@jbrowse/core/configuration';
+import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
+import { ElementId, Region as MUIRegion } from '@jbrowse/core/util/types/mst';
+import { ReturnToImportFormDialog } from '@jbrowse/core/ui';
+import { assembleLocString, clamp, findLastIndex, getContainingView, getSession, isViewContainer, isSessionModelWithWidgets, measureText, parseLocString, springAnimate, viewBpToPx, } from '@jbrowse/core/util';
+import calculateDynamicBlocks from '@jbrowse/core/util/calculateDynamicBlocks';
+import calculateStaticBlocks from '@jbrowse/core/util/calculateStaticBlocks';
+import { getParentRenderProps } from '@jbrowse/core/util/tracks';
+import { transaction, autorun } from 'mobx';
+import { addDisposer, cast, getSnapshot, getRoot, resolveIdentifier, types, } from 'mobx-state-tree';
+import Base1DView from '@jbrowse/core/util/Base1DViewModel';
+import clone from 'clone';
+import { saveAs } from 'file-saver';
+// icons
+import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
+import SyncAltIcon from '@mui/icons-material/SyncAlt';
+import VisibilityIcon from '@mui/icons-material/Visibility';
+import LabelIcon from '@mui/icons-material/Label';
+import FolderOpenIcon from '@mui/icons-material/FolderOpen';
+import PhotoCameraIcon from '@mui/icons-material/PhotoCamera';
+import ZoomInIcon from '@mui/icons-material/ZoomIn';
+import MenuOpenIcon from '@mui/icons-material/MenuOpen';
+// locals
+import { renderToSvg } from './components/LinearGenomeViewSvg';
+import RefNameAutocomplete from './components/RefNameAutocomplete';
+import SearchBox from './components/SearchBox';
+import ExportSvgDlg from './components/ExportSvgDialog';
+function calculateVisibleLocStrings(contentBlocks) {
+    if (!contentBlocks.length) {
+        return '';
+    }
+    const isSingleAssemblyName = contentBlocks.every(block => block.assemblyName === contentBlocks[0].assemblyName);
+    const locs = contentBlocks.map(block => assembleLocString({
+        ...block,
+        start: Math.round(block.start),
+        end: Math.round(block.end),
+        assemblyName: isSingleAssemblyName ? undefined : block.assemblyName,
+    }));
+    return locs.join(' ');
+}
+export const HEADER_BAR_HEIGHT = 48;
+export const HEADER_OVERVIEW_HEIGHT = 20;
+export const SCALE_BAR_HEIGHT = 17;
+export const RESIZE_HANDLE_HEIGHT = 3;
+export const INTER_REGION_PADDING_WIDTH = 2;
+export const SPACING = 7;
+export const WIDGET_HEIGHT = 32;
+function localStorageGetItem(item) {
+    return typeof localStorage !== 'undefined'
+        ? localStorage.getItem(item)
+        : undefined;
+}
+export function stateModelFactory(pluginManager) {
+    return types
+        .compose(BaseViewModel, types.model('LinearGenomeView', {
+        id: ElementId,
+        type: types.literal('LinearGenomeView'),
+        offsetPx: 0,
+        bpPerPx: 1,
+        displayedRegions: types.array(MUIRegion),
+        // we use an array for the tracks because the tracks are displayed in a
+        // specific order that we need to keep.
+        tracks: types.array(pluginManager.pluggableMstType('track', 'stateModel')),
+        hideHeader: false,
+        hideHeaderOverview: false,
+        hideNoTracksActive: false,
+        trackSelectorType: types.optional(types.enumeration(['hierarchical']), 'hierarchical'),
+        trackLabels: types.optional(types.string, () => localStorageGetItem('lgv-trackLabels') || 'overlapping'),
+        showCenterLine: types.optional(types.boolean, () => {
+            const setting = localStorageGetItem('lgv-showCenterLine');
+            return setting !== undefined && setting !== null ? !!+setting : false;
+        }),
+        showCytobandsSetting: types.optional(types.boolean, () => {
+            const setting = localStorageGetItem('lgv-showCytobands');
+            return setting !== undefined && setting !== null ? !!+setting : true;
+        }),
+    }))
+        .volatile(() => ({
+        volatileWidth: undefined,
+        minimumBlockWidth: 3,
+        draggingTrackId: undefined,
+        volatileError: undefined,
+        // array of callbacks to run after the next set of the displayedRegions,
+        // which is basically like an onLoad
+        afterDisplayedRegionsSetCallbacks: [],
+        scaleFactor: 1,
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        trackRefs: {},
+        coarseDynamicBlocks: [],
+        coarseTotalBp: 0,
+        leftOffset: undefined,
+        rightOffset: undefined,
+        searchResults: undefined,
+        searchQuery: undefined,
+        seqDialogDisplayed: false,
+    }))
+        .views(self => ({
+        get width() {
+            if (self.volatileWidth === undefined) {
+                throw new Error('width undefined, make sure to check for model.initialized');
+            }
+            return self.volatileWidth;
+        },
+        get interRegionPaddingWidth() {
+            return INTER_REGION_PADDING_WIDTH;
+        },
+        get assemblyNames() {
+            return [
+                ...new Set(self.displayedRegions.map(region => region.assemblyName)),
+            ];
+        },
+    }))
+        .views(self => ({
+        get assemblyErrors() {
+            const { assemblyManager } = getSession(self);
+            const { assemblyNames } = self;
+            return 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 } = getSession(self);
+            const { assemblyNames } = self;
+            return 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 isSearchDialogDisplayed() {
+            return self.searchResults !== undefined;
+        },
+        get scaleBarHeight() {
+            return SCALE_BAR_HEIGHT + RESIZE_HANDLE_HEIGHT;
+        },
+        get headerHeight() {
+            if (self.hideHeader) {
+                return 0;
+            }
+            if (self.hideHeaderOverview) {
+                return HEADER_BAR_HEIGHT;
+            }
+            return HEADER_BAR_HEIGHT + HEADER_OVERVIEW_HEIGHT;
+        },
+        get trackHeights() {
+            return self.tracks
+                .map(t => t.displays[0].height)
+                .reduce((a, b) => a + b, 0);
+        },
+        get trackHeightsWithResizeHandles() {
+            return this.trackHeights + self.tracks.length * RESIZE_HANDLE_HEIGHT;
+        },
+        get height() {
+            return (this.trackHeightsWithResizeHandles +
+                this.headerHeight +
+                this.scaleBarHeight);
+        },
+        get totalBp() {
+            return self.displayedRegions.reduce((a, b) => a + b.end - b.start, 0);
+        },
+        get maxBpPerPx() {
+            return this.totalBp / (self.width * 0.9);
+        },
+        get minBpPerPx() {
+            return 1 / 50;
+        },
+        get error() {
+            return self.volatileError || this.assemblyErrors;
+        },
+        get maxOffset() {
+            // objectively determined to keep the linear genome on the main screen
+            const leftPadding = 10;
+            return this.displayedRegionsTotalPx - leftPadding;
+        },
+        get minOffset() {
+            // objectively determined to keep the linear genome on the main screen
+            const rightPadding = 30;
+            return -self.width + rightPadding;
+        },
+        get displayedRegionsTotalPx() {
+            return this.totalBp / self.bpPerPx;
+        },
+        renderProps() {
+            return {
+                ...getParentRenderProps(self),
+                bpPerPx: self.bpPerPx,
+                highResolutionScaling: getConf(getSession(self), 'highResolutionScaling'),
+            };
+        },
+        searchScope(assemblyName) {
+            return {
+                assemblyName,
+                includeAggregateIndexes: true,
+                tracks: self.tracks,
+            };
+        },
+        bpToPx({ refName, coord, regionNumber, }) {
+            return viewBpToPx({ refName, coord, regionNumber, self });
+        },
+        /**
+         *
+         * @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) {
+            let bpSoFar = 0;
+            const bp = (self.offsetPx + px) * self.bpPerPx;
+            const n = self.displayedRegions.length;
+            if (bp < 0) {
+                const region = self.displayedRegions[0];
+                const offset = bp;
+                const snap = getSnapshot(region);
+                return {
+                    // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+                    ...snap,
+                    oob: true,
+                    coord: region.reversed
+                        ? Math.floor(region.end - offset) + 1
+                        : Math.floor(region.start + offset) + 1,
+                    offset,
+                    index: 0,
+                };
+            }
+            const interRegionPaddingBp = self.interRegionPaddingWidth * self.bpPerPx;
+            const minimumBlockBp = self.minimumBlockWidth * self.bpPerPx;
+            for (let index = 0; index < self.displayedRegions.length; index += 1) {
+                const region = self.displayedRegions[index];
+                const len = region.end - region.start;
+                const offset = bp - bpSoFar;
+                if (len + bpSoFar > bp && bpSoFar <= bp) {
+                    const snap = getSnapshot(region);
+                    return {
+                        // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+                        ...snap,
+                        oob: false,
+                        offset,
+                        coord: region.reversed
+                            ? Math.floor(region.end - offset) + 1
+                            : Math.floor(region.start + offset) + 1,
+                        index,
+                    };
+                }
+                // add the interRegionPaddingWidth if the boundary is in the screen
+                // e.g. offset>0 && offset<width
+                if (region.end - region.start > minimumBlockBp &&
+                    offset / self.bpPerPx > 0 &&
+                    offset / self.bpPerPx < self.width) {
+                    bpSoFar += len + interRegionPaddingBp;
+                }
+                else {
+                    bpSoFar += len;
+                }
+            }
+            if (bp >= bpSoFar) {
+                const region = self.displayedRegions[n - 1];
+                const len = region.end - region.start;
+                const offset = bp - bpSoFar + len;
+                const snap = getSnapshot(region);
+                return {
+                    // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+                    ...snap,
+                    oob: true,
+                    offset,
+                    coord: region.reversed
+                        ? Math.floor(region.end - offset) + 1
+                        : Math.floor(region.start + offset) + 1,
+                    index: n - 1,
+                };
+            }
+            return {
+                coord: 0,
+                index: 0,
+                refName: '',
+                oob: true,
+                assemblyName: '',
+                offset: 0,
+                start: 0,
+                end: 0,
+                reversed: false,
+            };
+        },
+        getTrack(id) {
+            return self.tracks.find(t => t.configuration.trackId === id);
+        },
+        rankSearchResults(results) {
+            // order of rank
+            const openTrackIds = self.tracks.map(track => track.configuration.trackId);
+            results.forEach(result => {
+                if (openTrackIds.includes(result.trackId)) {
+                    result.updateScore(result.getScore() + 1);
+                }
+            });
+            return results;
+        },
+        // modifies view menu action onClick to apply to all tracks of same type
+        rewriteOnClicks(trackType, viewMenuActions) {
+            viewMenuActions.forEach(action => {
+                // go to lowest level menu
+                if ('subMenu' in action) {
+                    this.rewriteOnClicks(trackType, action.subMenu);
+                }
+                if ('onClick' in action) {
+                    const holdOnClick = action.onClick;
+                    action.onClick = (...args) => {
+                        self.tracks.forEach(track => {
+                            if (track.type === trackType) {
+                                holdOnClick.apply(track, [track, ...args]);
+                            }
+                        });
+                    };
+                }
+            });
+        },
+        get trackTypeActions() {
+            const allActions = new Map();
+            self.tracks.forEach(track => {
+                const trackInMap = allActions.get(track.type);
+                if (!trackInMap) {
+                    const viewMenuActions = clone(track.viewMenuActions);
+                    this.rewriteOnClicks(track.type, viewMenuActions);
+                    allActions.set(track.type, viewMenuActions);
+                }
+            });
+            return allActions;
+        },
+        get centerLineInfo() {
+            return self.displayedRegions.length
+                ? this.pxToBp(self.width / 2)
+                : undefined;
+        },
+    }))
+        .actions(self => ({
+        setShowCytobands(flag) {
+            self.showCytobandsSetting = flag;
+            localStorage.setItem('lgv-showCytobands', `${+flag}`);
+        },
+        setWidth(newWidth) {
+            self.volatileWidth = newWidth;
+        },
+        setError(error) {
+            self.volatileError = error;
+        },
+        toggleHeader() {
+            self.hideHeader = !self.hideHeader;
+        },
+        toggleHeaderOverview() {
+            self.hideHeaderOverview = !self.hideHeaderOverview;
+        },
+        toggleNoTracksActive() {
+            self.hideNoTracksActive = !self.hideNoTracksActive;
+        },
+        scrollTo(offsetPx) {
+            const newOffsetPx = clamp(offsetPx, self.minOffset, self.maxOffset);
+            self.offsetPx = newOffsetPx;
+            return newOffsetPx;
+        },
+        zoomTo(bpPerPx) {
+            const newBpPerPx = clamp(bpPerPx, self.minBpPerPx, self.maxBpPerPx);
+            if (newBpPerPx === self.bpPerPx) {
+                return newBpPerPx;
+            }
+            const oldBpPerPx = self.bpPerPx;
+            self.bpPerPx = newBpPerPx;
+            if (Math.abs(oldBpPerPx - newBpPerPx) < 0.000001) {
+                console.warn('zoomTo bpPerPx rounding error');
+                return oldBpPerPx;
+            }
+            // tweak the offset so that the center of the view remains at the same coordinate
+            const viewWidth = self.width;
+            this.scrollTo(Math.round(((self.offsetPx + viewWidth / 2) * oldBpPerPx) / newBpPerPx -
+                viewWidth / 2));
+            return newBpPerPx;
+        },
+        setOffsets(left, right) {
+            // sets offsets used in the get sequence dialog
+            self.leftOffset = left;
+            self.rightOffset = right;
+        },
+        setSearchResults(results, query) {
+            self.searchResults = results;
+            self.searchQuery = query;
+        },
+        setSequenceDialogOpen(open) {
+            self.seqDialogDisplayed = open;
+        },
+        setNewView(bpPerPx, offsetPx) {
+            this.zoomTo(bpPerPx);
+            this.scrollTo(offsetPx);
+        },
+        horizontallyFlip() {
+            self.displayedRegions = cast(self.displayedRegions
+                .slice()
+                .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 = resolveIdentifier(schema, 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 = viewType.displayTypes.map(d => d.name);
+            const displayConf = conf.displays.find((d) => supportedDisplays.includes(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 = resolveIdentifier(schema, getRoot(self), trackId);
+            const t = self.tracks.filter(t => t.configuration === conf);
+            transaction(() => t.forEach(t => self.tracks.remove(t)));
+            return t.length;
+        },
+    }))
+        .actions(self => ({
+        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 ${targetId} not found`);
+            }
+            const track = getSnapshot(self.tracks[oldIndex]);
+            self.tracks.splice(oldIndex, 1);
+            self.tracks.splice(newIndex, 0, track);
+        },
+        closeView() {
+            const parent = getContainingView(self);
+            if (parent) {
+                // I am embedded in a some other view
+                if (isViewContainer(parent)) {
+                    parent.removeView(self);
+                }
+            }
+            else {
+                // I am part of a session
+                getSession(self).removeView(self);
+            }
+        },
+        toggleTrack(trackId) {
+            // if we have any tracks with that configuration, turn them off
+            const hiddenCount = self.hideTrack(trackId);
+            // if none had that configuration, turn one on
+            if (!hiddenCount) {
+                self.showTrack(trackId);
+            }
+        },
+        setTrackLabels(setting) {
+            self.trackLabels = setting;
+            localStorage.setItem('lgv-trackLabels', setting);
+        },
+        toggleCenterLine() {
+            self.showCenterLine = !self.showCenterLine;
+            localStorage.setItem('lgv-showCenterLine', `${+self.showCenterLine}`);
+        },
+        setDisplayedRegions(regions) {
+            self.displayedRegions = cast(regions);
+            self.zoomTo(self.bpPerPx);
+        },
+        activateTrackSelector() {
+            if (self.trackSelectorType === 'hierarchical') {
+                const session = getSession(self);
+                if (isSessionModelWithWidgets(session)) {
+                    const selector = session.addWidget('HierarchicalTrackSelectorWidget', 'hierarchicalTrackSelector', { view: self });
+                    session.showWidget(selector);
+                    return selector;
+                }
+            }
+            throw new Error(`invalid track selector type ${self.trackSelectorType}`);
+        },
+        navToLocString(locString, optAssemblyName) {
+            const { assemblyNames } = self;
+            const { assemblyManager } = getSession(self);
+            const { isValidRefName } = assemblyManager;
+            const assemblyName = optAssemblyName || assemblyNames[0];
+            let parsedLocStrings;
+            const inputs = locString
+                .split(/(\s+)/)
+                .map(f => f.trim())
+                .filter(f => !!f);
+            // first try interpreting as a whitespace-separated sequence of
+            // multiple locstrings
+            try {
+                parsedLocStrings = inputs.map(l => parseLocString(l, ref => isValidRefName(ref, assemblyName)));
+            }
+            catch (e) {
+                // if this fails, try interpreting as a whitespace-separated refname,
+                // start, end if start and end are integer inputs
+                const [refName, start, end] = inputs;
+                if (`${e}`.match(/Unknown reference sequence/) &&
+                    Number.isInteger(+start) &&
+                    Number.isInteger(+end)) {
+                    parsedLocStrings = [
+                        parseLocString(refName + ':' + start + '..' + end, ref => isValidRefName(ref, assemblyName)),
+                    ];
+                }
+                else {
+                    throw e;
+                }
+            }
+            const locations = parsedLocStrings === null || parsedLocStrings === void 0 ? void 0 : parsedLocStrings.map(region => {
+                const asmName = region.assemblyName || assemblyName;
+                const asm = assemblyManager.get(asmName);
+                const { refName } = region;
+                if (!asm) {
+                    throw new Error(`assembly ${asmName} not found`);
+                }
+                const { regions } = asm;
+                if (!regions) {
+                    throw new Error(`regions not loaded yet for ${asmName}`);
+                }
+                const canonicalRefName = asm.getCanonicalRefName(region.refName);
+                if (!canonicalRefName) {
+                    throw new Error(`Could not find refName ${refName} in ${asm.name}`);
+                }
+                const parentRegion = regions.find(region => region.refName === canonicalRefName);
+                if (!parentRegion) {
+                    throw new Error(`Could not find refName ${refName} in ${asmName}`);
+                }
+                return {
+                    ...region,
+                    assemblyName: asmName,
+                    parentRegion,
+                };
+            });
+            if (locations.length === 1) {
+                const loc = locations[0];
+                this.setDisplayedRegions([
+                    { reversed: loc.reversed, ...loc.parentRegion },
+                ]);
+                const { start, end, parentRegion } = loc;
+                this.navTo({
+                    ...loc,
+                    start: clamp(start !== null && start !== void 0 ? start : 0, 0, parentRegion.end),
+                    end: clamp(end !== null && end !== void 0 ? end : parentRegion.end, 0, parentRegion.end),
+                });
+            }
+            else {
+                this.setDisplayedRegions(
+                // @ts-ignore
+                locations.map(r => (r.start === undefined ? r.parentRegion : r)));
+                this.showAllRegions();
+            }
+        },
+        /**
+         * Navigate to a location based on its refName and optionally start, end,
+         * and assemblyName. Can handle if there are multiple displayedRegions
+         * from same refName. Only navigates to a location if it is entirely
+         * within a displayedRegion. Navigates to the first matching location
+         * encountered.
+         *
+         * Throws an error if navigation was unsuccessful
+         *
+         * @param location - a proposed location to navigate to
+         */
+        navTo(query) {
+            this.navToMultiple([query]);
+        },
+        navToMultiple(locations) {
+            const firstLocation = locations[0];
+            let { refName } = firstLocation;
+            const { start, end, assemblyName = self.assemblyNames[0], } = firstLocation;
+            if (start !== undefined && end !== undefined && start > end) {
+                throw new Error(`start "${start + 1}" is greater than end "${end}"`);
+            }
+            const session = getSession(self);
+            const { assemblyManager } = session;
+            const assembly = assemblyManager.get(assemblyName);
+            if (assembly) {
+                const canonicalRefName = assembly.getCanonicalRefName(refName);
+                if (canonicalRefName) {
+                    refName = canonicalRefName;
+                }
+            }
+            let s = start;
+            let e = end;
+            let refNameMatched = false;
+            const predicate = (r) => {
+                if (refName === r.refName) {
+                    refNameMatched = true;
+                    if (s === undefined) {
+                        s = r.start;
+                    }
+                    if (e === undefined) {
+                        e = r.end;
+                    }
+                    if (s >= r.start && s <= r.end && e <= r.end && e >= r.start) {
+                        return true;
+                    }
+                    s = start;
+                    e = end;
+                }
+                return false;
+            };
+            const lastIndex = findLastIndex(self.displayedRegions, predicate);
+            let index;
+            while (index !== lastIndex) {
+                try {
+                    const previousIndex = index;
+                    index = self.displayedRegions
+                        .slice(previousIndex === undefined ? 0 : previousIndex + 1)
+                        .findIndex(predicate);
+                    if (previousIndex !== undefined) {
+                        index += previousIndex + 1;
+                    }
+                    if (!refNameMatched) {
+                        throw new Error(`could not find a region with refName "${refName}"`);
+                    }
+                    if (s === undefined) {
+                        throw new Error(`could not find a region with refName "${refName}" that contained an end position ${e}`);
+                    }
+                    if (e === undefined) {
+                        throw new Error(`could not find a region with refName "${refName}" that contained a start position ${s + 1}`);
+                    }
+                    if (index === -1) {
+                        throw new Error(`could not find a region that completely contained "${assembleLocString(firstLocation)}"`);
+                    }
+                    if (locations.length === 1) {
+                        const f = self.displayedRegions[index];
+                        this.moveTo({ index, offset: f.reversed ? f.end - e : s - f.start }, { index, offset: f.reversed ? f.end - s : e - f.start });
+                        return;
+                    }
+                    let locationIndex = 0;
+                    let locationStart = 0;
+                    let locationEnd = 0;
+                    for (locationIndex; locationIndex < locations.length; locationIndex++) {
+                        const location = locations[locationIndex];
+                        const region = self.displayedRegions[index + locationIndex];
+                        locationStart = location.start || region.start;
+                        locationEnd = location.end || region.end;
+                        if (location.refName !== region.refName) {
+                            throw new Error(`Entered location ${assembleLocString(location)} does not match with displayed regions`);
+                        }
+                    }
+                    locationIndex -= 1;
+                    const startDisplayedRegion = self.displayedRegions[index];
+                    const endDisplayedRegion = self.displayedRegions[index + locationIndex];
+                    this.moveTo({
+                        index,
+                        offset: startDisplayedRegion.reversed
+                            ? startDisplayedRegion.end - e
+                            : s - startDisplayedRegion.start,
+                    }, {
+                        index: index + locationIndex,
+                        offset: endDisplayedRegion.reversed
+                            ? endDisplayedRegion.end - locationStart
+                            : locationEnd - endDisplayedRegion.start,
+                    });
+                    return;
+                }
+                catch (error) {
+                    if (index === lastIndex) {
+                        throw error;
+                    }
+                }
+            }
+        },
+        /**
+         * 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, rightPx) {
+            if (leftPx === undefined || rightPx === undefined) {
+                return;
+            }
+            const singleRefSeq = leftPx.refName === rightPx.refName && leftPx.index === rightPx.index;
+            // zooming into one displayed Region
+            if ((singleRefSeq && rightPx.offset < leftPx.offset) ||
+                leftPx.index > rightPx.index) {
+                ;
+                [leftPx, rightPx] = [rightPx, leftPx];
+            }
+            const startOffset = {
+                start: leftPx.start,
+                end: leftPx.end,
+                index: leftPx.index,
+                offset: leftPx.offset,
+            };
+            const endOffset = {
+                start: rightPx.start,
+                end: rightPx.end,
+                index: rightPx.index,
+                offset: rightPx.offset,
+            };
+            if (startOffset && endOffset) {
+                this.moveTo(startOffset, endOffset);
+            }
+            else {
+                const session = getSession(self);
+                session.notify('No regions found to navigate to', 'warning');
+            }
+        },
+        /**
+         * Helper method for the fetchSequence.
+         * Retrieves the corresponding regions that were selected by the rubberband
+         *
+         * @param leftOffset - `object as {start, end, index, offset}`, offset = start of user drag
+         * @param rightOffset - `object as {start, end, index, offset}`, offset = end of user drag
+         * @returns array of Region[]
+         */
+        getSelectedRegions(leftOffset, rightOffset) {
+            const snap = getSnapshot(self);
+            const simView = Base1DView.create({
+                // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+                ...snap,
+                interRegionPaddingWidth: self.interRegionPaddingWidth,
+            });
+            simView.setVolatileWidth(self.width);
+            simView.zoomToDisplayedRegions(leftOffset, rightOffset);
+            return simView.dynamicBlocks.contentBlocks.map(region => ({
+                ...region,
+                start: Math.floor(region.start),
+                end: Math.ceil(region.end),
+            }));
+        },
+        // schedule something to be run after the next time displayedRegions is set
+        afterDisplayedRegionsSet(cb) {
+            self.afterDisplayedRegionsSetCallbacks.push(cb);
+        },
+        /**
+         * 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, end) {
+            // find locations in the modellist
+            let bpSoFar = 0;
+            if (start.index === end.index) {
+                bpSoFar += end.offset - start.offset;
+            }
+            else {
+                const s = self.displayedRegions[start.index];
+                bpSoFar += s.end - s.start - start.offset;
+                if (end.index - start.index >= 2) {
+                    for (let i = start.index + 1; i < end.index; i += 1) {
+                        bpSoFar +=
+                            self.displayedRegions[i].end - self.displayedRegions[i].start;
+                    }
+                }
+                bpSoFar += end.offset;
+            }
+            const targetBpPerPx = bpSoFar /
+                (self.width -
+                    self.interRegionPaddingWidth * (end.index - start.index));
+            const newBpPerPx = self.zoomTo(targetBpPerPx);
+            // If our target bpPerPx was smaller than the allowed minBpPerPx, adjust
+            // the scroll so the requested range is in the middle of the screen
+            let extraBp = 0;
+            if (targetBpPerPx < newBpPerPx) {
+                extraBp = ((newBpPerPx - targetBpPerPx) * self.width) / 2;
+            }
+            let bpToStart = -extraBp;
+            for (let i = 0; i < self.displayedRegions.length; i += 1) {
+                const region = self.displayedRegions[i];
+                if (start.index === i) {
+                    bpToStart += start.offset;
+                    break;
+                }
+                else {
+                    bpToStart += region.end - region.start;
+                }
+            }
+            self.scrollTo(Math.round(bpToStart / self.bpPerPx) +
+                self.interRegionPaddingWidth * start.index);
+        },
+        horizontalScroll(distance) {
+            const oldOffsetPx = self.offsetPx;
+            // newOffsetPx is the actual offset after the scroll is clamped
+            const newOffsetPx = self.scrollTo(self.offsetPx + distance);
+            return newOffsetPx - oldOffsetPx;
+        },
+        /**
+         * 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, refName, regionIndex) {
+            const centerPx = self.bpToPx({
+                refName,
+                coord: bp,
+                regionNumber: regionIndex,
+            });
+            if (centerPx) {
+                self.scrollTo(Math.round(centerPx.offsetPx - self.width / 2));
+            }
+        },
+        center() {
+            const centerBp = self.totalBp / 2;
+            self.scrollTo(Math.round(centerBp / self.bpPerPx - self.width / 2));
+        },
+        showAllRegions() {
+            self.zoomTo(self.maxBpPerPx);
+            this.center();
+        },
+        showAllRegionsInAssembly(assemblyName) {
+            const session = getSession(self);
+            const { assemblyManager } = session;
+            if (!assemblyName) {
+                const assemblyNames = [
+                    ...new Set(self.displayedRegions.map(region => region.assemblyName)),
+                ];
+                if (assemblyNames.length > 1) {
+                    session.notify(`Can't perform this with multiple assemblies currently`);
+                    return;
+                }
+                ;
+                [assemblyName] = assemblyNames;
+            }
+            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;
+        },
+    }))
+        .actions(self => {
+        let cancelLastAnimation = () => { };
+        function slide(viewWidths) {
+            const [animate, cancelAnimation] = springAnimate(self.offsetPx, self.offsetPx + self.width * viewWidths, self.scrollTo);
+            cancelLastAnimation();
+            cancelLastAnimation = cancelAnimation;
+            animate();
+        }
+        return { slide };
+    })
+        .actions(self => {
+        let cancelLastAnimation = () => { };
+        function zoom(targetBpPerPx) {
+            self.zoomTo(self.bpPerPx);
+            if (
+            // already zoomed all the way in
+            (targetBpPerPx < self.bpPerPx && self.bpPerPx === self.minBpPerPx) ||
+                // already zoomed all the way out
+                (targetBpPerPx > self.bpPerPx && self.bpPerPx === self.maxBpPerPx)) {
+                return;
+            }
+            const factor = self.bpPerPx / targetBpPerPx;
+            const [animate, cancelAnimation] = 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 } = getSession(self);
+            const { assemblyNames } = self;
+            return assemblyNames.some(asm => { var _a, _b; return (_b = (_a = assemblyManager.get(asm)) === null || _a === void 0 ? void 0 : _a.cytobands) === null || _b === void 0 ? void 0 : _b.length; });
+        },
+        get cytobandOffset() {
+            return this.showCytobands
+                ? measureText(self.displayedRegions[0].refName, 12) + 15
+                : 0;
+        },
+    }))
+        .views(self => ({
+        menuItems() {
+            const { canShowCytobands, showCytobands } = self;
+            const menuItems = [
+                {
+                    label: 'Return to import form',
+                    onClick: () => {
+                        getSession(self).queueDialog(handleClose => [
+                            ReturnToImportFormDialog,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                    icon: FolderOpenIcon,
+                },
+                {
+                    label: 'Export SVG',
+                    icon: PhotoCameraIcon,
+                    onClick: () => {
+                        getSession(self).queueDialog(handleClose => [
+                            ExportSvgDlg,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                },
+                {
+                    label: 'Open track selector',
+                    onClick: self.activateTrackSelector,
+                    icon: TrackSelectorIcon,
+                },
+                {
+                    label: 'Horizontally flip',
+                    icon: SyncAltIcon,
+                    onClick: self.horizontallyFlip,
+                },
+                { type: 'divider' },
+                {
+                    label: 'Show all regions in assembly',
+                    icon: VisibilityIcon,
+                    onClick: self.showAllRegionsInAssembly,
+                },
+                {
+                    label: 'Show center line',
+                    icon: VisibilityIcon,
+                    type: 'checkbox',
+                    checked: self.showCenterLine,
+                    onClick: self.toggleCenterLine,
+                },
+                {
+                    label: 'Show header',
+                    icon: VisibilityIcon,
+                    type: 'checkbox',
+                    checked: !self.hideHeader,
+                    onClick: self.toggleHeader,
+                },
+                {
+                    label: 'Show header overview',
+                    icon: VisibilityIcon,
+                    type: 'checkbox',
+                    checked: !self.hideHeaderOverview,
+                    onClick: self.toggleHeaderOverview,
+                    disabled: self.hideHeader,
+                },
+                {
+                    label: 'Show no tracks active button',
+                    icon: VisibilityIcon,
+                    type: 'checkbox',
+                    checked: !self.hideNoTracksActive,
+                    onClick: self.toggleNoTracksActive,
+                },
+                {
+                    label: 'Track labels',
+                    icon: LabelIcon,
+                    subMenu: [
+                        {
+                            label: 'Overlapping',
+                            icon: VisibilityIcon,
+                            type: 'radio',
+                            checked: self.trackLabels === 'overlapping',
+                            onClick: () => self.setTrackLabels('overlapping'),
+                        },
+                        {
+                            label: 'Offset',
+                            icon: VisibilityIcon,
+                            type: 'radio',
+                            checked: self.trackLabels === 'offset',
+                            onClick: () => self.setTrackLabels('offset'),
+                        },
+                        {
+                            label: 'Hidden',
+                            icon: VisibilityIcon,
+                            type: 'radio',
+                            checked: self.trackLabels === 'hidden',
+                            onClick: () => self.setTrackLabels('hidden'),
+                        },
+                    ],
+                },
+                ...(canShowCytobands
+                    ? [
+                        {
+                            label: showCytobands ? 'Hide ideogram' : 'Show ideograms',
+                            onClick: () => {
+                                self.setShowCytobands(!showCytobands);
+                            },
+                        },
+                    ]
+                    : []),
+            ];
+            // add track's view level menu options
+            for (const [key, value] of self.trackTypeActions.entries()) {
+                if (value.length) {
+                    menuItems.push({ type: 'divider' }, { type: 'subHeader', label: key });
+                    value.forEach(action => {
+                        menuItems.push(action);
+                    });
+                }
+            }
+            return menuItems;
+        },
+    }))
+        .views(self => {
+        let currentlyCalculatedStaticBlocks;
+        let stringifiedCurrentlyCalculatedStaticBlocks = '';
+        return {
+            get staticBlocks() {
+                const ret = calculateStaticBlocks(self);
+                const sret = JSON.stringify(ret);
+                if (stringifiedCurrentlyCalculatedStaticBlocks !== sret) {
+                    currentlyCalculatedStaticBlocks = ret;
+                    stringifiedCurrentlyCalculatedStaticBlocks = sret;
+                }
+                return currentlyCalculatedStaticBlocks;
+            },
+            get dynamicBlocks() {
+                return calculateDynamicBlocks(self);
+            },
+            get roundedDynamicBlocks() {
+                return this.dynamicBlocks.contentBlocks.map(block => {
+                    return {
+                        ...block,
+                        start: Math.floor(block.start),
+                        end: Math.ceil(block.end),
+                    };
+                });
+            },
+            get visibleLocStrings() {
+                return calculateVisibleLocStrings(this.dynamicBlocks.contentBlocks);
+            },
+            get coarseVisibleLocStrings() {
+                return calculateVisibleLocStrings(self.coarseDynamicBlocks);
+            },
+        };
+    })
+        .actions(self => ({
+        // this "clears the view" and makes the view return to the import form
+        clearView() {
+            self.setDisplayedRegions([]);
+            self.tracks.clear();
+            // it is necessary to run these after setting displayed regions empty
+            // or else model.offsetPx gets set to Infinity and breaks
+            // mobx-state-tree snapshot
+            self.scrollTo(0);
+            self.zoomTo(10);
+        },
+        setCoarseDynamicBlocks(blocks) {
+            self.coarseDynamicBlocks = blocks.contentBlocks;
+            self.coarseTotalBp = blocks.totalBp;
+        },
+        afterAttach() {
+            addDisposer(self, autorun(() => {
+                if (self.initialized) {
+                    this.setCoarseDynamicBlocks(self.dynamicBlocks);
+                }
+            }, { delay: 150 }));
+        },
+    }))
+        .actions(self => ({
+        async exportSvg(opts = {}) {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            const html = await renderToSvg(self, opts);
+            const blob = new Blob([html], { type: 'image/svg+xml' });
+            saveAs(blob, opts.filename || 'image.svg');
+        },
+    }))
+        .views(self => ({
+        rubberBandMenuItems() {
+            return [
+                {
+                    label: 'Zoom to region',
+                    icon: ZoomInIcon,
+                    onClick: () => {
+                        const { leftOffset, rightOffset } = self;
+                        if (leftOffset && rightOffset) {
+                            self.moveTo(leftOffset, rightOffset);
+                        }
+                    },
+                },
+                {
+                    label: 'Get sequence',
+                    icon: MenuOpenIcon,
+                    onClick: () => {
+                        self.setSequenceDialogOpen(true);
+                    },
+                },
+            ];
+        },
+    }));
+}
+export { renderToSvg, RefNameAutocomplete, SearchBox };
+export { default as ReactComponent } from './components/LinearGenomeView';
+//# sourceMappingURL=index.js.map