@jbrowse/plugin-linear-genome-view 5.0.0-beta.2 → 5.0.0-beta.20

package/esm/LinearGenomeView/model.d.ts

@@ -1,4 +1,5 @@
-import type { BpOffset, ExportSvgOptions, HighlightType, InitState, NavLocation, VolatileGuide } from './types.ts';
+import type { BpOffset, ExportSvgOptions, HighlightInput, HighlightType, InitState, NavLocation, ViewTrackLabelMode, VolatileGuide } from './types.ts';
+import type { RegionEdit } from './util.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import type { MenuItem } from '@jbrowse/core/ui';
@@ -8,17 +9,48 @@ 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 { LaunchInput } from '@jbrowse/core/util/withLaunchInput';
+import type { LinearDisplayModel } from '@jbrowse/display-kit/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
-/** One span of the row that is not track data — see `paddingSpans`. */
-export interface PaddingSpan {
-    key: string;
-    x: number;
-    width: number;
-    kind: 'seam' | 'elided' | 'boundary';
+/** One place a name search points at, as a picker lists it. */
+export interface SearchPickerRow {
+    id: string;
+    label: string;
+    /** the canonical location string, or the hit's own when the assembly is not loaded */
+    location: string;
+    /** the name of the track the hit's index came from, or '' when the session has none */
+    trackName: string;
+}
+/**
+ * A name search's hits as a host lists them: what `view.search` returns, and
+ * what the picker holds.
+ */
+export interface SearchHits {
+    query: string;
+    assemblyName: string;
+    /** one row per hit, hits in a track the view already shows first */
+    rows: SearchPickerRow[];
+    /** lands on the row's place and reports a failure */
+    pick: (id: string) => Promise<unknown>;
+}
+/**
+ * The hits of a name search that point at more than one place, waiting for the
+ * user to choose; its `pick` also closes the picker. A host draws them however
+ * it likes: the Material view shows a dialog, and `SearchPicker` in
+ * `@jbrowse/display-ui/embed` a plain list.
+ */
+export type SearchPickerState = SearchHits;
+export type { PaddingSpan } from './util.ts';
+export interface HighlightRegion {
+    assemblyName?: string;
+    refName: string;
+    start: number;
+    end: number;
 }
 /**
  * #stateModel LinearGenomeView
  * #category view
+ * Stacks tracks under a horizontal axis of one or more genomic regions laid
+ * end to end, which the user scrolls, zooms and searches.
  *
  * #example
  * A `LinearGenomeView` is what you hand-author under `defaultSession.views`, and
@@ -30,7 +62,7 @@ export interface PaddingSpan {
  *   views: [
  *     {
  *       type: 'LinearGenomeView',
- *       colorByCDS: true,
+ *       colorByFrame: true,
  *       assembly: 'hg38',
  *       loc: 'chr1:1,000,000-1,100,000',
  *       tracks: ['genes', 'alignments'],
@@ -40,9 +72,8 @@ export interface PaddingSpan {
  * ```
  * `assembly`, `loc`, `tracks`, `tracklist`, `nav` and `highlight` need
  * on-attach resolution and are captured into the `launch` property below;
- * `colorByCDS`, `showAminoAcids`, `showCenterLine`, `trackLabels` and
- * `showHighlightChips` are plain view props MST restores natively. Both are
- * written the same way.
+ * `colorByFrame`, `showAminoAcids`, `showCenterLine` and `trackLabels` are plain
+ * view props MST restores natively. Both are written the same way.
  * At runtime the same model is driven imperatively — every property and action
  * below is reachable on `viewState.session.views[0]`:
  * ```js
@@ -52,31 +83,33 @@ export interface PaddingSpan {
  * view.zoomTo(view.bpPerPx * 2) // zoom out 2x
  * ```
  */
-export declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<{
+export declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<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").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" | "labelsVisible" | "launch" | "legacyBpPerPx" | "scalebarOnly" | "showAminoAcids" | "showCenterLine" | "showCytobands" | "showGridlines" | "showTrackOutlines" | "trackLabels" | "trackSelectorType" | "tracks" | "type" | "windowStartBp" | "windowWidthBp"> & {
+}, "axis" | "colorByFrame" | "displayedRegions" | "hideHeader" | "hideHeaderOverview" | "hideNoTracksActive" | "id" | "launch" | "legacyBpPerPx" | "scalebarOnly" | "showAminoAcids" | "showCenterLine" | "showCytobands" | "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>;
     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>;
+    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>;
     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]>;
     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").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]>;
+    trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"" | "hidden" | "offset" | "overlapping">, [undefined]>;
+    axis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly grid: {
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>, [undefined]>;
+    colorByFrame: 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]>;
@@ -85,50 +118,55 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     width: number;
     bodyMounted: boolean;
 } & {
+    readonly rendersDisplays: boolean;
     readonly effectiveBodyMounted: boolean;
     menuItems(): MenuItem[];
     readonly ownTracks: import("@jbrowse/core/util").AbstractTrackModel[];
-    readonly allViews: import("@jbrowse/core/util").AbstractViewModel[];
-} & {
-    readonly allTracks: import("@jbrowse/core/util").AbstractTrackModel[];
+    readonly ownViews: import("@jbrowse/core/util").AbstractViewModel[];
 } & {
     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
+     * Height of each track's in-flow label band, measured by
+     * TrackContainer as the rendering container's offset inside its Paper.
+     * Absent (0) while the label is hidden, overlapping, or not yet
+     * measured. Observable, so the offset and height getters re-derive
+     * when a band changes.
      */
-    volatileWidth: number | undefined;
+    trackLabelBands: import("mobx").ObservableMap<string, number>;
     /**
      * #volatile
+     * How much taller the view's box is than the scroll port it sits in,
+     * in px, negative when it is shorter. Measured by the view component
+     * for a top-level view; undefined until then, and for a nested one.
      */
-    minimumBlockWidth: number;
+    scrollPortExcess: number | undefined;
+    /**
+     * #volatile
+     */
+    volatileWidth: number | undefined;
     /**
      * #volatile
      */
     draggingTrackId: undefined | string;
     /**
      * #volatile
+     * Set by a search whose hits name more than one place, until the user
+     * picks one or closes it.
      */
-    lastTrackDragY: undefined | number;
+    searchPicker: SearchPickerState | undefined;
     /**
      * #volatile
      */
-    volatileError: unknown;
+    lastTrackDragY: undefined | number;
     /**
      * #volatile
      */
-    trackRefs: Record<string, HTMLDivElement>;
+    volatileError: unknown;
     /**
      * #volatile
      */
@@ -143,26 +181,34 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     coarseBpPerPx: number;
     /**
      * #volatile
+     * the scroll offset the coarse blocks were laid out at, in px at
+     * `coarseBpPerPx`: the settled viewport's left edge, which the first
+     * coarse block is not while the view is scrolled before the first region
      */
-    leftOffset: undefined | BpOffset;
+    coarseOffsetPx: number;
     /**
      * #volatile
      */
-    rightOffset: undefined | BpOffset;
+    leftOffset: undefined | BpOffset;
     /**
      * #volatile
      */
-    isScalebarRefNameMenuOpen: boolean;
+    rightOffset: undefined | BpOffset;
     /**
      * #volatile
      */
-    scalebarRefNameClickPending: boolean;
+    isScalebarRefNameMenuOpen: boolean;
     /**
      * #volatile
      * temporary vertical guides that can be set by displays (e.g., LD display hover)
      */
     volatileGuides: VolatileGuide[];
 } & {
+    /**
+     * #getter
+     * `axis.grid`: whether the ruler's ticks run down through the tracks.
+     */
+    readonly axisGrid: boolean;
     /**
      * #getter
      * the launch state that still has something to apply — the gate every
@@ -189,6 +235,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * corresponds roughly to the horizontal scroll of the LGV
      */
     readonly offsetPx: number;
+    /**
+     * #getter
+     * a displayed region narrower than this many pixels draws as an elided
+     * block
+     */
+    readonly minimumBlockWidth: number;
     /**
      * #getter
      * scroll-to-zoom is a global, personal preference resolved from the
@@ -198,17 +250,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      */
-    readonly pinnedTracks: any[];
+    readonly pinnedTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      */
-    readonly unpinnedTracks: any[];
+    readonly unpinnedTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      * the effective track labels setting, resolving the stored `trackLabels`
      * against the LinearGenomeViewPlugin config default
      */
-    readonly effectiveTrackLabels: any;
+    readonly effectiveTrackLabels: ViewTrackLabelMode;
     /**
      * #getter
      */
@@ -226,6 +278,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #getter
      */
     readonly assemblyDisplayNames: string[];
+    /**
+     * #getter
+     * the session's highlights on this view's assemblies
+     */
+    readonly highlights: HighlightType[];
     /**
      * #getter
      * checking if lgv is a 'top-level' view is used for toggling pin track
@@ -241,8 +298,19 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     /**
      * #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
+     * The census entry for this view: the tracks it holds itself. Declared
+     * rather than derived — see `BaseViewModel.ownTracks`.
+     */
+    readonly ownTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
+    /**
+     * #getter
+     * See `BaseViewModel.rendersDisplays`.
+     */
+    readonly rendersDisplays: boolean;
+    /**
+     * #getter
+     * Assembly name captioning the scalebar ahead of its 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
@@ -270,21 +338,63 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }> & {
         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;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
+        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
         statusMessage: string | undefined;
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -298,8 +408,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
         setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
             cytobands: import("@jbrowse/core/util").Feature[];
             geneticCodes: Record<string, number>;
@@ -313,7 +424,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         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;
@@ -331,27 +441,72 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | 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>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }, {
         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;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
+        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
         statusMessage: string | undefined;
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -365,8 +520,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
         setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
             cytobands: import("@jbrowse/core/util").Feature[];
             geneticCodes: Record<string, number>;
@@ -380,7 +536,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         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;
@@ -398,12 +553,25 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | undefined;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+    /**
+     * #getter
+     * The assembly a pending launch is for: the one it names, else the one
+     * the view already shows. A re-launch of a materialized view (a
+     * `jb.setSession` document writing `loc` beside the built state) need
+     * not restate it; without the default the readiness gate waited on
+     * `assemblyManager.get(undefined)` for good. Undefined on a fresh view
+     * whose blob names none, which `error` reports.
+     */
+    readonly launchAssemblyName: string | undefined;
     /**
      * #getter
      */
@@ -419,21 +587,63 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }> & {
         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;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
+        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
         statusMessage: string | undefined;
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -447,8 +657,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
         setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
             cytobands: import("@jbrowse/core/util").Feature[];
             geneticCodes: Record<string, number>;
@@ -462,7 +673,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         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;
@@ -480,27 +690,72 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | 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>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }, {
         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;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
+        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
         statusMessage: string | undefined;
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -514,8 +769,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
         setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
             cytobands: import("@jbrowse/core/util").Feature[];
             geneticCodes: Record<string, number>;
@@ -529,7 +785,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         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;
@@ -547,34 +802,21 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | 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)
+     * The loading screen's text while `showLoading`, taken from the
+     * assembly being waited on; undefined otherwise.
      */
-    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;
+    readonly loading: import("@jbrowse/core/util/viewStatus").ViewLoading | undefined;
     /**
      * #getter
      */
@@ -614,12 +856,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * `width`/`staticBlocks` throw by design before the view has been
      * measured and navigated.
      *
-     * **Not `initialized`**, which is the trap this getter exists to close.
+     * Use this getter rather than `initialized`.
      * 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
+     * folds in `awaitingInitNavigation`, the getter for exactly
      * that gap.
      *
      * `error` is the third outcome and is why this is not a bare
@@ -657,42 +899,31 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #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.
+     * The track *label* is not counted here: an offset label is an in-flow
+     * box whose height is whatever the theme renders a Paper of icon buttons
+     * at, so it is measured into `trackLabelBands` per track and added by
+     * `trackLabelBand` rather than derived.
      */
     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
+     * rendered height of a single track, using 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;
+    trackHeight(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>)[number]): number;
+    /**
+     * #method
+     * the measured in-flow label band above a track's rendering container,
+     * 0 until TrackContainer has measured one or when no label is in flow
+     */
+    trackLabelBand(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>)[number]): number;
     /**
      * #getter
      */
@@ -705,6 +936,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #getter
      */
     readonly height: number;
+    /**
+     * #getter
+     * The display height of each track a whole-stack resize moves, by track
+     * instance id: every shown track that is not minimized.
+     */
+    readonly resizableTrackHeights: Map<string, number>;
     /**
      * #method
      * Y offset (in pixels, from the top of the view) where a track's
@@ -712,19 +949,24 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
+     * Includes each track's measured label band, this track's own included,
+     * since an in-flow label sits above the rendering container inside the
+     * same Paper. Exact once TrackContainer has measured; before that it is
+     * short by the unmeasured bands.
      */
     getTrackYOffset(trackId: string): number | undefined;
+    /**
+     * #getter
+     * `getTrackYOffset` for every shown track, by trackId, from one walk
+     */
+    readonly trackYOffsets: Map<string, number>;
     /**
      * #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[];
+    trackSection(id: string): (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      */
@@ -735,16 +977,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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.
+     * The zoom-out limit. Equal to the fit for this view's regions, except
+     * while a container holds it on a coarser shared scale, such as 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.
+     * The shared scale raises the limit. A bpPerPx written past the limit
+     * would be undone by the first operation that clamps (a wheel tick, a
+     * rubberband, a `setDisplayedRegions`), as with the dotplot's locked
+     * aspect ratio turning "zoom out" into a zoom in (`axisMaxBpPerPx`).
+     * Every zoom clamps against the same ceiling, so full zoom-out stops at
+     * the shared scale.
      */
     readonly maxBpPerPx: number;
     /**
@@ -753,8 +995,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
+     * A getter rather than a volatile the container writes: the number is a
+     * function of every row's fit, all of which change on a resize, and a
      * stored copy would be stale by the next layout.
      */
     readonly sharedFitBpPerPx: number;
@@ -791,11 +1033,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      */
-    readonly trackMap: Map<string, any>;
+    readonly trackMap: Map<string, import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>;
     /**
      * #method
      */
-    getTrack(id: string): any;
+    getTrack(id: string): (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>) | undefined;
     /**
      * #method
      * displayId of the active (shown) display for a track in this view, used
@@ -803,6 +1045,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * track's other displays
      */
     getActiveDisplayId(trackId: string): string | undefined;
+} & {
+    /**
+     * #action
+     * Dismiss the search picker without choosing a place.
+     */
+    closeSearchPicker(): void;
 } & {
     /**
      * #action
@@ -815,7 +1063,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setColorByCDS(flag: boolean): void;
+    setColorByFrame(flag: boolean): void;
     /**
      * #action
      */
@@ -827,19 +1075,34 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setWidth(newWidth: number): void;
+    setTrackLabelBand(trackId: string, band: number): void;
     /**
      * #action
      */
-    setError(error: unknown): void;
+    setScrollPortExcess(px: number | undefined): void;
     /**
      * #action
+     * Grow or shrink every unminimized track by `distance` px in all, each
+     * by its share of the height it has above the display minimum. `from` is
+     * the heights to scale, by track instance id; a drag passes the heights
+     * it started with, so whole-pixel rounding does not compound frame by
+     * frame. Returns how far the stack moved.
      */
-    setIsScalebarRefNameMenuOpen(isOpen: boolean): void;
+    resizeTracks(distance: number, from?: any): number;
+    /**
+     * #action
+     * A resize keeps the window in bp, so `bpPerPx` follows the new width
+     * and the view keeps framing the same sequence (ADR-070).
+     */
+    setWidth(newWidth: number): void;
+    /**
+     * #action
+     */
+    setError(error: unknown): void;
     /**
      * #action
      */
-    setScalebarRefNameClickPending(pending: boolean): void;
+    setIsScalebarRefNameMenuOpen(isOpen: boolean): void;
     /**
      * #action
      */
@@ -859,11 +1122,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setShowGridlines(b: boolean): void;
-    /**
-     * #action
-     */
-    setLabelsVisible(arg: boolean): void;
+    setAxisGrid(grid: boolean): void;
     /**
      * #action
      * set temporary vertical guides (e.g., for LD display hover)
@@ -898,8 +1157,20 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setOffsets(left?: BpOffset, right?: BpOffset): void;
     /**
      * #action
+     * Raise the picker over search results that name more than one place.
+     * @param onPick - where a picked result lands; by default it navigates
+     * there and shows the track its index came from
      */
-    setSearchResults(searchResults: BaseResult[], searchQuery: string, assemblyName: string): void;
+    setSearchResults(searchResults: BaseResult[], searchQuery: string, assemblyName: string, onPick?: (result: BaseResult) => Promise<unknown>): void;
+    /**
+     * #action
+     * Search the view's assembly by name, for a host listing the hits
+     * itself. A row's `pick` lands as the search box does: it navigates
+     * there and shows the track the hit's index came from.
+     */
+    search(query: string, opts?: {
+        signal?: AbortSignal;
+    }): Promise<SearchHits>;
     /**
      * #action
      */
@@ -909,33 +1180,62 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     hideTrack(trackId: string): boolean;
 } & {
+    /**
+     * #action
+     * Resize every unminimized track so the view is exactly as tall as the
+     * scroll port it sits in. Does nothing until the view has measured one.
+     */
+    fitTracksToWindow(): void;
     /**
      * #action
      * showTrack for a track whose display state model may be lazily
      * loaded: loads it, then shows
      */
     launchTrack(trackId: string, initialSnapshot?: any, displayInitialSnapshot?: any, inlineConf?: Record<string, unknown>): Promise<any>;
-} & {
     /**
      * #action
+     * Replace the highlights `highlights` reads, each written as the launch
+     * spec's `highlight` writes one: a locstring, or an object whose
+     * `assemblyName` defaults to the view's. Throws on one that names no
+     * region, writing none.
+     */
+    setHighlights(highlights: readonly (string | HighlightInput)[]): void;
+    /**
+     * #action
+     * Show files from the user's disk as session tracks: one per data file,
+     * beside the index among them that names it, its type guessed from its
+     * name. Adds nothing when one file has no known type. Resolves the new
+     * tracks' ids.
+     */
+    showFiles(files: readonly File[]): Promise<string[]>;
+} & {
+    /**
+     * #method
+     * The shown track a move action means: the menu passes a track model's
+     * own `id`, an agent passes the `trackId` it knows the track by, and
+     * both name one shown track. Answers the model id, or the argument
+     * unchanged when nothing shown matches, so the move reports it.
      */
-    moveTrackDown(id: string): void;
+    trackModelId(idOrTrackId: string): string;
+} & {
+    moveTrack: (moving: string, target: string) => void;
     /**
      * #action
      */
-    moveTrackUp(id: string): void;
+    moveTrackDown(idOrTrackId: string): void;
     /**
      * #action
      */
-    moveTrackToTop(id: string): void;
+    moveTrackUp(idOrTrackId: string): void;
     /**
      * #action
      */
-    moveTrackToBottom(id: string): void;
+    moveTrackToTop(idOrTrackId: string): void;
     /**
      * #action
      */
-    moveTrack(movingId: string, targetId: string): void;
+    moveTrackToBottom(idOrTrackId: string): void;
+} & {
     /**
      * #action
      */
@@ -948,7 +1248,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden'): void;
+    setTrackLabels(setting: ViewTrackLabelMode): void;
     /**
      * #action
      */
@@ -961,24 +1261,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #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
      */
@@ -987,10 +1269,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setDraggingTrackId(idx?: string): void;
-    /**
-     * #action
-     */
-    setLastTrackDragY(y: number): void;
     /**
      * #action
      * called while dragging a track over the track at `targetId`; reorders
@@ -1002,11 +1280,25 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setLaunch(launch?: LaunchInput<InitState>): void;
+} & {
     /**
      * #method
-     * creates an svg export and save using FileSaver
+     * Helper method for the fetchSequence.
+     * Returns the regions the user selected with 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[]
      */
-    exportSvg(opts?: ExportSvgOptions): Promise<void>;
+    getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
+        assemblyName: string;
+        refName: string;
+        start: number;
+        end: number;
+    }[];
 } & {
     slide: (viewWidths: number) => void;
     zoom: (targetBpPerPx: number) => void;
@@ -1020,19 +1312,18 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #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
+     * up as a lone half-triangle. The chromosome also needs bands: a cytoband
+     * file often lists only the main chromosomes, not chrM or the
+     * unplaced scaffolds
      */
     readonly canShowCytobands: boolean;
     /**
      * #getter
      * the `showCytobands` setting gated by whether cytobands can be shown at
-     * all (whole chromosome + data present) — i.e. actually on screen
+     * all (whole chromosome with bands in the cytoband file) and by the header
+     * overview they draw in being on, which the SVG export follows too
      */
     readonly effectiveShowCytobands: boolean;
-    /**
-     * #getter
-     */
-    readonly anyCytobandsExist: boolean;
     /**
      * #getter
      * the cytoband is displayed to the right of the chromosome name, and
@@ -1049,6 +1340,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * return the view menu items
      */
     menuItems(): MenuItem[];
+    /**
+     * #method
+     * the view menu's Highlights submenu; extend this to add a row there
+     */
+    highlightsSubMenuItems(): MenuItem[];
     /**
      * #method
      * what a plugin can start from the selected region — a synteny view, a
@@ -1077,9 +1373,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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
+     * visible genome regions on the screen. Static blocks can go
+     * offscreen, while dynamic blocks represent exactly what is on screen
      */
     readonly dynamicBlocks: BlockSet;
     /**
@@ -1111,12 +1406,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
+     * this number moves. `scalebarRefNameLabels` is the exception: 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 —
+     * **The subtraction must happen here, in float64.** `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
@@ -1128,13 +1421,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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 —
+     * This applies the GPU side's rule one layer up; see
      * `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
+     * copies written out at each call site disagree about rounding. Round it where the content is text
      * (a fractional offset blurs a label); leave it alone for paths and
      * boxes.
      */
@@ -1177,11 +1469,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
+     * does not scroll the chromosome's 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:
+     * This getter applies three rules that a host drawing region names would
+     * otherwise have to rediscover, 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
@@ -1193,7 +1485,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *   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` —
+     *   run leaves. Clipped to that space, `chr16` reads as `chr1` —
      *   a different chromosome rather than a shortened name, which is why
      *   this is a fit test rather than an ellipsis.
      *
@@ -1209,10 +1501,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
+     * orientation. `captionSpanPx` is the width it takes: the sticky label
+     * pins to its right edge rather than the viewport's, and the coordinate
+     * numbers stay out from under it. The SVG export deliberately
      * calls `getScalebarRefNameLabels` itself with no prefix rather than
-     * reading this, since it draws its own assembly name above the ruler.
+     * reading this, since it draws the assembly name itself above the ruler.
      */
     readonly scalebarRefNameLabels: {
         labels: import("./util.ts").ScalebarRefNameLabel[];
@@ -1224,36 +1517,36 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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:
+     * three. A host that draws the row's chrome itself needs all three kinds:
      *
      * - `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
+     *   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.
+     *   two-region view looks like a single region.
+     *   `isRightEndOfDisplayedRegion` marks it; the right edge of the
+     *   currently *loaded* blocks, which block geometry gives you, is a
+     *   different set.
      * - `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.
+     *   a real assembly is mostly these (hg38 has 455 sequences, and all
+     *   but the 24 chromosomes are under a pixel wide), so a host that
+     *   skips them leaves that part of the row empty.
      * - `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.
+     *   last. Greying it makes the last region's seam read as the edge of a
+     *   filled area, where it would otherwise look like a line in the
+     *   middle of the track.
+     *
+     * Elided blocks get no seam even though they have the flag: at the
+     * zoom where regions elide, one bar per region would fill the row solid
+     * grey.
+     *
+     * PaddingBlocks is the in-tree consumer. The SVG export does not use
+     * it: `SVGRegionSeparators` walks dynamicBlocks itself and draws only
+     * the seam, because `elided` and `boundary` mark state for an
+     * interactive row. In a static figure the striped grey would cover most
+     * of the row at whole-genome zoom. The export keeps the seam because
+     * regions lay out contiguously and the seam is all that separates two
+     * of them.
      */
     readonly paddingSpans: readonly {
         key: string;
@@ -1285,8 +1578,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
+     * describe. The SVG export checks it before drawing its header.
+     * Distinct from `hasDisplayedRegions`, which only asks whether the
      * view has been given regions, not whether any are on screen.
      */
     readonly hasVisibleContent: boolean;
@@ -1322,7 +1615,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      * Right edge (px, viewport-relative) of the on-screen content, clamped
-     * to the track — where a right-pinned overlay such as a wiggle's colour
+     * to the track — where a right-pinned overlay such as a wiggle's color
      * or score legend belongs, rather than out in the empty gutter the
      * regions can leave at whole-genome zoom. `@jbrowse/display-kit`'s
      * `contentRightEdgePx` states the rule; an SVG export applies the same
@@ -1332,7 +1625,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * array of fresh objects on every pan and zoom frame, so a component
      * that derived this number itself re-rendered on every frame of every
      * gesture — to produce, whenever content fills the track, the unchanged
-     * `trackWidthPx`. Reading the scalar lets MobX's `===` stop the chain at
+     * `trackWidthPx`. A component that reads the scalar lets MobX's `===` stop the chain at
      * this computed instead. Measured over 20 zoom frames: the wiggle
      * family's three body instances fell from 66 renders to 7.
      */
@@ -1362,23 +1655,22 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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 blocks 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.
+     * The coarse blocks stop a per-bp scan from recomputing on every
+     * animation frame during a pan or zoom. Wiggle's autoscale domain, the
+     * alignments coverage scale and MAF's coverage band use them. While the
+     * coarse blocks are stale the result is a frame or two old, as the
+     * debounce intends. **Empty coarse blocks are a different case.** A scan
+     * over no blocks yields no entries, and the consumer falls back to the
+     * domain `[0,1]`, which draws a line plot blank and a density plot
+     * saturated. The coarse blocks are empty for the 500ms between a view
+     * initializing and the coarse autorun's first run, and data can load
+     * within that window.
      *
-     * One recompute at that transition, against N per frame, which is the
-     * trade the guard was making anyway.
+     * Falling back to the live blocks costs one extra recompute at that
+     * transition, compared with N per frame without the debounce.
      */
     readonly settledDynamicBlocks: ContentBlock[];
     /**
@@ -1411,7 +1703,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *
      * 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
+     * the feature display'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
@@ -1419,21 +1711,29 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
+     * 4040bp on screen.
      *
-     * **The continuous paths deliberately do not come through here.** The
+     * **The continuous paths do not call this.** 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.
+     * autorun's 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
+     * Every placer calls it, and `placersSettleCoarseBlocks.test.ts` enforces
+     * that for 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;
+} & {
+    /**
+     * #method
+     * renders the view to SVG markup, which it returns; saves it through
+     * FileSaver unless `save: false`. A `viewWidth` lays the view out at
+     * that many pixels for the export, as a window that wide would, and
+     * puts the on-screen width back after.
+     */
+    exportSvg(opts?: ExportSvgOptions): Promise<string>;
 } & {
     /**
      * #action
@@ -1446,17 +1746,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     moveTo(start?: BpOffset, end?: BpOffset): 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
+     * Place the viewport by `bpPerPx` and `offsetPx`, the pixel pair the view
+     * stored before it stored the window. 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.
+     * gesture, a rubberband.
      */
     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
+     * width and left edge, both in bp. The bp-space counterpart of `setNewView`, 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.
@@ -1478,8 +1778,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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
+     * Settles the coarse blocks, since this is the worst jump to leave
+     * unsettled: they 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;
@@ -1624,6 +1924,24 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * adds 20% padding on each side)
      */
     navToLocation(parsedLocString: ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+    /**
+     * #action
+     * adds the region in view to the session's highlights
+     */
+    highlightCurrentRegion(): void;
+    /**
+     * #action
+     * navigates to a highlight, zoomed out a little for context. Goes through
+     * a locstring so it reaches a refName the view is not displaying
+     */
+    navToHighlight(highlight: HighlightType): Promise<boolean>;
+} & {
+    /**
+     * #action
+     * navigates to the most recently added highlight on this view's
+     * assemblies
+     */
+    navigateNewestHighlight(): Promise<void>;
 } & {
     /**
      * #method
@@ -1642,31 +1960,30 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } | undefined;
     /**
      * #method
-     * Map a highlight or bookmark region to its pixel position+width inside
+     * Map a highlight 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;
-        start: number;
-        end: number;
-    }): {
+    getHighlightCoords(region: HighlightRegion): {
         width: number;
         left: number;
     } | undefined;
+    /**
+     * #method
+     * y ranges, from the top of the highlight bands, of tracks whose display
+     * sets `drawsGenomicCoordinates` to false; the bands skip them
+     */
+    nonGenomicTrackBands(): {
+        top: number;
+        height: number;
+    }[];
     /**
      * #method
      * like getHighlightCoords but laid out against the overview scalebar and
      * shifted by the cytoband offset
      */
-    getOverviewHighlightCoords(region: {
-        assemblyName?: string;
-        refName: string;
-        start: number;
-        end: number;
-    }): {
+    getOverviewHighlightCoords(region: HighlightRegion): {
         width: number;
         left: number;
     } | undefined;
@@ -1688,6 +2005,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #getter
      */
     readonly centerLineInfo: import("@jbrowse/core/util/Base1DUtils").PxToBpResult | undefined;
+} & {
+    /**
+     * #action
+     * a region edit from the ruler's menu as one action, which a synteny
+     * stack's follow reads as the reader's gesture on this row; see
+     * `setDisplayedRegionsKeepingCenter`
+     */
+    editDisplayedRegions(edit: RegionEdit): void;
 } & {
     /**
      * #method
@@ -1695,8 +2020,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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
+     * a highlight chip's menu rows after Dismiss; extend this to add one
      */
     highlightMenuItems(_highlight: HighlightType): MenuItem[];
 } & {
@@ -1706,35 +2030,45 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * `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;
+    flyToCenter(coord: number, refName: string, displayedRegionIndex?: number): void;
+    /**
+     * #action
+     * A flight to a linear bp centre at the zoom the view is on, or is
+     * already flying to, widened where that is narrower than `fitWidthBp`.
+     * The current width mid-flight is a point on the arc, so a second
+     * flight read from it would land pulled back.
+     */
+    flyToFit(centerBp: number, fitWidthBp: number): void;
 } & {
     afterCreate(): void;
     afterAttach(): void;
-}, import("@jbrowse/core/util/withLaunchInput").LaunchSnapshotIn<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<{
+}, import("@jbrowse/core/util/withLaunchInput").LaunchSnapshotIn<import("@jbrowse/mobx-state-tree").IModelType<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").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" | "labelsVisible" | "launch" | "legacyBpPerPx" | "scalebarOnly" | "showAminoAcids" | "showCenterLine" | "showCytobands" | "showGridlines" | "showTrackOutlines" | "trackLabels" | "trackSelectorType" | "tracks" | "type" | "windowStartBp" | "windowWidthBp"> & {
+}, "axis" | "colorByFrame" | "displayedRegions" | "hideHeader" | "hideHeaderOverview" | "hideNoTracksActive" | "id" | "launch" | "legacyBpPerPx" | "scalebarOnly" | "showAminoAcids" | "showCenterLine" | "showCytobands" | "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>;
     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>;
+    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>;
     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]>;
     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").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]>;
+    trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"" | "hidden" | "offset" | "overlapping">, [undefined]>;
+    axis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly grid: {
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>, [undefined]>;
+    colorByFrame: 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]>;
@@ -1743,50 +2077,55 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     width: number;
     bodyMounted: boolean;
 } & {
+    readonly rendersDisplays: boolean;
     readonly effectiveBodyMounted: boolean;
     menuItems(): MenuItem[];
     readonly ownTracks: import("@jbrowse/core/util").AbstractTrackModel[];
-    readonly allViews: import("@jbrowse/core/util").AbstractViewModel[];
-} & {
-    readonly allTracks: import("@jbrowse/core/util").AbstractTrackModel[];
+    readonly ownViews: import("@jbrowse/core/util").AbstractViewModel[];
 } & {
     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
+     * Height of each track's in-flow label band, measured by
+     * TrackContainer as the rendering container's offset inside its Paper.
+     * Absent (0) while the label is hidden, overlapping, or not yet
+     * measured. Observable, so the offset and height getters re-derive
+     * when a band changes.
      */
-    volatileWidth: number | undefined;
+    trackLabelBands: import("mobx").ObservableMap<string, number>;
+    /**
+     * #volatile
+     * How much taller the view's box is than the scroll port it sits in,
+     * in px, negative when it is shorter. Measured by the view component
+     * for a top-level view; undefined until then, and for a nested one.
+     */
+    scrollPortExcess: number | undefined;
     /**
      * #volatile
      */
-    minimumBlockWidth: number;
+    volatileWidth: number | undefined;
     /**
      * #volatile
      */
     draggingTrackId: undefined | string;
     /**
      * #volatile
+     * Set by a search whose hits name more than one place, until the user
+     * picks one or closes it.
      */
-    lastTrackDragY: undefined | number;
+    searchPicker: SearchPickerState | undefined;
     /**
      * #volatile
      */
-    volatileError: unknown;
+    lastTrackDragY: undefined | number;
     /**
      * #volatile
      */
-    trackRefs: Record<string, HTMLDivElement>;
+    volatileError: unknown;
     /**
      * #volatile
      */
@@ -1801,26 +2140,34 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     coarseBpPerPx: number;
     /**
      * #volatile
+     * the scroll offset the coarse blocks were laid out at, in px at
+     * `coarseBpPerPx`: the settled viewport's left edge, which the first
+     * coarse block is not while the view is scrolled before the first region
      */
-    leftOffset: undefined | BpOffset;
+    coarseOffsetPx: number;
     /**
      * #volatile
      */
-    rightOffset: undefined | BpOffset;
+    leftOffset: undefined | BpOffset;
     /**
      * #volatile
      */
-    isScalebarRefNameMenuOpen: boolean;
+    rightOffset: undefined | BpOffset;
     /**
      * #volatile
      */
-    scalebarRefNameClickPending: boolean;
+    isScalebarRefNameMenuOpen: boolean;
     /**
      * #volatile
      * temporary vertical guides that can be set by displays (e.g., LD display hover)
      */
     volatileGuides: VolatileGuide[];
 } & {
+    /**
+     * #getter
+     * `axis.grid`: whether the ruler's ticks run down through the tracks.
+     */
+    readonly axisGrid: boolean;
     /**
      * #getter
      * the launch state that still has something to apply — the gate every
@@ -1847,6 +2194,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * corresponds roughly to the horizontal scroll of the LGV
      */
     readonly offsetPx: number;
+    /**
+     * #getter
+     * a displayed region narrower than this many pixels draws as an elided
+     * block
+     */
+    readonly minimumBlockWidth: number;
     /**
      * #getter
      * scroll-to-zoom is a global, personal preference resolved from the
@@ -1856,17 +2209,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      */
-    readonly pinnedTracks: any[];
+    readonly pinnedTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      */
-    readonly unpinnedTracks: any[];
+    readonly unpinnedTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      * the effective track labels setting, resolving the stored `trackLabels`
      * against the LinearGenomeViewPlugin config default
      */
-    readonly effectiveTrackLabels: any;
+    readonly effectiveTrackLabels: ViewTrackLabelMode;
     /**
      * #getter
      */
@@ -1884,6 +2237,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #getter
      */
     readonly assemblyDisplayNames: string[];
+    /**
+     * #getter
+     * the session's highlights on this view's assemblies
+     */
+    readonly highlights: HighlightType[];
     /**
      * #getter
      * checking if lgv is a 'top-level' view is used for toggling pin track
@@ -1899,8 +2257,19 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     /**
      * #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
+     * The census entry for this view: the tracks it holds itself. Declared
+     * rather than derived — see `BaseViewModel.ownTracks`.
+     */
+    readonly ownTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
+    /**
+     * #getter
+     * See `BaseViewModel.rendersDisplays`.
+     */
+    readonly rendersDisplays: boolean;
+    /**
+     * #getter
+     * Assembly name captioning the scalebar ahead of its 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
@@ -1928,21 +2297,63 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }> & {
         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;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
+        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
         statusMessage: string | undefined;
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -1956,8 +2367,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
         setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
             cytobands: import("@jbrowse/core/util").Feature[];
             geneticCodes: Record<string, number>;
@@ -1971,7 +2383,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         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;
@@ -1989,27 +2400,72 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | 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>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }, {
         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;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
+        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
         statusMessage: string | undefined;
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -2023,8 +2479,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
         setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
             cytobands: import("@jbrowse/core/util").Feature[];
             geneticCodes: Record<string, number>;
@@ -2038,7 +2495,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         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;
@@ -2056,12 +2512,25 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | undefined;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+    /**
+     * #getter
+     * The assembly a pending launch is for: the one it names, else the one
+     * the view already shows. A re-launch of a materialized view (a
+     * `jb.setSession` document writing `loc` beside the built state) need
+     * not restate it; without the default the readiness gate waited on
+     * `assemblyManager.get(undefined)` for good. Undefined on a fresh view
+     * whose blob names none, which `error` reports.
+     */
+    readonly launchAssemblyName: string | undefined;
     /**
      * #getter
      */
@@ -2077,21 +2546,63 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }> & {
         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;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
+        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
         statusMessage: string | undefined;
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -2105,8 +2616,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
         setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
             cytobands: import("@jbrowse/core/util").Feature[];
             geneticCodes: Record<string, number>;
@@ -2120,7 +2632,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         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;
@@ -2138,27 +2649,72 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | 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>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }, {
         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;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
+        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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;
+        lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
         statusMessage: string | undefined;
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -2172,8 +2728,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
         setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
             cytobands: import("@jbrowse/core/util").Feature[];
             geneticCodes: Record<string, number>;
@@ -2187,7 +2744,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         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;
@@ -2205,34 +2761,21 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | 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)
+     * The loading screen's text while `showLoading`, taken from the
+     * assembly being waited on; undefined otherwise.
      */
-    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;
+    readonly loading: import("@jbrowse/core/util/viewStatus").ViewLoading | undefined;
     /**
      * #getter
      */
@@ -2272,12 +2815,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * `width`/`staticBlocks` throw by design before the view has been
      * measured and navigated.
      *
-     * **Not `initialized`**, which is the trap this getter exists to close.
+     * Use this getter rather than `initialized`.
      * 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
+     * folds in `awaitingInitNavigation`, the getter for exactly
      * that gap.
      *
      * `error` is the third outcome and is why this is not a bare
@@ -2315,42 +2858,31 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #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.
+     * The track *label* is not counted here: an offset label is an in-flow
+     * box whose height is whatever the theme renders a Paper of icon buttons
+     * at, so it is measured into `trackLabelBands` per track and added by
+     * `trackLabelBand` rather than derived.
      */
     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
+     * rendered height of a single track, using 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;
+    trackHeight(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>)[number]): number;
+    /**
+     * #method
+     * the measured in-flow label band above a track's rendering container,
+     * 0 until TrackContainer has measured one or when no label is in flow
+     */
+    trackLabelBand(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>)[number]): number;
     /**
      * #getter
      */
@@ -2363,6 +2895,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #getter
      */
     readonly height: number;
+    /**
+     * #getter
+     * The display height of each track a whole-stack resize moves, by track
+     * instance id: every shown track that is not minimized.
+     */
+    readonly resizableTrackHeights: Map<string, number>;
     /**
      * #method
      * Y offset (in pixels, from the top of the view) where a track's
@@ -2370,19 +2908,24 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
+     * Includes each track's measured label band, this track's own included,
+     * since an in-flow label sits above the rendering container inside the
+     * same Paper. Exact once TrackContainer has measured; before that it is
+     * short by the unmeasured bands.
      */
     getTrackYOffset(trackId: string): number | undefined;
+    /**
+     * #getter
+     * `getTrackYOffset` for every shown track, by trackId, from one walk
+     */
+    readonly trackYOffsets: Map<string, number>;
     /**
      * #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[];
+    trackSection(id: string): (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      */
@@ -2393,16 +2936,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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.
+     * The zoom-out limit. Equal to the fit for this view's regions, except
+     * while a container holds it on a coarser shared scale, such as 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.
+     * The shared scale raises the limit. A bpPerPx written past the limit
+     * would be undone by the first operation that clamps (a wheel tick, a
+     * rubberband, a `setDisplayedRegions`), as with the dotplot's locked
+     * aspect ratio turning "zoom out" into a zoom in (`axisMaxBpPerPx`).
+     * Every zoom clamps against the same ceiling, so full zoom-out stops at
+     * the shared scale.
      */
     readonly maxBpPerPx: number;
     /**
@@ -2411,8 +2954,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
+     * A getter rather than a volatile the container writes: the number is a
+     * function of every row's fit, all of which change on a resize, and a
      * stored copy would be stale by the next layout.
      */
     readonly sharedFitBpPerPx: number;
@@ -2449,11 +2992,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      */
-    readonly trackMap: Map<string, any>;
+    readonly trackMap: Map<string, import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>;
     /**
      * #method
      */
-    getTrack(id: string): any;
+    getTrack(id: string): (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>) | undefined;
     /**
      * #method
      * displayId of the active (shown) display for a track in this view, used
@@ -2461,6 +3004,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * track's other displays
      */
     getActiveDisplayId(trackId: string): string | undefined;
+} & {
+    /**
+     * #action
+     * Dismiss the search picker without choosing a place.
+     */
+    closeSearchPicker(): void;
 } & {
     /**
      * #action
@@ -2473,7 +3022,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setColorByCDS(flag: boolean): void;
+    setColorByFrame(flag: boolean): void;
     /**
      * #action
      */
@@ -2485,19 +3034,34 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setWidth(newWidth: number): void;
+    setTrackLabelBand(trackId: string, band: number): void;
     /**
      * #action
      */
-    setError(error: unknown): void;
+    setScrollPortExcess(px: number | undefined): void;
     /**
      * #action
+     * Grow or shrink every unminimized track by `distance` px in all, each
+     * by its share of the height it has above the display minimum. `from` is
+     * the heights to scale, by track instance id; a drag passes the heights
+     * it started with, so whole-pixel rounding does not compound frame by
+     * frame. Returns how far the stack moved.
      */
-    setIsScalebarRefNameMenuOpen(isOpen: boolean): void;
+    resizeTracks(distance: number, from?: any): number;
     /**
      * #action
+     * A resize keeps the window in bp, so `bpPerPx` follows the new width
+     * and the view keeps framing the same sequence (ADR-070).
      */
-    setScalebarRefNameClickPending(pending: boolean): void;
+    setWidth(newWidth: number): void;
+    /**
+     * #action
+     */
+    setError(error: unknown): void;
+    /**
+     * #action
+     */
+    setIsScalebarRefNameMenuOpen(isOpen: boolean): void;
     /**
      * #action
      */
@@ -2517,11 +3081,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setShowGridlines(b: boolean): void;
-    /**
-     * #action
-     */
-    setLabelsVisible(arg: boolean): void;
+    setAxisGrid(grid: boolean): void;
     /**
      * #action
      * set temporary vertical guides (e.g., for LD display hover)
@@ -2556,8 +3116,20 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setOffsets(left?: BpOffset, right?: BpOffset): void;
     /**
      * #action
+     * Raise the picker over search results that name more than one place.
+     * @param onPick - where a picked result lands; by default it navigates
+     * there and shows the track its index came from
+     */
+    setSearchResults(searchResults: BaseResult[], searchQuery: string, assemblyName: string, onPick?: (result: BaseResult) => Promise<unknown>): void;
+    /**
+     * #action
+     * Search the view's assembly by name, for a host listing the hits
+     * itself. A row's `pick` lands as the search box does: it navigates
+     * there and shows the track the hit's index came from.
      */
-    setSearchResults(searchResults: BaseResult[], searchQuery: string, assemblyName: string): void;
+    search(query: string, opts?: {
+        signal?: AbortSignal;
+    }): Promise<SearchHits>;
     /**
      * #action
      */
@@ -2567,33 +3139,62 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     hideTrack(trackId: string): boolean;
 } & {
+    /**
+     * #action
+     * Resize every unminimized track so the view is exactly as tall as the
+     * scroll port it sits in. Does nothing until the view has measured one.
+     */
+    fitTracksToWindow(): void;
     /**
      * #action
      * showTrack for a track whose display state model may be lazily
      * loaded: loads it, then shows
      */
     launchTrack(trackId: string, initialSnapshot?: any, displayInitialSnapshot?: any, inlineConf?: Record<string, unknown>): Promise<any>;
-} & {
     /**
      * #action
+     * Replace the highlights `highlights` reads, each written as the launch
+     * spec's `highlight` writes one: a locstring, or an object whose
+     * `assemblyName` defaults to the view's. Throws on one that names no
+     * region, writing none.
      */
-    moveTrackDown(id: string): void;
+    setHighlights(highlights: readonly (string | HighlightInput)[]): void;
     /**
      * #action
+     * Show files from the user's disk as session tracks: one per data file,
+     * beside the index among them that names it, its type guessed from its
+     * name. Adds nothing when one file has no known type. Resolves the new
+     * tracks' ids.
+     */
+    showFiles(files: readonly File[]): Promise<string[]>;
+} & {
+    /**
+     * #method
+     * The shown track a move action means: the menu passes a track model's
+     * own `id`, an agent passes the `trackId` it knows the track by, and
+     * both name one shown track. Answers the model id, or the argument
+     * unchanged when nothing shown matches, so the move reports it.
      */
-    moveTrackUp(id: string): void;
+    trackModelId(idOrTrackId: string): string;
+} & {
+    moveTrack: (moving: string, target: string) => void;
     /**
      * #action
      */
-    moveTrackToTop(id: string): void;
+    moveTrackDown(idOrTrackId: string): void;
     /**
      * #action
      */
-    moveTrackToBottom(id: string): void;
+    moveTrackUp(idOrTrackId: string): void;
     /**
      * #action
      */
-    moveTrack(movingId: string, targetId: string): void;
+    moveTrackToTop(idOrTrackId: string): void;
+    /**
+     * #action
+     */
+    moveTrackToBottom(idOrTrackId: string): void;
+} & {
     /**
      * #action
      */
@@ -2606,7 +3207,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden'): void;
+    setTrackLabels(setting: ViewTrackLabelMode): void;
     /**
      * #action
      */
@@ -2619,24 +3220,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #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
      */
@@ -2645,10 +3228,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setDraggingTrackId(idx?: string): void;
-    /**
-     * #action
-     */
-    setLastTrackDragY(y: number): void;
     /**
      * #action
      * called while dragging a track over the track at `targetId`; reorders
@@ -2660,11 +3239,25 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setLaunch(launch?: LaunchInput<InitState>): void;
+} & {
     /**
      * #method
-     * creates an svg export and save using FileSaver
+     * Helper method for the fetchSequence.
+     * Returns the regions the user selected with 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[]
      */
-    exportSvg(opts?: ExportSvgOptions): Promise<void>;
+    getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
+        assemblyName: string;
+        refName: string;
+        start: number;
+        end: number;
+    }[];
 } & {
     slide: (viewWidths: number) => void;
     zoom: (targetBpPerPx: number) => void;
@@ -2678,19 +3271,18 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #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
+     * up as a lone half-triangle. The chromosome also needs bands: a cytoband
+     * file often lists only the main chromosomes, not chrM or the
+     * unplaced scaffolds
      */
     readonly canShowCytobands: boolean;
     /**
      * #getter
      * the `showCytobands` setting gated by whether cytobands can be shown at
-     * all (whole chromosome + data present) — i.e. actually on screen
+     * all (whole chromosome with bands in the cytoband file) and by the header
+     * overview they draw in being on, which the SVG export follows too
      */
     readonly effectiveShowCytobands: boolean;
-    /**
-     * #getter
-     */
-    readonly anyCytobandsExist: boolean;
     /**
      * #getter
      * the cytoband is displayed to the right of the chromosome name, and
@@ -2707,6 +3299,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * return the view menu items
      */
     menuItems(): MenuItem[];
+    /**
+     * #method
+     * the view menu's Highlights submenu; extend this to add a row there
+     */
+    highlightsSubMenuItems(): MenuItem[];
     /**
      * #method
      * what a plugin can start from the selected region — a synteny view, a
@@ -2735,9 +3332,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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
+     * visible genome regions on the screen. Static blocks can go
+     * offscreen, while dynamic blocks represent exactly what is on screen
      */
     readonly dynamicBlocks: BlockSet;
     /**
@@ -2769,12 +3365,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
+     * this number moves. `scalebarRefNameLabels` is the exception: 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 —
+     * **The subtraction must happen here, in float64.** `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
@@ -2786,13 +3380,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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 —
+     * This applies the GPU side's rule one layer up; see
      * `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
+     * copies written out at each call site disagree about rounding. Round it where the content is text
      * (a fractional offset blurs a label); leave it alone for paths and
      * boxes.
      */
@@ -2835,11 +3428,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
+     * does not scroll the chromosome's 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:
+     * This getter applies three rules that a host drawing region names would
+     * otherwise have to rediscover, 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
@@ -2851,7 +3444,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *   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` —
+     *   run leaves. Clipped to that space, `chr16` reads as `chr1` —
      *   a different chromosome rather than a shortened name, which is why
      *   this is a fit test rather than an ellipsis.
      *
@@ -2867,10 +3460,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
+     * orientation. `captionSpanPx` is the width it takes: the sticky label
+     * pins to its right edge rather than the viewport's, and the coordinate
+     * numbers stay out from under it. The SVG export deliberately
      * calls `getScalebarRefNameLabels` itself with no prefix rather than
-     * reading this, since it draws its own assembly name above the ruler.
+     * reading this, since it draws the assembly name itself above the ruler.
      */
     readonly scalebarRefNameLabels: {
         labels: import("./util.ts").ScalebarRefNameLabel[];
@@ -2882,36 +3476,36 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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:
+     * three. A host that draws the row's chrome itself needs all three kinds:
      *
      * - `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
+     *   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.
+     *   two-region view looks like a single region.
+     *   `isRightEndOfDisplayedRegion` marks it; the right edge of the
+     *   currently *loaded* blocks, which block geometry gives you, is a
+     *   different set.
      * - `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.
+     *   a real assembly is mostly these (hg38 has 455 sequences, and all
+     *   but the 24 chromosomes are under a pixel wide), so a host that
+     *   skips them leaves that part of the row empty.
      * - `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.
+     *   last. Greying it makes the last region's seam read as the edge of a
+     *   filled area, where it would otherwise look like a line in the
+     *   middle of the track.
+     *
+     * Elided blocks get no seam even though they have the flag: at the
+     * zoom where regions elide, one bar per region would fill the row solid
+     * grey.
+     *
+     * PaddingBlocks is the in-tree consumer. The SVG export does not use
+     * it: `SVGRegionSeparators` walks dynamicBlocks itself and draws only
+     * the seam, because `elided` and `boundary` mark state for an
+     * interactive row. In a static figure the striped grey would cover most
+     * of the row at whole-genome zoom. The export keeps the seam because
+     * regions lay out contiguously and the seam is all that separates two
+     * of them.
      */
     readonly paddingSpans: readonly {
         key: string;
@@ -2943,8 +3537,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
+     * describe. The SVG export checks it before drawing its header.
+     * Distinct from `hasDisplayedRegions`, which only asks whether the
      * view has been given regions, not whether any are on screen.
      */
     readonly hasVisibleContent: boolean;
@@ -2980,7 +3574,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      * Right edge (px, viewport-relative) of the on-screen content, clamped
-     * to the track — where a right-pinned overlay such as a wiggle's colour
+     * to the track — where a right-pinned overlay such as a wiggle's color
      * or score legend belongs, rather than out in the empty gutter the
      * regions can leave at whole-genome zoom. `@jbrowse/display-kit`'s
      * `contentRightEdgePx` states the rule; an SVG export applies the same
@@ -2990,7 +3584,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * array of fresh objects on every pan and zoom frame, so a component
      * that derived this number itself re-rendered on every frame of every
      * gesture — to produce, whenever content fills the track, the unchanged
-     * `trackWidthPx`. Reading the scalar lets MobX's `===` stop the chain at
+     * `trackWidthPx`. A component that reads the scalar lets MobX's `===` stop the chain at
      * this computed instead. Measured over 20 zoom frames: the wiggle
      * family's three body instances fell from 66 renders to 7.
      */
@@ -3020,23 +3614,22 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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 blocks 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.
+     * The coarse blocks stop a per-bp scan from recomputing on every
+     * animation frame during a pan or zoom. Wiggle's autoscale domain, the
+     * alignments coverage scale and MAF's coverage band use them. While the
+     * coarse blocks are stale the result is a frame or two old, as the
+     * debounce intends. **Empty coarse blocks are a different case.** A scan
+     * over no blocks yields no entries, and the consumer falls back to the
+     * domain `[0,1]`, which draws a line plot blank and a density plot
+     * saturated. The coarse blocks are empty for the 500ms between a view
+     * initializing and the coarse autorun's first run, and data can load
+     * within that window.
      *
-     * One recompute at that transition, against N per frame, which is the
-     * trade the guard was making anyway.
+     * Falling back to the live blocks costs one extra recompute at that
+     * transition, compared with N per frame without the debounce.
      */
     readonly settledDynamicBlocks: ContentBlock[];
     /**
@@ -3069,7 +3662,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *
      * 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
+     * the feature display'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
@@ -3077,21 +3670,29 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
+     * 4040bp on screen.
      *
-     * **The continuous paths deliberately do not come through here.** The
+     * **The continuous paths do not call this.** 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.
+     * autorun's 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
+     * Every placer calls it, and `placersSettleCoarseBlocks.test.ts` enforces
+     * that for 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;
+} & {
+    /**
+     * #method
+     * renders the view to SVG markup, which it returns; saves it through
+     * FileSaver unless `save: false`. A `viewWidth` lays the view out at
+     * that many pixels for the export, as a window that wide would, and
+     * puts the on-screen width back after.
+     */
+    exportSvg(opts?: ExportSvgOptions): Promise<string>;
 } & {
     /**
      * #action
@@ -3104,17 +3705,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     moveTo(start?: BpOffset, end?: BpOffset): 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
+     * Place the viewport by `bpPerPx` and `offsetPx`, the pixel pair the view
+     * stored before it stored the window. 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.
+     * gesture, a rubberband.
      */
     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
+     * width and left edge, both in bp. The bp-space counterpart of `setNewView`, 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.
@@ -3136,8 +3737,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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
+     * Settles the coarse blocks, since this is the worst jump to leave
+     * unsettled: they 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;
@@ -3282,6 +3883,24 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * adds 20% padding on each side)
      */
     navToLocation(parsedLocString: ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+    /**
+     * #action
+     * adds the region in view to the session's highlights
+     */
+    highlightCurrentRegion(): void;
+    /**
+     * #action
+     * navigates to a highlight, zoomed out a little for context. Goes through
+     * a locstring so it reaches a refName the view is not displaying
+     */
+    navToHighlight(highlight: HighlightType): Promise<boolean>;
+} & {
+    /**
+     * #action
+     * navigates to the most recently added highlight on this view's
+     * assemblies
+     */
+    navigateNewestHighlight(): Promise<void>;
 } & {
     /**
      * #method
@@ -3300,31 +3919,30 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } | undefined;
     /**
      * #method
-     * Map a highlight or bookmark region to its pixel position+width inside
+     * Map a highlight 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;
-        start: number;
-        end: number;
-    }): {
+    getHighlightCoords(region: HighlightRegion): {
         width: number;
         left: number;
     } | undefined;
+    /**
+     * #method
+     * y ranges, from the top of the highlight bands, of tracks whose display
+     * sets `drawsGenomicCoordinates` to false; the bands skip them
+     */
+    nonGenomicTrackBands(): {
+        top: number;
+        height: number;
+    }[];
     /**
      * #method
      * like getHighlightCoords but laid out against the overview scalebar and
      * shifted by the cytoband offset
      */
-    getOverviewHighlightCoords(region: {
-        assemblyName?: string;
-        refName: string;
-        start: number;
-        end: number;
-    }): {
+    getOverviewHighlightCoords(region: HighlightRegion): {
         width: number;
         left: number;
     } | undefined;
@@ -3346,6 +3964,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #getter
      */
     readonly centerLineInfo: import("@jbrowse/core/util/Base1DUtils").PxToBpResult | undefined;
+} & {
+    /**
+     * #action
+     * a region edit from the ruler's menu as one action, which a synteny
+     * stack's follow reads as the reader's gesture on this row; see
+     * `setDisplayedRegionsKeepingCenter`
+     */
+    editDisplayedRegions(edit: RegionEdit): void;
 } & {
     /**
      * #method
@@ -3353,8 +3979,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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
+     * a highlight chip's menu rows after Dismiss; extend this to add one
      */
     highlightMenuItems(_highlight: HighlightType): MenuItem[];
 } & {
@@ -3364,38 +3989,45 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * `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;
+    flyToCenter(coord: number, refName: string, displayedRegionIndex?: number): void;
+    /**
+     * #action
+     * A flight to a linear bp centre at the zoom the view is on, or is
+     * already flying to, widened where that is narrower than `fitWidthBp`.
+     * The current width mid-flight is a point on the arc, so a second
+     * flight read from it would land pulled back.
+     */
+    flyToFit(centerBp: number, fitWidthBp: number): void;
 } & {
     afterCreate(): void;
     afterAttach(): void;
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, InitState, "bpPerPx" | "offsetPx">, {
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, InitState, "bpPerPx" | "colorByCDS" | "offsetPx" | "showCytobandsSetting">, {
     displayName: string | undefined;
     minimized: boolean;
-    highlight: HighlightType[];
-    showHighlightChips: boolean;
     id: string;
     type: string;
     windowStartBp: number;
     windowWidthBp: number;
     legacyBpPerPx: number;
     displayedRegions: Region[];
-    tracks: any[];
+    tracks: import("@jbrowse/core/util/tracks").TrackSnapshot[];
     hideHeader: boolean;
     hideHeaderOverview: boolean;
     hideNoTracksActive: boolean;
     trackSelectorType: string;
-    showGridlines: boolean;
-    labelsVisible: boolean;
+    showCytobands: boolean;
+    trackLabels: "" | "hidden" | "offset" | "overlapping";
+    axis: import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, import("@jbrowse/mobx-state-tree").IAnyType>>;
+    colorByFrame: boolean;
+    showAminoAcids: boolean;
+    showTrackOutlines: boolean;
     scalebarOnly: boolean;
-    launch?: LaunchInput<InitState> | undefined;
-    showCytobands?: false | undefined;
-    trackLabels?: string | undefined;
-    colorByCDS?: true | undefined;
-    showAminoAcids?: false | undefined;
-    showTrackOutlines?: false | undefined;
+    launch: LaunchInput<InitState> | undefined;
 }>;
-export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
+export interface LinearGenomeViewStateModel extends ReturnType<typeof stateModelFactory> {
+}
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
+export type LinearGenomeViewTrack = LinearGenomeViewModel['tracks'][number];
 declare module '@jbrowse/core/PluginManager' {
     interface ViewTypeRegistry {
         LinearGenomeView: LinearGenomeViewStateModel;