@jbrowse/plugin-linear-genome-view 4.3.0 → 5.0.0-beta.1

package/esm/LinearGenomeView/model.d.ts

@@ -1,209 +1,1598 @@
-import type React from 'react';
 import type { BpOffset, ExportSvgOptions, HighlightType, InitState, NavLocation, VolatileGuide } from './types.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
 import type { MenuItem } from '@jbrowse/core/ui';
 import type { ParsedLocString } from '@jbrowse/core/util';
-import type { BaseBlock, BlockSet } from '@jbrowse/core/util/blockTypes';
+import type { ViewLayout } from '@jbrowse/core/util/Base1DUtils';
+import type { BlockSet, ContentBlock } from '@jbrowse/core/util/blockTypes';
 import type { Region } from '@jbrowse/core/util/types';
+import type { ViewStatus } from '@jbrowse/core/util/viewStatus';
 import type { Instance } from '@jbrowse/mobx-state-tree';
-export declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+/**
+ * #stateModel LinearGenomeView
+ * #category view
+ *
+ * #example
+ * A `LinearGenomeView` is what you hand-author under `defaultSession.views`. The
+ * `init` shorthand fills in `displayedRegions`/`bpPerPx`/`offsetPx` for you:
+ * ```js
+ * defaultSession: {
+ *   name: 'My session',
+ *   views: [
+ *     {
+ *       type: 'LinearGenomeView',
+ *       // plain persisted props sit alongside init, not inside it
+ *       colorByCDS: true,
+ *       init: {
+ *         assembly: 'hg38',
+ *         loc: 'chr1:1,000,000-1,100,000',
+ *         tracks: ['genes', 'alignments'],
+ *       },
+ *     },
+ *   ],
+ * }
+ * ```
+ * `init` holds only keys that need on-attach resolution — also `tracklist`,
+ * `nav`, `highlight` (see the `init` property below). Plain view props like
+ * `colorByCDS`, `showAminoAcids`, `showCenterLine`, `trackLabels`,
+ * `showHighlightChips` are set
+ * directly on the view (MST restores them natively).
+ * At runtime the same model is driven imperatively — every property and action
+ * below is reachable on `viewState.session.views[0]`:
+ * ```js
+ * const view = viewState.session.views[0]
+ * await view.navToLocString('chr1:2,000,000-2,100,000')
+ * view.showTrack('alignments')
+ * view.zoomTo(view.bpPerPx * 2) // zoom out 2x
+ * ```
+ */
+export declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<{
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-} & {
+    minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}, "highlight" | "showHighlightChips"> & {
+    highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<HighlightType, HighlightType, HighlightType>>, [undefined]>;
+    showHighlightChips: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}, "colorByCDS" | "displayedRegions" | "hideHeader" | "hideHeaderOverview" | "hideNoTracksActive" | "id" | "init" | "labelsVisible" | "legacyBpPerPx" | "scalebarOnly" | "showAminoAcids" | "showCenterLine" | "showCytobands" | "showGridlines" | "showTrackOutlines" | "trackLabels" | "trackSelectorType" | "tracks" | "type" | "windowStartBp" | "windowWidthBp"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-    offsetPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    bpPerPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    windowStartBp: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    windowWidthBp: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    legacyBpPerPx: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     displayedRegions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Region[], Region[], Region[]>, [undefined]>;
     tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
-    hideHeader: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideHeaderOverview: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideNoTracksActive: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hideHeader: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    hideHeaderOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    hideNoTracksActive: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     trackSelectorType: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showCenterLine: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showCytobands: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<HighlightType, HighlightType, HighlightType>>, [undefined]>;
-    highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showGridlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showAminoAcids: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    scalebarOnly: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     init: import("@jbrowse/mobx-state-tree").IType<InitState | undefined, InitState | undefined, InitState | undefined>;
 }, {
     width: number;
+    bodyMounted: boolean;
 } & {
+    readonly effectiveBodyMounted: boolean;
     menuItems(): MenuItem[];
 } & {
     setDisplayName(name: string): void;
     setWidth(newWidth: number): void;
+    setBodyMounted(flag: boolean): void;
     setMinimized(flag: boolean): void;
 } & {
+    addToHighlights(highlight: HighlightType): void;
+    setHighlight(highlight?: HighlightType[]): void;
+    removeHighlight(highlight: HighlightType): void;
+    updateHighlight(old: HighlightType, updates: Partial<HighlightType>): void;
+    setShowHighlightChips(arg: boolean): void;
+} & {
+    afterAttach(): void;
+} & {
+    /**
+     * #volatile
+     */
     volatileWidth: number | undefined;
+    /**
+     * #volatile
+     */
     minimumBlockWidth: number;
+    /**
+     * #volatile
+     */
     draggingTrackId: undefined | string;
+    /**
+     * #volatile
+     */
     lastTrackDragY: undefined | number;
+    /**
+     * #volatile
+     */
     volatileError: unknown;
-    scaleFactor: number;
-    targetBpPerPx: number | undefined;
+    /**
+     * #volatile
+     */
     trackRefs: Record<string, HTMLDivElement>;
-    coarseDynamicBlocks: BaseBlock[];
+    /**
+     * #volatile
+     */
+    coarseDynamicBlocks: ContentBlock[];
+    /**
+     * #volatile
+     */
     coarseTotalBp: number;
+    /**
+     * #volatile
+     */
+    coarseBpPerPx: number;
+    /**
+     * #volatile
+     */
     leftOffset: undefined | BpOffset;
+    /**
+     * #volatile
+     */
     rightOffset: undefined | BpOffset;
+    /**
+     * #volatile
+     */
     isScalebarRefNameMenuOpen: boolean;
+    /**
+     * #volatile
+     */
     scalebarRefNameClickPending: boolean;
+    /**
+     * #volatile
+     * temporary vertical guides that can be set by displays (e.g., LD display hover)
+     */
     volatileGuides: VolatileGuide[];
 } & {
+    /**
+     * #getter
+     * corresponds roughly to the zoom level, base-pairs per pixel.
+     *
+     * Zero before a width is measured, which is the same not-yet-measured
+     * sentinel `Base1DView` uses and which `displayedRegionsTotalPx` and the
+     * offset getters already guard for. Reads `volatileWidth` rather than the
+     * `width` getter on purpose: that one throws when unmeasured, and these
+     * are read from the first render.
+     */
+    readonly bpPerPx: number;
+    /**
+     * #getter
+     * corresponds roughly to the horizontal scroll of the LGV
+     */
+    readonly offsetPx: number;
+    /**
+     * #getter
+     * scroll-to-zoom is a global, personal preference resolved from the
+     * session; toggling it in any view applies everywhere
+     */
+    readonly scrollZoom: boolean;
+    /**
+     * #getter
+     */
     readonly pinnedTracks: any[];
+    /**
+     * #getter
+     */
     readonly unpinnedTracks: any[];
-    readonly trackLabelsSetting: any;
+    /**
+     * #getter
+     * the effective track labels setting, resolving the stored `trackLabels`
+     * against the LinearGenomeViewPlugin config default
+     */
+    readonly effectiveTrackLabels: any;
+    /**
+     * #getter
+     */
     readonly width: number;
-    readonly interRegionPaddingWidth: number;
+    /**
+     * #getter
+     * width minus track outline borders (1px each side when shown)
+     */
+    readonly trackWidthPx: number;
+    /**
+     * #getter
+     */
     readonly assemblyNames: string[];
+    /**
+     * #getter
+     */
     readonly assemblyDisplayNames: string[];
+    /**
+     * #getter
+     * checking if lgv is a 'top-level' view is used for toggling pin track
+     * capability, sticky positioning
+     */
     readonly isTopLevelView: boolean;
+    /**
+     * #getter
+     * only uses sticky view headers when it is a 'top-level' view and
+     * session allows it
+     */
     readonly stickyViewHeaders: boolean;
-    readonly rubberbandTop: number;
-    readonly pinnedTracksTop: number;
 } & {
-    scalebarDisplayPrefix(): string | undefined;
-    MiniControlsComponent(): React.FC<any>;
-    HeaderComponent(): React.FC<any>;
+    /**
+     * #getter
+     * Assembly-name prefix for the scalebar refName labels, or undefined for
+     * none. A container view (e.g. LinearSyntenyView) opts its sub-views in by
+     * exposing showAssemblyNameInSubviewScalebar; duck-typed rather than
+     * matching a concrete view type so no upward plugin dependency is needed
+     * and any container can opt in. A wrong nesting depth simply yields no
+     * prefix — hence the hasParent guard, since getParent throws (rather than
+     * returning undefined) when the view sits shallower than depth 2.
+     */
+    readonly scalebarDisplayPrefix: string | undefined;
+    /**
+     * #getter
+     */
     readonly assembliesNotFound: string | undefined;
+    /**
+     * #getter
+     */
     readonly assemblyErrors: string;
+    /**
+     * #getter
+     */
     readonly assembliesInitialized: boolean;
+    /**
+     * #getter
+     * the assembly named by a pending `init`, or undefined when no init is
+     * set. `init`'s assembly isn't in `assemblyNames` yet (that derives from
+     * displayedRegions, still empty pre-navigation), so init-phase readiness
+     * and error checks resolve it directly through here.
+     */
+    readonly initAssembly: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    }> & {
+        error: unknown;
+        loadingP: Promise<void> | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+        canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+    } & {
+        getConf(arg: string): any;
+    } & {
+        readonly name: string;
+        readonly aliases: string[];
+        readonly displayName: string;
+        readonly refNameColors: string[];
+    } & {
+        readonly allAliases: string[];
+        hasName(name: string): boolean;
+    } & {
+        setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+    } & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            regions: import("@jbrowse/core/util").Region[];
+            cytobands: import("@jbrowse/core/util").Feature[];
+            geneticCodes: Record<string, number>;
+        }): void;
+        setError(e: unknown): void;
+        setLoadingP(p?: Promise<void>): void;
+        loadPre(): Promise<void>;
+    } & {
+        load(): Promise<void>;
+    } & {
+        afterAttach(): void;
+    } & {
+        readonly initialized: boolean;
+        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        readonly allRefNames: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string | undefined;
+        getRefNameColor(refName: string): string | undefined;
+        getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
+        getSeqAdapterRefName(canonicalRefName: string): string;
+    } & {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getAliasesForRefName(refName: string): string[];
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    }, {
+        error: unknown;
+        loadingP: Promise<void> | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+        canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+    } & {
+        getConf(arg: string): any;
+    } & {
+        readonly name: string;
+        readonly aliases: string[];
+        readonly displayName: string;
+        readonly refNameColors: string[];
+    } & {
+        readonly allAliases: string[];
+        hasName(name: string): boolean;
+    } & {
+        setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+    } & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            regions: import("@jbrowse/core/util").Region[];
+            cytobands: import("@jbrowse/core/util").Feature[];
+            geneticCodes: Record<string, number>;
+        }): void;
+        setError(e: unknown): void;
+        setLoadingP(p?: Promise<void>): void;
+        loadPre(): Promise<void>;
+    } & {
+        load(): Promise<void>;
+    } & {
+        afterAttach(): void;
+    } & {
+        readonly initialized: boolean;
+        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        readonly allRefNames: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string | undefined;
+        getRefNameColor(refName: string): string | undefined;
+        getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
+        getSeqAdapterRefName(canonicalRefName: string): string;
+    } & {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getAliasesForRefName(refName: string): string[];
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+    /**
+     * #getter
+     */
     readonly initialized: boolean;
+    /**
+     * #getter
+     */
     readonly hasDisplayedRegions: boolean;
-    readonly loadingMessage: "Loading" | undefined;
+    /**
+     * #getter
+     * The assembly whose load the spinner is waiting on: the one `init` names
+     * before navigation (it isn't in assemblyNames yet), else the first of the
+     * displayed assemblies that hasn't finished loading.
+     */
+    readonly loadingAssembly: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    }> & {
+        error: unknown;
+        loadingP: Promise<void> | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+        canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+    } & {
+        getConf(arg: string): any;
+    } & {
+        readonly name: string;
+        readonly aliases: string[];
+        readonly displayName: string;
+        readonly refNameColors: string[];
+    } & {
+        readonly allAliases: string[];
+        hasName(name: string): boolean;
+    } & {
+        setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+    } & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            regions: import("@jbrowse/core/util").Region[];
+            cytobands: import("@jbrowse/core/util").Feature[];
+            geneticCodes: Record<string, number>;
+        }): void;
+        setError(e: unknown): void;
+        setLoadingP(p?: Promise<void>): void;
+        loadPre(): Promise<void>;
+    } & {
+        load(): Promise<void>;
+    } & {
+        afterAttach(): void;
+    } & {
+        readonly initialized: boolean;
+        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        readonly allRefNames: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string | undefined;
+        getRefNameColor(refName: string): string | undefined;
+        getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
+        getSeqAdapterRefName(canonicalRefName: string): string;
+    } & {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getAliasesForRefName(refName: string): string[];
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    }, {
+        error: unknown;
+        loadingP: Promise<void> | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+        canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+    } & {
+        getConf(arg: string): any;
+    } & {
+        readonly name: string;
+        readonly aliases: string[];
+        readonly displayName: string;
+        readonly refNameColors: string[];
+    } & {
+        readonly allAliases: string[];
+        hasName(name: string): boolean;
+    } & {
+        setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+    } & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            regions: import("@jbrowse/core/util").Region[];
+            cytobands: import("@jbrowse/core/util").Feature[];
+            geneticCodes: Record<string, number>;
+        }): void;
+        setError(e: unknown): void;
+        setLoadingP(p?: Promise<void>): void;
+        loadPre(): Promise<void>;
+    } & {
+        load(): Promise<void>;
+    } & {
+        afterAttach(): void;
+    } & {
+        readonly initialized: boolean;
+        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        readonly allRefNames: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string | undefined;
+        getRefNameColor(refName: string): string | undefined;
+        getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
+        getSeqAdapterRefName(canonicalRefName: string): string;
+    } & {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getAliasesForRefName(refName: string): string[];
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+    /**
+     * #getter
+     * What the spinner says. The assembly reports which of its files it is
+     * downloading, so this is "Downloading chromosome aliases" rather than a bare
+     * "Loading" for the part of startup that actually takes time. Falls back
+     * once the assembly is loaded and the remaining wait is the init autorun's
+     * own navigation, which is local.
+     */
+    readonly loadingMessage: string | undefined;
+    /**
+     * #getter
+     * Determinate fraction for the spinner's bar, when the assembly load
+     * reports one (a whole-file download with a Content-Length)
+     */
+    readonly loadingProgress: number | undefined;
+    /**
+     * #getter
+     * The URL the assembly load is currently fetching, when the phase named
+     * one. Only the stalled-load notice reads it — see
+     * {@link ViewLoadingScreen}.
+     */
+    readonly loadingSource: string | undefined;
+    /**
+     * #getter
+     */
     readonly hasSomethingToShow: boolean;
+    /**
+     * #getter
+     * init is set but its async navigation (the afterAttach autorun) hasn't
+     * populated displayedRegions yet. `initialized` can already be true here
+     * (it only tracks assembly readiness), so without this the container
+     * would mount over empty regions and pxToBp/hover would throw.
+     *
+     * **Not dotplot's or synteny's `initPending`**, which is the bare
+     * `!!self.init` — "an init blob has not been applied" — and which those
+     * views read from their `settled` gate rather than from `showLoading`.
+     * This one is narrower on purpose: it closes only the window where there
+     * is nothing on screen. Once navigation has produced regions the view is
+     * usable and gets shown, even though `init` is still set while the tracks
+     * and highlights land. Renamed away from the shared spelling because the
+     * two predicates disagree exactly there, and the bare name reads as
+     * theirs.
+     */
+    readonly awaitingInitNavigation: boolean;
+    /**
+     * #getter
+     * Whether to show a loading indicator instead of the import form or view
+     */
     readonly showLoading: boolean;
+    /**
+     * #getter
+     * Whether to show the import form
+     */
     readonly showImportForm: boolean;
+    /**
+     * #getter
+     * Is there anything to draw yet? The gate anything reading block geometry
+     * — a ruler, a scalebar, a display — has to pass first, because
+     * `width`/`staticBlocks` throw by design before the view has been
+     * measured and navigated.
+     *
+     * **Not `initialized`**, which is the trap this getter exists to close.
+     * That one answers "have the assembly's regions loaded", which is only
+     * the first of two async steps: navigating then populates
+     * `displayedRegions`, and in the window between the two `initialized` is
+     * already true while there is still nothing on screen. `showLoading`
+     * folds in `awaitingInitNavigation`, the getter that exists for exactly
+     * that gap.
+     *
+     * `error` is the third outcome and is why this is not a bare
+     * `!showLoading`: a failed assembly load also ends the loading state, so
+     * that alone would mount over the wreckage. Read `error` yourself if you
+     * want to draw it.
+     */
+    readonly ready: boolean;
+    /**
+     * #getter
+     * The same question as `ready` with the other three outcomes named, for a
+     * host that draws its own chrome and has to render all four. See
+     * `computeViewStatus`, whose precedence this defers to — and note its
+     * `ready` is narrower than the getter above, which is true when nothing
+     * has told the view where to look.
+     */
+    readonly status: ViewStatus;
+    /**
+     * #getter
+     */
     readonly scalebarHeight: number;
+    /**
+     * #getter
+     * What TrackContainer puts *above* a track's rendering container: the gap
+     * over its Paper, and the Paper's own top border when outlines are on.
+     */
+    readonly trackLeadingChrome: number;
+    /**
+     * #getter
+     * ...and what it puts below: the resize divider, plus the matching bottom
+     * border.
+     */
+    readonly trackTrailingChrome: number;
+    /**
+     * #getter
+     * A track's full cost beyond its display height.
+     *
+     * The track *label* is not counted, and cannot be: an offset label is an
+     * in-flow box whose height is whatever the theme renders a Paper of icon
+     * buttons at — 31.140625px on the stock theme, and not a number this file
+     * can derive. So these getters are exact while labels are hidden or
+     * overlapping, and short by one label box per labelled track otherwise.
+     * Anything needing the offset to the pixel with labels showing measures
+     * the DOM; `BreakpointSplitViewOverlay` does, and falls back to this
+     * arithmetic only for a track with no mounted div.
+     */
+    readonly trackChromeHeight: number;
+    /**
+     * #getter
+     */
     readonly headerHeight: number;
+    /**
+     * #getter
+     * Where the scalebar pins when the view's chrome is sticky: everything
+     * stacked above it, which is the view's own title bar plus this view's
+     * header. Expressed from `headerHeight` rather than re-summing its
+     * constants — the two are the same box, and a second spelling of the sum
+     * is free to drift from the first while both typecheck.
+     */
+    readonly rubberbandTop: number;
+    /**
+     * #getter
+     */
+    readonly pinnedTracksTop: number;
+    /**
+     * #method
+     * rendered height of a single track, collapsing to a fixed height when
+     * minimized. Shared by trackHeights and getTrackYOffset so the two can't
+     * disagree. Reads `activeDisplay` — the display TrackContainer actually
+     * mounts — rather than re-picking `displays[0]`, so the view's height math
+     * can't diverge from what is on screen.
+     */
+    trackHeight(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IAnyType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>>)[number]): any;
+    /**
+     * #getter
+     */
     readonly trackHeights: number;
-    readonly trackHeightsWithResizeHandles: number;
+    /**
+     * #getter
+     */
+    readonly trackHeightsWithChrome: number;
+    /**
+     * #getter
+     */
     readonly height: number;
+    /**
+     * #method
+     * Y offset (in pixels, from the top of the view) where a track's
+     * rendering container starts. Walks tracks in DOM render order (pinned
+     * first, then unpinned), from the same constants TrackContainer lays its
+     * Paper out with. Returns `undefined` if the track is not present.
+     *
+     * Exact while track labels are hidden or overlapping. With an offset
+     * label the answer is short by one label box per labelled track above
+     * this one — see `trackChromeHeight` for why that box is not derivable
+     * here.
+     */
+    getTrackYOffset(trackId: string): number | undefined;
+    /**
+     * #method
+     * the pinned or unpinned sibling list a track renders within; move
+     * up/down/top/bottom reorder inside this section rather than the full
+     * `tracks` array, since the two sections lay out independently
+     */
+    trackSection(id: string): any[];
+    /**
+     * #getter
+     */
     readonly totalBp: number;
-    getNonElidedRegionCount(bpPerPx: number): number;
-    getInterRegionPaddingPx(bpPerPx: number): number;
+    /**
+     * #getter
+     */
+    readonly fitBpPerPx: number;
+    /**
+     * #getter
+     * The zoom-out limit. This view's own fit, except while a container holds
+     * it on a shared scale coarser than that — a small genome next to a large
+     * one, drawn short so the two compare by length.
+     *
+     * Raising the LIMIT is what makes such a scale survive: written past the
+     * limit instead, it is undone by the first thing that clamps — a wheel
+     * tick, a rubberband, a `setDisplayedRegions` — which is how the dotplot's
+     * locked aspect ratio once turned "zoom out" into a zoom in
+     * (`axisMaxBpPerPx`). Here every route to a zoom clamps against the same
+     * ceiling, so full zoom-out LANDS on the shared scale.
+     */
     readonly maxBpPerPx: number;
+    /**
+     * #getter
+     * The zoom-out ceiling a containing comparative view holds this row to,
+     * or 0 for a standalone view, a mode that is off, and a stack that cannot
+     * answer yet.
+     *
+     * Pulled rather than pushed down into a volatile: the number is a
+     * function of every row's fit, all of which move on a resize, and a
+     * stored copy would be stale by the next layout.
+     */
+    readonly sharedFitBpPerPx: number;
+    /**
+     * #getter
+     */
     readonly minBpPerPx: number;
+    /**
+     * #getter
+     */
     readonly error: unknown;
+    /**
+     * #getter
+     */
     readonly maxOffset: number;
+    /**
+     * #getter
+     */
     readonly minOffset: number;
+    /**
+     * #getter
+     * Whether the displayed regions read left-to-right, right-to-left, or
+     * some of each. `horizontallyFlip` reverses the order and flips every
+     * region at once, so a flipped row is uniformly `reversed` and `mixed`
+     * takes going out of your way — the scalebar label menu's per-region
+     * "Reverse region". Read off `displayedRegions` rather than off blocks
+     * because blocks cover the window and this is a fact about the row.
+     */
+    readonly displayedRegionsOrientation: import("./util.ts").RegionsOrientation;
+    /**
+     * #getter
+     */
     readonly displayedRegionsTotalPx: number;
-    renderProps(): any;
-    searchScope(assemblyName: string): {
-        assemblyName: string;
-        includeAggregateIndexes: boolean;
-        tracks: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IAnyType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>>;
-    };
-    readonly trackMap: Map<any, any>;
+    /**
+     * #getter
+     */
+    readonly trackMap: Map<string, any>;
+    /**
+     * #method
+     */
     getTrack(id: string): any;
-    rankSearchResults(results: BaseResult[]): BaseResult[];
-    readonly trackTypeActions: Map<string, MenuItem[]>;
+    /**
+     * #method
+     * displayId of the active (shown) display for a track in this view, used
+     * by the config editor to expand the relevant display and collapse the
+     * track's other displays
+     */
+    getActiveDisplayId(trackId: string): string | undefined;
 } & {
+    /**
+     * #action
+     */
     setShowTrackOutlines(arg: boolean): void;
+    /**
+     * #action
+     */
+    setScrollZoom(flag: boolean): void;
+    /**
+     * #action
+     */
     setColorByCDS(flag: boolean): void;
+    /**
+     * #action
+     */
+    setShowAminoAcids(flag: boolean): void;
+    /**
+     * #action
+     */
     setShowCytobands(flag: boolean): void;
+    /**
+     * #action
+     */
     setWidth(newWidth: number): void;
+    /**
+     * #action
+     */
     setError(error: unknown): void;
+    /**
+     * #action
+     */
     setIsScalebarRefNameMenuOpen(isOpen: boolean): void;
+    /**
+     * #action
+     */
     setScalebarRefNameClickPending(pending: boolean): void;
+    /**
+     * #action
+     */
     setHideHeader(b: boolean): void;
+    /**
+     * #action
+     */
     setHideHeaderOverview(b: boolean): void;
+    /**
+     * #action
+     */
+    setScalebarOnly(b: boolean): void;
+    /**
+     * #action
+     */
     setHideNoTracksActive(b: boolean): void;
+    /**
+     * #action
+     */
     setShowGridlines(b: boolean): void;
-    addToHighlights(highlight: HighlightType): void;
-    setHighlight(highlight?: HighlightType[]): void;
-    removeHighlight(highlight: HighlightType): void;
-    updateHighlight(old: HighlightType, updates: Partial<HighlightType>): void;
-    setHighlightsVisible(arg: boolean): void;
+    /**
+     * #action
+     */
     setLabelsVisible(arg: boolean): void;
+    /**
+     * #action
+     * set temporary vertical guides (e.g., for LD display hover)
+     */
     setVolatileGuides(guides: VolatileGuide[]): void;
+    /**
+     * #action
+     */
     scrollTo(offsetPx: number): number;
-    zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
+    /**
+     * #action
+     * `scrollTo`'s bp-space twin: place the window's left edge at a
+     * linearized bp coordinate, clamped to the same scroll limits.
+     *
+     * It exists so a caller that already knows where it wants to be in bp —
+     * zoomTo, anchoring the base under the cursor — does not have to convert
+     * to pixels and let this convert back. That round trip is lossy once per
+     * frame, and a scroll-zoom burst is a few dozen frames, which is enough
+     * to walk the base out from under the cursor.
+     */
+    scrollToBp(startBp: number): number;
+    /**
+     * #action
+     */
+    zoomTo(bpPerPx: number, offset?: any): number;
+    /**
+     * #action
+     * sets offsets of rubberband, used in the get sequence dialog can call
+     * view.getSelectedRegions(view.leftOffset,view.rightOffset) to compute
+     * the selected regions from the offsets
+     */
     setOffsets(left?: BpOffset, right?: BpOffset): void;
-    setSearchResults(searchResults: BaseResult[], searchQuery: string, assemblyName?: string): void;
-    setNewView(bpPerPx: number, offsetPx: number): void;
-    horizontallyFlip(): void;
-    showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
-    hideTrack(trackId: string): 0 | 1;
+    /**
+     * #action
+     */
+    setSearchResults(searchResults: BaseResult[], searchQuery: string, assemblyName: string): void;
+    /**
+     * #action
+     */
+    showTrack(trackId: string, initialSnapshot?: any, displayInitialSnapshot?: any, inlineConf?: Record<string, unknown>): any;
+    /**
+     * #action
+     */
+    hideTrack(trackId: string): boolean;
 } & {
+    /**
+     * #action
+     */
     moveTrackDown(id: string): void;
+    /**
+     * #action
+     */
     moveTrackUp(id: string): void;
+    /**
+     * #action
+     */
     moveTrackToTop(id: string): void;
+    /**
+     * #action
+     */
     moveTrackToBottom(id: string): void;
+    /**
+     * #action
+     */
     moveTrack(movingId: string, targetId: string): void;
-    toggleTrack(trackId: string): void;
-    setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
+    /**
+     * #action
+     */
+    toggleTrack(trackId: string): boolean;
+    /**
+     * #action
+     */
+    setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden'): void;
+    /**
+     * #action
+     */
     setShowCenterLine(b: boolean): void;
-    setDisplayedRegions(regions: Region[]): void;
+    /**
+     * #action
+     */
     activateTrackSelector(): import("@jbrowse/core/util").Widget;
+    /**
+     * #action
+     */
+    toggleTrackSelector(): import("@jbrowse/core/util").Widget;
+    /**
+     * #method
+     * Helper method for the fetchSequence.
+     * Retrieves the corresponding regions that were selected by the
+     * rubberband
+     *
+     * @param leftOffset - `object as {start, end, index, offset}`, offset = start
+     * of user drag
+     * @param rightOffset - `object as {start, end, index, offset}`,
+     * offset = end of user drag
+     * @returns array of Region[]
+     */
     getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
         assemblyName: string;
         refName: string;
         start: number;
         end: number;
     }[];
+    /**
+     * #action
+     */
     horizontalScroll(distance: number): number;
-    showAllRegions(): void;
-    showAllRegionsInAssembly(assemblyName?: string): void;
+    /**
+     * #action
+     */
     setDraggingTrackId(idx?: string): void;
+    /**
+     * #action
+     */
     setLastTrackDragY(y: number): void;
-    setScaleFactor(factor: number): void;
-    setTargetBpPerPx(target: number | undefined): void;
-    clearView(): void;
+    /**
+     * #action
+     * called while dragging a track over the track at `targetId`; reorders
+     * once the cursor has moved far enough (see shouldSwapTracks) to avoid
+     * jitter when a short track is dragged over a tall one
+     */
+    onTrackDragOver(targetId: string, currentY: number): void;
+    /**
+     * #action
+     */
     setInit(arg?: InitState): void;
+    /**
+     * #method
+     * creates an svg export and save using FileSaver
+     */
     exportSvg(opts?: ExportSvgOptions): Promise<void>;
 } & {
     slide: (viewWidths: number) => void;
-} & {
     zoom: (targetBpPerPx: number) => void;
+    cancelZoomAnimation: () => void;
 } & {
+    /**
+     * #getter
+     */
+    readonly showsWholeChromosome: boolean;
+    /**
+     * #getter
+     * an ideogram only reads correctly against an entire chromosome: on a
+     * sub-region it is a meaningless slice of bands, and the centromere shows
+     * up as a lone half-triangle
+     */
     readonly canShowCytobands: boolean;
-    readonly showCytobands: boolean;
+    /**
+     * #getter
+     * the `showCytobands` setting gated by whether cytobands can be shown at
+     * all (whole chromosome + data present) — i.e. actually on screen
+     */
+    readonly effectiveShowCytobands: boolean;
+    /**
+     * #getter
+     */
     readonly anyCytobandsExist: boolean;
+    /**
+     * #getter
+     * the cytoband is displayed to the right of the chromosome name, and
+     * that offset is calculated manually with this method
+     */
     readonly cytobandOffset: number;
+    /**
+     * #getter
+     */
+    readonly isTrackSelectorOpen: boolean;
 } & {
+    /**
+     * #method
+     * return the view menu items
+     */
     menuItems(): MenuItem[];
+    /**
+     * #method
+     * what a plugin can start from the selected region — a synteny view, a
+     * consensus call. Extend this rather than `rubberBandMenuItems` so the
+     * entries collect under the menu's "Launch" submenu; that grouping is
+     * decided once here rather than by whichever contributor runs first, and
+     * keeps the rubberband menu itself short as plugins pile on.
+     */
+    rubberBandLaunchMenuItems(): MenuItem[];
+    /**
+     * #getter
+     * geometry of the overview scalebar — derived from displayedRegions,
+     * width, and cytobandOffset so it stays cached by MobX
+     */
+    readonly overviewLayout: ViewLayout;
 } & {
+    /**
+     * #getter
+     * static blocks are an important concept jbrowse uses to avoid
+     * re-rendering when you scroll to the side. when you horizontally
+     * scroll to the right, old blocks to the left may be removed, and new
+     * blocks may be instantiated on the right. tracks may use the static
+     * blocks to render their data for the region represented by the block
+     */
     readonly staticBlocks: BlockSet;
+    /**
+     * #getter
+     * dynamic blocks represent the exact coordinates of the currently
+     * visible genome regions on the screen. they are similar to static
+     * blocks, but static blocks can go offscreen while dynamic blocks
+     * represent exactly what is on screen
+     */
     readonly dynamicBlocks: BlockSet;
-    readonly roundedDynamicBlocks: BaseBlock[];
+    /**
+     * #getter
+     * all overview scalebar blocks (content + elided), laid out on the
+     * overviewLayout. memoized so the scalebar doesn't recompute it per
+     * render
+     */
+    readonly overviewBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
+    /**
+     * #getter
+     * leading/trailing pixel span of the visible regions projected onto the
+     * overviewLayout — the geometry of the overview's "you are here"
+     * rectangle, and of the top edge of the polygon drawn under it. Elided
+     * regions count: at whole-genome zoom the tail of an assembly is all
+     * coalesced tiny contigs, and stopping at the last *content* block left
+     * the rectangle short of (or, scrolled onto that tail, absent from) the
+     * polygon it sits on.
+     */
+    readonly overviewRegionPxSpan: import("@jbrowse/core/util/Base1DUtils").PxSpan | undefined;
+    /**
+     * #getter
+     * The x shift that maps the **staticBlocks frame** onto the viewport:
+     * `translateX(view.staticBlocksTranslateX)` on one container places
+     * every `gridlineTicks`, `scalebarLabels` and `paddingSpans` entry at
+     * once, and a pan then moves that single transform rather than each
+     * child.
+     *
+     * The frame exists because those three are laid out across every
+     * displayed region rather than across the viewport — it overhangs on
+     * both sides — so their `x` values are stable under a scroll and only
+     * this number moves. `scalebarRefNameLabels` is the exception and says
+     * so: its `transform` is already a screen x, because a sticky label's
+     * position is a function of the scroll rather than of block geometry.
+     *
+     * **The subtraction must happen here, in float64, and that is the
+     * load-bearing part.** `offsetPx` is a whole-genome pixel coordinate —
+     * hg38 chr1 at base resolution is already past 1e10 — and a length that
+     * size does not survive the trip through CSS: the transform matrix is
+     * float32 by the time it reaches the compositor, where consecutive
+     * representable values at 1e10 are ~1024px apart, and layout saturates
+     * sooner still (Blink's `LayoutUnit` is int32 at 1/64px, so ±33.5M px).
+     * So the shape that looks obvious — lay an overlay out in absolute
+     * genome pixels, write `translateX(-view.offsetPx)` — does not lose a
+     * subpixel, it puts the row somewhere else entirely, and only on large
+     * assemblies at high zoom, which is not where anyone tests. Both
+     * operands here are large and their difference is bounded by the
+     * overhang (a block or two), so what reaches CSS is small and exact.
+     * Same rule as the GPU side, one layer up —
+     * `agent-docs/reference/BP_PRECISION.md`.
+     *
+     * Published because it is the one piece of coordinate arithmetic a host
+     * drawing its own chrome would otherwise have to know, and because
+     * having it written out at each call site is how the two in-tree copies
+     * came to disagree about rounding. Round it where the content is text
+     * (a fractional offset blurs a label); leave it alone for paths and
+     * boxes.
+     */
+    readonly staticBlocksTranslateX: number;
+    /**
+     * #getter
+     * Gridline tick positions (x relative to the staticBlocks frame),
+     * derived from staticBlocks + bpPerPx. Computed once and shared by every
+     * Gridlines instance (scalebar, main view, each pinned track) rather
+     * than recomputing the makeTicks loop per component.
+     */
+    readonly gridlineTicks: {
+        x: number;
+        major: boolean;
+    }[];
+    /**
+     * #getter
+     * Scalebar coordinate labels (x in the staticBlocks frame + display
+     * text). Sibling of gridlineTicks sharing the same makeBlockTicks
+     * formula, so labels line up exactly with their gridlines. staticBlocks
+     * chop a region into ~800px chunks; groupContiguousBlocks merges them
+     * back per region so a label on an internal chunk boundary isn't clipped
+     * away by both neighbors — only genuine region edges clip a label.
+     *
+     * A run that can hold too few labels to make a ruler goes unnumbered
+     * (`tickLabelsWorthDrawing`), the same rule the overview scalebar and
+     * the dotplot axes apply: with a whole genome displayed each chromosome
+     * catches one lone coordinate, which conveys no scale by itself and
+     * reads as the same number repeated across the row.
+     */
+    readonly scalebarLabels: {
+        x: number;
+        label: string;
+        key: string;
+    }[];
+    /**
+     * #getter
+     * The bold refName labels drawn along the scalebar, as plain data:
+     * `{key, refName, displayedRegionIndex, lastDisplayedRegionIndex,
+     * sticky, transform, maxWidth, paddingLeft, text}` each. One per run of
+     * same-refName regions, plus a "sticky" one pinned to the viewport's
+     * left edge naming the refName under it, so panning into a chromosome
+     * does not scroll its own name off the screen.
+     *
+     * Three rules live in here that a host drawing region names will
+     * otherwise rediscover the hard way, and two of them are invisible until
+     * the data is awkward:
+     *
+     * - the sticky label rides the rightmost run that has scrolled off the
+     *   left, not the region's first block — that one is gone from
+     *   staticBlocks entirely once you zoom into a region's interior, taking
+     *   the chromosome name off screen at exactly the zoom where nothing
+     *   else names it.
+     * - adjacent regions of the same refName (collapsed introns) get one
+     *   label between them, not one each. That label names the whole run and
+     *   is fitted to the whole run, and `displayedRegionIndex` /
+     *   `lastDisplayedRegionIndex` bracket what it stands for.
+     * - a name is drawn whole or not at all, measured against the space its
+     *   run leaves. Clipped to its own width, `chr16` reads as `chr1` —
+     *   a different chromosome rather than a shortened name, which is why
+     *   this is a fit test rather than an ellipsis.
+     *
+     * **Viewport frame, unlike its siblings.** `transform` is a screen x,
+     * already net of `offsetPx`, where gridlineTicks / scalebarLabels /
+     * paddingSpans are all in the staticBlocks frame. The sticky label's
+     * position is a function of `offsetPx` rather than of block geometry, so
+     * it has no fixed position in that frame — and for the same reason this
+     * getter recomputes on every scroll frame where those three do not.
+     *
+     * `caption` accompanies the labels: the chip at the row's left edge,
+     * saying which assembly the row is (a container view — synteny — opts
+     * into that through `scalebarDisplayPrefix`) and whether it is flipped.
+     * A ` [rev]` there is a fact about the ROW; the same marker on a
+     * chromosome name means that one region, which only happens under mixed
+     * orientation. `captionSpanPx` is the width it takes, which the
+     * coordinate numbers stay out from under. The SVG export deliberately
+     * calls `getScalebarRefNameLabels` itself with no prefix rather than
+     * reading this, since it draws its own assembly name above the ruler.
+     */
+    readonly scalebarRefNameLabels: {
+        labels: import("./util.ts").ScalebarRefNameLabel[];
+        caption: string | undefined;
+        captionSpanPx: number;
+    };
+    /**
+     * #getter
+     * Every span along the row that is not track data, as plain geometry in
+     * the staticBlocks frame — the same frame as gridlineTicks and
+     * scalebarLabels, so one `translateX(staticBlocksTranslateX)` places all
+     * three. Three kinds, and a host drawing its own chrome needs all of
+     * them:
+     *
+     * - `seam`: the 3px bar at a region's right edge. Displayed regions are
+     *   laid out **contiguously** — calculateStaticBlocks emits boundary
+     *   padding only before the first region and after the last — so this
+     *   bar is the only thing separating two of them. Without it a
+     *   two-region view reads as a one-region view scrolled somewhere
+     *   strange. `isRightEndOfDisplayedRegion` is what marks it, and the
+     *   right edge of the blocks currently *loaded* — which is what block
+     *   geometry hands you — is not the same filter.
+     * - `elided`: a region too narrow to draw at this zoom. Whole-genome on
+     *   a real assembly is mostly these — hg38 has 455 sequences and all
+     *   but the 24 chromosomes land sub-pixel — so a host that skips them
+     *   renders that tail as nothing at all.
+     * - `boundary`: past the start of the first region or the end of the
+     *   last. Greying it is what makes the last region's seam read as the
+     *   edge of a filled area rather than a rule floating in the track.
+     *
+     * Elided blocks get no seam even though they carry the flag: at the
+     * zoom where regions elide, one bar per region is a solid grey wall.
+     *
+     * PaddingBlocks is the in-tree consumer. The SVG export is deliberately
+     * NOT one: `SVGRegionSeparators` walks dynamicBlocks itself and draws
+     * only the seam, because `elided` and `boundary` are chrome for an
+     * interactive row rather than information a figure carries — striped
+     * grey saying "regions here are too narrow to draw" is noise in a
+     * static image, and at whole-genome zoom it would be most of the row.
+     * The seam is the one that must survive: regions lay out contiguously,
+     * so it is all that separates two of them.
+     */
+    readonly paddingSpans: {
+        key: string;
+        x: number;
+        width: number;
+        kind: 'seam' | 'elided' | 'boundary';
+    }[];
+    /**
+     * #getter
+     * Integer-rounded sum of all visible block widths. Slightly less than
+     * view.width when the genome ends before the right edge; use view.width
+     * for SVG clip rects (display boundary) and this for paint canvas sizing
+     * (actual content width).
+     */
+    readonly totalWidthPx: number;
+    /**
+     * #getter
+     * Like totalWidthPx but excluding inter-region boundary blocks. Used
+     * when column layout divides the canvas width by feature count.
+     */
+    readonly totalWidthPxWithoutBorders: number;
+    /**
+     * #getter
+     */
+    readonly visibleBp: number;
+    /**
+     * #getter
+     * Whether any part of a displayed region actually falls inside the
+     * viewport. False both when the view holds no regions at all and when
+     * it holds some but is scrolled entirely off them; either way there is
+     * no visible span for the scalebar, ruler and refName labels to
+     * describe, which is what the SVG export's header checks before drawing
+     * one. Distinct from `hasDisplayedRegions`, which only asks whether the
+     * view has been given regions, not whether any are on screen.
+     */
+    readonly hasVisibleContent: boolean;
+    /**
+     * #getter
+     * What is on screen, as regions that address whole bases — what a
+     * reader means by "the visible region" when they ask to fetch it,
+     * bookmark it or read it back in a locString field. `visibleRegions`
+     * below is the other half: pixels, and fractional by design.
+     */
+    readonly visibleWholeBaseRegions: {
+        assemblyName: string;
+        refName: string;
+        start: number;
+        end: number;
+    }[];
+    /**
+     * #getter
+     * Returns the currently visible content blocks with screen pixel
+     * positions and displayedRegionIndex guaranteed.
+     * Used by WebGL displays for per-region data fetching and rendering.
+     */
+    readonly visibleRegions: {
+        refName: string;
+        start: number;
+        end: number;
+        assemblyName: string;
+        reversed: boolean | undefined;
+        displayedRegionIndex: number;
+        screenStartPx: number;
+        screenEndPx: number;
+    }[];
+    /**
+     * #getter
+     * visibleRegions expanded by a half-screen buffer on each side,
+     * clamped to displayedRegion bounds, with integer-rounded coordinates.
+     * Use this when fetching data that should extend slightly beyond the
+     * viewport for smooth scrolling.
+     */
+    readonly bufferedVisibleRegions: {
+        region: {
+            refName: string;
+            start: number;
+            end: number;
+            assemblyName: string;
+            reversed: boolean | undefined;
+        };
+        displayedRegionIndex: number;
+    }[];
+    /**
+     * #getter
+     * a single "combo-locstring" representing all the regions visible on
+     * the screen
+     */
     readonly visibleLocStrings: string;
+    /**
+     * #getter
+     * **What a debounced consumer clips to**: the coarse blocks once the
+     * view has settled at least once, the live ones before that.
+     *
+     * The coarse blocks exist so a per-bp scan does not recompute on every
+     * animation frame during a pan or zoom — wiggle's autoscale domain, the
+     * alignments coverage scale and MAF's coverage band are the three — and
+     * while they are stale
+     * the answer is merely a frame or two old, which is what the debounce
+     * means. **Empty is different in kind.** A scan over no blocks yields no
+     * entries, and no entries is not a stale domain, it is the fallback one:
+     * `[0,1]`, which draws a line plot blank and a density plot saturated.
+     * That window is the 500ms between a view initializing and the coarse
+     * autorun's first run, and data can now land inside it — the per-region
+     * fetch used to be trailing-edge at 600ms, so it never did.
+     *
+     * One recompute at that transition, against N per frame, which is the
+     * trade the guard was making anyway.
+     */
+    readonly settledDynamicBlocks: ContentBlock[];
+    /**
+     * #getter
+     * same as visibleLocStrings, but only updated every 500ms
+     */
     readonly coarseVisibleLocStrings: string;
+    /**
+     * #getter
+     */
     readonly coarseTotalBpDisplayStr: string;
-    readonly effectiveBpPerPx: number;
+    /**
+     * #getter
+     */
     readonly effectiveTotalBp: number;
+    /**
+     * #getter
+     */
     readonly effectiveTotalBpDisplayStr: string;
 } & {
-    setCoarseDynamicBlocks(blocks: BlockSet): void;
+    /**
+     * #action
+     */
+    setCoarseDynamicBlocks(blocks: BlockSet, bpPerPx: number): void;
 } & {
+    /**
+     * #action
+     * Bring the coarse blocks to the viewport as it stands now, for a
+     * placement that JUMPED rather than travelled.
+     *
+     * The coarse blocks are a 500ms throttle, and every consumer trades
+     * freshness for not recomputing per animation frame — the location box,
+     * canvas's on-screen feature set, and the two per-bp scans behind
+     * `settledDynamicBlocks`. That trade is only sound while the answer is a
+     * few frames old. **A jump makes it unrelated instead**, because there is
+     * nothing to coalesce: the viewport left behind is not an approximation of
+     * the new one, it is a different place. Unsettled, the location box reads
+     * as a navigation that didn't happen, and wiggle's autoscale domain is
+     * computed over the window the user just left — measured at `[0,200]`
+     * against a correct `[0,300]` when a 40bp coarse window survived a jump to
+     * 4040bp on screen. Only the per-region fetch moving to the leading edge
+     * made that reachable: at 600ms the data never landed inside the hole.
+     *
+     * **The continuous paths deliberately do not come through here.** The
+     * spring zoom writes through `zoomTo` per frame and a drag through
+     * `scrollTo`, so this adds no per-frame work; the settle is idempotent
+     * (`setCoarseDynamicBlocks` compares block keys), so the debounced
+     * autorun's own follow-up run costs nothing.
+     *
+     * Every placer calls it, and `placersSettleCoarseBlocks.test.ts` is what
+     * makes that true of the next one — it scans this file for the writes and
+     * fails on a placer that reaches neither the settle nor its named list of
+     * continuous paths. Two passes by hand missed four.
+     */
+    settleCoarseBlocks(): void;
+} & {
+    /**
+     * #action
+     * offset is the base-pair-offset in the displayed region, index is the
+     * index of the displayed region in the linear genome view
+     *
+     * @param start - object as `{start, end, offset, index}`
+     * @param end - object as `{start, end, offset, index}`
+     */
     moveTo(start?: BpOffset, end?: BpOffset): void;
-    navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
-    navToSearchString({ input, assembly, }: {
-        input: string;
-        assembly: Assembly;
-    }): Promise<void>;
-    navToLocation(parsedLocString: ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
-    navToLocations(regions: ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
+    /**
+     * #action
+     * Place the viewport by the pair of PIXEL quantities it used to be stored
+     * as. Prefer `setWindow`: pixels mean nothing without the width they were
+     * measured at, so a round trip through here is only exact while the width
+     * holds still. Kept for callers that genuinely have pixels — a wheel
+     * gesture, a rubberband — and for reading old snapshots.
+     */
+    setNewView(bpPerPx: number, offsetPx: number): void;
+    /**
+     * #action
+     * Place the viewport by the pair it is actually STORED as: the window's
+     * width and left edge, both in bp. `setNewView`'s bp-space twin, and the
+     * right one for anything that captures a viewport and puts it back later
+     * (an Undo, a saved location) — those two moments can be a window resize
+     * apart, and this pair survives one where a pixel pair does not.
+     *
+     * Still clamped, by the same zoom and scroll limits as every other mover:
+     * the regions may have changed under it, and a window the new set can't
+     * hold is not restorable however it was spelled.
+     */
+    setWindow(windowWidthBp: number, windowStartBp: number): void;
+    /**
+     * #action
+     * `setWindow` without the settle, for a writer that runs per animation
+     * frame. Flushing the coarse blocks sixty times a second is the one thing
+     * such a writer must not do: they are a 500ms throttle that a synteny
+     * follow pass and two autoscale domains hang off, and settling each frame
+     * turns each of those into per-frame work — `positionViewOnSpans` states
+     * the same rule for the same reason.
+     */
+    setWindowFrame(windowWidthBp: number, windowStartBp: number): void;
+    /**
+     * #action
+     * The worst jump of them to leave unsettled: the coarse blocks are keyed
+     * by `displayedRegionIndex`, so a set that outlives the region list has a
+     * consumer reading one contig's data against another's blocks.
+     */
+    setDisplayedRegions(regions: Region[]): void;
+    /**
+     * #action
+     * Re-assert `maxBpPerPx` over the current zoom, for a container whose
+     * shared ceiling just fell — otherwise the view is stranded above it with
+     * zoom-out disabled and the slider's min past its value. Goes through
+     * `zoomTo` so the clamp keeps one definition, and settles because a
+     * ceiling drop moves the window in one step.
+     *
+     * Requires an `initialized` view; the caller checks, since an MST action
+     * reads untracked and a guard here would never re-run once the row
+     * arrived.
+     */
+    clampZoomToCeiling(): void;
+    /**
+     * #action
+     */
+    showAllRegions(): void;
+    /**
+     * #action
+     * Fit the displayed regions to the width exactly, edge to edge.
+     *
+     * Not the same as `showAllRegions`, which goes to `maxBpPerPx` — the
+     * zoom-out LIMIT, where `SHOW_ALL_REGIONS_FILL` deliberately keeps a 10%
+     * margin so the whole genome doesn't sit flush against both edges. That
+     * margin is right for "show me everything" and wrong for a caller that
+     * named the regions it wants: it draws them at 1/0.9 of fit-to-width,
+     * centered, which is a silent 11% scale difference from the
+     * single-region path (`moveTo`, span/width) reached through the same
+     * location box.
+     *
+     * The scale comes from `fitAllRegionsWindow`, which is where the rule is
+     * written — a snapshot builder that cannot call an action needs the same
+     * answer, and the two agreeing matters more than either being local. Where
+     * it clamps up to `minBpPerPx` the content is narrower than the view, and
+     * the centering is what frames it.
+     */
+    fitAllRegions(): void;
+    /**
+     * #action
+     */
+    horizontallyFlip(): void;
+} & {
+    /**
+     * #action
+     */
+    showAllRegionsInAssembly(assemblyName?: string): void;
+    /**
+     * #action
+     * this "clears the view" and makes the view return to the import form
+     */
+    clearView(): void;
+    /**
+     * #action
+     * Navigate to a location based on its refName and optionally start, end,
+     * and assemblyName. Will not try to change displayed regions, use
+     * `navToLocations` instead. Only navigates to a location if it is
+     * entirely within a displayedRegion. Navigates to the first matching
+     * location encountered.
+     *
+     * Throws an error if navigation was unsuccessful
+     *
+     * @param query - a proposed location to navigate to
+     * @param grow - optional multiplier to expand the region by (e.g., 0.2
+     * adds 20% padding on each side)
+     */
     navTo(query: NavLocation, grow?: number): void;
+    /**
+     * #action
+     * Navigate to a location based on its refName and optionally start, end,
+     * and assemblyName. Will not try to change displayed regions, use
+     * navToLocations instead. Only navigates to a location if it is entirely
+     * within a displayedRegion. Navigates to the first matching location
+     * encountered.
+     *
+     * Throws an error if navigation was unsuccessful
+     *
+     * @param locations - proposed location to navigate to
+     * @param grow - optional multiplier to expand the region by (e.g., 0.2
+     * adds 20% padding on each side)
+     */
     navToMultiple(locations: NavLocation[], grow?: number): void;
 } & {
+    /**
+     * #action
+     * Replace the region list and place the viewport in one step. The pair is
+     * the unit a coarse-block consumer can act on: called separately they
+     * publish the viewport in between, and post-await in `navToLocations`
+     * they are two transactions, so a per-bp scan runs over a window that was
+     * never on screen.
+     *
+     * With no location named it fits the regions rather than going through
+     * `showAllRegions`: the caller named the regions it wants, so it gets the
+     * width, where showAllRegions goes to the zoom-out LIMIT and its 10%
+     * margin is dead frame for a named subset.
+     */
+    showRegions(regions: Region[], location?: NavLocation): void;
+} & {
+    /**
+     * #action
+     * Navigate to the given locstring, will change displayed regions if
+     * needed, and wait for assemblies to be initialized
+     *
+     * @param input - e.g. "chr1:1-100", "chr1:1-100 chr2:1-100", "chr 1 100"
+     * @param optAssemblyName - (optional) the assembly name to use when
+     * navigating to the locstring
+     * @param grow - optional multiplier to expand the region by (e.g., 0.2
+     * adds 20% padding on each side)
+     * @returns whether the view moved. A multi-hit search raises the picker
+     * instead of navigating, and both resolve — see `handleSelectedRegion`.
+     */
+    navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<boolean>;
+    /**
+     * #action
+     * Similar to `navToLocString`, but accepts a list of parsed location
+     * objects instead of a locstring. Will try to perform
+     * `setDisplayedRegions` if changing regions
+     *
+     * @param regions - array of parsed location objects
+     * @param assemblyName - optional assembly name
+     * @param grow - optional multiplier to expand the region by (e.g., 0.2
+     * adds 20% padding on each side)
+     */
+    navToLocations(regions: ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
+} & {
+    /**
+     * #action
+     * Similar to `navToLocString`, but accepts a parsed location object
+     * instead of a locstring. Will try to perform `setDisplayedRegions` if
+     * changing regions
+     *
+     * @param parsedLocString - a parsed location object with refName, start,
+     * end, etc.
+     * @param assemblyName - optional assembly name
+     * @param grow - optional multiplier to expand the region by (e.g., 0.2
+     * adds 20% padding on each side)
+     */
+    navToLocation(parsedLocString: ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+} & {
+    /**
+     * #method
+     */
     rubberBandMenuItems(): MenuItem[];
-    bpToPx({ refName, coord, regionNumber, }: {
+    /**
+     * #method
+     */
+    bpToPx({ refName, coord, displayedRegionIndex, }: {
         refName: string;
         coord: number;
-        regionNumber?: number;
+        displayedRegionIndex?: number;
     }): {
         index: number;
         offsetPx: number;
     } | undefined;
+    /**
+     * #method
+     * Map a highlight or bookmark region to its pixel position+width inside
+     * the tracks container. Falls back to the raw refName if the region's
+     * assemblyName is missing or unknown so highlights authored without an
+     * assembly still render in single-assembly views.
+     */
     getHighlightCoords(region: {
         assemblyName?: string;
         refName: string;
@@ -213,89 +1602,90 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         width: number;
         left: 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;
+    /**
+     * #method
+     * like getHighlightCoords but laid out against the overview scalebar and
+     * shifted by the cytoband offset
+     */
+    getOverviewHighlightCoords(region: {
+        assemblyName?: string;
         refName: string;
-        oob: boolean;
-        assemblyName: string;
-        offset: number;
         start: number;
         end: number;
-        reversed?: boolean;
+    }): {
+        width: number;
+        left: number;
     } | undefined;
-    readonly visibleRegions: BaseBlock[];
+    /**
+     * #method
+     * scrolls the view to center on the given bp. if that is not in any of
+     * the displayed regions, does nothing
+     *
+     * @param coord - basepair at which you want to center the view
+     * @param refName - refName of the displayedRegion you are centering at
+     * @param displayedRegionIndex - index of the displayedRegion
+     */
+    centerAt(coord: number, refName: string, displayedRegionIndex?: number): void;
+    /**
+     * #method
+     */
+    pxToBp(px: number): import("@jbrowse/core/util/Base1DUtils").PxToBpResult;
+    /**
+     * #getter
+     */
+    readonly centerLineInfo: import("@jbrowse/core/util/Base1DUtils").PxToBpResult | undefined;
 } & {
+    /**
+     * #method
+     */
     rubberbandClickMenuItems(clickOffset: BpOffset): MenuItem[];
+    /**
+     * #method
+     * returns menu items for a highlight context menu. plugins can extend
+     * this via Core-extendPluggableElement to add their own items
+     */
+    highlightMenuItems(_highlight: HighlightType): MenuItem[];
+} & {
+    flyTo: (centerBp: number, windowWidthBp: number) => void;
+    /**
+     * #action
+     * `centerAt`'s animated twin: the same destination, reached along the
+     * arc instead of jumped to, at the zoom the view is already on.
+     */
+    flyToCenter(coord: number, refName: string): void;
 } & {
     afterCreate(): void;
     afterAttach(): void;
-}, import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
-    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-} & {
-    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-    offsetPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    bpPerPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    displayedRegions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Region[], Region[], Region[]>, [undefined]>;
-    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
-    hideHeader: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideHeaderOverview: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideNoTracksActive: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    trackSelectorType: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    showCenterLine: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<HighlightType, HighlightType, HighlightType>>, [undefined]>;
-    highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    labelsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    init: import("@jbrowse/mobx-state-tree").IType<InitState | undefined, InitState | undefined, InitState | undefined>;
-}>>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-} & {
-    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-    offsetPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    bpPerPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    displayedRegions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Region[], Region[], Region[]>, [undefined]>;
-    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
-    hideHeader: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideHeaderOverview: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideNoTracksActive: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    trackSelectorType: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    showCenterLine: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    showCytobandsSetting: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    showGridlines: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<HighlightType, HighlightType, HighlightType>>, [undefined]>;
-    highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    labelsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    init: import("@jbrowse/mobx-state-tree").IType<InitState | undefined, InitState | undefined, InitState | undefined>;
-}>>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, {
+    displayName: string | undefined;
+    minimized: boolean;
+    highlight: HighlightType[];
+    showHighlightChips: boolean;
+    id: string;
+    type: string;
+    windowStartBp: number;
+    windowWidthBp: number;
+    legacyBpPerPx: number;
+    displayedRegions: Region[];
+    tracks: any[];
+    hideHeader: boolean;
+    hideHeaderOverview: boolean;
+    hideNoTracksActive: boolean;
+    trackSelectorType: string;
+    showGridlines: boolean;
+    labelsVisible: boolean;
+    scalebarOnly: boolean;
+    init?: InitState | undefined;
+    showCytobands?: false | undefined;
+    trackLabels?: string | undefined;
+    colorByCDS?: true | undefined;
+    showAminoAcids?: false | undefined;
+    showTrackOutlines?: false | undefined;
+}>;
 export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
-export { default as LinearGenomeView, default as ReactComponent, } from './components/LinearGenomeView.tsx';
-export { default as RefNameAutocomplete } from './components/RefNameAutocomplete/index.tsx';
-export { default as SearchBox } from './components/SearchBox.tsx';
-export { renderToSvg } from './svgcomponents/SVGLinearGenomeView.tsx';
+declare module '@jbrowse/core/PluginManager' {
+    interface ViewTypeRegistry {
+        LinearGenomeView: LinearGenomeViewStateModel;
+    }
+}