@jbrowse/plugin-linear-genome-view 5.0.0-beta.7 → 5.0.0-beta.9

package/esm/LinearGenomeView/model.d.ts

@@ -1,4 +1,5 @@
-import type { BpOffset, ExportSvgOptions, HighlightType, InitState, NavLocation, VolatileGuide } from './types.ts';
+import type { CloseUp } from './closeUps.ts';
+import type { BpOffset, ExportSvgOptions, HighlightType, InitState, NavLocation, ViewTrackLabelMode, VolatileGuide } from './types.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import type { MenuItem } from '@jbrowse/core/ui';
@@ -40,9 +41,8 @@ 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.
+ * `colorByCDS`, `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
@@ -52,14 +52,11 @@ 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"> & {
+}, "closeUpConnectorHeight" | "closeUps" | "colorByCDS" | "displayedRegions" | "hideHeader" | "hideHeaderOverview" | "hideNoTracksActive" | "id" | "labelsVisible" | "launch" | "legacyBpPerPx" | "scalebarOnly" | "showAminoAcids" | "showCenterLine" | "showCytobands" | "showGridlines" | "showTrackOutlines" | "trackLabels" | "trackSelectorType" | "tracks" | "type" | "windowStartBp" | "windowWidthBp"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
     windowStartBp: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -69,6 +66,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
     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]>;
+    closeUps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>, [undefined]>;
+    closeUpConnectorHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [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]>;
@@ -85,6 +84,7 @@ 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[];
@@ -94,14 +94,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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
@@ -211,7 +203,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * the effective track labels setting, resolving the stored `trackLabels`
      * against the LinearGenomeViewPlugin config default
      */
-    readonly effectiveTrackLabels: any;
+    readonly effectiveTrackLabels: ViewTrackLabelMode;
     /**
      * #getter
      */
@@ -229,6 +221,11 @@ 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
@@ -250,8 +247,30 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly ownTracks: any[];
     /**
      * #getter
-     * Assembly-name prefix for the scalebar refName labels, or undefined for
-     * none. A container view (e.g. LinearSyntenyView) opts its sub-views in by
+     * The census entry for this view's close-ups, which are views in
+     * their own right.
+     */
+    readonly ownViews: any[];
+    /**
+     * #getter
+     * The close-ups as what the host reads off them. The array element
+     * is a late type back onto this view, so this is where it gets a shape.
+     */
+    readonly closeUpViews: CloseUp[];
+    /**
+     * #getter
+     * Whether this view is itself a close-up of another
+     */
+    readonly isCloseUp: boolean;
+    /**
+     * #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
@@ -413,6 +432,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+    /**
+     * #getter
+     * 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
      */
@@ -564,26 +593,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
      * #getter
-     * What the spinner says. The assembly reports which of its files it is
-     * downloading, so this is "Downloading chromosome aliases" rather than a bare
-     * "Loading" for the part of startup that actually takes time. Falls back
-     * once the assembly is loaded and the remaining wait is the init autorun's
-     * own navigation, which is local.
-     */
-    readonly loadingMessage: string | undefined;
-    /**
-     * #getter
-     * Determinate fraction for the spinner's bar, when the assembly load
-     * reports one (a whole-file download with a Content-Length)
-     */
-    readonly loadingProgress: number | undefined;
-    /**
-     * #getter
-     * The URL the assembly load is currently fetching, when the phase named
-     * one. Only the stalled-load notice reads it — see
-     * {@link ViewLoadingScreen}.
+     * What the loading screen says while `showLoading`, read off the
+     * assembly whose load is the wait; undefined otherwise.
      */
-    readonly loadingSource: string | undefined;
+    readonly loading: import("@jbrowse/core/util/viewStatus").ViewLoading | undefined;
     /**
      * #getter
      */
@@ -679,10 +692,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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.
+     * stacked above it, which is the view's own title bar, where the session
+     * draws one, 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;
     /**
@@ -746,16 +760,16 @@ 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;
     /**
@@ -860,6 +874,31 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setHideHeaderOverview(b: boolean): void;
+    /**
+     * #action
+     * Add a close-up showing `trackIds`, spanning `windowWidthBp` bases or a
+     * tenth of the closest close-up there is. The stack stays widest first,
+     * so a span between two existing close-ups lands between them, and one
+     * wider than this view is pulled back in to it by the sync.
+     *
+     * Answers the close-up, which is a LinearGenomeView: its own actions
+     * navigate it, name its tracks and take it away again.
+     */
+    addCloseUp({ windowWidthBp, trackIds, }?: {
+        windowWidthBp?: number;
+        trackIds?: string[];
+    }): CloseUp;
+    /**
+     * #action
+     */
+    removeCloseUp(closeUp: CloseUp): void;
+    /**
+     * #action
+     * Set the height of every band between this view's close-ups.
+     * Floored at the drag surface's own height rather than at 0: the band IS
+     * the handle, so a band dragged shut could never be dragged open again.
+     */
+    setCloseUpConnectorHeight(height: number): void;
     /**
      * #action
      */
@@ -921,33 +960,59 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     hideTrack(trackId: string): boolean;
 } & {
+    /**
+     * #action
+     * Open a close-up over a rubberband selection, showing this view's
+     * tracks. The view recentres on the span first, because every close-up
+     * shares its host's centre — a close-up is a closer look at the middle of
+     * this view, and a selection off to one side would otherwise open
+     * somewhere else.
+     *
+     * The span is `computeMoveToLayout`'s, the pure half of the `moveTo` the
+     * same selection's "Zoom to region" runs, so the close-up covers exactly
+     * what zooming would have navigated to.
+     */
+    addCloseUpForSpan(start?: BpOffset, end?: BpOffset, { trackIds }?: {
+        trackIds?: string[];
+    }): CloseUp | undefined;
     /**
      * #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>;
+} & {
+    /**
+     * #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.
+     */
+    trackModelId(idOrTrackId: string): any;
 } & {
     /**
      * #action
      */
-    moveTrackDown(id: string): void;
+    moveTrackDown(idOrTrackId: string): void;
     /**
      * #action
      */
-    moveTrackUp(id: string): void;
+    moveTrackUp(idOrTrackId: string): void;
     /**
      * #action
      */
-    moveTrackToTop(id: string): void;
+    moveTrackToTop(idOrTrackId: string): void;
     /**
      * #action
      */
-    moveTrackToBottom(id: string): void;
+    moveTrackToBottom(idOrTrackId: string): void;
     /**
      * #action
+     * Move one shown track to another's position; each is a track model id
+     * or a trackId.
      */
-    moveTrack(movingId: string, targetId: string): void;
+    moveTrack(moving: string, target: string): void;
     /**
      * #action
      */
@@ -960,7 +1025,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden'): void;
+    setTrackLabels(setting: ViewTrackLabelMode): void;
     /**
      * #action
      */
@@ -1222,8 +1287,9 @@ 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.
      */
@@ -1237,36 +1303,36 @@ 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 drawing its own chrome 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.
+     *   last. Greying it shows the last region's seam 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 carry the flag: at the
-     * zoom where regions elide, one bar per region is a solid grey wall.
+     * zoom where regions elide, one bar per region would fill the row solid
+     * grey.
      *
-     * 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.
+     * 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;
@@ -1298,8 +1364,8 @@ 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;
@@ -1375,23 +1441,22 @@ 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[];
     /**
@@ -1637,6 +1702,17 @@ 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 the most recently added highlight on this view's
+     * assemblies, zoomed out a little for context
+     */
+    navigateNewestHighlight(): Promise<void>;
 } & {
     /**
      * #method
@@ -1655,7 +1731,7 @@ 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.
@@ -1720,17 +1796,22 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * arc instead of jumped to, at the zoom the view is already on.
      */
     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"> & {
+}, "closeUpConnectorHeight" | "closeUps" | "colorByCDS" | "displayedRegions" | "hideHeader" | "hideHeaderOverview" | "hideNoTracksActive" | "id" | "labelsVisible" | "launch" | "legacyBpPerPx" | "scalebarOnly" | "showAminoAcids" | "showCenterLine" | "showCytobands" | "showGridlines" | "showTrackOutlines" | "trackLabels" | "trackSelectorType" | "tracks" | "type" | "windowStartBp" | "windowWidthBp"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
     windowStartBp: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -1740,6 +1821,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
     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]>;
+    closeUps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>, [undefined]>;
+    closeUpConnectorHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [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]>;
@@ -1756,6 +1839,7 @@ 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[];
@@ -1765,14 +1849,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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
@@ -1882,7 +1958,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * the effective track labels setting, resolving the stored `trackLabels`
      * against the LinearGenomeViewPlugin config default
      */
-    readonly effectiveTrackLabels: any;
+    readonly effectiveTrackLabels: ViewTrackLabelMode;
     /**
      * #getter
      */
@@ -1900,6 +1976,11 @@ 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
@@ -1921,8 +2002,30 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly ownTracks: any[];
     /**
      * #getter
-     * Assembly-name prefix for the scalebar refName labels, or undefined for
-     * none. A container view (e.g. LinearSyntenyView) opts its sub-views in by
+     * The census entry for this view's close-ups, which are views in
+     * their own right.
+     */
+    readonly ownViews: any[];
+    /**
+     * #getter
+     * The close-ups as what the host reads off them. The array element
+     * is a late type back onto this view, so this is where it gets a shape.
+     */
+    readonly closeUpViews: CloseUp[];
+    /**
+     * #getter
+     * Whether this view is itself a close-up of another
+     */
+    readonly isCloseUp: boolean;
+    /**
+     * #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
@@ -2084,6 +2187,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+    /**
+     * #getter
+     * 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
      */
@@ -2235,26 +2348,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
      * #getter
-     * What the spinner says. The assembly reports which of its files it is
-     * downloading, so this is "Downloading chromosome aliases" rather than a bare
-     * "Loading" for the part of startup that actually takes time. Falls back
-     * once the assembly is loaded and the remaining wait is the init autorun's
-     * own navigation, which is local.
-     */
-    readonly loadingMessage: string | undefined;
-    /**
-     * #getter
-     * Determinate fraction for the spinner's bar, when the assembly load
-     * reports one (a whole-file download with a Content-Length)
-     */
-    readonly loadingProgress: number | undefined;
-    /**
-     * #getter
-     * The URL the assembly load is currently fetching, when the phase named
-     * one. Only the stalled-load notice reads it — see
-     * {@link ViewLoadingScreen}.
+     * What the loading screen says while `showLoading`, read off the
+     * assembly whose load is the wait; undefined otherwise.
      */
-    readonly loadingSource: string | undefined;
+    readonly loading: import("@jbrowse/core/util/viewStatus").ViewLoading | undefined;
     /**
      * #getter
      */
@@ -2350,10 +2447,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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.
+     * stacked above it, which is the view's own title bar, where the session
+     * draws one, 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;
     /**
@@ -2417,16 +2515,16 @@ 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;
     /**
@@ -2531,6 +2629,31 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setHideHeaderOverview(b: boolean): void;
+    /**
+     * #action
+     * Add a close-up showing `trackIds`, spanning `windowWidthBp` bases or a
+     * tenth of the closest close-up there is. The stack stays widest first,
+     * so a span between two existing close-ups lands between them, and one
+     * wider than this view is pulled back in to it by the sync.
+     *
+     * Answers the close-up, which is a LinearGenomeView: its own actions
+     * navigate it, name its tracks and take it away again.
+     */
+    addCloseUp({ windowWidthBp, trackIds, }?: {
+        windowWidthBp?: number;
+        trackIds?: string[];
+    }): CloseUp;
+    /**
+     * #action
+     */
+    removeCloseUp(closeUp: CloseUp): void;
+    /**
+     * #action
+     * Set the height of every band between this view's close-ups.
+     * Floored at the drag surface's own height rather than at 0: the band IS
+     * the handle, so a band dragged shut could never be dragged open again.
+     */
+    setCloseUpConnectorHeight(height: number): void;
     /**
      * #action
      */
@@ -2592,33 +2715,59 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     hideTrack(trackId: string): boolean;
 } & {
+    /**
+     * #action
+     * Open a close-up over a rubberband selection, showing this view's
+     * tracks. The view recentres on the span first, because every close-up
+     * shares its host's centre — a close-up is a closer look at the middle of
+     * this view, and a selection off to one side would otherwise open
+     * somewhere else.
+     *
+     * The span is `computeMoveToLayout`'s, the pure half of the `moveTo` the
+     * same selection's "Zoom to region" runs, so the close-up covers exactly
+     * what zooming would have navigated to.
+     */
+    addCloseUpForSpan(start?: BpOffset, end?: BpOffset, { trackIds }?: {
+        trackIds?: string[];
+    }): CloseUp | undefined;
     /**
      * #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>;
+} & {
+    /**
+     * #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.
+     */
+    trackModelId(idOrTrackId: string): any;
 } & {
     /**
      * #action
      */
-    moveTrackDown(id: string): void;
+    moveTrackDown(idOrTrackId: string): void;
     /**
      * #action
      */
-    moveTrackUp(id: string): void;
+    moveTrackUp(idOrTrackId: string): void;
     /**
      * #action
      */
-    moveTrackToTop(id: string): void;
+    moveTrackToTop(idOrTrackId: string): void;
     /**
      * #action
      */
-    moveTrackToBottom(id: string): void;
+    moveTrackToBottom(idOrTrackId: string): void;
     /**
      * #action
+     * Move one shown track to another's position; each is a track model id
+     * or a trackId.
      */
-    moveTrack(movingId: string, targetId: string): void;
+    moveTrack(moving: string, target: string): void;
     /**
      * #action
      */
@@ -2631,7 +2780,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden'): void;
+    setTrackLabels(setting: ViewTrackLabelMode): void;
     /**
      * #action
      */
@@ -2893,8 +3042,9 @@ 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.
      */
@@ -2908,36 +3058,36 @@ 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 drawing its own chrome 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.
+     *   last. Greying it shows the last region's seam 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 carry the flag: at the
-     * zoom where regions elide, one bar per region is a solid grey wall.
+     * zoom where regions elide, one bar per region would fill the row solid
+     * grey.
      *
-     * 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.
+     * 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;
@@ -2969,8 +3119,8 @@ 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;
@@ -3046,23 +3196,22 @@ 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[];
     /**
@@ -3308,6 +3457,17 @@ 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 the most recently added highlight on this view's
+     * assemblies, zoomed out a little for context
+     */
+    navigateNewestHighlight(): Promise<void>;
 } & {
     /**
      * #method
@@ -3326,7 +3486,7 @@ 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.
@@ -3391,14 +3551,20 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * arc instead of jumped to, at the zoom the view is already on.
      */
     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" | "cytobandsVisible" | "offsetPx" | "showCytobandsSetting">, {
     displayName: string | undefined;
     minimized: boolean;
-    highlight: HighlightType[];
-    showHighlightChips: boolean;
     id: string;
     type: string;
     windowStartBp: number;
@@ -3408,6 +3574,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     tracks: any[];
     hideHeader: boolean;
     hideHeaderOverview: boolean;
+    closeUps: any[];
+    closeUpConnectorHeight: number;
     hideNoTracksActive: boolean;
     trackSelectorType: string;
     showGridlines: boolean;