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

package/dist/LinearSyntenyDisplay/components/SyntenyContextMenu.js

@@ -39,15 +39,11 @@ function SyntenyContextMenu({ model, onClose, anchorEl, }) {
                     const end = f.get('end');
                     const refName = f.get('refName');
                     const mate = f.get('mate');
-                    view.views[0]
-                        .navToLocString(`${refName}:${start}-${end}`)
-                        .catch(e => {
+                    view.views[0].navToLocString(`${refName}:${start}-${end}`).catch((e) => {
                         console.error(e);
                         (0, util_1.getSession)(model).notifyError(`${e}`, e);
                     });
-                    view.views[1]
-                        .navToLocString(`${mate.refName}:${mate.start}-${mate.end}`)
-                        .catch(e => {
+                    view.views[1].navToLocString(`${mate.refName}:${mate.start}-${mate.end}`).catch((e) => {
                         console.error(e);
                         (0, util_1.getSession)(model).notifyError(`${e}`, e);
                     });

package/dist/LinearSyntenyDisplay/components/SyntenyTooltip.js

@@ -39,7 +39,7 @@ const SyntenyTooltip = (0, mobx_react_1.observer)(function ({ title }) {
     });
     const clientPoint = (0, react_2.useClientPoint)(context);
     const { getFloatingProps } = (0, react_2.useInteractions)([clientPoint]);
-    const popperTheme = (_a = theme === null || theme === void 0 ? void 0 : theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
+    const popperTheme = (_a = theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
     return title ? (react_1.default.createElement(material_1.Portal, { container: (_b = popperTheme === null || popperTheme === void 0 ? void 0 : popperTheme.defaultProps) === null || _b === void 0 ? void 0 : _b.container },
         react_1.default.createElement("div", { className: classes.tooltip, ref: refs.setFloating, style: {
                 ...floatingStyles,

package/dist/LinearSyntenyDisplay/components/util.d.ts

@@ -7,7 +7,9 @@ interface Pos {
 export interface ClickCoord {
     clientX: number;
     clientY: number;
-    feature: any;
+    feature: {
+        f: Feature;
+    };
 }
 interface FeatPos {
     p11: Pos;

package/dist/LinearSyntenyDisplay/drawSynteny.d.ts

@@ -1,5 +1,5 @@
 import { LinearSyntenyDisplayModel } from './model';
 export declare const MAX_COLOR_RANGE: number;
 export declare function getId(r: number, g: number, b: number, unitMultiplier: number): number;
-export declare function drawRef(model: LinearSyntenyDisplayModel, ctx1: CanvasRenderingContext2D, ctx3?: CanvasRenderingContext2D): void;
+export declare function drawRef(model: LinearSyntenyDisplayModel, ctx1: CanvasRenderingContext2D, ctx3?: CanvasRenderingContext2D): undefined;
 export declare function drawMouseoverSynteny(model: LinearSyntenyDisplayModel): void;

package/dist/LinearSyntenyDisplay/drawSynteny.js

@@ -99,7 +99,7 @@ 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
@@ -123,6 +123,7 @@ 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;
                     }
@@ -140,12 +141,12 @@ 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;
                             (0, util_2.draw)(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);
                             if (ctx3) {
                                 ctx3.fillStyle = makeColor(idx);
@@ -173,7 +174,9 @@ function drawRef(model, ctx1, ctx3) {
         ctx2.fillStyle = makeColor(idx);
         // too many click map false positives with colored stroked lines
         (0, util_2.drawMatchSimple)({
-            cb: ctx => ctx.fill(),
+            cb: ctx => {
+                ctx.fill();
+            },
             feature,
             ctx: ctx2,
             drawCurves,
@@ -184,6 +187,7 @@ function drawRef(model, ctx1, ctx3) {
             height,
         });
     }
+    return undefined;
 }
 function drawMouseoverSynteny(model) {
     var _a;
@@ -205,7 +209,9 @@ function drawMouseoverSynteny(model) {
     if (feature1) {
         ctx.fillStyle = 'rgb(0,0,0,0.1)';
         (0, util_2.drawMatchSimple)({
-            cb: ctx => ctx.fill(),
+            cb: ctx => {
+                ctx.fill();
+            },
             feature: feature1,
             ctx,
             oobLimit,
@@ -219,7 +225,9 @@ function drawMouseoverSynteny(model) {
     if (feature2) {
         ctx.strokeStyle = 'rgb(0, 0, 0, 0.9)';
         (0, util_2.drawMatchSimple)({
-            cb: ctx => ctx.stroke(),
+            cb: ctx => {
+                ctx.stroke();
+            },
             feature: feature2,
             ctx,
             oobLimit,

package/dist/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/dist/LinearSyntenyView/components/ExportSvgDialog.js

@@ -34,7 +34,7 @@ function LoadingMessage() {
         react_1.default.createElement(material_1.Typography, { display: "inline" }, "Creating SVG")));
 }
 function useSvgLocal(key, val) {
-    return (0, util_1.useLocalStorage)('svg-' + key, val);
+    return (0, util_1.useLocalStorage)(`svg-${key}`, val);
 }
 function TextField2({ children, ...rest }) {
     return (react_1.default.createElement("div", null,
@@ -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", value: trackLabels, style: { width: 150 }, 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", value: trackLabels, style: { width: 150 }, 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/LinearSyntenyView/components/ImportForm/ImportCustomTrack.js

@@ -130,7 +130,9 @@ const OpenTrack = (0, mobx_react_1.observer)(({ assembly1, assembly2, setSession
     return (react_1.default.createElement(material_1.Paper, { style: { padding: 12 } },
         error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
         react_1.default.createElement(material_1.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_1.default.createElement(material_1.RadioGroup, { value: radioOption, onChange: event => setValue(event.target.value) },
+        react_1.default.createElement(material_1.RadioGroup, { value: radioOption, onChange: event => {
+                setValue(event.target.value);
+            } },
             react_1.default.createElement(material_1.Grid, { container: true, justifyContent: "center" },
                 react_1.default.createElement(material_1.Grid, { item: true },
                     react_1.default.createElement(material_1.FormControlLabel, { value: ".paf", control: react_1.default.createElement(material_1.Radio, null), label: ".paf" })),
@@ -154,10 +156,18 @@ const OpenTrack = (0, mobx_react_1.observer)(({ assembly1, assembly2, setSession
                     react_1.default.createElement("a", { href: "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)" }, "(more info)")),
                 react_1.default.createElement("div", { style: { display: 'flex' } },
                     react_1.default.createElement("div", null,
-                        react_1.default.createElement(ui_1.FileSelector, { name: ".anchors file", description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) })),
+                        react_1.default.createElement(ui_1.FileSelector, { name: ".anchors file", description: "", location: fileLocation, setLocation: loc => {
+                                setFileLocation(loc);
+                            } })),
                     react_1.default.createElement("div", null,
-                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => setBed1Location(loc) })),
+                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => {
+                                setBed1Location(loc);
+                            } })),
                     react_1.default.createElement("div", null,
-                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => setBed2Location(loc) }))))) : (react_1.default.createElement(ui_1.FileSelector, { name: value ? value + ' location' : '', description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) }))))));
+                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => {
+                                setBed2Location(loc);
+                            } }))))) : (react_1.default.createElement(ui_1.FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
+                    setFileLocation(loc);
+                } }))))));
 });
 exports.default = OpenTrack;

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

@@ -57,6 +57,8 @@ const Selector = (0, mobx_react_1.observer)(({ model, assembly1, assembly2, setS
     }, [value, setShowTrackId]);
     return (react_1.default.createElement(material_1.Paper, { style: { padding: 12 } },
         react_1.default.createElement(material_1.Typography, { paragraph: true }, "Select a track from the select box below, the track will be shown when you hit \"Launch\"."),
-        filteredTracks.length ? (react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, filteredTracks.map(track => (react_1.default.createElement(material_1.MenuItem, { key: track.trackId, value: track.trackId }, (0, tracks_1.getTrackName)(track, session)))))) : (react_1.default.createElement(ui_1.ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
+        filteredTracks.length ? (react_1.default.createElement(material_1.Select, { value: value, onChange: event => {
+                setValue(event.target.value);
+            } }, filteredTracks.map(track => (react_1.default.createElement(material_1.MenuItem, { key: track.trackId, value: track.trackId }, (0, tracks_1.getTrackName)(track, session)))))) : (react_1.default.createElement(ui_1.ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
 });
 exports.default = Selector;

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

@@ -55,7 +55,9 @@ function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData,
     return (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(material_1.FormControl, null,
             react_1.default.createElement(material_1.FormLabel, { id: "group-label" }, "(Optional) Select or add a synteny track"),
-            react_1.default.createElement(material_1.RadioGroup, { row: true, value: choice, onChange: event => setChoice(event.target.value), "aria-labelledby": "group-label" },
+            react_1.default.createElement(material_1.RadioGroup, { row: true, value: choice, onChange: event => {
+                    setChoice(event.target.value);
+                }, "aria-labelledby": "group-label" },
                 react_1.default.createElement(material_1.FormControlLabel, { value: "none", control: react_1.default.createElement(material_1.Radio, null), label: "None" }),
                 react_1.default.createElement(material_1.FormControlLabel, { value: "tracklist", control: react_1.default.createElement(material_1.Radio, null), label: "Existing track" }),
                 react_1.default.createElement(material_1.FormControlLabel, { value: "custom", control: react_1.default.createElement(material_1.Radio, null), label: "New track" }))),
@@ -92,8 +94,12 @@ const LinearSyntenyViewImportForm = (0, mobx_react_1.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);
@@ -117,9 +123,13 @@ const LinearSyntenyViewImportForm = (0, mobx_react_1.observer)(function ({ model
                     react_1.default.createElement("p", { style: { textAlign: 'center' } }, "Select assemblies for linear synteny view"),
                     react_1.default.createElement(material_1.Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
                         react_1.default.createElement(material_1.Grid, { item: true },
-                            react_1.default.createElement(ui_1.AssemblySelector, { selected: assembly1, onChange: val => setAssembly1(val), session: session })),
+                            react_1.default.createElement(ui_1.AssemblySelector, { selected: assembly1, onChange: val => {
+                                    setAssembly1(val);
+                                }, session: session })),
                         react_1.default.createElement(material_1.Grid, { item: true },
-                            react_1.default.createElement(ui_1.AssemblySelector, { selected: assembly2, onChange: val => setAssembly2(val), session: session })),
+                            react_1.default.createElement(ui_1.AssemblySelector, { selected: assembly2, onChange: val => {
+                                    setAssembly2(val);
+                                }, session: session })),
                         react_1.default.createElement(material_1.Grid, { item: true },
                             react_1.default.createElement(material_1.FormControl, null,
                                 react_1.default.createElement(material_1.Button, { onClick: onOpenClick, variant: "contained", color: "primary" }, "Launch"))))),

package/dist/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/dist/LinearSyntenyView/model.js

@@ -80,7 +80,9 @@ function stateModelFactory(pluginManager) {
          */
         showAllRegions() {
             (0, mobx_1.transaction)(() => {
-                self.views.forEach(view => view.showAllRegionsInAssembly());
+                self.views.forEach(view => {
+                    view.showAllRegionsInAssembly();
+                });
             });
         },
     }))

package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -25,7 +25,6 @@ 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 } = (0, mobx_state_tree_1.getRoot)(model);
     const heights = views.map(v => (0, plugin_linear_genome_view_1.totalHeight)(v.tracks, textHeight, trackLabels) + offset);
     const totalHeightSvg = (0, util_1.sum)(heights) + synH + 100;
@@ -43,11 +42,14 @@ async function renderToSvg(model, opts) {
     const renderings = await Promise.all(tracks.map(async (track) => {
         const d = track.displays[0];
         await (0, mobx_1.when)(() => (d.ready !== undefined ? d.ready : true));
-        const r = await (0, util_1.renderToAbstractCanvas)(width, synH, { exportSVG: opts }, ctx => (0, drawSynteny_1.drawRef)(d, ctx));
+        const r = await (0, util_1.renderToAbstractCanvas)(width, synH, { exportSVG: opts }, ctx => {
+            (0, drawSynteny_1.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 (0, util_1.getSerializedSvg)({
                     ...r,
@@ -56,9 +58,7 @@ async function renderToSvg(model, opts) {
                 }),
             };
         }
-        else {
-            return r;
-        }
+        return r;
     }));
     const trackLabelMaxLen = (0, util_1.max)(views.flatMap(view => view.tracks.map(t => (0, util_1.measureText)((0, tracks_1.getTrackName)(t.configuration, session), fontSize))), 0) + 40;
     const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
@@ -77,7 +77,9 @@ async function renderToSvg(model, opts) {
                 react_1.default.createElement("defs", null,
                     react_1.default.createElement("clipPath", { id: 'synclip' },
                         react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: synH }))),
-                react_1.default.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize + heights[0]})`, clipPath: `url(#synclip)` }, renderings.map((r, i) => (react_1.default.createElement(util_1.ReactRendering, { key: i, rendering: r })))),
+                react_1.default.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize + heights[0]})`, clipPath: 'url(#synclip)' }, renderings.map((r, i) => (
+                /* biome-ignore lint/suspicious/noArrayIndexKey: */
+                react_1.default.createElement(util_1.ReactRendering, { key: i, rendering: r })))),
                 react_1.default.createElement("g", { transform: `translate(${shift} ${fontSize + heights[0] + synH})` },
                     react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
                         react_1.default.createElement("text", { x: 0, fontSize: fontSize, ...(0, util_1.getFillProps)(theme.palette.text.primary) }, views[1].assemblyNames.join(', ')),

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -44,7 +44,9 @@ function Formatter({ value }) {
                         setCopied(false);
                     }, 700);
                 } }, copied ? 'Copied to clipboard' : 'Copy'),
-            react_1.default.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
+            react_1.default.createElement("button", { type: "button", onClick: () => {
+                    setShow(val => !val);
+                } }, show ? 'Show less' : 'Show more'),
             react_1.default.createElement("div", null, show ? display : `${display.slice(0, 100)}...`)));
     }
     return react_1.default.createElement("div", null, display);

package/dist/util.js

@@ -15,10 +15,11 @@ 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);
 }
 function getTrackPos(view, trackConfigId) {

package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -17,8 +17,12 @@ export default function LaunchSyntenyViewDialog({ model, feature, handleClose, }
     const [windowSize, setWindowSize] = useState('1000');
     return (React.createElement(Dialog, { open: true, title: "Launch synteny view", onClose: handleClose },
         React.createElement(DialogContent, null,
-            inverted ? (React.createElement(FormControlLabel, { className: classes.padding, control: React.createElement(Checkbox, { checked: horizontallyFlip, onChange: event => setHorizontallyFlip(event.target.checked) }), label: "Note: The feature is inverted in orientation on the target\n            sequence. This will result in the lower panel having genomic\n            coordinates decreasing left to right. Horizontally flip?" })) : null,
-            React.createElement(TextField, { label: "Add window size in bp", value: windowSize, onChange: event => setWindowSize(event.target.value) })),
+            inverted ? (React.createElement(FormControlLabel, { className: classes.padding, control: React.createElement(Checkbox, { checked: horizontallyFlip, onChange: event => {
+                        setHorizontallyFlip(event.target.checked);
+                    } }), label: "Note: The feature is inverted in orientation on the target\n            sequence. This will result in the lower panel having genomic\n            coordinates decreasing left to right. Horizontally flip?" })) : null,
+            React.createElement(TextField, { label: "Add window size in bp", value: windowSize, onChange: event => {
+                    setWindowSize(event.target.value);
+                } })),
         React.createElement(DialogActions, null,
             React.createElement(Button, { variant: "contained", onClick: () => {
                     // eslint-disable-next-line @typescript-eslint/no-floating-promises
@@ -39,5 +43,7 @@ export default function LaunchSyntenyViewDialog({ model, feature, handleClose, }
                     })();
                     handleClose();
                 } }, "Submit"),
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"))));
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"))));
 }

package/esm/LGVSyntenyDisplay/components/util.js

@@ -1,6 +1,5 @@
 import { getSession, getContainingTrack, getContainingView, } from '@jbrowse/core/util';
 import { MismatchParser } from '@jbrowse/plugin-alignments';
-import { when } from 'mobx';
 const { parseCigar } = MismatchParser;
 function f(n) {
     return Math.floor(n);
@@ -15,7 +14,7 @@ function findPosInCigar(cigar, startX) {
         if (featX >= startX) {
             break;
         }
-        else if (op === 'I') {
+        if (op === 'I') {
             mateX += len;
         }
         else if (op === 'D') {
@@ -33,6 +32,9 @@ export async function navToSynteny({ feature, windowSize: ws, model, horizontall
     const track = getContainingTrack(model);
     const view = getContainingView(model);
     const reg = view.dynamicBlocks.contentBlocks[0];
+    if (!reg) {
+        throw new Error('no visible region');
+    }
     const cigar = feature.get('CIGAR');
     const strand = feature.get('strand');
     const regStart = reg.start;
@@ -99,7 +101,6 @@ export async function navToSynteny({ feature, windowSize: ws, model, horizontall
     const m1 = Math.min(rMateStart, rMateEnd);
     const m2 = Math.max(rMateStart, rMateEnd);
     const l2 = `${mateRef}:${f(m1 - ws)}-${f(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
-    await when(() => view2.width !== undefined);
     await Promise.all([
         view2.views[0].navToLocString(l1, featAsm),
         view2.views[1].navToLocString(l2, mateAsm),

package/esm/LGVSyntenyDisplay/model.d.ts

@@ -117,7 +117,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             tag: import("mobx-state-tree").ISimpleType<string>;
-            value: import("mobx-state-tree").ISimpleType<string>;
+            value: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
@@ -153,7 +153,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
             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<{
@@ -263,7 +263,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     readonly autorunReady: boolean;
 } & {
     setTagsReady(flag: boolean): void;
-    setMaxHeight(n: number): void;
+    setMaxHeight(n?: number): void;
     setFeatureHeight(n?: number): void;
     setNoSpacing(flag?: boolean): void;
     setColorScheme(colorScheme: {
@@ -329,6 +329,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
+        priority: number;
         onClick: () => void;
     })[];
 } & {