@jbrowse/plugin-breakpoint-split-view 2.18.0 → 3.0.1

package/esm/BreakpointSplitView/components/PairedFeatures.js

@@ -1,4 +1,5 @@
-import React, { useMemo, useState } from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useMemo, useState } from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { getSnapshot } from 'mobx-state-tree';
@@ -6,7 +7,7 @@ import { getMatchedPairedFeatures } from './util';
 import { getPxFromCoordinate, useNextFrame, yPos } from '../util';
 const [LEFT] = [0, 1, 2, 3];
 const PairedFeatures = observer(function ({ model, trackId, parentRef: ref, getTrackYPosOverride, }) {
-    const { views } = model;
+    const { interactiveOverlay, views } = model;
     const session = getSession(model);
     const { assemblyManager } = session;
     const totalFeatures = model.getTrackFeatures(trackId);
@@ -23,50 +24,50 @@ const PairedFeatures = observer(function ({ model, trackId, parentRef: ref, getT
         const rect = ref.current.getBoundingClientRect();
         yoff = rect.top;
     }
-    return (React.createElement("g", { stroke: "green", strokeWidth: 5, fill: "none", "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
-        const ret = [];
-        for (let i = 0; i < chunk.length - 1; i += 1) {
-            const { layout: c1, feature: f1, level: level1 } = chunk[i];
-            const { layout: c2, feature: f2, level: level2 } = chunk[i + 1];
-            const id = f1.id();
-            if (!c1 || !c2) {
-                return null;
+    return (_jsx("g", { stroke: "green", strokeWidth: 5, fill: "none", "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId, children: layoutMatches.map(chunk => {
+            const ret = [];
+            for (let i = 0; i < chunk.length - 1; i += 1) {
+                const { layout: c1, feature: f1, level: level1 } = chunk[i];
+                const { layout: c2, feature: f2, level: level2 } = chunk[i + 1];
+                const id = f1.id();
+                if (!c1 || !c2) {
+                    return null;
+                }
+                const f1origref = f1.get('refName');
+                const f2origref = f2.get('refName');
+                const f1ref = assembly.getCanonicalRefName(f1origref);
+                const f2ref = assembly.getCanonicalRefName(f2origref);
+                if (!f1ref || !f2ref) {
+                    throw new Error(`unable to find ref for ${f1ref || f2ref}`);
+                }
+                const x1 = getPxFromCoordinate(views[level1], f1ref, c1[LEFT]);
+                const x2 = getPxFromCoordinate(views[level2], f2ref, c2[LEFT]);
+                const tracks = views.map(v => v.getTrack(trackId));
+                const y1 = yPos(trackId, level1, views, tracks, c1, getTrackYPosOverride) -
+                    yoff;
+                const y2 = yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
+                    yoff;
+                const path = [
+                    'M',
+                    x1,
+                    y1,
+                    'L',
+                    x2,
+                    y2,
+                ].join(' ');
+                ret.push(_jsx("path", { d: path, "data-testid": "r2", pointerEvents: interactiveOverlay ? 'auto' : undefined, strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
+                        var _a, _b, _c;
+                        const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
+                            featureData: (_b = totalFeatures.get(id)) === null || _b === void 0 ? void 0 : _b.toJSON(),
+                        });
+                        (_c = session.showWidget) === null || _c === void 0 ? void 0 : _c.call(session, featureWidget);
+                    }, onMouseOver: () => {
+                        setMouseoverElt(id);
+                    }, onMouseOut: () => {
+                        setMouseoverElt(undefined);
+                    } }, JSON.stringify(path)));
             }
-            const f1origref = f1.get('refName');
-            const f2origref = f2.get('refName');
-            const f1ref = assembly.getCanonicalRefName(f1origref);
-            const f2ref = assembly.getCanonicalRefName(f2origref);
-            if (!f1ref || !f2ref) {
-                throw new Error(`unable to find ref for ${f1ref || f2ref}`);
-            }
-            const x1 = getPxFromCoordinate(views[level1], f1ref, c1[LEFT]);
-            const x2 = getPxFromCoordinate(views[level2], f2ref, c2[LEFT]);
-            const tracks = views.map(v => v.getTrack(trackId));
-            const y1 = yPos(trackId, level1, views, tracks, c1, getTrackYPosOverride) -
-                yoff;
-            const y2 = yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
-                yoff;
-            const path = [
-                'M',
-                x1,
-                y1,
-                'L',
-                x2,
-                y2,
-            ].join(' ');
-            ret.push(React.createElement("path", { d: path, "data-testid": "r2", key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
-                    var _a, _b, _c;
-                    const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
-                        featureData: (_b = totalFeatures.get(id)) === null || _b === void 0 ? void 0 : _b.toJSON(),
-                    });
-                    (_c = session.showWidget) === null || _c === void 0 ? void 0 : _c.call(session, featureWidget);
-                }, onMouseOver: () => {
-                    setMouseoverElt(id);
-                }, onMouseOut: () => {
-                    setMouseoverElt(undefined);
-                } }));
-        }
-        return ret;
-    })));
+            return ret;
+        }) }));
 });
 export default PairedFeatures;

package/esm/BreakpointSplitView/components/Translocations.d.ts

@@ -1,9 +1,8 @@
-import React from 'react';
 import type { BreakpointViewModel } from '../model';
 declare const Translocations: ({ model, trackId, parentRef: ref, getTrackYPosOverride, }: {
     model: BreakpointViewModel;
     trackId: string;
-    parentRef: React.RefObject<SVGSVGElement>;
+    parentRef: React.RefObject<SVGSVGElement | null>;
     getTrackYPosOverride?: (trackId: string, level: number) => number;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default Translocations;

package/esm/BreakpointSplitView/components/Translocations.js

@@ -1,4 +1,5 @@
-import React, { useMemo, useState } from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useMemo, useState } from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { getSnapshot } from 'mobx-state-tree';
@@ -17,7 +18,7 @@ function str(s) {
     }
 }
 const Translocations = observer(function ({ model, trackId, parentRef: ref, getTrackYPosOverride, }) {
-    const { views } = model;
+    const { interactiveOverlay, views } = model;
     const session = getSession(model);
     const { assemblyManager } = session;
     const totalFeatures = model.getTrackFeatures(trackId);
@@ -37,60 +38,60 @@ const Translocations = observer(function ({ model, trackId, parentRef: ref, getT
     if (views.length < 2) {
         return null;
     }
-    return (React.createElement("g", { fill: "none", stroke: "green", strokeWidth: 5, "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
-        var _a, _b;
-        const ret = [];
-        for (const { layout: c1, feature: f1, level: level1 } of chunk) {
-            const level2 = level1 === 0 ? 1 : 0;
-            const id = f1.id();
-            if (!c1) {
-                return null;
+    return (_jsx("g", { fill: "none", stroke: "green", strokeWidth: 5, "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId, children: layoutMatches.map(chunk => {
+            var _a, _b;
+            const ret = [];
+            for (const { layout: c1, feature: f1, level: level1 } of chunk) {
+                const level2 = level1 === 0 ? 1 : 0;
+                const id = f1.id();
+                if (!c1) {
+                    return null;
+                }
+                const info = f1.get('INFO');
+                const chr2 = info.CHR2[0];
+                const end2 = info.END[0];
+                const res = (_b = (_a = info.STRANDS) === null || _a === void 0 ? void 0 : _a[0]) === null || _b === void 0 ? void 0 : _b.split('');
+                const [myDirection, mateDirection] = res !== null && res !== void 0 ? res : ['.', '.'];
+                const r = getPxFromCoordinate(views[level2], chr2, end2);
+                if (r) {
+                    const c2 = [r, 0, r + 1, 0];
+                    const x1 = getPxFromCoordinate(views[level1], f1.get('refName'), c1[LEFT]);
+                    const x2 = r;
+                    const reversed1 = views[level1].pxToBp(x1).reversed;
+                    const reversed2 = views[level2].pxToBp(x2).reversed;
+                    const tracks = views.map(v => v.getTrack(trackId));
+                    const y1 = yPos(trackId, level1, views, tracks, c1, getTrackYPosOverride) -
+                        yOffset;
+                    const y2 = yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
+                        yOffset;
+                    const path = [
+                        'M',
+                        x1 - 20 * str(myDirection) * (reversed1 ? -1 : 1),
+                        y1,
+                        'L',
+                        x1,
+                        y1,
+                        'L',
+                        x2,
+                        y2,
+                        'L',
+                        x2 - 20 * str(mateDirection) * (reversed2 ? -1 : 1),
+                        y2,
+                    ].join(' ');
+                    ret.push(_jsx("path", { d: path, pointerEvents: interactiveOverlay ? 'auto' : undefined, strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
+                            var _a, _b;
+                            const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
+                                featureData: (totalFeatures.get(id) || { toJSON: () => { } }).toJSON(),
+                            });
+                            (_b = session.showWidget) === null || _b === void 0 ? void 0 : _b.call(session, featureWidget);
+                        }, onMouseOver: () => {
+                            setMouseoverElt(id);
+                        }, onMouseOut: () => {
+                            setMouseoverElt(undefined);
+                        } }, JSON.stringify(path)));
+                }
             }
-            const info = f1.get('INFO');
-            const chr2 = info.CHR2[0];
-            const end2 = info.END[0];
-            const res = (_b = (_a = info.STRANDS) === null || _a === void 0 ? void 0 : _a[0]) === null || _b === void 0 ? void 0 : _b.split('');
-            const [myDirection, mateDirection] = res !== null && res !== void 0 ? res : ['.', '.'];
-            const r = getPxFromCoordinate(views[level2], chr2, end2);
-            if (r) {
-                const c2 = [r, 0, r + 1, 0];
-                const x1 = getPxFromCoordinate(views[level1], f1.get('refName'), c1[LEFT]);
-                const x2 = r;
-                const reversed1 = views[level1].pxToBp(x1).reversed;
-                const reversed2 = views[level2].pxToBp(x2).reversed;
-                const tracks = views.map(v => v.getTrack(trackId));
-                const y1 = yPos(trackId, level1, views, tracks, c1, getTrackYPosOverride) -
-                    yOffset;
-                const y2 = yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
-                    yOffset;
-                const path = [
-                    'M',
-                    x1 - 20 * str(myDirection) * (reversed1 ? -1 : 1),
-                    y1,
-                    'L',
-                    x1,
-                    y1,
-                    'L',
-                    x2,
-                    y2,
-                    'L',
-                    x2 - 20 * str(mateDirection) * (reversed2 ? -1 : 1),
-                    y2,
-                ].join(' ');
-                ret.push(React.createElement("path", { d: path, key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
-                        var _a, _b;
-                        const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
-                            featureData: (totalFeatures.get(id) || { toJSON: () => { } }).toJSON(),
-                        });
-                        (_b = session.showWidget) === null || _b === void 0 ? void 0 : _b.call(session, featureWidget);
-                    }, onMouseOver: () => {
-                        setMouseoverElt(id);
-                    }, onMouseOut: () => {
-                        setMouseoverElt(undefined);
-                    } }));
-            }
-        }
-        return ret;
-    })));
+            return ret;
+        }) }));
 });
 export default Translocations;

package/esm/BreakpointSplitView/model.d.ts

@@ -1,32 +1,7 @@
-import type React from 'react';
+import type { ExportSvgOptions } from './types';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 import type { Instance } from 'mobx-state-tree';
-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];
 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>>;
@@ -37,7 +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>>;
@@ -57,7 +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]>;
     }, {
@@ -78,8 +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;
@@ -126,12 +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;
@@ -148,7 +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;
@@ -170,7 +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;
     } & {
@@ -192,15 +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, }: {
@@ -255,7 +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>>;
@@ -284,7 +259,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     getTrackFeatures(trackConfigId: string): Map<string, Feature>;
     getMatchedFeaturesInLayout(trackConfigId: string, features: Feature[][]): {
         feature: Feature;
-        layout: LayoutRecord | undefined;
+        layout: import("./types").LayoutRecord | undefined;
         level: number;
         clipPos: number;
     }[][];
@@ -292,10 +267,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     afterAttach(): void;
     onSubviewAction(actionName: string, path: string, args?: unknown[]): void;
     setWidth(newWidth: number): void;
-    removeView(view: LGV): void;
-    toggleInteract(): void;
-    toggleIntraviewLinks(): void;
-    toggleLinkViews(): void;
+    setInteractiveOverlay(arg: boolean): void;
+    setShowIntraviewLinks(arg: boolean): void;
+    setLinkViews(arg: boolean): void;
     setMatchedTrackFeatures(obj: Record<string, Feature[][]>): void;
     reverseViewOrder(): void;
 } & {
@@ -335,4 +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

@@ -1,5 +1,4 @@
 import { lazy } from 'react';
-import { getConf } from '@jbrowse/core/configuration';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { getSession, notEmpty } from '@jbrowse/core/util';
 import LinkIcon from '@mui/icons-material/Link';
@@ -7,38 +6,8 @@ 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 { intersect } from './util';
+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;
-    }
-    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;
@@ -49,7 +18,7 @@ export default function stateModelFactory(pluginManager) {
         trackSelectorType: 'hierarchical',
         showIntraviewLinks: true,
         linkViews: false,
-        interactToggled: false,
+        interactiveOverlay: true,
         views: types.array(pluginManager.getViewType('LinearGenomeView')
             .stateModel),
     }))
@@ -137,17 +106,14 @@ export default function stateModelFactory(pluginManager) {
                 v.setWidth(newWidth);
             });
         },
-        removeView(view) {
-            self.views.remove(view);
-        },
-        toggleInteract() {
-            self.interactToggled = !self.interactToggled;
+        setInteractiveOverlay(arg) {
+            self.interactiveOverlay = arg;
         },
-        toggleIntraviewLinks() {
-            self.showIntraviewLinks = !self.showIntraviewLinks;
+        setShowIntraviewLinks(arg) {
+            self.showIntraviewLinks = arg;
         },
-        toggleLinkViews() {
-            self.linkViews = !self.linkViews;
+        setLinkViews(arg) {
+            self.linkViews = arg;
         },
         setMatchedTrackFeatures(obj) {
             self.matchedTrackFeatures = obj;
@@ -182,26 +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);
                     },
                 },
                 {
@@ -210,7 +180,7 @@ export default function stateModelFactory(pluginManager) {
                     icon: LinkIcon,
                     checked: self.linkViews,
                     onClick: () => {
-                        self.toggleLinkViews();
+                        self.setLinkViews(!self.linkViews);
                     },
                 },
                 {
@@ -219,7 +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 { 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 type { BreakpointViewModel, ExportSvgOptions } 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

@@ -1,17 +1,15 @@
-import React from 'react';
+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 { when } from 'mobx';
-import { getRoot } from 'mobx-state-tree';
 import SVGBackground from './SVGBackground';
 import { getTrackNameMaxLen, getTrackOffsets } from './util';
 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;
@@ -33,24 +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);
-    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))) })] }) }) }));
 }