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

package/dist/index.d.ts

@@ -123,7 +123,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     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<{
@@ -360,419 +360,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
         ZoomControls: ({ model, }: {
             model: import("./LinearGenomeView").LinearGenomeViewModel;
         }) => import("react").JSX.Element;
-        LinearGenomeView: ({ model }: {
-            model: {
-                id: string;
-                displayName: string | undefined;
-                minimized: boolean;
-                type: string;
-                offsetPx: number;
-                bpPerPx: number;
-                displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
-                tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
-                hideHeader: boolean;
-                hideHeaderOverview: boolean;
-                hideNoTracksActive: boolean;
-                trackSelectorType: string;
-                showCenterLine: boolean;
-                showCytobandsSetting: boolean;
-                trackLabels: string;
-                showGridlines: boolean;
-                highlight: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>> & import("mobx-state-tree").IStateTreeNode<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]>>;
-                colorByCDS: boolean;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                width: number;
-            } & {
-                menuItems(): import("@jbrowse/core/ui").MenuItem[];
-            } & {
-                setDisplayName(name: string): void;
-                setWidth(newWidth: number): void;
-                setMinimized(flag: boolean): void;
-            } & {
-                volatileWidth: number | undefined;
-                minimumBlockWidth: number;
-                draggingTrackId: undefined | string;
-                volatileError: unknown;
-                afterDisplayedRegionsSetCallbacks: Function[];
-                scaleFactor: number;
-                trackRefs: Record<string, HTMLDivElement>;
-                coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
-                coarseTotalBp: number;
-                leftOffset: undefined | import("./LinearGenomeView").BpOffset;
-                rightOffset: undefined | import("./LinearGenomeView").BpOffset;
-            } & {
-                scaleBarDisplayPrefix(): "";
-                readonly trackLabelsSetting: any;
-                readonly width: number;
-                readonly interRegionPaddingWidth: number;
-                readonly assemblyNames: string[];
-            } & {
-                MiniControlsComponent(): import("react").FC<any>;
-                HeaderComponent(): import("react").FC<any>;
-                readonly assemblyErrors: string;
-                readonly assembliesInitialized: boolean;
-                readonly initialized: boolean;
-                readonly hasDisplayedRegions: boolean;
-                readonly scaleBarHeight: number;
-                readonly headerHeight: number;
-                readonly trackHeights: number;
-                readonly trackHeightsWithResizeHandles: number;
-                readonly height: number;
-                readonly totalBp: number;
-                readonly maxBpPerPx: number;
-                readonly minBpPerPx: number;
-                readonly error: {};
-                readonly maxOffset: number;
-                readonly minOffset: number;
-                readonly displayedRegionsTotalPx: number;
-                renderProps(): any;
-                searchScope(assemblyName: string): {
-                    assemblyName: string;
-                    includeAggregateIndexes: boolean;
-                    tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
-                };
-                getTrack(id: string): any;
-                rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
-                rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
-                readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
-            } & {
-                setColorByCDS(flag: boolean): void;
-                setShowCytobands(flag: boolean): void;
-                setWidth(newWidth: number): void;
-                setError(error: unknown): void;
-                setHideHeader(b: boolean): void;
-                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;
-                scrollTo(offsetPx: number): number;
-                zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
-                setOffsets(left?: import("./LinearGenomeView").BpOffset, right?: import("./LinearGenomeView").BpOffset): void;
-                setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
-                setNewView(bpPerPx: number, offsetPx: number): void;
-                horizontallyFlip(): void;
-                showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
-                hideTrack(trackId: string): number;
-            } & {
-                moveTrackDown(id: string): void;
-                moveTrackUp(id: string): void;
-                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;
-                setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                activateTrackSelector(): import("@jbrowse/core/util").Widget;
-                getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset, rightOffset?: import("./LinearGenomeView").BpOffset): {
-                    start: number;
-                    end: number;
-                    type: string;
-                    regionNumber?: number;
-                    reversed?: boolean;
-                    refName: string;
-                    assemblyName: string;
-                    key: string;
-                    offsetPx: number;
-                    widthPx: number;
-                    variant?: string;
-                    isLeftEndOfDisplayedRegion?: boolean;
-                }[];
-                afterDisplayedRegionsSet(cb: Function): void;
-                horizontalScroll(distance: number): number;
-                center(): void;
-                showAllRegions(): void;
-                showAllRegionsInAssembly(assemblyName?: string): void;
-                setDraggingTrackId(idx?: string): void;
-                setScaleFactor(factor: number): void;
-                clearView(): void;
-                exportSvg(opts?: import("./LinearGenomeView").ExportSvgOptions): Promise<void>;
-            } & {
-                slide: (viewWidths: number) => void;
-            } & {
-                zoom: (targetBpPerPx: number) => void;
-            } & {
-                readonly canShowCytobands: boolean;
-                readonly showCytobands: boolean;
-                readonly anyCytobandsExist: boolean;
-                readonly cytobandOffset: number;
-            } & {
-                menuItems(): import("@jbrowse/core/ui").MenuItem[];
-            } & {
-                readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
-                readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
-                readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
-                readonly visibleLocStrings: string;
-                readonly coarseVisibleLocStrings: string;
-            } & {
-                setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
-                afterAttach(): void;
-            } & {
-                moveTo(start?: import("./LinearGenomeView").BpOffset, end?: import("./LinearGenomeView").BpOffset): void;
-                navToLocString(input: string, optAssemblyName?: string): Promise<void>;
-                navToSearchString({ input, assembly, }: {
-                    input: string;
-                    assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
-                }): Promise<void>;
-                navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
-                navTo(query: import("./LinearGenomeView").NavLocation): void;
-                navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
-            } & {
-                rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-                bpToPx({ refName, coord, regionNumber, }: {
-                    refName: string;
-                    coord: number;
-                    regionNumber?: number;
-                }): {
-                    index: number;
-                    offsetPx: number;
-                } | undefined;
-                centerAt(coord: number, refName: string, regionNumber?: number): void;
-                pxToBp(px: number): {
-                    coord: number;
-                    index: number;
-                    refName: string;
-                    oob: boolean;
-                    assemblyName: string;
-                    offset: number;
-                    start: number;
-                    end: number;
-                    reversed?: boolean;
-                };
-                readonly centerLineInfo: {
-                    coord: number;
-                    index: number;
-                    refName: string;
-                    oob: boolean;
-                    assemblyName: string;
-                    offset: number;
-                    start: number;
-                    end: number;
-                    reversed?: boolean;
-                } | undefined;
-            } & {
-                afterCreate(): void;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-                minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-            } & {
-                id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                type: import("mobx-state-tree").IType<string | undefined, string, string>;
-                offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-                bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-                displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
-                tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
-                hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-                hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-                hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-                trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-                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]>;
-                colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-            }, {
-                width: number;
-            } & {
-                menuItems(): import("@jbrowse/core/ui").MenuItem[];
-            } & {
-                setDisplayName(name: string): void;
-                setWidth(newWidth: number): void;
-                setMinimized(flag: boolean): void;
-            } & {
-                volatileWidth: number | undefined;
-                minimumBlockWidth: number;
-                draggingTrackId: undefined | string;
-                volatileError: unknown;
-                afterDisplayedRegionsSetCallbacks: Function[];
-                scaleFactor: number;
-                trackRefs: Record<string, HTMLDivElement>;
-                coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
-                coarseTotalBp: number;
-                leftOffset: undefined | import("./LinearGenomeView").BpOffset;
-                rightOffset: undefined | import("./LinearGenomeView").BpOffset;
-            } & {
-                scaleBarDisplayPrefix(): "";
-                readonly trackLabelsSetting: any;
-                readonly width: number;
-                readonly interRegionPaddingWidth: number;
-                readonly assemblyNames: string[];
-            } & {
-                MiniControlsComponent(): import("react").FC<any>;
-                HeaderComponent(): import("react").FC<any>;
-                readonly assemblyErrors: string;
-                readonly assembliesInitialized: boolean;
-                readonly initialized: boolean;
-                readonly hasDisplayedRegions: boolean;
-                readonly scaleBarHeight: number;
-                readonly headerHeight: number;
-                readonly trackHeights: number;
-                readonly trackHeightsWithResizeHandles: number;
-                readonly height: number;
-                readonly totalBp: number;
-                readonly maxBpPerPx: number;
-                readonly minBpPerPx: number;
-                readonly error: {};
-                readonly maxOffset: number;
-                readonly minOffset: number;
-                readonly displayedRegionsTotalPx: number;
-                renderProps(): any;
-                searchScope(assemblyName: string): {
-                    assemblyName: string;
-                    includeAggregateIndexes: boolean;
-                    tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
-                };
-                getTrack(id: string): any;
-                rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
-                rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
-                readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
-            } & {
-                setColorByCDS(flag: boolean): void;
-                setShowCytobands(flag: boolean): void;
-                setWidth(newWidth: number): void;
-                setError(error: unknown): void;
-                setHideHeader(b: boolean): void;
-                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;
-                scrollTo(offsetPx: number): number;
-                zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
-                setOffsets(left?: import("./LinearGenomeView").BpOffset, right?: import("./LinearGenomeView").BpOffset): void;
-                setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
-                setNewView(bpPerPx: number, offsetPx: number): void;
-                horizontallyFlip(): void;
-                showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
-                hideTrack(trackId: string): number;
-            } & {
-                moveTrackDown(id: string): void;
-                moveTrackUp(id: string): void;
-                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;
-                setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                activateTrackSelector(): import("@jbrowse/core/util").Widget;
-                getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset, rightOffset?: import("./LinearGenomeView").BpOffset): {
-                    start: number;
-                    end: number;
-                    type: string;
-                    regionNumber?: number;
-                    reversed?: boolean;
-                    refName: string;
-                    assemblyName: string;
-                    key: string;
-                    offsetPx: number;
-                    widthPx: number;
-                    variant?: string;
-                    isLeftEndOfDisplayedRegion?: boolean;
-                }[];
-                afterDisplayedRegionsSet(cb: Function): void;
-                horizontalScroll(distance: number): number;
-                center(): void;
-                showAllRegions(): void;
-                showAllRegionsInAssembly(assemblyName?: string): void;
-                setDraggingTrackId(idx?: string): void;
-                setScaleFactor(factor: number): void;
-                clearView(): void;
-                exportSvg(opts?: import("./LinearGenomeView").ExportSvgOptions): Promise<void>;
-            } & {
-                slide: (viewWidths: number) => void;
-            } & {
-                zoom: (targetBpPerPx: number) => void;
-            } & {
-                readonly canShowCytobands: boolean;
-                readonly showCytobands: boolean;
-                readonly anyCytobandsExist: boolean;
-                readonly cytobandOffset: number;
-            } & {
-                menuItems(): import("@jbrowse/core/ui").MenuItem[];
-            } & {
-                readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
-                readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
-                readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
-                readonly visibleLocStrings: string;
-                readonly coarseVisibleLocStrings: string;
-            } & {
-                setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
-                afterAttach(): void;
-            } & {
-                moveTo(start?: import("./LinearGenomeView").BpOffset, end?: import("./LinearGenomeView").BpOffset): void;
-                navToLocString(input: string, optAssemblyName?: string): Promise<void>;
-                navToSearchString({ input, assembly, }: {
-                    input: string;
-                    assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
-                }): Promise<void>;
-                navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
-                navTo(query: import("./LinearGenomeView").NavLocation): void;
-                navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
-            } & {
-                rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-                bpToPx({ refName, coord, regionNumber, }: {
-                    refName: string;
-                    coord: number;
-                    regionNumber?: number;
-                }): {
-                    index: number;
-                    offsetPx: number;
-                } | undefined;
-                centerAt(coord: number, refName: string, regionNumber?: number): void;
-                pxToBp(px: number): {
-                    coord: number;
-                    index: number;
-                    refName: string;
-                    oob: boolean;
-                    assemblyName: string;
-                    offset: number;
-                    start: number;
-                    end: number;
-                    reversed?: boolean;
-                };
-                readonly centerLineInfo: {
-                    coord: number;
-                    index: number;
-                    refName: string;
-                    oob: boolean;
-                    assemblyName: string;
-                    offset: number;
-                    start: number;
-                    end: number;
-                    reversed?: boolean;
-                } | undefined;
-            } & {
-                afterCreate(): void;
-            }, 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>>;
-                minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-            } & {
-                id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                type: import("mobx-state-tree").IType<string | undefined, string, string>;
-                offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-                bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-                displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
-                tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
-                hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-                hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-                hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-                trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-                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]>;
-                colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-            }>>, import("mobx-state-tree")._NotCustomized>>;
+        LinearGenomeView: ({ model, }: {
+            model: import("./LinearGenomeView").LinearGenomeViewModel;
         }) => import("react").JSX.Element;
     };
     /**

package/dist/searchUtils.js

@@ -27,7 +27,7 @@ async function navToOption({ option, model, assemblyName, }) {
 // 2) if it's a single result navigate to it
 // 3) else assume it's a locstring and navigate to it
 async function handleSelectedRegion({ input, model, assembly, }) {
-    const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNamesWithLowerCase) || [];
+    const allRefs = assembly.allRefNamesWithLowerCase || [];
     const assemblyName = assembly.name;
     if (input.split(' ').every(entry => checkRef(entry, allRefs))) {
         await model.navToLocString(input, assembly.name);
@@ -81,9 +81,7 @@ function splitLast(str, split) {
     if (lastIndex === -1) {
         return [str, ''];
     }
-    else {
-        const before = str.slice(0, lastIndex);
-        const after = str.slice(lastIndex + 1);
-        return [before, after];
-    }
+    const before = str.slice(0, lastIndex);
+    const after = str.slice(lastIndex + 1);
+    return [before, after];
 }

package/esm/BaseLinearDisplay/components/LinearBlocks.js

@@ -39,10 +39,10 @@ const RenderedBlocks = observer(function ({ model, }) {
                         height: 16,
                     } }, "Max height reached")) : null));
         }
-        else if (block.type === 'ElidedBlock') {
+        if (block.type === 'ElidedBlock') {
             return React.createElement(ElidedBlockComponent, { key: key, width: block.widthPx });
         }
-        else if (block.type === 'InterRegionPaddingBlock') {
+        if (block.type === 'InterRegionPaddingBlock') {
             return (React.createElement(InterRegionPaddingBlockComponent, { key: key, width: block.widthPx, style: { background: 'none' }, boundary: block.variant === 'boundary' }));
         }
         throw new Error(`invalid block type ${JSON.stringify(block)}`);

package/esm/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js

@@ -34,7 +34,9 @@ const ServerSideRenderedBlockContent = observer(function ({ model, }) {
     if (model.error) {
         return (React.createElement(BlockMsg, { message: `${model.error}`, severity: "error", action: React.createElement(React.Fragment, null,
                 React.createElement(Tooltip, { title: "Reload track" },
-                    React.createElement(IconButton, { "data-testid": "reload_button", onClick: () => model.reload() },
+                    React.createElement(IconButton, { "data-testid": "reload_button", onClick: () => {
+                            model.reload();
+                        } },
                         React.createElement(RefreshIcon, null))),
                 React.createElement(Tooltip, { title: "Show stack trace" },
                     React.createElement(IconButton, { onClick: () => {

package/esm/BaseLinearDisplay/components/Tooltip.js

@@ -42,7 +42,7 @@ const Tooltip = observer(function ({ model, clientMouseCoord, }) {
     const contents = featureUnderMouse
         ? getConf(model, 'mouseover', { feature: featureUnderMouse })
         : undefined;
-    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 featureUnderMouse && contents ? (React.createElement(Portal, { container: (_b = popperTheme === null || popperTheme === void 0 ? void 0 : popperTheme.defaultProps) === null || _b === void 0 ? void 0 : _b.container },
         React.createElement("div", { className: classes.tooltip, ref: refs.setFloating, style: {
                 ...floatingStyles,

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -139,7 +139,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             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: React.FC<{

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -108,7 +108,7 @@ function stateModelFactory() {
         get features() {
             const featureMaps = [];
             for (const block of self.blockState.values()) {
-                if (block === null || block === void 0 ? void 0 : block.features) {
+                if (block.features) {
                     featureMaps.push(block.features);
                 }
             }
@@ -142,7 +142,7 @@ function stateModelFactory() {
             let ret;
             self.blockState.forEach(block => {
                 var _a;
-                const val = (_a = block === null || block === void 0 ? void 0 : block.layout) === null || _a === void 0 ? void 0 : _a.getByID(id);
+                const val = (_a = block.layout) === null || _a === void 0 ? void 0 : _a.getByID(id);
                 if (val) {
                     ret = val;
                 }
@@ -223,7 +223,9 @@ function stateModelFactory() {
                 self.setError();
                 self.setCurrStatsBpPerPx(0);
                 self.clearFeatureDensityStats();
-                [...self.blockState.values()].map(val => val.doReload());
+                [...self.blockState.values()].forEach(val => {
+                    val.doReload();
+                });
                 superReload();
             },
         };
@@ -345,6 +347,7 @@ function stateModelFactory() {
         },
     }))
         .preProcessSnapshot(snap => {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!snap) {
             return snap;
         }
@@ -354,9 +357,9 @@ function stateModelFactory() {
         const { height, ...rest } = snap;
         return { heightPreConfig: height, ...rest };
     })
-        .postProcessSnapshot(self => {
+        .postProcessSnapshot(snap => {
         // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
-        const r = self;
+        const r = snap;
         const { blockState, ...rest } = r;
         return rest;
     });

package/esm/BaseLinearDisplay/models/FeatureDensityMixin.js

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
 import React from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { getContainingView } from '@jbrowse/core/util';
@@ -97,9 +96,9 @@ export default function FeatureDensityMixin() {
         /**
          * #action
          */
-        async getFeatureDensityStats() {
+        getFeatureDensityStats() {
             if (!self.featureDensityStatsP) {
-                self.featureDensityStatsP = getFeatureDensityStatsPre(self).catch(e => {
+                self.featureDensityStatsP = getFeatureDensityStatsPre(self).catch((e) => {
                     if (isAlive(self)) {
                         this.setFeatureDensityStatsP(undefined);
                     }

package/esm/BaseLinearDisplay/models/renderSvg.d.ts

@@ -4,5 +4,5 @@ import { ExportSvgOptions } from '../../LinearGenomeView';
 import { BaseLinearDisplayModel } from './BaseLinearDisplayModel';
 export declare function renderBaseLinearDisplaySvg(self: BaseLinearDisplayModel, opts: ExportSvgOptions & {
     overrideHeight: number;
-    theme: ThemeOptions;
+    theme?: ThemeOptions;
 }): Promise<React.JSX.Element>;

package/esm/BaseLinearDisplay/models/renderSvg.js

@@ -42,7 +42,9 @@ export async function renderBaseLinearDisplaySvg(self, opts) {
         const { offsetPx, widthPx } = block;
         const offset = offsetPx - viewOffsetPx;
         const clipid = getId(id, index);
-        return (React.createElement(React.Fragment, { key: `frag-${index}` },
+        return (
+        /* biome-ignore lint/suspicious/noArrayIndexKey: */
+        React.createElement(React.Fragment, { key: `frag-${index}` },
             React.createElement("defs", null,
                 React.createElement("clipPath", { id: clipid },
                     React.createElement("rect", { x: 0, y: 0, width: widthPx, height: overrideHeight || height }))),

package/esm/BaseLinearDisplay/models/util.d.ts

@@ -7,7 +7,7 @@ export interface RenderProps {
     renderProps: Record<string, any>;
     displayError: unknown;
     rpcManager: {
-        call: Function;
+        call: (...args: unknown[]) => void;
     };
     cannotBeRenderedReason: string;
 }

package/esm/BaseLinearDisplay/models/util.js

@@ -2,17 +2,15 @@ import { getContainingView, getSession } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { isAlive } from 'mobx-state-tree';
 export function getDisplayStr(totalBytes) {
-    let displayBp;
     if (Math.floor(totalBytes / 1000000) > 0) {
-        displayBp = `${Number.parseFloat((totalBytes / 1000000).toPrecision(3))} Mb`;
+        return `${Number.parseFloat((totalBytes / 1000000).toPrecision(3))} Mb`;
     }
     else if (Math.floor(totalBytes / 1000) > 0) {
-        displayBp = `${Number.parseFloat((totalBytes / 1000).toPrecision(3))} Kb`;
+        return `${Number.parseFloat((totalBytes / 1000).toPrecision(3))} Kb`;
     }
     else {
-        displayBp = `${Math.floor(totalBytes)} bytes`;
+        return `${Math.floor(totalBytes)} bytes`;
     }
-    return displayBp;
 }
 // stabilize clipid under test for snapshot
 export function getId(id, index) {