@jbrowse/plugin-breakpoint-split-view 2.13.1 → 2.15.0

package/dist/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.d.ts

@@ -1,5 +1,7 @@
 import React from 'react';
-declare const BreakpointAlignmentsFeatureDetail: ({ model }: {
-    model: any;
+declare const BreakpointAlignmentsFeatureDetail: ({ model, }: {
+    model: {
+        featureData: Record<string, unknown>;
+    };
 }) => React.JSX.Element;
 export default BreakpointAlignmentsFeatureDetail;

package/dist/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.js

@@ -3,15 +3,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const Paper_1 = __importDefault(require("@mui/material/Paper"));
-const mobx_react_1 = require("mobx-react");
 const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
-const BreakpointAlignmentsFeatureDetail = (0, mobx_react_1.observer)(
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-({ model }) => {
+const BreakpointAlignmentsFeatureDetail = (0, mobx_react_1.observer)(function ({ model, }) {
     const { feature1, feature2 } = JSON.parse(JSON.stringify(model.featureData));
-    return (react_1.default.createElement(Paper_1.default, { "data-testid": "alignment-side-drawer" },
+    return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
         react_1.default.createElement(BaseFeatureDetail_1.BaseCoreDetails, { title: "Feature 1", feature: feature1 }),
         react_1.default.createElement(BaseFeatureDetail_1.BaseCoreDetails, { title: "Feature 2", feature: feature2 }),
         react_1.default.createElement(BaseFeatureDetail_1.BaseAttributes, { title: "Feature 1 attributes", feature: feature1 }),

package/dist/BreakpointSplitView/BreakpointSplitView.js

@@ -52,12 +52,15 @@ class BreakpointSplitViewType extends ViewType_1.default {
             mateRefName = assembly.getCanonicalRefName(mate.refName);
             endPos = mate.start;
         }
+        else {
+            endPos = startPos + 1;
+        }
         if (!mateRefName) {
             throw new Error(`unable to resolve mate refName ${mateRefName} in reference genome`);
         }
         const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
         if (!topRegion || !bottomRegion) {
-            throw new Error(`unable to find the refName for the top or bottom of the breakpoint view`);
+            throw new Error('unable to find the refName for the top or bottom of the breakpoint view');
         }
         const topMarkedRegion = [{ ...topRegion }, { ...topRegion }];
         const bottomMarkedRegion = [{ ...bottomRegion }, { ...bottomRegion }];

package/dist/BreakpointSplitView/components/AlignmentConnections.js

@@ -121,7 +121,11 @@ const AlignmentConnections = (0, mobx_react_1.observer)(function ({ model, track
                         },
                     });
                     (_b = session.showWidget) === null || _b === void 0 ? void 0 : _b.call(session, featureWidget);
-                }, onMouseOver: () => setMouseoverElt(id), onMouseOut: () => setMouseoverElt(undefined) }));
+                }, onMouseOver: () => {
+                    setMouseoverElt(id);
+                }, onMouseOut: () => {
+                    setMouseoverElt(undefined);
+                } }));
         }
         return ret;
     }))) : null;

package/dist/BreakpointSplitView/components/Breakends.js

@@ -107,7 +107,11 @@ const Breakends = (0, mobx_react_1.observer)(function ({ model, trackId, parentR
                             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) }));
+                    }, onMouseOver: () => {
+                        setMouseoverElt(id);
+                    }, onMouseOut: () => {
+                        setMouseoverElt(undefined);
+                    } }));
             }
         }
         return ret;

package/dist/BreakpointSplitView/components/ExportSvgDialog.js

@@ -38,7 +38,7 @@ function TextField2({ children, ...rest }) {
         react_1.default.createElement(material_1.TextField, { ...rest }, children)));
 }
 function useSvgLocal(key, val) {
-    return (0, util_1.useLocalStorage)('svg-' + key, val);
+    return (0, util_1.useLocalStorage)(`svg-${key}`, val);
 }
 function ExportSvgDialog({ model, handleClose, }) {
     const session = (0, util_1.getSession)(model);
@@ -52,19 +52,29 @@ function ExportSvgDialog({ model, handleClose, }) {
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         react_1.default.createElement(material_1.DialogContent, null,
             error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : loading ? (react_1.default.createElement(LoadingMessage, null)) : null,
-            react_1.default.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
-            react_1.default.createElement(TextField2, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
+            react_1.default.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => {
+                    setFilename(event.target.value);
+                } }),
+            react_1.default.createElement(TextField2, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => {
+                    setTrackLabels(event.target.value);
+                } },
                 react_1.default.createElement(material_1.MenuItem, { value: "offset" }, "Offset"),
                 react_1.default.createElement(material_1.MenuItem, { value: "overlay" }, "Overlay"),
                 react_1.default.createElement(material_1.MenuItem, { value: "left" }, "Left"),
                 react_1.default.createElement(material_1.MenuItem, { value: "none" }, "None")),
             react_1.default.createElement("br", null),
-            session.allThemes ? (react_1.default.createElement(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
+            session.allThemes ? (react_1.default.createElement(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => {
+                    setThemeName(event.target.value);
+                } }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
             // @ts-expect-error
             val.name || '(Unknown name)'))))) : null,
-            offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
+            offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => {
+                        setRasterizeLayers(val => !val);
+                    } }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
         react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
                     setLoading(true);
                     setError(undefined);

package/dist/BreakpointSplitView/components/Translocations.js

@@ -102,7 +102,7 @@ const Translocations = (0, mobx_react_1.observer)(function ({ model, trackId, pa
                     'L', // line to
                     x1,
                     y1,
-                    'L', // line to
+                    'L', // line to as const
                     x2,
                     y2,
                     'L', // line to
@@ -115,7 +115,11 @@ const Translocations = (0, mobx_react_1.observer)(function ({ model, trackId, pa
                             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) }));
+                    }, onMouseOver: () => {
+                        setMouseoverElt(id);
+                    }, onMouseOut: () => {
+                        setMouseoverElt(undefined);
+                    } }));
             }
         }
         return ret;

package/dist/BreakpointSplitView/components/util.js

@@ -70,7 +70,10 @@ function hasPairedReads(features) {
 function findMatchingAlt(feat1, feat2) {
     const alts = feat1.get('ALT');
     if (alts) {
-        return new Map(alts === null || alts === void 0 ? void 0 : alts.map(alt => (0, vcf_1.parseBreakend)(alt)).filter(util_1.notEmpty).map(bnd => [bnd.MatePosition, bnd])).get(`${feat2.get('refName')}:${feat2.get('start') + 1}`);
+        return new Map(alts
+            .map(alt => (0, vcf_1.parseBreakend)(alt))
+            .filter(util_1.notEmpty)
+            .map(bnd => [bnd.MatePosition, bnd])).get(`${feat2.get('refName')}:${feat2.get('start') + 1}`);
     }
     return undefined;
 }

package/dist/BreakpointSplitView/model.d.ts

@@ -61,7 +61,7 @@ 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<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").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]>;
     }, {
@@ -77,7 +77,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         minimumBlockWidth: number;
         draggingTrackId: undefined | string;
         volatileError: unknown;
-        afterDisplayedRegionsSetCallbacks: Function[];
+        afterDisplayedRegionsSetCallbacks: (() => void)[];
         scaleFactor: number;
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
@@ -90,7 +90,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
     } & {
-        scaleBarDisplayPrefix(): string;
+        scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
         readonly assemblyErrors: string;
@@ -105,7 +105,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly totalBp: number;
         readonly maxBpPerPx: number;
         readonly minBpPerPx: number;
-        readonly error: {};
+        readonly error: unknown;
         readonly maxOffset: number;
         readonly minOffset: number;
         readonly displayedRegionsTotalPx: number;
@@ -129,9 +129,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
-        setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
-        removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): 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;
         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;
@@ -146,7 +146,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         moveTrackToTop(id: string): void;
         moveTrackToBottom(id: string): void;
         moveTrack(movingId: string, targetId: string): void;
-        closeView(): void;
         toggleTrack(trackId: string): boolean;
         setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
         setShowCenterLine(b: boolean): void;
@@ -166,7 +165,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             variant?: string;
             isLeftEndOfDisplayedRegion?: boolean;
         }[];
-        afterDisplayedRegionsSet(cb: Function): void;
+        afterDisplayedRegionsSet(cb: () => void): void;
         horizontalScroll(distance: number): number;
         center(): void;
         showAllRegions(): void;
@@ -259,7 +258,7 @@ 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<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").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>>;
@@ -323,10 +322,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     removeView(view: LGV): void;
-    /**
-     * #action
-     */
-    closeView(): void;
     /**
      * #action
      */

package/dist/BreakpointSplitView/model.js

@@ -205,7 +205,9 @@ function stateModelFactory(pluginManager) {
          */
         setWidth(newWidth) {
             self.width = newWidth;
-            self.views.forEach(v => v.setWidth(newWidth));
+            self.views.forEach(v => {
+                v.setWidth(newWidth);
+            });
         },
         /**
          * #action
@@ -213,13 +215,6 @@ function stateModelFactory(pluginManager) {
         removeView(view) {
             self.views.remove(view);
         },
-        /**
-         * #action
-         */
-        closeView() {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            (0, mobx_state_tree_1.getParent)(self, 2).removeView(self);
-        },
         /**
          * #action
          */
@@ -254,7 +249,6 @@ function stateModelFactory(pluginManager) {
                     }
                     self.setMatchedTrackFeatures(Object.fromEntries(await Promise.all(self.matchedTracks.map(async (track) => [
                         track.configuration.trackId,
-                        // eslint-disable-next-line @typescript-eslint/no-explicit-any
                         await getBlockFeatures(self, track),
                     ]))));
                 }
@@ -270,20 +264,23 @@ function stateModelFactory(pluginManager) {
         menuItems() {
             return [
                 ...self.views
-                    .map((view, idx) => { var _a; return [idx, (_a = view.menuItems) === null || _a === void 0 ? void 0 : _a.call(view)]; })
-                    .filter(f => !!f[1])
+                    .map((view, idx) => [idx, view.menuItems()])
                     .map(f => ({ label: `View ${f[0] + 1} Menu`, subMenu: f[1] })),
                 {
                     label: 'Show intra-view links',
                     type: 'checkbox',
                     checked: self.showIntraviewLinks,
-                    onClick: () => self.toggleIntraviewLinks(),
+                    onClick: () => {
+                        self.toggleIntraviewLinks();
+                    },
                 },
                 {
                     label: 'Allow clicking alignment squiggles?',
                     type: 'checkbox',
                     checked: self.interactToggled,
-                    onClick: () => self.toggleInteract(),
+                    onClick: () => {
+                        self.toggleInteract();
+                    },
                 },
                 {
                     label: 'Link views',

package/dist/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js

@@ -19,7 +19,6 @@ const util_2 = require("./util");
 async function renderToSvg(model, opts) {
     var _a;
     const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => children, themeName = 'default', } = opts;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     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];

package/esm/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.d.ts

@@ -1,5 +1,7 @@
 import React from 'react';
-declare const BreakpointAlignmentsFeatureDetail: ({ model }: {
-    model: any;
+declare const BreakpointAlignmentsFeatureDetail: ({ model, }: {
+    model: {
+        featureData: Record<string, unknown>;
+    };
 }) => React.JSX.Element;
 export default BreakpointAlignmentsFeatureDetail;

package/esm/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.js

@@ -1,10 +1,8 @@
-import Paper from '@mui/material/Paper';
-import { observer } from 'mobx-react';
 import React from 'react';
+import { Paper } from '@mui/material';
+import { observer } from 'mobx-react';
 import { BaseCoreDetails, BaseAttributes, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
-const BreakpointAlignmentsFeatureDetail = observer(
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-({ model }) => {
+const BreakpointAlignmentsFeatureDetail = observer(function ({ model, }) {
     const { feature1, feature2 } = JSON.parse(JSON.stringify(model.featureData));
     return (React.createElement(Paper, { "data-testid": "alignment-side-drawer" },
         React.createElement(BaseCoreDetails, { title: "Feature 1", feature: feature1 }),

package/esm/BreakpointSplitView/BreakpointSplitView.js

@@ -47,12 +47,15 @@ export default class BreakpointSplitViewType extends ViewType {
             mateRefName = assembly.getCanonicalRefName(mate.refName);
             endPos = mate.start;
         }
+        else {
+            endPos = startPos + 1;
+        }
         if (!mateRefName) {
             throw new Error(`unable to resolve mate refName ${mateRefName} in reference genome`);
         }
         const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
         if (!topRegion || !bottomRegion) {
-            throw new Error(`unable to find the refName for the top or bottom of the breakpoint view`);
+            throw new Error('unable to find the refName for the top or bottom of the breakpoint view');
         }
         const topMarkedRegion = [{ ...topRegion }, { ...topRegion }];
         const bottomMarkedRegion = [{ ...bottomRegion }, { ...bottomRegion }];

package/esm/BreakpointSplitView/components/AlignmentConnections.js

@@ -96,7 +96,11 @@ const AlignmentConnections = observer(function ({ model, trackId, parentRef, get
                         },
                     });
                     (_b = session.showWidget) === null || _b === void 0 ? void 0 : _b.call(session, featureWidget);
-                }, onMouseOver: () => setMouseoverElt(id), onMouseOut: () => setMouseoverElt(undefined) }));
+                }, onMouseOver: () => {
+                    setMouseoverElt(id);
+                }, onMouseOut: () => {
+                    setMouseoverElt(undefined);
+                } }));
         }
         return ret;
     }))) : null;

package/esm/BreakpointSplitView/components/Breakends.js

@@ -82,7 +82,11 @@ const Breakends = observer(function ({ model, trackId, parentRef: ref, getTrackY
                             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) }));
+                    }, onMouseOver: () => {
+                        setMouseoverElt(id);
+                    }, onMouseOut: () => {
+                        setMouseoverElt(undefined);
+                    } }));
             }
         }
         return ret;

package/esm/BreakpointSplitView/components/ExportSvgDialog.js

@@ -12,7 +12,7 @@ function TextField2({ children, ...rest }) {
         React.createElement(TextField, { ...rest }, children)));
 }
 function useSvgLocal(key, val) {
-    return useLocalStorage('svg-' + key, val);
+    return useLocalStorage(`svg-${key}`, val);
 }
 export default function ExportSvgDialog({ model, handleClose, }) {
     const session = getSession(model);
@@ -26,19 +26,29 @@ export default function ExportSvgDialog({ model, handleClose, }) {
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         React.createElement(DialogContent, null,
             error ? (React.createElement(ErrorMessage, { error: error })) : loading ? (React.createElement(LoadingMessage, null)) : null,
-            React.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
-            React.createElement(TextField2, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
+            React.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => {
+                    setFilename(event.target.value);
+                } }),
+            React.createElement(TextField2, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => {
+                    setTrackLabels(event.target.value);
+                } },
                 React.createElement(MenuItem, { value: "offset" }, "Offset"),
                 React.createElement(MenuItem, { value: "overlay" }, "Overlay"),
                 React.createElement(MenuItem, { value: "left" }, "Left"),
                 React.createElement(MenuItem, { value: "none" }, "None")),
             React.createElement("br", null),
-            session.allThemes ? (React.createElement(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key }, 
+            session.allThemes ? (React.createElement(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => {
+                    setThemeName(event.target.value);
+                } }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key }, 
             // @ts-expect-error
             val.name || '(Unknown name)'))))) : null,
-            offscreenCanvas ? (React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (React.createElement(Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
+            offscreenCanvas ? (React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: rasterizeLayers, onChange: () => {
+                        setRasterizeLayers(val => !val);
+                    } }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (React.createElement(Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
             React.createElement(Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
                     setLoading(true);
                     setError(undefined);

package/esm/BreakpointSplitView/components/Translocations.js

@@ -77,7 +77,7 @@ const Translocations = observer(function ({ model, trackId, parentRef: ref, getT
                     'L', // line to
                     x1,
                     y1,
-                    'L', // line to
+                    'L', // line to as const
                     x2,
                     y2,
                     'L', // line to
@@ -90,7 +90,11 @@ const Translocations = observer(function ({ model, trackId, parentRef: ref, getT
                             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) }));
+                    }, onMouseOver: () => {
+                        setMouseoverElt(id);
+                    }, onMouseOut: () => {
+                        setMouseoverElt(undefined);
+                    } }));
             }
         }
         return ret;

package/esm/BreakpointSplitView/components/util.js

@@ -62,7 +62,10 @@ export function hasPairedReads(features) {
 export function findMatchingAlt(feat1, feat2) {
     const alts = feat1.get('ALT');
     if (alts) {
-        return new Map(alts === null || alts === void 0 ? void 0 : alts.map(alt => parseBreakend(alt)).filter(notEmpty).map(bnd => [bnd.MatePosition, bnd])).get(`${feat2.get('refName')}:${feat2.get('start') + 1}`);
+        return new Map(alts
+            .map(alt => parseBreakend(alt))
+            .filter(notEmpty)
+            .map(bnd => [bnd.MatePosition, bnd])).get(`${feat2.get('refName')}:${feat2.get('start') + 1}`);
     }
     return undefined;
 }

package/esm/BreakpointSplitView/model.d.ts

@@ -61,7 +61,7 @@ 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<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").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]>;
     }, {
@@ -77,7 +77,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         minimumBlockWidth: number;
         draggingTrackId: undefined | string;
         volatileError: unknown;
-        afterDisplayedRegionsSetCallbacks: Function[];
+        afterDisplayedRegionsSetCallbacks: (() => void)[];
         scaleFactor: number;
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
@@ -90,7 +90,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
     } & {
-        scaleBarDisplayPrefix(): string;
+        scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
         readonly assemblyErrors: string;
@@ -105,7 +105,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly totalBp: number;
         readonly maxBpPerPx: number;
         readonly minBpPerPx: number;
-        readonly error: {};
+        readonly error: unknown;
         readonly maxOffset: number;
         readonly minOffset: number;
         readonly displayedRegionsTotalPx: number;
@@ -129,9 +129,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
-        setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
-        removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): 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;
         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;
@@ -146,7 +146,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         moveTrackToTop(id: string): void;
         moveTrackToBottom(id: string): void;
         moveTrack(movingId: string, targetId: string): void;
-        closeView(): void;
         toggleTrack(trackId: string): boolean;
         setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
         setShowCenterLine(b: boolean): void;
@@ -166,7 +165,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             variant?: string;
             isLeftEndOfDisplayedRegion?: boolean;
         }[];
-        afterDisplayedRegionsSet(cb: Function): void;
+        afterDisplayedRegionsSet(cb: () => void): void;
         horizontalScroll(distance: number): number;
         center(): void;
         showAllRegions(): void;
@@ -259,7 +258,7 @@ 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<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [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").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").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>>;
@@ -323,10 +322,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     removeView(view: LGV): void;
-    /**
-     * #action
-     */
-    closeView(): void;
     /**
      * #action
      */

package/esm/BreakpointSplitView/model.js

@@ -1,5 +1,5 @@
 import { lazy } from 'react';
-import { types, getParent, onAction, addDisposer, getPath, } from 'mobx-state-tree';
+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';
@@ -176,7 +176,9 @@ export default function stateModelFactory(pluginManager) {
          */
         setWidth(newWidth) {
             self.width = newWidth;
-            self.views.forEach(v => v.setWidth(newWidth));
+            self.views.forEach(v => {
+                v.setWidth(newWidth);
+            });
         },
         /**
          * #action
@@ -184,13 +186,6 @@ export default function stateModelFactory(pluginManager) {
         removeView(view) {
             self.views.remove(view);
         },
-        /**
-         * #action
-         */
-        closeView() {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            getParent(self, 2).removeView(self);
-        },
         /**
          * #action
          */
@@ -225,7 +220,6 @@ export default function stateModelFactory(pluginManager) {
                     }
                     self.setMatchedTrackFeatures(Object.fromEntries(await Promise.all(self.matchedTracks.map(async (track) => [
                         track.configuration.trackId,
-                        // eslint-disable-next-line @typescript-eslint/no-explicit-any
                         await getBlockFeatures(self, track),
                     ]))));
                 }
@@ -241,20 +235,23 @@ export default function stateModelFactory(pluginManager) {
         menuItems() {
             return [
                 ...self.views
-                    .map((view, idx) => { var _a; return [idx, (_a = view.menuItems) === null || _a === void 0 ? void 0 : _a.call(view)]; })
-                    .filter(f => !!f[1])
+                    .map((view, idx) => [idx, view.menuItems()])
                     .map(f => ({ label: `View ${f[0] + 1} Menu`, subMenu: f[1] })),
                 {
                     label: 'Show intra-view links',
                     type: 'checkbox',
                     checked: self.showIntraviewLinks,
-                    onClick: () => self.toggleIntraviewLinks(),
+                    onClick: () => {
+                        self.toggleIntraviewLinks();
+                    },
                 },
                 {
                     label: 'Allow clicking alignment squiggles?',
                     type: 'checkbox',
                     checked: self.interactToggled,
-                    onClick: () => self.toggleInteract(),
+                    onClick: () => {
+                        self.toggleInteract();
+                    },
                 },
                 {
                     label: 'Link views',

package/esm/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js

@@ -13,7 +13,6 @@ import { getTrackNameMaxLen, getTrackOffsets } from './util';
 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;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { createRootFn } = getRoot(model);
     const session = getSession(model);
     const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-breakpoint-split-view",
-  "version": "2.13.1",
+  "version": "2.15.0",
   "description": "JBrowse 2 breakpoint detail split view",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/breakpoint-split-view",
+    "test": "cd ../..; jest --passWithNoTests plugins/breakpoint-split-view",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -37,14 +37,14 @@
   },
   "dependencies": {
     "@gmod/vcf": "^5.0.9",
-    "@mui/icons-material": "^5.0.1",
+    "@mui/icons-material": "^6.0.0",
     "@types/file-saver": "^2.0.1",
     "file-saver": "^2.0.0"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
     "@jbrowse/plugin-linear-genome-view": "^2.0.0",
-    "@mui/material": "^5.0.0",
+    "@mui/material": "^6.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
+  "gitHead": "87eeb1fbf8311dbf88d5e75b5a265f03beffdda8"
 }