@jbrowse/plugin-linear-comparative-view 2.13.1 → 2.14.0

package/dist/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -43,8 +43,12 @@ function LaunchSyntenyViewDialog({ model, feature, handleClose, }) {
     const [windowSize, setWindowSize] = (0, react_1.useState)('1000');
     return (react_1.default.createElement(ui_1.Dialog, { open: true, title: "Launch synteny view", onClose: handleClose },
         react_1.default.createElement(material_1.DialogContent, null,
-            inverted ? (react_1.default.createElement(material_1.FormControlLabel, { className: classes.padding, control: react_1.default.createElement(material_1.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_1.default.createElement(material_1.TextField, { label: "Add window size in bp", value: windowSize, onChange: event => setWindowSize(event.target.value) })),
+            inverted ? (react_1.default.createElement(material_1.FormControlLabel, { className: classes.padding, control: react_1.default.createElement(material_1.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_1.default.createElement(material_1.TextField, { label: "Add window size in bp", value: windowSize, onChange: event => {
+                    setWindowSize(event.target.value);
+                } })),
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
                     // eslint-disable-next-line @typescript-eslint/no-floating-promises
@@ -65,5 +69,7 @@ function LaunchSyntenyViewDialog({ model, feature, handleClose, }) {
                     })();
                     handleClose();
                 } }, "Submit"),
-            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"))));
 }

package/dist/LGVSyntenyDisplay/components/util.js

@@ -3,7 +3,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.navToSynteny = navToSynteny;
 const util_1 = require("@jbrowse/core/util");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-const mobx_1 = require("mobx");
 const { parseCigar } = plugin_alignments_1.MismatchParser;
 function f(n) {
     return Math.floor(n);
@@ -18,7 +17,7 @@ function findPosInCigar(cigar, startX) {
         if (featX >= startX) {
             break;
         }
-        else if (op === 'I') {
+        if (op === 'I') {
             mateX += len;
         }
         else if (op === 'D') {
@@ -36,6 +35,9 @@ async function navToSynteny({ feature, windowSize: ws, model, horizontallyFlip,
     const track = (0, util_1.getContainingTrack)(model);
     const view = (0, util_1.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;
@@ -102,7 +104,6 @@ async function navToSynteny({ feature, windowSize: ws, model, horizontallyFlip,
     const m1 = Math.min(rMateStart, rMateEnd);
     const m2 = Math.max(rMateStart, rMateEnd);
     const l2 = `${mateRef}:${f(m1 - ws)}-${f(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
-    await (0, mobx_1.when)(() => view2.width !== undefined);
     await Promise.all([
         view2.views[0].navToLocString(l1, featAsm),
         view2.views[1].navToLocString(l2, mateAsm),

package/dist/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;
     })[];
 } & {

package/dist/LaunchLinearSyntenyView.js

@@ -33,9 +33,13 @@ function LaunchLinearSyntenyView(pluginManager) {
                     throw new Error(`Assembly ${data.assembly} failed to load`);
                 }
                 await view.navToSearchString({ input: loc, assembly: asm });
-                tracks.forEach(track => tryTrack(view, track, idsNotFound));
+                tracks.forEach(track => {
+                    tryTrack(view, track, idsNotFound);
+                });
             }));
-            tracks.forEach(track => tryTrack(model, track, idsNotFound));
+            tracks.forEach(track => {
+                tryTrack(model, track, idsNotFound);
+            });
             if (idsNotFound.length) {
                 throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
             }
@@ -51,7 +55,7 @@ function tryTrack(model, trackId, idsNotFound) {
         model.showTrack(trackId);
     }
     catch (e) {
-        if (`${e}`.match('Could not resolve identifier')) {
+        if (/Could not resolve identifier/.exec(`${e}`)) {
             idsNotFound.push(trackId);
         }
         else {

package/dist/LinearComparativeDisplay/configSchemaF.js

@@ -1,6 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const configuration_1 = require("@jbrowse/core/configuration");
 /**
  * #config LinearComparativeDisplay

package/dist/LinearComparativeDisplay/stateModelFactory.d.ts

@@ -39,7 +39,7 @@ 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<{
@@ -125,7 +125,7 @@ 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<{
@@ -195,7 +195,7 @@ 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/LinearComparativeDisplay/stateModelFactory.js

@@ -77,8 +77,8 @@ function stateModelFactory(configSchema) {
                 }
                 const { features } = args;
                 const existingFeatures = self.features || [];
-                const featIds = new Set(existingFeatures.map(f => f.id()) || []);
-                const newFeatIds = new Set((features === null || features === void 0 ? void 0 : features.map(f => f.id())) || []);
+                const featIds = new Set(existingFeatures.map(f => f.id()));
+                const newFeatIds = new Set(features.map(f => f.id()));
                 let foundNewFeatureNotInExistingMap = false;
                 let foundExistingFeatureNotInNewMap = false;
                 for (const feat of features) {

package/dist/LinearComparativeView/components/Header.js

@@ -78,7 +78,9 @@ const Header = (0, mobx_react_1.observer)(function ({ model }) {
     const anyShowHeaders = model.views.some(view => !view.hideHeader);
     return (react_1.default.createElement("div", { className: classes.headerBar },
         react_1.default.createElement(TrackSelector, { model: model }),
-        react_1.default.createElement(material_1.IconButton, { onClick: event => setMenuAnchorEl(event.currentTarget), className: classes.iconButton },
+        react_1.default.createElement(material_1.IconButton, { onClick: event => {
+                setMenuAnchorEl(event.currentTarget);
+            }, className: classes.iconButton },
             react_1.default.createElement(MoreVert_1.default, null)),
         !anyShowHeaders
             ? model.views.map(view => (react_1.default.createElement("div", { key: view.id, className: classes.searchBox },
@@ -93,6 +95,8 @@ const Header = (0, mobx_react_1.observer)(function ({ model }) {
         menuAnchorEl ? (react_1.default.createElement(ui_1.Menu, { anchorEl: menuAnchorEl, open: true, onMenuItemClick: (_event, callback) => {
                 callback();
                 setMenuAnchorEl(undefined);
-            }, menuItems: model.headerMenuItems(), onClose: () => setMenuAnchorEl(undefined) })) : null));
+            }, menuItems: model.headerMenuItems(), onClose: () => {
+                setMenuAnchorEl(undefined);
+            } })) : null));
 });
 exports.default = Header;

package/dist/LinearComparativeView/components/Rubberband.js

@@ -34,14 +34,10 @@ const util_1 = require("@jbrowse/core/util");
 const ui_1 = require("@jbrowse/core/ui");
 const VerticalGuide_1 = __importDefault(require("./VerticalGuide"));
 const useStyles = (0, mui_1.makeStyles)()(theme => {
-    const { tertiary, primary } = theme.palette;
-    const background = tertiary
-        ? (0, material_1.alpha)(tertiary.main, 0.7)
-        : (0, material_1.alpha)(primary.main, 0.7);
     return {
         rubberband: {
             height: '100%',
-            background,
+            background: (0, material_1.alpha)(theme.palette.tertiary.main, 0.7),
             position: 'absolute',
             zIndex: 10,
             textAlign: 'center',
@@ -53,7 +49,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => {
             minHeight: 8,
         },
         rubberbandText: {
-            color: tertiary ? tertiary.contrastText : primary.contrastText,
+            color: theme.palette.tertiary.contrastText,
         },
         popover: {
             mouseEvents: 'none',
@@ -129,7 +125,7 @@ const LinearComparativeRubberband = (0, mobx_react_1.observer)(function Rubberba
             };
         }
         return () => { };
-    }, [startX, mouseDragging, anchorPosition, model]);
+    }, [startX, mouseDragging, model]);
     (0, react_1.useEffect)(() => {
         if (!mouseDragging &&
             currentX !== undefined &&
@@ -152,7 +148,9 @@ const LinearComparativeRubberband = (0, mobx_react_1.observer)(function Rubberba
     }
     function mouseOut() {
         setGuideX(undefined);
-        model.views.forEach(view => view.setOffsets(undefined, undefined));
+        model.views.forEach(view => {
+            view.setOffsets(undefined, undefined);
+        });
     }
     function handleClose() {
         setAnchorPosition(undefined);
@@ -193,7 +191,9 @@ const LinearComparativeRubberband = (0, mobx_react_1.observer)(function Rubberba
                     horizontal: 'left',
                 }, keepMounted: true, disableRestoreFocus: true }, rightBpOffset.map((l, idx) => (react_1.default.createElement(material_1.Typography, { key: [JSON.stringify(l), idx, 'right'].join('-') }, (0, util_1.stringify)(l, true))))))) : null,
         react_1.default.createElement("div", { ref: rubberbandRef, className: classes.rubberband, style: { left, width } },
-            react_1.default.createElement(material_1.Typography, { variant: "h6", className: classes.rubberbandText }, numOfBpSelected.map((n, i) => (react_1.default.createElement(material_1.Typography, { key: `${n}_${i}` }, `${n.toLocaleString('en-US')}bp`))))),
+            react_1.default.createElement(material_1.Typography, { variant: "h6", className: classes.rubberbandText }, numOfBpSelected.map((n, i) => (
+            /* biome-ignore lint/suspicious/noArrayIndexKey: */
+            react_1.default.createElement(material_1.Typography, { key: `${n}_${i}` }, `${n.toLocaleString('en-US')}bp`))))),
         react_1.default.createElement("div", { className: classes.rubberbandControl, ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent),
         anchorPosition ? (react_1.default.createElement(ui_1.Menu, { anchorReference: "anchorPosition", anchorPosition: {
                 left: anchorPosition.clientX,

package/dist/LinearComparativeView/model.d.ts

@@ -38,7 +38,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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]>;
     }, {
@@ -54,7 +54,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         minimumBlockWidth: number;
         draggingTrackId: undefined | string;
         volatileError: unknown;
-        afterDisplayedRegionsSetCallbacks: Function[];
+        afterDisplayedRegionsSetCallbacks: (() => void)[];
         scaleFactor: number;
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
@@ -67,7 +67,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
     } & {
-        scaleBarDisplayPrefix(): string;
+        scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): import("react").FC<any>;
         HeaderComponent(): import("react").FC<any>;
         readonly assemblyErrors: string;
@@ -82,7 +82,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         readonly totalBp: number;
         readonly maxBpPerPx: number;
         readonly minBpPerPx: number;
-        readonly error: {};
+        readonly error: unknown;
         readonly maxOffset: number;
         readonly minOffset: number;
         readonly displayedRegionsTotalPx: number;
@@ -106,9 +106,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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;
@@ -123,7 +123,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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;
@@ -143,7 +142,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             variant?: string;
             isLeftEndOfDisplayedRegion?: boolean;
         }[];
-        afterDisplayedRegionsSet(cb: Function): void;
+        afterDisplayedRegionsSet(cb: () => void): void;
         horizontalScroll(distance: number): number;
         center(): void;
         showAllRegions(): void;
@@ -236,7 +235,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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>>;
@@ -286,12 +285,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
      * #action
      */
     removeView(view: LinearGenomeViewModel): void;
-    /**
-     * #action
-     * removes the view itself from the state tree entirely by calling the
-     * parent removeView
-     */
-    closeView(): void;
     /**
      * #action
      */

package/dist/LinearComparativeView/model.js

@@ -105,7 +105,9 @@ function stateModelFactory(pluginManager) {
          * #getter
          */
         get initialized() {
-            return (self.width !== undefined &&
+            return (
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+            self.width !== undefined &&
                 self.views.length > 0 &&
                 self.views.every(view => view.initialized));
         },
@@ -161,15 +163,6 @@ function stateModelFactory(pluginManager) {
         removeView(view) {
             self.views.remove(view);
         },
-        /**
-         * #action
-         * removes the view itself from the state tree entirely by calling the
-         * parent removeView
-         */
-        closeView() {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            (0, mobx_state_tree_1.getParent)(self, 2).removeView(self);
-        },
         /**
          * #action
          */
@@ -236,7 +229,9 @@ function stateModelFactory(pluginManager) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const config = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
             const shownTracks = self.tracks.filter(t => t.configuration === config);
-            (0, mobx_1.transaction)(() => shownTracks.forEach(t => self.tracks.remove(t)));
+            (0, mobx_1.transaction)(() => {
+                shownTracks.forEach(t => self.tracks.remove(t));
+            });
             return shownTracks.length;
         },
         /**
@@ -278,8 +273,7 @@ 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: 'Return to import form',
@@ -321,7 +315,9 @@ function stateModelFactory(pluginManager) {
         afterAttach() {
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
                 if (self.width) {
-                    self.views.forEach(v => v.setWidth(self.width));
+                    self.views.forEach(v => {
+                        v.setWidth(self.width);
+                    });
                 }
             }));
         },

package/dist/LinearReadVsRef/LinearReadVsRef.js

@@ -136,7 +136,7 @@ function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
             const totalLength = flags & 2048 ? getLength(suppAlns[0].CIGAR) : getLength(cigar);
             const features = [feat, ...suppAlns];
             features.forEach((f, idx) => {
-                f.refName = (assembly === null || assembly === void 0 ? void 0 : assembly.getCanonicalRefName(f.refName)) || f.refName;
+                f.refName = assembly.getCanonicalRefName(f.refName) || f.refName;
                 f.syntenyId = idx;
                 f.mate.syntenyId = idx;
                 f.mate.uniqueId = `${f.uniqueId}_mate`;
@@ -157,10 +157,10 @@ function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
                 assemblyName: trackAssembly,
             })));
             (_a = session.addTemporaryAssembly) === null || _a === void 0 ? void 0 : _a.call(session, {
-                name: `${readAssembly}`,
+                name: readAssembly,
                 sequence: {
                     type: 'ReferenceSequenceTrack',
-                    name: `Read sequence`,
+                    name: 'Read sequence',
                     trackId: seqTrackId,
                     assemblyNames: [readAssembly],
                     adapter: {
@@ -277,7 +277,9 @@ function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
             react_1.default.createElement(material_1.CircularProgress, null))) : (react_1.default.createElement("div", { className: classes.root },
             primaryFeature.get('flags') & 256 ? (react_1.default.createElement(material_1.Typography, { style: { color: 'orange' } }, "Note: You selected a secondary alignment (which generally does not have SA tags or SEQ fields) so do a full reconstruction of the alignment")) : null,
             react_1.default.createElement(material_1.Typography, null, "Show an extra window size around each part of the split alignment. Using a larger value can allow you to see more genomic context."),
-            react_1.default.createElement(material_1.TextField, { value: windowSize, onChange: event => setWindowSize(event.target.value), label: "Set window size" })))),
+            react_1.default.createElement(material_1.TextField, { value: windowSize, onChange: event => {
+                    setWindowSize(event.target.value);
+                }, label: "Set window size" })))),
         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, { disabled: !primaryFeature, variant: "contained", color: "primary", onClick: onSubmit }, "Submit"))));

package/dist/LinearSyntenyDisplay/afterAttach.js

@@ -72,8 +72,8 @@ function doAfterAttach(self) {
                 ;
                 [f1e, f1s] = [f1s, f1e];
             }
-            const a1 = assemblyManager === null || assemblyManager === void 0 ? void 0 : assemblyManager.get(f.get('assemblyName'));
-            const a2 = assemblyManager === null || assemblyManager === void 0 ? void 0 : assemblyManager.get(mate.assemblyName);
+            const a1 = assemblyManager.get(f.get('assemblyName'));
+            const a2 = assemblyManager.get(mate.assemblyName);
             const r1 = f.get('refName');
             const r2 = mate.refName;
             const ref1 = (a1 === null || a1 === void 0 ? void 0 : a1.getCanonicalRefName(r1)) || r1;

package/dist/LinearSyntenyDisplay/components/Component.js

@@ -57,8 +57,12 @@ function LoadingMessage() {
     const [shown, setShown] = (0, react_1.useState)(false);
     const { classes } = useStyles();
     (0, react_1.useEffect)(() => {
-        const timeout = setTimeout(() => setShown(true), 300);
-        return () => clearTimeout(timeout);
+        const timeout = setTimeout(() => {
+            setShown(true);
+        }, 300);
+        return () => {
+            clearTimeout(timeout);
+        };
     });
     return shown ? (react_1.default.createElement("div", { className: classes.loading },
         react_1.default.createElement(ui_1.LoadingEllipses, null))) : null;

package/dist/LinearSyntenyDisplay/components/LinearSyntenyRendering.js

@@ -69,15 +69,20 @@ const LinearSyntenyRendering = (0, mobx_react_1.observer)(function ({ model, })
     const [mouseInitialDownX, setMouseInitialDownX] = (0, react_1.useState)();
     const [currY, setCurrY] = (0, react_1.useState)();
     const { mouseoverId } = model;
-    // these useCallbacks avoid new refs from being created on any mouseover, etc.
-    const k1 = (0, react_1.useCallback)((ref) => model.setMouseoverCanvasRef(ref), 
+    // these useCallbacks avoid new refs from being created on any mouseover,
+    // etc.
+    // biome-ignore lint/correctness/useExhaustiveDependencies:
+    const k1 = (0, react_1.useCallback)((ref) => {
+        model.setMouseoverCanvasRef(ref);
+    }, 
     // eslint-disable-next-line react-hooks/exhaustive-deps
     [model, height, width]);
+    // biome-ignore lint/correctness/useExhaustiveDependencies:
     const k2 = (0, react_1.useCallback)((ref) => {
         model.setMainCanvasRef(ref);
         function onWheel(event) {
             event.preventDefault();
-            if (event.ctrlKey === true) {
+            if (event.ctrlKey) {
                 delta.current += event.deltaY / 500;
                 for (const v of view.views) {
                     v.setScaleFactor(delta.current < 0 ? 1 - delta.current : 1 / (1 + delta.current));
@@ -112,21 +117,26 @@ const LinearSyntenyRendering = (0, mobx_react_1.observer)(function ({ model, })
                 }
             }
         }
-        if (ref) {
-            ref.addEventListener('wheel', onWheel);
-            // this is a react 19-ism to have a cleanup in the ref callback
-            // https://react.dev/blog/2024/04/25/react-19#cleanup-functions-for-refs
-            // note: it warns in earlier versions of react
-            return () => ref.removeEventListener('wheel', onWheel);
-        }
-        return () => { };
+        ref === null || ref === void 0 ? void 0 : ref.addEventListener('wheel', onWheel);
+        // this is a react 19-ism to have a cleanup in the ref callback
+        // https://react.dev/blog/2024/04/25/react-19#cleanup-functions-for-refs
+        // note: it warns in earlier versions of react
+        return () => {
+            ref === null || ref === void 0 ? void 0 : ref.removeEventListener('wheel', onWheel);
+        };
     }, 
     // eslint-disable-next-line react-hooks/exhaustive-deps
     [model, height, width]);
-    const k3 = (0, react_1.useCallback)((ref) => model.setClickMapCanvasRef(ref), 
+    // biome-ignore lint/correctness/useExhaustiveDependencies:
+    const k3 = (0, react_1.useCallback)((ref) => {
+        model.setClickMapCanvasRef(ref);
+    }, 
     // eslint-disable-next-line react-hooks/exhaustive-deps
     [model, height, width]);
-    const k4 = (0, react_1.useCallback)((ref) => model.setCigarClickMapCanvasRef(ref), 
+    // biome-ignore lint/correctness/useExhaustiveDependencies:
+    const k4 = (0, react_1.useCallback)((ref) => {
+        model.setCigarClickMapCanvasRef(ref);
+    }, 
     // eslint-disable-next-line react-hooks/exhaustive-deps
     [model, height, width]);
     return (react_1.default.createElement("div", { className: classes.rel },
@@ -193,10 +203,14 @@ const LinearSyntenyRendering = (0, mobx_react_1.observer)(function ({ model, })
                     Math.abs(evt.clientX - mouseInitialDownX) < 5) {
                     (0, util_2.onSynClick)(evt, model);
                 }
-            }, onContextMenu: evt => (0, util_2.onSynContextClick)(evt, model, setAnchorEl), "data-testid": "synteny_canvas", className: classes.abs, width: width, height: height }),
+            }, onContextMenu: evt => {
+                (0, util_2.onSynContextClick)(evt, model, setAnchorEl);
+            }, "data-testid": "synteny_canvas", className: classes.abs, width: width, height: height }),
         react_1.default.createElement("canvas", { ref: k3, className: classes.pix, width: width, height: height }),
         react_1.default.createElement("canvas", { ref: k4, className: classes.pix, width: width, height: height }),
         mouseoverId && tooltip && currX && currY ? (react_1.default.createElement(SyntenyTooltip_1.default, { title: tooltip })) : null,
-        anchorEl ? (react_1.default.createElement(SyntenyContextMenu_1.default, { model: model, anchorEl: anchorEl, onClose: () => setAnchorEl(undefined) })) : null));
+        anchorEl ? (react_1.default.createElement(SyntenyContextMenu_1.default, { model: model, anchorEl: anchorEl, onClose: () => {
+                setAnchorEl(undefined);
+            } })) : null));
 });
 exports.default = LinearSyntenyRendering;

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

@@ -1,9 +1,12 @@
 import React from 'react';
+import { Feature } from '@jbrowse/core/util';
 import { LinearSyntenyDisplayModel } from '../model';
 interface ClickCoord {
     clientX: number;
     clientY: number;
-    feature: any;
+    feature: {
+        f: Feature;
+    };
 }
 export default function SyntenyContextMenu({ model, onClose, anchorEl, }: {
     onClose: () => void;

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;