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

package/dist/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/dist/BreakpointSplitView/model.js

@@ -15,21 +15,29 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getClip = getClip;
 exports.default = stateModelFactory;
 const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const util_1 = require("@jbrowse/core/util");
 const Link_1 = __importDefault(require("@mui/icons-material/Link"));
@@ -39,36 +47,6 @@ const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const util_2 = require("./util");
 const ExportSvgDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ExportSvgDialog'))));
-const startClip = new RegExp(/(\d+)[SH]$/);
-const endClip = new RegExp(/^(\d+)([SH])/);
-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 } = (0, util_1.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: (0, configuration_1.getConf)(track, ['adapter']),
-        sessionId,
-        regions: view.staticBlocks.contentBlocks,
-    })).flat()));
-}
 function stateModelFactory(pluginManager) {
     const minHeight = 40;
     const defaultHeight = 400;
@@ -79,7 +57,7 @@ function stateModelFactory(pluginManager) {
         trackSelectorType: 'hierarchical',
         showIntraviewLinks: true,
         linkViews: false,
-        interactToggled: false,
+        interactiveOverlay: true,
         views: mobx_state_tree_1.types.array(pluginManager.getViewType('LinearGenomeView')
             .stateModel),
     }))
@@ -120,13 +98,13 @@ function stateModelFactory(pluginManager) {
             const tracks = this.getMatchedTracks(trackConfigId);
             return features.map(c => c
                 .map(feature => {
-                const level = tracks.findIndex(track => calc(track, feature));
+                const level = tracks.findIndex(track => (0, util_2.calc)(track, feature));
                 return level !== -1
                     ? {
                         feature,
-                        layout: calc(tracks[level], feature),
+                        layout: (0, util_2.calc)(tracks[level], feature),
                         level,
-                        clipPos: getClip(feature.get('CIGAR'), feature.get('strand')),
+                        clipPos: (0, util_2.getClip)(feature.get('CIGAR'), feature.get('strand')),
                     }
                     : undefined;
             })
@@ -167,17 +145,14 @@ function stateModelFactory(pluginManager) {
                 v.setWidth(newWidth);
             });
         },
-        removeView(view) {
-            self.views.remove(view);
+        setInteractiveOverlay(arg) {
+            self.interactiveOverlay = arg;
         },
-        toggleInteract() {
-            self.interactToggled = !self.interactToggled;
+        setShowIntraviewLinks(arg) {
+            self.showIntraviewLinks = arg;
         },
-        toggleIntraviewLinks() {
-            self.showIntraviewLinks = !self.showIntraviewLinks;
-        },
-        toggleLinkViews() {
-            self.linkViews = !self.linkViews;
+        setLinkViews(arg) {
+            self.linkViews = arg;
         },
         setMatchedTrackFeatures(obj) {
             self.matchedTrackFeatures = obj;
@@ -195,7 +170,7 @@ function stateModelFactory(pluginManager) {
                     }
                     self.setMatchedTrackFeatures(Object.fromEntries(await Promise.all(self.matchedTracks.map(async (track) => [
                         track.configuration.trackId,
-                        await getBlockFeatures(self, track),
+                        await (0, util_2.getBlockFeatures)(self, track),
                     ]))));
                 }
                 catch (e) {
@@ -212,26 +187,30 @@ 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);
                     },
                 },
                 {
@@ -240,7 +219,7 @@ function stateModelFactory(pluginManager) {
                     icon: Link_1.default,
                     checked: self.linkViews,
                     onClick: () => {
-                        self.toggleLinkViews();
+                        self.setLinkViews(!self.linkViews);
                     },
                 },
                 {
@@ -249,7 +228,10 @@ function stateModelFactory(pluginManager) {
                     onClick: () => {
                         (0, util_1.getSession)(self).queueDialog(handleClose => [
                             ExportSvgDialog,
-                            { model: self, handleClose },
+                            {
+                                model: self,
+                                handleClose,
+                            },
                         ]);
                     },
                 },

package/dist/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/dist/BreakpointSplitView/svgcomponents/SVGBackground.js

@@ -1,13 +1,10 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SVGBackground;
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
 function SVGBackground({ width, height, shift, }) {
     const theme = (0, material_1.useTheme)();
-    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));
+    return ((0, jsx_runtime_1.jsx)("rect", { width: width + shift * 2, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));
 }

package/dist/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/dist/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js

@@ -4,20 +4,18 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderToSvg = renderToSvg;
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const material_1 = require("@mui/material");
 const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const SVGBackground_1 = __importDefault(require("./SVGBackground"));
 const util_2 = require("./util");
 const Overlay_1 = __importDefault(require("../components/Overlay"));
 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 } = (0, mobx_state_tree_1.getRoot)(model);
     const session = (0, util_1.getSession)(model);
     const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
     const { width, views } = model;
@@ -39,24 +37,5 @@ async function renderToSvg(model, opts) {
     const trackOffsets = views.map((view, idx) => (0, util_2.getTrackOffsets)(view, textOffset, fontSize + (idx > 0 ? heights[idx - 1] : 0) + offset));
     const w = width + trackLabelOffset;
     const t = (0, ui_1.createJBrowseTheme)(theme);
-    return (0, util_1.renderToStaticMarkup)(react_1.default.createElement(material_1.ThemeProvider, { theme: t },
-        react_1.default.createElement(Wrapper, null,
-            react_1.default.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_1.default.createElement(SVGBackground_1.default, { width: w, height: totalHeightSvg, shift: shift }),
-                views[0] ? (react_1.default.createElement("g", { transform: `translate(${shift} ${fontSize})` },
-                    react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
-                        react_1.default.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[0].assemblyNames.join(', ')),
-                        react_1.default.createElement(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[0].view, fontSize: fontSize })),
-                    react_1.default.createElement("g", { transform: `translate(0 ${offset})` },
-                        react_1.default.createElement(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, trackLabelOffset: trackLabelOffset })))) : null,
-                views[1] ? (react_1.default.createElement("g", { transform: `translate(${shift} ${fontSize + heights[0]})` },
-                    react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
-                        react_1.default.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[1].assemblyNames.join(', ')),
-                        react_1.default.createElement(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[1].view, fontSize: fontSize })),
-                    react_1.default.createElement("g", { transform: `translate(0 ${offset})` },
-                        react_1.default.createElement(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, trackLabelOffset: trackLabelOffset })))) : null,
-                react_1.default.createElement("defs", null,
-                    react_1.default.createElement("clipPath", { id: "clip-bsv" },
-                        react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: totalHeightSvg }))),
-                react_1.default.createElement("g", { transform: `translate(${trackLabelOffset + shift})`, clipPath: "url(#clip-bsv)" }, model.matchedTracks.map(track => (react_1.default.createElement(Overlay_1.default, { parentRef: { current: null }, key: track.configuration.trackId, model: model, trackId: track.configuration.trackId, getTrackYPosOverride: (id, level) => trackOffsets[level][id] }))))))), createRootFn);
+    return (0, util_1.renderToStaticMarkup)((0, jsx_runtime_1.jsx)(material_1.ThemeProvider, { theme: t, children: (0, jsx_runtime_1.jsx)(Wrapper, { children: (0, jsx_runtime_1.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: [(0, jsx_runtime_1.jsx)(SVGBackground_1.default, { width: w, height: totalHeightSvg, shift: shift }), views[0] ? ((0, jsx_runtime_1.jsxs)("g", { transform: `translate(${shift} ${fontSize})`, children: [(0, jsx_runtime_1.jsxs)("g", { transform: `translate(${trackLabelOffset})`, children: [(0, jsx_runtime_1.jsx)("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary, children: views[0].assemblyNames.join(', ') }), (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[0].view, fontSize: fontSize })] }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${offset})`, children: (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, trackLabelOffset: trackLabelOffset }) })] })) : null, views[1] ? ((0, jsx_runtime_1.jsxs)("g", { transform: `translate(${shift} ${fontSize + heights[0]})`, children: [(0, jsx_runtime_1.jsxs)("g", { transform: `translate(${trackLabelOffset})`, children: [(0, jsx_runtime_1.jsx)("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary, children: views[1].assemblyNames.join(', ') }), (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[1].view, fontSize: fontSize })] }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${offset})`, children: (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, trackLabelOffset: trackLabelOffset }) })] })) : null, (0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: "clip-bsv", children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: width, height: totalHeightSvg }) }) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(${trackLabelOffset + shift})`, clipPath: "url(#clip-bsv)", children: model.matchedTracks.map(track => ((0, jsx_runtime_1.jsx)(Overlay_1.default, { parentRef: { current: null }, model: model, trackId: track.configuration.trackId, getTrackYPosOverride: (id, level) => trackOffsets[level][id] }, track.configuration.trackId))) })] }) }) }));
 }

package/dist/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/dist/BreakpointSplitView/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/dist/BreakpointSplitView/util.d.ts

@@ -1,4 +1,6 @@
-import type { LayoutRecord } from './model';
+import type { LayoutRecord } from './types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 type LGV = LinearGenomeViewModel;
 interface Display {
@@ -7,6 +9,7 @@ interface Display {
     SNPCoverageDisplay?: {
         height: number;
     };
+    searchFeatureByID?: (str: string) => LayoutRecord;
 }
 interface Track {
     displays: Display[];
@@ -16,4 +19,11 @@ export declare function getPxFromCoordinate(view: LGV, refName: string, coord: n
 export declare function yPos(trackId: string, level: number, views: LGV[], tracks: Track[], c: LayoutRecord, getYPosOverride?: (trackId: string, level: number) => number): number;
 export declare const useNextFrame: (variable: unknown) => void;
 export declare function intersect<T>(cb: (l: T) => string, a1?: T[], a2?: T[], ...rest: T[][]): T[];
+export declare function getClip(cigar: string, strand: number): number;
+export declare function calc(track: Track, f: Feature): LayoutRecord | undefined;
+export declare function getBlockFeatures(model: {
+    views: LinearGenomeViewModel[];
+}, track: {
+    configuration: AnyConfigurationModel;
+}): Promise<Feature[][] | undefined>;
 export {};

package/dist/BreakpointSplitView/util.js

@@ -5,7 +5,11 @@ exports.heightFromSpecificLevel = heightFromSpecificLevel;
 exports.getPxFromCoordinate = getPxFromCoordinate;
 exports.yPos = yPos;
 exports.intersect = intersect;
+exports.getClip = getClip;
+exports.calc = calc;
+exports.getBlockFeatures = getBlockFeatures;
 const react_1 = require("react");
+const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const [, TOP, , BOTTOM] = [0, 1, 2, 3];
 function cheight(chunk) {
@@ -47,3 +51,33 @@ function intersect(cb, a1 = [], a2 = [], ...rest) {
     const a12 = a1.filter(value => ids.has(cb(value)));
     return rest.length === 0 ? a12 : intersect(cb, a12, ...rest);
 }
+const startClip = new RegExp(/(\d+)[SH]$/);
+const endClip = new RegExp(/^(\d+)([SH])/);
+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 } = (0, util_1.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: (0, configuration_1.getConf)(track, ['adapter']),
+        sessionId,
+        regions: view.staticBlocks.contentBlocks,
+    })).flat()));
+}

package/esm/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 declare const BreakpointAlignmentsFeatureDetail: ({ model, }: {
     model: {
@@ -7,5 +6,5 @@ declare const BreakpointAlignmentsFeatureDetail: ({ model, }: {
             feature2: SimpleFeatureSerialized;
         };
     };
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default BreakpointAlignmentsFeatureDetail;

package/esm/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.js

@@ -1,14 +1,10 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { BaseAttributes, BaseCoreDetails, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
 const BreakpointAlignmentsFeatureDetail = observer(function ({ model, }) {
     const { featureData } = model;
     const { feature1, feature2 } = structuredClone(featureData);
-    return (React.createElement(Paper, null,
-        React.createElement(BaseCoreDetails, { title: "Feature 1", feature: feature1 }),
-        React.createElement(BaseCoreDetails, { title: "Feature 2", feature: feature2 }),
-        React.createElement(BaseAttributes, { title: "Feature 1 attributes", feature: feature1 }),
-        React.createElement(BaseAttributes, { title: "Feature 2 attributes", feature: feature2 })));
+    return (_jsxs(Paper, { children: [_jsx(BaseCoreDetails, { title: "Feature 1", feature: feature1 }), _jsx(BaseCoreDetails, { title: "Feature 2", feature: feature2 }), _jsx(BaseAttributes, { title: "Feature 1 attributes", feature: feature1 }), _jsx(BaseAttributes, { title: "Feature 2 attributes", feature: feature2 })] }));
 });
 export default BreakpointAlignmentsFeatureDetail;

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

@@ -1,9 +1,8 @@
-import React from 'react';
 import type { BreakpointViewModel } from '../model';
 declare const AlignmentConnections: ({ model, trackId, parentRef, 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 AlignmentConnections;