@jbrowse/plugin-breakpoint-split-view 2.17.0 → 3.0.0

package/esm/BreakpointSplitView/model.d.ts

@@ -1,37 +1,7 @@
-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 declare function getClip(cigar: string, strand: number): number;
-export interface ExportSvgOptions {
-    rasterizeLayers?: boolean;
-    filename?: string;
-    Wrapper?: React.FC<{
-        children: React.ReactNode;
-    }>;
-    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];
-/**
- * #stateModel BreakpointSplitView
- * extends
- * - [BaseViewModel](../baseviewmodel)
- */
+import type { ExportSvgOptions } from './types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Feature } from '@jbrowse/core/util';
+import type { Instance } from 'mobx-state-tree';
 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>>;
@@ -42,7 +12,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     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>;
+    interactiveOverlay: 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>>;
@@ -62,7 +32,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
@@ -83,8 +53,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
-        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
-        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
+        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
+        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
     } & {
         readonly trackLabelsSetting: any;
         readonly width: number;
@@ -94,6 +64,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
+        readonly assembliesNotFound: string | undefined;
         readonly assemblyErrors: string;
         readonly assembliesInitialized: boolean;
         readonly initialized: boolean;
@@ -130,12 +101,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
-        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType[]): void;
-        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
+        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
+        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
+        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
-        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
@@ -152,7 +123,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setShowCenterLine(b: boolean): 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, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
+        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
             start: number;
             end: number;
             type: string;
@@ -174,7 +145,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setDraggingTrackId(idx?: string): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {
@@ -196,15 +167,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
         afterAttach(): void;
     } & {
-        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         navToLocString(input: string, optAssemblyName?: string): Promise<void>;
         navToSearchString({ input, assembly, }: {
             input: string;
             assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
         }): Promise<void>;
         navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): 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;
+        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
+        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
     } & {
         rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
         bpToPx({ refName, coord, regionNumber, }: {
@@ -259,7 +230,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }>>, import("mobx-state-tree")._NotCustomized>>;
@@ -275,89 +246,34 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     width: number;
     matchedTrackFeatures: Record<string, Feature[][]>;
 } & {
-    /**
-     * #method
-     * creates an svg export and save using FileSaver
-     */
     exportSvg(opts?: ExportSvgOptions): Promise<void>;
 } & {
-    /**
-     * #getter
-     * Find all track ids that match across multiple views, or return just
-     * the single view's track if only a single row is used
-     */
     readonly matchedTracks: (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>>) | {
         configuration: {
             trackId: string;
         };
     }[];
-    /**
-     * #method
-     * Get tracks with a given trackId across multiple views
-     */
     getMatchedTracks(trackConfigId: string): any[];
-    /**
-     * #method
-     * Translocation features are handled differently since they do not have
-     * a mate e.g. they are one sided
-     */
     hasTranslocations(trackConfigId: string): Feature | undefined;
-    /**
-     * #method
-     * Paired features similar to breakends, but simpler, like BEDPE
-     */
     hasPairedFeatures(trackConfigId: string): Feature | undefined;
-    /**
-     * #method
-     * Get a composite map of featureId-\>feature map for a track across
-     * multiple views
-     */
     getTrackFeatures(trackConfigId: string): Map<string, Feature>;
-    /**
-     * #method
-     */
     getMatchedFeaturesInLayout(trackConfigId: string, features: Feature[][]): {
         feature: Feature;
-        layout: LayoutRecord | undefined;
+        layout: import("./types").LayoutRecord | undefined;
         level: number;
         clipPos: number;
     }[][];
 } & {
     afterAttach(): void;
     onSubviewAction(actionName: string, path: string, args?: unknown[]): void;
-    /**
-     * #action
-     */
     setWidth(newWidth: number): void;
-    /**
-     * #action
-     */
-    removeView(view: LGV): void;
-    /**
-     * #action
-     */
-    toggleInteract(): void;
-    /**
-     * #action
-     */
-    toggleIntraviewLinks(): void;
-    /**
-     * #action
-     */
-    toggleLinkViews(): void;
-    /**
-     * #action
-     */
+    setInteractiveOverlay(arg: boolean): void;
+    setShowIntraviewLinks(arg: boolean): void;
+    setLinkViews(arg: boolean): void;
     setMatchedTrackFeatures(obj: Record<string, Feature[][]>): void;
-    /**
-     * #action
-     */
     reverseViewOrder(): void;
 } & {
     afterAttach(): void;
-    /**
-     * #method
-     */
     menuItems(): ({
         label: string;
         subMenu: import("@jbrowse/core/ui").MenuItem[];
@@ -393,4 +309,3 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
 }, 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

@@ -1,84 +1,24 @@
 import { lazy } from 'react';
-import { types, 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
+import PhotoCamera from '@mui/icons-material/PhotoCamera';
+import { saveAs } from 'file-saver';
+import { autorun } from 'mobx';
+import { addDisposer, getPath, onAction, types } from 'mobx-state-tree';
+import { calc, getBlockFeatures, getClip, intersect } from './util';
 const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
-const startClip = new RegExp(/(\d+)[SH]$/);
-const endClip = new RegExp(/^(\d+)([SH])/);
-export function getClip(cigar, strand) {
-    return strand === -1
-        ? +(startClip.exec(cigar) || [])[1] || 0
-        : +(endClip.exec(cigar) || [])[1] || 0;
-}
-function calc(track, f) {
-    var _a, _b;
-    return (_b = (_a = track.displays[0]).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, f.id());
-}
-async function getBlockFeatures(model, track) {
-    var _a;
-    const { views } = model;
-    const { rpcManager, assemblyManager } = getSession(model);
-    const assemblyName = (_a = model.views[0]) === null || _a === void 0 ? void 0 : _a.assemblyNames[0];
-    if (!assemblyName) {
-        return undefined;
-    }
-    const assembly = await assemblyManager.waitForAssembly(assemblyName);
-    if (!assembly) {
-        return undefined; // throw new Error(`assembly not found: "${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()));
-}
-/**
- * #stateModel BreakpointSplitView
- * extends
- * - [BaseViewModel](../baseviewmodel)
- */
 export default function stateModelFactory(pluginManager) {
     const minHeight = 40;
     const defaultHeight = 400;
     return types
         .compose('BreakpointSplitView', BaseViewModel, types.model({
-        /**
-         * #property
-         */
         type: types.literal('BreakpointSplitView'),
-        /**
-         * #property
-         */
         height: types.optional(types.refinement('viewHeight', types.number, (n) => n >= minHeight), defaultHeight),
-        /**
-         * #property
-         */
         trackSelectorType: 'hierarchical',
-        /**
-         * #property
-         */
         showIntraviewLinks: true,
-        /**
-         * #property
-         */
         linkViews: false,
-        /**
-         * #property
-         */
-        interactToggled: false,
-        /**
-         * #property
-         */
+        interactiveOverlay: true,
         views: types.array(pluginManager.getViewType('LinearGenomeView')
             .stateModel),
     }))
@@ -87,10 +27,6 @@ export default function stateModelFactory(pluginManager) {
         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);
@@ -99,54 +35,27 @@ export default function stateModelFactory(pluginManager) {
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         * Find all track ids that match across multiple views, or return just
-         * the single view's track if only a single row is used
-         */
         get matchedTracks() {
             return self.views.length === 1
                 ? self.views[0].tracks
                 : intersect(elt => elt.configuration.trackId, ...self.views.map(view => view.tracks));
         },
-        /**
-         * #method
-         * Get tracks with a given trackId across multiple views
-         */
         getMatchedTracks(trackConfigId) {
             return self.views
                 .map(view => view.getTrack(trackConfigId))
                 .filter(f => !!f);
         },
-        /**
-         * #method
-         * 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');
         },
-        /**
-         * #method
-         * Paired features similar to breakends, but simpler, like BEDPE
-         */
         hasPairedFeatures(trackConfigId) {
             return [...this.getTrackFeatures(trackConfigId).values()].find(f => f.get('type') === 'paired_feature');
         },
-        /**
-         * #method
-         * 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]));
         },
-        /**
-         * #method
-         */
         getMatchedFeaturesInLayout(trackConfigId, features) {
-            // use reverse to search the second track first
             const tracks = this.getMatchedTracks(trackConfigId);
             return features.map(c => c
                 .map(feature => {
@@ -187,53 +96,28 @@ export default function stateModelFactory(pluginManager) {
             self.views.forEach(view => {
                 const ret = getPath(view);
                 if (!ret.endsWith(path)) {
-                    // @ts-ignore
                     view[actionName](args === null || args === void 0 ? void 0 : args[0]);
                 }
             });
         },
-        /**
-         * #action
-         */
         setWidth(newWidth) {
             self.width = newWidth;
             self.views.forEach(v => {
                 v.setWidth(newWidth);
             });
         },
-        /**
-         * #action
-         */
-        removeView(view) {
-            self.views.remove(view);
+        setInteractiveOverlay(arg) {
+            self.interactiveOverlay = arg;
         },
-        /**
-         * #action
-         */
-        toggleInteract() {
-            self.interactToggled = !self.interactToggled;
+        setShowIntraviewLinks(arg) {
+            self.showIntraviewLinks = arg;
         },
-        /**
-         * #action
-         */
-        toggleIntraviewLinks() {
-            self.showIntraviewLinks = !self.showIntraviewLinks;
+        setLinkViews(arg) {
+            self.linkViews = arg;
         },
-        /**
-         * #action
-         */
-        toggleLinkViews() {
-            self.linkViews = !self.linkViews;
-        },
-        /**
-         * #action
-         */
         setMatchedTrackFeatures(obj) {
             self.matchedTrackFeatures = obj;
         },
-        /**
-         * #action
-         */
         reverseViewOrder() {
             self.views.reverse();
         },
@@ -256,9 +140,6 @@ export default function stateModelFactory(pluginManager) {
                 }
             }));
         },
-        /**
-         * #method
-         */
         menuItems() {
             return [
                 ...self.views
@@ -267,26 +148,30 @@ export default function stateModelFactory(pluginManager) {
                     label: `Row ${f[0] + 1} view menu`,
                     subMenu: f[1],
                 })),
-                {
-                    label: 'Reverse view order',
-                    onClick: () => {
-                        self.reverseViewOrder();
-                    },
-                },
+                ...(self.views.length > 1
+                    ? [
+                        {
+                            label: 'Reverse view order',
+                            onClick: () => {
+                                self.reverseViewOrder();
+                            },
+                        },
+                    ]
+                    : []),
                 {
                     label: 'Show intra-view links',
                     type: 'checkbox',
                     checked: self.showIntraviewLinks,
                     onClick: () => {
-                        self.toggleIntraviewLinks();
+                        self.setShowIntraviewLinks(!self.showIntraviewLinks);
                     },
                 },
                 {
                     label: 'Allow clicking alignment squiggles?',
                     type: 'checkbox',
-                    checked: self.interactToggled,
+                    checked: self.interactiveOverlay,
                     onClick: () => {
-                        self.toggleInteract();
+                        self.setInteractiveOverlay(!self.interactiveOverlay);
                     },
                 },
                 {
@@ -295,7 +180,7 @@ export default function stateModelFactory(pluginManager) {
                     icon: LinkIcon,
                     checked: self.linkViews,
                     onClick: () => {
-                        self.toggleLinkViews();
+                        self.setLinkViews(!self.linkViews);
                     },
                 },
                 {
@@ -304,7 +189,10 @@ export default function stateModelFactory(pluginManager) {
                     onClick: () => {
                         getSession(self).queueDialog(handleClose => [
                             ExportSvgDialog,
-                            { model: self, handleClose },
+                            {
+                                model: self,
+                                handleClose,
+                            },
                         ]);
                     },
                 },

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

@@ -1,6 +1,5 @@
-import React from 'react';
 export default function SVGBackground({ width, height, shift, }: {
     width: number;
     height: number;
     shift: number;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/BreakpointSplitView/svgcomponents/SVGBackground.js

@@ -1,7 +1,7 @@
-import React from 'react';
-import { useTheme } from '@mui/material';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { stripAlpha } from '@jbrowse/core/util';
+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: stripAlpha(theme.palette.background.default) }));
+    return (_jsx("rect", { width: width + shift * 2, height: height, fill: stripAlpha(theme.palette.background.default) }));
 }

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

@@ -1,4 +1,5 @@
-import { ExportSvgOptions, BreakpointViewModel } from '../model';
+import type { BreakpointViewModel } from '../model';
+import type { ExportSvgOptions } from '../types';
 type BSV = BreakpointViewModel;
 export declare function renderToSvg(model: BSV, opts: ExportSvgOptions): Promise<string>;
 export {};

package/esm/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js

@@ -1,19 +1,15 @@
-import React from 'react';
-import { when } from 'mobx';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { getSession, renderToStaticMarkup, sum } from '@jbrowse/core/util';
+import { SVGRuler, SVGTracks, totalHeight, } from '@jbrowse/plugin-linear-genome-view';
 import { ThemeProvider } from '@mui/material';
-import { createJBrowseTheme } from '@jbrowse/core/ui';
-import { getRoot } from 'mobx-state-tree';
-import { SVGTracks, SVGRuler, totalHeight, } from '@jbrowse/plugin-linear-genome-view';
-// locals
+import { when } from 'mobx';
 import SVGBackground from './SVGBackground';
-import Overlay from '../components/Overlay';
 import { getTrackNameMaxLen, getTrackOffsets } from './util';
-// render LGV to SVG
+import Overlay from '../components/Overlay';
 export async function renderToSvg(model, opts) {
     var _a;
     const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => children, themeName = 'default', } = opts;
-    const { createRootFn } = getRoot(model);
     const session = getSession(model);
     const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
     const { width, views } = model;
@@ -35,25 +31,5 @@ export async function renderToSvg(model, opts) {
     const trackOffsets = views.map((view, idx) => getTrackOffsets(view, textOffset, fontSize + (idx > 0 ? heights[idx - 1] : 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 }),
-                views[0] ? (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("g", { transform: `translate(0 ${offset})` },
-                        React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, trackLabelOffset: trackLabelOffset })))) : null,
-                views[1] ? (React.createElement("g", { transform: `translate(${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("g", { transform: `translate(0 ${offset})` },
-                        React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, trackLabelOffset: trackLabelOffset })))) : null,
-                React.createElement("defs", null,
-                    React.createElement("clipPath", { id: "clip-bsv" },
-                        React.createElement("rect", { x: 0, y: 0, width: width, height: totalHeightSvg }))),
-                React.createElement("g", { transform: `translate(${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] }))))))), createRootFn);
+    return renderToStaticMarkup(_jsx(ThemeProvider, { theme: t, children: _jsx(Wrapper, { children: _jsxs("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(), children: [_jsx(SVGBackground, { width: w, height: totalHeightSvg, shift: shift }), views[0] ? (_jsxs("g", { transform: `translate(${shift} ${fontSize})`, children: [_jsxs("g", { transform: `translate(${trackLabelOffset})`, children: [_jsx("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary, children: views[0].assemblyNames.join(', ') }), _jsx(SVGRuler, { model: displayResults[0].view, fontSize: fontSize })] }), _jsx("g", { transform: `translate(0 ${offset})`, children: _jsx(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, trackLabelOffset: trackLabelOffset }) })] })) : null, views[1] ? (_jsxs("g", { transform: `translate(${shift} ${fontSize + heights[0]})`, children: [_jsxs("g", { transform: `translate(${trackLabelOffset})`, children: [_jsx("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary, children: views[1].assemblyNames.join(', ') }), _jsx(SVGRuler, { model: displayResults[1].view, fontSize: fontSize })] }), _jsx("g", { transform: `translate(0 ${offset})`, children: _jsx(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, trackLabelOffset: trackLabelOffset }) })] })) : null, _jsx("defs", { children: _jsx("clipPath", { id: "clip-bsv", children: _jsx("rect", { x: 0, y: 0, width: width, height: totalHeightSvg }) }) }), _jsx("g", { transform: `translate(${trackLabelOffset + shift})`, clipPath: "url(#clip-bsv)", children: model.matchedTracks.map(track => (_jsx(Overlay, { parentRef: { current: null }, model: model, trackId: track.configuration.trackId, getTrackYPosOverride: (id, level) => trackOffsets[level][id] }, track.configuration.trackId))) })] }) }) }));
 }

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

@@ -1,4 +1,4 @@
-import { AbstractSessionModel } from '@jbrowse/core/util';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { AbstractSessionModel } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function getTrackNameMaxLen(views: LinearGenomeViewModel[], fontSize: number, session: AbstractSessionModel): number;
 export declare function getTrackOffsets(view: LinearGenomeViewModel, textOffset: number, extra?: number): Record<string, number>;

package/esm/BreakpointSplitView/svgcomponents/util.js

@@ -1,5 +1,4 @@
 import { max, measureText } from '@jbrowse/core/util';
-// locals
 import { getTrackName } from '@jbrowse/core/util/tracks';
 export function getTrackNameMaxLen(views, fontSize, session) {
     return max(views.flatMap(view => view.tracks.map(t => measureText(getTrackName(t.configuration, session), fontSize))), 0);

package/esm/BreakpointSplitView/types.d.ts

@@ -0,0 +1,22 @@
+export interface ExportSvgOptions {
+    rasterizeLayers?: boolean;
+    filename?: string;
+    Wrapper?: React.FC<{
+        children: React.ReactNode;
+    }>;
+    fontSize?: number;
+    rulerHeight?: number;
+    textHeight?: number;
+    paddingHeight?: number;
+    headerHeight?: number;
+    cytobandHeight?: number;
+    trackLabels?: string;
+    themeName?: string;
+}
+export interface Breakend {
+    MateDirection: string;
+    Join: string;
+    Replacement: string;
+    MatePosition: string;
+}
+export type LayoutRecord = [number, number, number, number];

package/esm/BreakpointSplitView/types.js

@@ -0,0 +1 @@
+export {};