@jbrowse/plugin-breakpoint-split-view 2.6.1

package/esm/BreakpointSplitView/model.d.ts

@@ -0,0 +1,299 @@
+import React from 'react';
+import { Instance } from 'mobx-state-tree';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { Feature } from '@jbrowse/core/util';
+export interface ExportSvgOptions {
+    rasterizeLayers?: boolean;
+    filename?: string;
+    Wrapper?: React.FC<any>;
+    fontSize?: number;
+    rulerHeight?: number;
+    textHeight?: number;
+    paddingHeight?: number;
+    headerHeight?: number;
+    cytobandHeight?: number;
+    trackLabels?: string;
+    themeName?: string;
+}
+type LGV = LinearGenomeViewModel;
+export interface Breakend {
+    MateDirection: string;
+    Join: string;
+    Replacement: string;
+    MatePosition: string;
+}
+export type LayoutRecord = [number, number, number, number];
+export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"BreakpointSplitView">;
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
+    showIntraviewLinks: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    linkViews: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    interactToggled: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    views: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+        id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    } & {
+        id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        type: import("mobx-state-tree").IType<string | undefined, string, string>;
+        offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+        bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+        displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
+        hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        width: number;
+    } & {
+        menuItems(): import("@jbrowse/core/ui").MenuItem[];
+    } & {
+        setDisplayName(name: string): void;
+        setWidth(newWidth: number): void;
+        setMinimized(flag: boolean): void;
+    } & {
+        volatileWidth: number | undefined;
+        minimumBlockWidth: number;
+        draggingTrackId: string | undefined;
+        volatileError: Error | undefined;
+        afterDisplayedRegionsSetCallbacks: Function[];
+        scaleFactor: number;
+        trackRefs: {
+            [key: string]: HTMLDivElement;
+        };
+        coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
+        coarseTotalBp: number;
+        leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
+        rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
+    } & {
+        readonly width: number;
+        readonly interRegionPaddingWidth: number;
+        readonly assemblyNames: string[];
+    } & {
+        MiniControlsComponent(): React.FC<any>;
+        HeaderComponent(): React.FC<any>;
+        readonly assemblyErrors: string;
+        readonly assembliesInitialized: boolean;
+        readonly initialized: boolean;
+        readonly hasDisplayedRegions: boolean;
+        readonly scaleBarHeight: number;
+        readonly headerHeight: number;
+        readonly trackHeights: number;
+        readonly trackHeightsWithResizeHandles: number;
+        readonly height: number;
+        readonly totalBp: number;
+        readonly maxBpPerPx: number;
+        readonly minBpPerPx: number;
+        readonly error: string | Error;
+        readonly maxOffset: number;
+        readonly minOffset: number;
+        readonly displayedRegionsTotalPx: number;
+        renderProps(): any;
+        searchScope(assemblyName: string): {
+            assemblyName: string;
+            includeAggregateIndexes: boolean;
+            tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
+        };
+        getTrack(id: string): any;
+        rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
+        rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
+        readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
+    } & {
+        setShowCytobands(flag: boolean): void;
+        setWidth(newWidth: number): void;
+        setError(error: Error | undefined): void;
+        toggleHeader(): void;
+        toggleHeaderOverview(): void;
+        toggleNoTracksActive(): void;
+        toggleShowGridlines(): void;
+        scrollTo(offsetPx: number): number;
+        zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
+        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
+        setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
+        setNewView(bpPerPx: number, offsetPx: number): void;
+        horizontallyFlip(): void;
+        showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
+        hideTrack(trackId: string): number;
+    } & {
+        moveTrack(movingId: string, targetId: string): void;
+        closeView(): void;
+        toggleTrack(trackId: string): void;
+        setTrackLabels(setting: "hidden" | "offset" | "overlapping"): void;
+        toggleCenterLine(): void;
+        setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
+        activateTrackSelector(): import("@jbrowse/core/util").Widget;
+        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
+            start: number;
+            end: number;
+            regionNumber?: number | undefined;
+            reversed?: boolean | undefined;
+            refName: string;
+            assemblyName: string;
+            key: string;
+            offsetPx: number;
+            widthPx: number;
+            variant?: string | undefined;
+            isLeftEndOfDisplayedRegion?: boolean | undefined;
+        }[];
+        afterDisplayedRegionsSet(cb: Function): void;
+        horizontalScroll(distance: number): number;
+        center(): void;
+        showAllRegions(): void;
+        showAllRegionsInAssembly(assemblyName?: string | undefined): void;
+        setDraggingTrackId(idx?: string | undefined): void;
+        setScaleFactor(factor: number): void;
+        clearView(): void;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
+    } & {
+        slide: (viewWidths: number) => void;
+    } & {
+        zoom: (targetBpPerPx: number) => void;
+    } & {
+        readonly canShowCytobands: boolean;
+        readonly showCytobands: boolean;
+        readonly anyCytobandsExist: boolean;
+        readonly cytobandOffset: number;
+    } & {
+        menuItems(): import("@jbrowse/core/ui").MenuItem[];
+    } & {
+        readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
+        readonly visibleLocStrings: string;
+        readonly coarseVisibleLocStrings: string;
+    } & {
+        setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
+        afterAttach(): void;
+    } & {
+        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
+        navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+        navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
+        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
+        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
+    } & {
+        rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+        bpToPx({ refName, coord, regionNumber, }: {
+            refName: string;
+            coord: number;
+            regionNumber?: number | undefined;
+        }): {
+            index: number;
+            offsetPx: number;
+        } | undefined;
+        centerAt(coord: number, refName: string, regionNumber: number): void;
+        pxToBp(px: number): {
+            coord: number;
+            index: number;
+            refName: string;
+            oob: boolean;
+            assemblyName: string;
+            offset: number;
+            start: number;
+            end: number;
+            reversed: boolean;
+        };
+        readonly centerLineInfo: {
+            coord: number;
+            index: number;
+            refName: string;
+            oob: boolean;
+            assemblyName: string;
+            offset: number;
+            start: number;
+            end: number;
+            reversed: boolean;
+        } | undefined;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+}, {
+    width: number;
+} & {
+    menuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    setDisplayName(name: string): void;
+    setWidth(newWidth: number): void;
+    setMinimized(flag: boolean): void;
+} & {
+    width: number;
+    matchedTrackFeatures: {
+        [key: string]: Feature[][];
+    };
+} & {
+    /**
+     * #method
+     * creates an svg export and save using FileSaver
+     */
+    exportSvg(opts?: ExportSvgOptions): Promise<void>;
+} & {
+    readonly matchedTracks: any[];
+    getMatchedTracks(trackConfigId: string): any[];
+    hasTranslocations(trackConfigId: string): Feature | undefined;
+    getTrackFeatures(trackConfigId: string): Map<string, Feature>;
+    getMatchedFeaturesInLayout(trackConfigId: string, features: Feature[][]): {
+        feature: Feature;
+        layout: LayoutRecord;
+        level: number;
+    }[][];
+} & {
+    afterAttach(): void;
+    onSubviewAction(actionName: string, path: string, args?: unknown[]): void;
+    setWidth(newWidth: number): void;
+    removeView(view: LGV): void;
+    closeView(): void;
+    toggleInteract(): void;
+    toggleIntraviewLinks(): void;
+    toggleLinkViews(): void;
+    setMatchedTrackFeatures(obj: {
+        [key: string]: Feature[][];
+    }): void;
+} & {
+    afterAttach(): void;
+    menuItems(): ({
+        label: string;
+        subMenu: import("@jbrowse/core/ui").MenuItem[];
+    } | {
+        label: string;
+        type: string;
+        checked: boolean;
+        onClick: () => void;
+        icon?: undefined;
+    } | {
+        label: string;
+        type: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        checked: boolean;
+        onClick: () => void;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+        type?: undefined;
+        checked?: undefined;
+    })[];
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type BreakpointViewStateModel = ReturnType<typeof stateModelFactory>;
+export type BreakpointViewModel = Instance<BreakpointViewStateModel>;
+export {};

package/esm/BreakpointSplitView/model.js

@@ -0,0 +1,216 @@
+import { lazy } from 'react';
+import { types, getParent, onAction, addDisposer, getPath, } from 'mobx-state-tree';
+import { autorun } from 'mobx';
+import { saveAs } from 'file-saver';
+import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
+import { getSession, notEmpty } from '@jbrowse/core/util';
+import { getConf } from '@jbrowse/core/configuration';
+// icons
+import PhotoCamera from '@mui/icons-material/PhotoCamera';
+import LinkIcon from '@mui/icons-material/Link';
+// locals
+import { intersect } from './util';
+// lazies
+const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
+function calc(track, feat) {
+    return track.displays[0].searchFeatureByID(feat.id());
+}
+async function getBlockFeatures(model, track) {
+    const { views } = model;
+    const { rpcManager, assemblyManager } = getSession(model);
+    const assemblyName = model.views[0].assemblyNames[0];
+    const assembly = await assemblyManager.waitForAssembly(assemblyName);
+    if (!assembly) {
+        return undefined; // throw new Error(`assembly not found: "${assemblyName}"`)
+    }
+    const sessionId = track.configuration.trackId;
+    return Promise.all(views.map(async (view) => (await rpcManager.call(sessionId, 'CoreGetFeatures', {
+        adapterConfig: getConf(track, ['adapter']),
+        sessionId,
+        regions: view.staticBlocks.contentBlocks,
+    })).flat()));
+}
+export default function stateModelFactory(pluginManager) {
+    const minHeight = 40;
+    const defaultHeight = 400;
+    const model = types
+        .model('BreakpointSplitView', {
+        type: types.literal('BreakpointSplitView'),
+        height: types.optional(types.refinement('viewHeight', types.number, (n) => n >= minHeight), defaultHeight),
+        trackSelectorType: 'hierarchical',
+        showIntraviewLinks: true,
+        linkViews: false,
+        interactToggled: false,
+        views: types.array(pluginManager.getViewType('LinearGenomeView')
+            .stateModel),
+    })
+        .volatile(() => ({
+        width: 800,
+        matchedTrackFeatures: {},
+    }))
+        .views(self => ({
+        /**
+         * #method
+         * creates an svg export and save using FileSaver
+         */
+        async exportSvg(opts = {}) {
+            const { renderToSvg } = await import('./svgcomponents/SVGBreakpointSplitView');
+            const html = await renderToSvg(self, opts);
+            const blob = new Blob([html], { type: 'image/svg+xml' });
+            saveAs(blob, opts.filename || 'image.svg');
+        },
+    }))
+        .views(self => ({
+        // Find all track ids that match across multiple views
+        get matchedTracks() {
+            return intersect(elt => elt.configuration.trackId, ...self.views.map(view => view.tracks));
+        },
+        // Get tracks with a given trackId across multiple views
+        getMatchedTracks(trackConfigId) {
+            return self.views
+                .map(view => view.getTrack(trackConfigId))
+                .filter(f => !!f);
+        },
+        // Translocation features are handled differently
+        // since they do not have a mate e.g. they are one sided
+        hasTranslocations(trackConfigId) {
+            return [...this.getTrackFeatures(trackConfigId).values()].find(f => f.get('type') === 'translocation');
+        },
+        // Get a composite map of featureId->feature map for a track across
+        // multiple views
+        getTrackFeatures(trackConfigId) {
+            var _a;
+            return new Map((_a = self.matchedTrackFeatures[trackConfigId]) === null || _a === void 0 ? void 0 : _a.flat().map(f => [f.id(), f]));
+        },
+        getMatchedFeaturesInLayout(trackConfigId, features) {
+            // use reverse to search the second track first
+            const tracks = this.getMatchedTracks(trackConfigId);
+            return features.map(c => c
+                .map(feature => {
+                const level = tracks.findIndex(track => calc(track, feature));
+                return level !== -1
+                    ? {
+                        feature,
+                        layout: calc(tracks[level], feature),
+                        level,
+                    }
+                    : undefined;
+            })
+                .filter(notEmpty));
+        },
+    }))
+        .actions(self => ({
+        afterAttach() {
+            addDisposer(self, onAction(self, ({ name, path, args, }) => {
+                if (self.linkViews) {
+                    const actions = [
+                        'horizontalScroll',
+                        'zoomTo',
+                        'setScaleFactor',
+                        'showTrack',
+                        'toggleTrack',
+                        'hideTrack',
+                        'setTrackLabels',
+                        'toggleCenterLine',
+                    ];
+                    if (actions.includes(name) && path) {
+                        this.onSubviewAction(name, path, args);
+                    }
+                }
+            }));
+        },
+        onSubviewAction(actionName, path, args) {
+            self.views.forEach(view => {
+                const ret = getPath(view);
+                if (ret.lastIndexOf(path) !== ret.length - path.length) {
+                    // @ts-ignore
+                    view[actionName](args === null || args === void 0 ? void 0 : args[0]);
+                }
+            });
+        },
+        setWidth(newWidth) {
+            self.width = newWidth;
+            self.views.forEach(v => v.setWidth(newWidth));
+        },
+        removeView(view) {
+            self.views.remove(view);
+        },
+        closeView() {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            getParent(self, 2).removeView(self);
+        },
+        toggleInteract() {
+            self.interactToggled = !self.interactToggled;
+        },
+        toggleIntraviewLinks() {
+            self.showIntraviewLinks = !self.showIntraviewLinks;
+        },
+        toggleLinkViews() {
+            self.linkViews = !self.linkViews;
+        },
+        setMatchedTrackFeatures(obj) {
+            self.matchedTrackFeatures = obj;
+        },
+    }))
+        .actions(self => ({
+        afterAttach() {
+            addDisposer(self, autorun(async () => {
+                try {
+                    if (!self.views.every(view => view.initialized)) {
+                        return;
+                    }
+                    self.setMatchedTrackFeatures(Object.fromEntries(await Promise.all(self.matchedTracks.map(async (track) => [
+                        track.configuration.trackId,
+                        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                        await getBlockFeatures(self, track),
+                    ]))));
+                }
+                catch (e) {
+                    console.error(e);
+                    getSession(self).notify(`${e}`, 'error');
+                }
+            }));
+        },
+        menuItems() {
+            return [
+                ...self.views
+                    .map((view, idx) => { var _a; return [idx, (_a = view.menuItems) === null || _a === void 0 ? void 0 : _a.call(view)]; })
+                    .filter(f => !!f[1])
+                    .map(f => ({ label: `View ${f[0] + 1} Menu`, subMenu: f[1] })),
+                {
+                    label: 'Show intra-view links',
+                    type: 'checkbox',
+                    checked: self.showIntraviewLinks,
+                    onClick: () => self.toggleIntraviewLinks(),
+                },
+                {
+                    label: 'Allow clicking alignment squiggles?',
+                    type: 'checkbox',
+                    checked: self.interactToggled,
+                    onClick: () => self.toggleInteract(),
+                },
+                {
+                    label: 'Link views',
+                    type: 'checkbox',
+                    icon: LinkIcon,
+                    checked: self.linkViews,
+                    onClick: () => {
+                        self.toggleLinkViews();
+                    },
+                },
+                {
+                    label: 'Export SVG',
+                    icon: PhotoCamera,
+                    onClick: () => {
+                        getSession(self).queueDialog(handleClose => [
+                            ExportSvgDialog,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                },
+            ];
+        },
+    }));
+    return types.compose(BaseViewModel, model);
+}
+//# sourceMappingURL=model.js.map

package/esm/BreakpointSplitView/model.js.map

@@ -0,0 +1 @@
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package/esm/BreakpointSplitView/svgcomponents/SVGBackground.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+export default function SVGBackground({ width, height, shift, }: {
+    width: number;
+    height: number;
+    shift: number;
+}): React.JSX.Element;

package/esm/BreakpointSplitView/svgcomponents/SVGBackground.js

@@ -0,0 +1,7 @@
+import React from 'react';
+import { useTheme } from '@mui/material';
+export default function SVGBackground({ width, height, shift, }) {
+    const theme = useTheme();
+    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+}
+//# sourceMappingURL=SVGBackground.js.map

package/esm/BreakpointSplitView/svgcomponents/SVGBackground.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGBackground.js","sourceRoot":"","sources":["../../../src/BreakpointSplitView/svgcomponents/SVGBackground.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,EACpC,KAAK,EACL,MAAM,EACN,KAAK,GAKN;IACC,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,OAAO,CACL,8BACE,KAAK,EAAE,KAAK,GAAG,KAAK,GAAG,CAAC,EACxB,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,GACtC,CACH,CAAA;AACH,CAAC"}

package/esm/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.d.ts

@@ -0,0 +1,4 @@
+import { ExportSvgOptions, BreakpointViewModel } from '../model';
+type BSV = BreakpointViewModel;
+export declare function renderToSvg(model: BSV, opts: ExportSvgOptions): Promise<string>;
+export {};

package/esm/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js

@@ -0,0 +1,76 @@
+import React from 'react';
+import { renderToStaticMarkup } from 'react-dom/server';
+import { when } from 'mobx';
+import { getSession, max, measureText, sum, } from '@jbrowse/core/util';
+import { ThemeProvider } from '@mui/material';
+import { createJBrowseTheme } from '@jbrowse/core/ui';
+// locals
+import { SVGTracks, SVGRuler, totalHeight, } from '@jbrowse/plugin-linear-genome-view';
+// locals
+import SVGBackground from './SVGBackground';
+import { getTrackName } from '@jbrowse/core/util/tracks';
+import Overlay from '../components/Overlay';
+function getTrackNameMaxLen(views, fontSize, session) {
+    return max(views.flatMap(view => view.tracks.map(t => measureText(getTrackName(t.configuration, session), fontSize))), 0);
+}
+function getTrackOffsets(view, textOffset, extra = 0) {
+    const offsets = {};
+    let curr = textOffset;
+    for (let i = 0; i < view.tracks.length; i++) {
+        const track = view.tracks[i];
+        offsets[track.configuration.trackId] = curr + extra;
+        curr += track.displays[0].height + textOffset;
+    }
+    return offsets;
+}
+// render LGV to SVG
+export async function renderToSvg(model, opts) {
+    var _a;
+    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', 
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    Wrapper = ({ children }) => React.createElement(React.Fragment, null, children), themeName = 'default', } = opts;
+    const session = getSession(model);
+    const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
+    const { width, views } = model;
+    const shift = 50;
+    const offset = headerHeight + rulerHeight;
+    const heights = views.map(v => totalHeight(v.tracks, textHeight, trackLabels) + offset);
+    const totalHeightSvg = sum(heights) + 100;
+    const displayResults = await Promise.all(views.map(async (view) => ({
+        view,
+        data: await Promise.all(view.tracks.map(async (track) => {
+            const d = track.displays[0];
+            await when(() => (d.ready !== undefined ? d.ready : true));
+            return { track, result: await d.renderSvg({ ...opts, theme }) };
+        })),
+    })));
+    const trackLabelMaxLen = getTrackNameMaxLen(views, fontSize, session) + 40;
+    const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
+    const textOffset = trackLabels === 'offset' ? textHeight : 0;
+    const trackOffsets = [
+        getTrackOffsets(views[0], textOffset, fontSize + offset),
+        getTrackOffsets(views[1], textOffset, fontSize + heights[0] + offset),
+    ];
+    const w = width + trackLabelOffset;
+    const t = createJBrowseTheme(theme);
+    // the xlink namespace is used for rendering <image> tag
+    return renderToStaticMarkup(React.createElement(ThemeProvider, { theme: t },
+        React.createElement(Wrapper, null,
+            React.createElement("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString() },
+                React.createElement(SVGBackground, { width: w, height: totalHeightSvg, shift: shift }),
+                React.createElement("g", { transform: `translate(${shift} ${fontSize})` },
+                    React.createElement("g", { transform: `translate(${trackLabelOffset})` },
+                        React.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[0].assemblyNames.join(', ')),
+                        React.createElement(SVGRuler, { model: displayResults[0].view, fontSize: fontSize })),
+                    React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, offset: offset, trackLabelOffset: trackLabelOffset })),
+                React.createElement("g", { transform: `translate(${shift} ${fontSize + heights[0]})` },
+                    React.createElement("g", { transform: `translate(${trackLabelOffset})` },
+                        React.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[1].assemblyNames.join(', ')),
+                        React.createElement(SVGRuler, { model: displayResults[1].view, fontSize: fontSize })),
+                    React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, offset: offset, trackLabelOffset: trackLabelOffset })),
+                React.createElement("defs", null,
+                    React.createElement("clipPath", { id: "clip-bsv" },
+                        React.createElement("rect", { x: 0, y: 0, width: width, height: totalHeightSvg }))),
+                React.createElement("g", { transform: `translate(${trackLabelOffset + shift})`, clipPath: "url(#clip-bsv)" }, model.matchedTracks.map(track => (React.createElement(Overlay, { parentRef: { current: null }, key: track.configuration.trackId, model: model, trackId: track.configuration.trackId, getTrackYPosOverride: (id, level) => trackOffsets[level][id] }))))))));
+}
+//# sourceMappingURL=SVGBreakpointSplitView.js.map

package/esm/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js.map

@@ -0,0 +1 @@
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