@jbrowse/plugin-linear-comparative-view 2.13.0 → 2.14.0

package/esm/LinearSyntenyDisplay/drawSynteny.js

@@ -93,7 +93,7 @@ export function drawRef(model, ctx1, ctx3) {
             // cx1/cx2 are the current x positions on top and bottom rows
             let cx1 = k1;
             let cx2 = s1 === -1 ? x22 : x21;
-            if ((cigar === null || cigar === void 0 ? void 0 : cigar.length) && drawCIGAR) {
+            if (cigar.length && drawCIGAR) {
                 // continuingFlag skips drawing commands on very small CIGAR features
                 let continuingFlag = false;
                 // px1/px2 are the previous x positions on the top and bottom rows
@@ -117,6 +117,7 @@ export function drawRef(model, ctx1, ctx3) {
                     else if (op === 'D' || op === 'N') {
                         cx1 += d1 * rev1;
                     }
+                    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                     else if (op === 'I') {
                         cx2 += d2 * rev2;
                     }
@@ -134,12 +135,12 @@ export function drawRef(model, ctx1, ctx3) {
                             continuingFlag = true;
                         }
                         else {
-                            continuingFlag = false;
-                            // allow rendering the dominant color when using continuing
-                            // flag if the last element of continuing was a large
-                            // feature, else just use match
+                            // allow rendering the dominant color when using continuing flag
+                            // if the last element of continuing was a large feature, else
+                            // just use match
                             ctx1.fillStyle =
                                 colorMap[(continuingFlag && d1 > 1) || d2 > 1 ? op : 'M'];
+                            continuingFlag = false;
                             draw(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);
                             if (ctx3) {
                                 ctx3.fillStyle = makeColor(idx);
@@ -167,7 +168,9 @@ export function drawRef(model, ctx1, ctx3) {
         ctx2.fillStyle = makeColor(idx);
         // too many click map false positives with colored stroked lines
         drawMatchSimple({
-            cb: ctx => ctx.fill(),
+            cb: ctx => {
+                ctx.fill();
+            },
             feature,
             ctx: ctx2,
             drawCurves,
@@ -178,6 +181,7 @@ export function drawRef(model, ctx1, ctx3) {
             height,
         });
     }
+    return undefined;
 }
 export function drawMouseoverSynteny(model) {
     var _a;
@@ -199,7 +203,9 @@ export function drawMouseoverSynteny(model) {
     if (feature1) {
         ctx.fillStyle = 'rgb(0,0,0,0.1)';
         drawMatchSimple({
-            cb: ctx => ctx.fill(),
+            cb: ctx => {
+                ctx.fill();
+            },
             feature: feature1,
             ctx,
             oobLimit,
@@ -213,7 +219,9 @@ export function drawMouseoverSynteny(model) {
     if (feature2) {
         ctx.strokeStyle = 'rgb(0, 0, 0, 0.9)';
         drawMatchSimple({
-            cb: ctx => ctx.stroke(),
+            cb: ctx => {
+                ctx.stroke();
+            },
             feature: feature2,
             ctx,
             oobLimit,

package/esm/LinearSyntenyDisplay/model.d.ts

@@ -57,7 +57,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
@@ -77,7 +77,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree" /**
+         * #action
+         */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
@@ -138,7 +140,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-                onHorizontalScroll?: Function;
+                onHorizontalScroll?: () => void;
                 blockState?: Record<string, any>;
             }>;
             readonly DisplayBlurb: import("react").FC<{
@@ -158,7 +160,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                }, import("mobx-state-tree" /**
+                 * #action
+                 */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: any;
@@ -208,7 +212,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-                onHorizontalScroll?: Function;
+                onHorizontalScroll?: () => void;
                 blockState?: Record<string, any>;
             }>;
             readonly DisplayBlurb: import("react").FC<{

package/esm/LinearSyntenyView/components/ExportSvgDialog.js

@@ -8,7 +8,7 @@ function LoadingMessage() {
         React.createElement(Typography, { display: "inline" }, "Creating SVG")));
 }
 function useSvgLocal(key, val) {
-    return useLocalStorage('svg-' + key, val);
+    return useLocalStorage(`svg-${key}`, val);
 }
 function TextField2({ children, ...rest }) {
     return (React.createElement("div", null,
@@ -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", value: trackLabels, style: { width: 150 }, 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", value: trackLabels, style: { width: 150 }, 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/LinearSyntenyView/components/ImportForm/ImportCustomTrack.js

@@ -105,7 +105,9 @@ const OpenTrack = observer(({ assembly1, assembly2, setSessionTrackData, }) => {
     return (React.createElement(Paper, { style: { padding: 12 } },
         error ? React.createElement(ErrorMessage, { error: error }) : null,
         React.createElement(Typography, { style: { textAlign: 'center' } }, "Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or .anchors.simple (MCScan) file to view in the dotplot. These file types can also be gzipped. The first assembly should be the query sequence (e.g. left column of the PAF) and the second assembly should be the target sequence (e.g. right column of the PAF)"),
-        React.createElement(RadioGroup, { value: radioOption, onChange: event => setValue(event.target.value) },
+        React.createElement(RadioGroup, { value: radioOption, onChange: event => {
+                setValue(event.target.value);
+            } },
             React.createElement(Grid, { container: true, justifyContent: "center" },
                 React.createElement(Grid, { item: true },
                     React.createElement(FormControlLabel, { value: ".paf", control: React.createElement(Radio, null), label: ".paf" })),
@@ -129,10 +131,18 @@ const OpenTrack = observer(({ assembly1, assembly2, setSessionTrackData, }) => {
                     React.createElement("a", { href: "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)" }, "(more info)")),
                 React.createElement("div", { style: { display: 'flex' } },
                     React.createElement("div", null,
-                        React.createElement(FileSelector, { name: ".anchors file", description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) })),
+                        React.createElement(FileSelector, { name: ".anchors file", description: "", location: fileLocation, setLocation: loc => {
+                                setFileLocation(loc);
+                            } })),
                     React.createElement("div", null,
-                        React.createElement(FileSelector, { name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => setBed1Location(loc) })),
+                        React.createElement(FileSelector, { name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => {
+                                setBed1Location(loc);
+                            } })),
                     React.createElement("div", null,
-                        React.createElement(FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => setBed2Location(loc) }))))) : (React.createElement(FileSelector, { name: value ? value + ' location' : '', description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) }))))));
+                        React.createElement(FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => {
+                                setBed2Location(loc);
+                            } }))))) : (React.createElement(FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
+                    setFileLocation(loc);
+                } }))))));
 });
 export default OpenTrack;

package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelector.js

@@ -32,6 +32,8 @@ const Selector = observer(({ model, assembly1, assembly2, setShowTrackId, }) =>
     }, [value, setShowTrackId]);
     return (React.createElement(Paper, { style: { padding: 12 } },
         React.createElement(Typography, { paragraph: true }, "Select a track from the select box below, the track will be shown when you hit \"Launch\"."),
-        filteredTracks.length ? (React.createElement(Select, { value: value, onChange: event => setValue(event.target.value) }, filteredTracks.map(track => (React.createElement(MenuItem, { key: track.trackId, value: track.trackId }, getTrackName(track, session)))))) : (React.createElement(ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
+        filteredTracks.length ? (React.createElement(Select, { value: value, onChange: event => {
+                setValue(event.target.value);
+            } }, filteredTracks.map(track => (React.createElement(MenuItem, { key: track.trackId, value: track.trackId }, getTrackName(track, session)))))) : (React.createElement(ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
 });
 export default Selector;

package/esm/LinearSyntenyView/components/ImportForm/index.js

@@ -27,7 +27,9 @@ function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData,
     return (React.createElement(React.Fragment, null,
         React.createElement(FormControl, null,
             React.createElement(FormLabel, { id: "group-label" }, "(Optional) Select or add a synteny track"),
-            React.createElement(RadioGroup, { row: true, value: choice, onChange: event => setChoice(event.target.value), "aria-labelledby": "group-label" },
+            React.createElement(RadioGroup, { row: true, value: choice, onChange: event => {
+                    setChoice(event.target.value);
+                }, "aria-labelledby": "group-label" },
                 React.createElement(FormControlLabel, { value: "none", control: React.createElement(Radio, null), label: "None" }),
                 React.createElement(FormControlLabel, { value: "tracklist", control: React.createElement(Radio, null), label: "Existing track" }),
                 React.createElement(FormControlLabel, { value: "custom", control: React.createElement(Radio, null), label: "New track" }))),
@@ -64,8 +66,12 @@ const LinearSyntenyViewImportForm = observer(function ({ model, }) {
                     displayedRegions: asm.regions,
                 };
             })));
-            model.views.forEach(view => view.setWidth(model.width));
-            model.views.forEach(view => view.showAllRegions());
+            model.views.forEach(view => {
+                view.setWidth(model.width);
+            });
+            model.views.forEach(view => {
+                view.showAllRegions();
+            });
             if (sessionTrackData) {
                 session.addTrackConf(sessionTrackData);
                 model.toggleTrack(sessionTrackData.trackId);
@@ -89,9 +95,13 @@ const LinearSyntenyViewImportForm = observer(function ({ model, }) {
                     React.createElement("p", { style: { textAlign: 'center' } }, "Select assemblies for linear synteny view"),
                     React.createElement(Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
                         React.createElement(Grid, { item: true },
-                            React.createElement(AssemblySelector, { selected: assembly1, onChange: val => setAssembly1(val), session: session })),
+                            React.createElement(AssemblySelector, { selected: assembly1, onChange: val => {
+                                    setAssembly1(val);
+                                }, session: session })),
                         React.createElement(Grid, { item: true },
-                            React.createElement(AssemblySelector, { selected: assembly2, onChange: val => setAssembly2(val), session: session })),
+                            React.createElement(AssemblySelector, { selected: assembly2, onChange: val => {
+                                    setAssembly2(val);
+                                }, session: session })),
                         React.createElement(Grid, { item: true },
                             React.createElement(FormControl, null,
                                 React.createElement(Button, { onClick: onOpenClick, variant: "contained", color: "primary" }, "Launch"))))),

package/esm/LinearSyntenyView/model.d.ts

@@ -54,8 +54,9 @@ 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]>;
     }, {
         width: number;
     } & {
@@ -69,7 +70,7 @@ 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[];
@@ -77,12 +78,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
         rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
     } & {
-        scaleBarDisplayPrefix(): "";
         readonly trackLabelsSetting: any;
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
     } & {
+        scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
         readonly assemblyErrors: string;
@@ -97,7 +98,7 @@ 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;
@@ -112,6 +113,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
         readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
     } & {
+        setShowTrackOutlines(arg: boolean): void;
         setColorByCDS(flag: boolean): void;
         setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
@@ -120,9 +122,9 @@ 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;
@@ -137,7 +139,6 @@ 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;
@@ -157,7 +158,7 @@ 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;
@@ -231,8 +232,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         } | undefined;
     } & {
         afterCreate(): void;
-    } & {
-        scaleBarDisplayPrefix(): string;
     }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         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>>;
@@ -252,8 +251,9 @@ 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>>;
     viewTrackConfigs: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 } & {
@@ -281,7 +281,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     setWidth(newWidth: number): void;
     setViews(views: import("mobx-state-tree").SnapshotIn<import("@jbrowse/plugin-linear-genome-view").LinearGenomeViewModel>[]): void;
     removeView(view: import("@jbrowse/plugin-linear-genome-view").LinearGenomeViewModel): void;
-    closeView(): void;
     setMiddleComparativeHeight(n: number): number;
     activateTrackSelector(): import("@jbrowse/core/util").Widget | undefined;
     toggleTrack(trackId: string): boolean;

package/esm/LinearSyntenyView/model.js

@@ -51,7 +51,9 @@ export default function stateModelFactory(pluginManager) {
          */
         showAllRegions() {
             transaction(() => {
-                self.views.forEach(view => view.showAllRegionsInAssembly());
+                self.views.forEach(view => {
+                    view.showAllRegionsInAssembly();
+                });
             });
         },
     }))

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -19,7 +19,6 @@ export async function renderToSvg(model, opts) {
     const { width, views, middleComparativeHeight: synH, tracks } = model;
     const shift = 50;
     const offset = headerHeight + rulerHeight;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { createRootFn } = getRoot(model);
     const heights = views.map(v => totalHeight(v.tracks, textHeight, trackLabels) + offset);
     const totalHeightSvg = sum(heights) + synH + 100;
@@ -37,11 +36,14 @@ export async function renderToSvg(model, opts) {
     const renderings = await Promise.all(tracks.map(async (track) => {
         const d = track.displays[0];
         await when(() => (d.ready !== undefined ? d.ready : true));
-        const r = await renderToAbstractCanvas(width, synH, { exportSVG: opts }, ctx => drawRef(d, ctx));
+        const r = await renderToAbstractCanvas(width, synH, { exportSVG: opts }, ctx => {
+            drawRef(d, ctx);
+            return undefined;
+        });
         if ('imageData' in r) {
             throw new Error('found a canvas in svg export, probably a bug');
         }
-        else if ('canvasRecordedData' in r) {
+        if ('canvasRecordedData' in r) {
             return {
                 html: await getSerializedSvg({
                     ...r,
@@ -50,9 +52,7 @@ export async function renderToSvg(model, opts) {
                 }),
             };
         }
-        else {
-            return r;
-        }
+        return r;
     }));
     const trackLabelMaxLen = max(views.flatMap(view => view.tracks.map(t => measureText(getTrackName(t.configuration, session), fontSize))), 0) + 40;
     const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
@@ -71,7 +71,9 @@ export async function renderToSvg(model, opts) {
                 React.createElement("defs", null,
                     React.createElement("clipPath", { id: 'synclip' },
                         React.createElement("rect", { x: 0, y: 0, width: width, height: synH }))),
-                React.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize + heights[0]})`, clipPath: `url(#synclip)` }, renderings.map((r, i) => (React.createElement(ReactRendering, { key: i, rendering: r })))),
+                React.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize + heights[0]})`, clipPath: 'url(#synclip)' }, renderings.map((r, i) => (
+                /* biome-ignore lint/suspicious/noArrayIndexKey: */
+                React.createElement(ReactRendering, { key: i, rendering: r })))),
                 React.createElement("g", { transform: `translate(${shift} ${fontSize + heights[0] + synH})` },
                     React.createElement("g", { transform: `translate(${trackLabelOffset})` },
                         React.createElement("text", { x: 0, fontSize: fontSize, ...getFillProps(theme.palette.text.primary) }, views[1].assemblyNames.join(', ')),

package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -16,7 +16,9 @@ function Formatter({ value }) {
                         setCopied(false);
                     }, 700);
                 } }, copied ? 'Copied to clipboard' : 'Copy'),
-            React.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
+            React.createElement("button", { type: "button", onClick: () => {
+                    setShow(val => !val);
+                } }, show ? 'Show less' : 'Show more'),
             React.createElement("div", null, show ? display : `${display.slice(0, 100)}...`)));
     }
     return React.createElement("div", null, display);

package/esm/util.js

@@ -8,10 +8,11 @@ function heightFromSpecificLevel(views, trackConfigId, level) {
         .slice(0, level)
         .map(v => v.height + 7)
         .reduce((a, b) => a + b, 0);
+    const v = views[level];
     return (heightUpUntilThisPoint +
-        views[level].headerHeight +
-        views[level].scaleBarHeight +
-        getTrackPos(views[level], trackConfigId) +
+        v.headerHeight +
+        v.scaleBarHeight +
+        getTrackPos(v, trackConfigId) +
         1);
 }
 export function getTrackPos(view, trackConfigId) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "2.13.0",
+  "version": "2.14.0",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/linear-comparative-view",
+    "test": "cd ../..; jest --passWithNoTests plugins/linear-comparative-view",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -61,5 +61,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "efe02fb9616e20e929cceeed46eb96420c1b6923"
+  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
 }