@jbrowse/plugin-linear-genome-view 5.0.0-beta.13 → 5.0.0-beta.16

package/esm/LinearGenomeView/model.d.ts

@@ -10,13 +10,29 @@ 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 { 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;
+}
+/**
+ * The hits of a name search that point at more than one place, waiting for the
+ * user to choose. A host draws them however it likes: the Material view shows
+ * a dialog, and `SearchPicker` in `@jbrowse/display-ui/embed` a plain list.
+ */
+export interface SearchPickerState {
+    query: string;
+    assemblyName: string;
+    /** one row per place, hits in a track the view already shows first */
+    rows: SearchPickerRow[];
+    /** navigates to the row's place, reports a failure and closes the picker */
+    pick: (id: string) => Promise<unknown>;
 }
+export type { PaddingSpan } from './util.ts';
 export interface HighlightRegion {
     assemblyName?: string;
     refName: string;
@@ -26,6 +42,8 @@ export interface HighlightRegion {
 /**
  * #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
@@ -122,6 +140,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #volatile
      */
     draggingTrackId: undefined | string;
+    /**
+     * #volatile
+     * Set by a search whose hits name more than one place, until the user
+     * picks one or closes it.
+     */
+    searchPicker: SearchPickerState | undefined;
     /**
      * #volatile
      */
@@ -293,13 +317,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        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/assembly").RefNameAliases | 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;
@@ -318,7 +342,7 @@ 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;
     } & {
-        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>;
@@ -349,24 +373,25 @@ 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;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
         configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
     }, {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        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/assembly").RefNameAliases | 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;
@@ -385,7 +410,7 @@ 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;
     } & {
-        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>;
@@ -416,11 +441,12 @@ 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;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
@@ -452,13 +478,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        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/assembly").RefNameAliases | 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;
@@ -477,7 +503,7 @@ 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;
     } & {
-        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>;
@@ -508,24 +534,25 @@ 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;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
         configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
     }, {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        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/assembly").RefNameAliases | 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;
@@ -544,7 +571,7 @@ 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;
     } & {
-        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>;
@@ -575,17 +602,18 @@ 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;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
      * #getter
-     * What the loading screen says while `showLoading`, read off the
-     * assembly whose load is the wait; undefined otherwise.
+     * The loading screen's text while `showLoading`, taken from the
+     * assembly being waited on; undefined otherwise.
      */
     readonly loading: import("@jbrowse/core/util/viewStatus").ViewLoading | undefined;
     /**
@@ -627,12 +655,12 @@ 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
@@ -682,7 +710,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly headerHeight: 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
@@ -761,8 +789,8 @@ 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;
@@ -811,6 +839,12 @@ 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
@@ -999,7 +1033,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #method
      * Helper method for the fetchSequence.
-     * Retrieves the corresponding regions that were selected by the
+     * Returns the regions the user selected with the
      * rubberband
      *
      * @param leftOffset - `object as {start, end, index, offset}`, offset = start
@@ -1033,12 +1067,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setLaunch(launch?: LaunchInput<InitState>): void;
-    /**
-     * #method
-     * renders the view to SVG markup, which it returns; saves it through
-     * FileSaver unless `save: false`
-     */
-    exportSvg(opts?: ExportSvgOptions): Promise<string>;
 } & {
     slide: (viewWidths: number) => void;
     zoom: (targetBpPerPx: number) => void;
@@ -1052,15 +1080,15 @@ 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. The chromosome needs bands of its own too:
-     * a cytoband file often lists only the main chromosomes, not chrM or the
+     * 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 with bands of its own) and by the header
+     * 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;
@@ -1113,9 +1141,8 @@ 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;
     /**
@@ -1147,12 +1174,10 @@ 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
@@ -1164,13 +1189,12 @@ 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.
      */
@@ -1213,11 +1237,11 @@ 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
@@ -1229,7 +1253,7 @@ 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.
      *
@@ -1249,7 +1273,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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[];
@@ -1261,7 +1285,7 @@ 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. A host drawing its own chrome needs all three kinds:
+     * 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
@@ -1276,11 +1300,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *   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 shows the last region's seam as the edge of a
+     *   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 carry the flag: at the
+     * 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.
      *
@@ -1359,7 +1383,7 @@ 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
@@ -1369,7 +1393,7 @@ 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.
      */
@@ -1455,21 +1479,29 @@ 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
@@ -1482,8 +1514,8 @@ 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.
@@ -1492,7 +1524,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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.
@@ -1514,8 +1546,8 @@ 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;
@@ -1750,7 +1782,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #method
      * returns menu items for a highlight context menu. plugins can extend
-     * this via Core-extendPluggableElement to add their own items
+     * this via Core-extendPluggableElement to add items
      */
     highlightMenuItems(_highlight: HighlightType): MenuItem[];
 } & {
@@ -1836,6 +1868,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #volatile
      */
     draggingTrackId: undefined | string;
+    /**
+     * #volatile
+     * Set by a search whose hits name more than one place, until the user
+     * picks one or closes it.
+     */
+    searchPicker: SearchPickerState | undefined;
     /**
      * #volatile
      */
@@ -2007,13 +2045,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        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/assembly").RefNameAliases | 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;
@@ -2032,7 +2070,7 @@ 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;
     } & {
-        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>;
@@ -2063,24 +2101,25 @@ 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;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
         configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
     }, {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        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/assembly").RefNameAliases | 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;
@@ -2099,7 +2138,7 @@ 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;
     } & {
-        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>;
@@ -2130,11 +2169,12 @@ 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;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
@@ -2166,13 +2206,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        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/assembly").RefNameAliases | 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;
@@ -2191,7 +2231,7 @@ 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;
     } & {
-        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>;
@@ -2222,24 +2262,25 @@ 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;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
         configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
     }, {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+        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/assembly").RefNameAliases | 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;
@@ -2258,7 +2299,7 @@ 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;
     } & {
-        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>;
@@ -2289,17 +2330,18 @@ 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;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
      * #getter
-     * What the loading screen says while `showLoading`, read off the
-     * assembly whose load is the wait; undefined otherwise.
+     * The loading screen's text while `showLoading`, taken from the
+     * assembly being waited on; undefined otherwise.
      */
     readonly loading: import("@jbrowse/core/util/viewStatus").ViewLoading | undefined;
     /**
@@ -2341,12 +2383,12 @@ 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
@@ -2396,7 +2438,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly headerHeight: 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
@@ -2475,8 +2517,8 @@ 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;
@@ -2525,6 +2567,12 @@ 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
@@ -2713,7 +2761,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #method
      * Helper method for the fetchSequence.
-     * Retrieves the corresponding regions that were selected by the
+     * Returns the regions the user selected with the
      * rubberband
      *
      * @param leftOffset - `object as {start, end, index, offset}`, offset = start
@@ -2747,12 +2795,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setLaunch(launch?: LaunchInput<InitState>): void;
-    /**
-     * #method
-     * renders the view to SVG markup, which it returns; saves it through
-     * FileSaver unless `save: false`
-     */
-    exportSvg(opts?: ExportSvgOptions): Promise<string>;
 } & {
     slide: (viewWidths: number) => void;
     zoom: (targetBpPerPx: number) => void;
@@ -2766,15 +2808,15 @@ 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. The chromosome needs bands of its own too:
-     * a cytoband file often lists only the main chromosomes, not chrM or the
+     * 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 with bands of its own) and by the header
+     * 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;
@@ -2827,9 +2869,8 @@ 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;
     /**
@@ -2861,12 +2902,10 @@ 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
@@ -2878,13 +2917,12 @@ 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.
      */
@@ -2927,11 +2965,11 @@ 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
@@ -2943,7 +2981,7 @@ 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.
      *
@@ -2963,7 +3001,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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[];
@@ -2975,7 +3013,7 @@ 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. A host drawing its own chrome needs all three kinds:
+     * 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
@@ -2990,11 +3028,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *   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 shows the last region's seam as the edge of a
+     *   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 carry the flag: at the
+     * 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.
      *
@@ -3073,7 +3111,7 @@ 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
@@ -3083,7 +3121,7 @@ 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.
      */
@@ -3169,21 +3207,29 @@ 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
@@ -3196,8 +3242,8 @@ 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.
@@ -3206,7 +3252,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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.
@@ -3228,8 +3274,8 @@ 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;
@@ -3464,7 +3510,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #method
      * returns menu items for a highlight context menu. plugins can extend
-     * this via Core-extendPluggableElement to add their own items
+     * this via Core-extendPluggableElement to add items
      */
     highlightMenuItems(_highlight: HighlightType): MenuItem[];
 } & {
@@ -3500,14 +3546,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     hideHeaderOverview: boolean;
     hideNoTracksActive: boolean;
     trackSelectorType: "hierarchical";
+    showCytobands: boolean;
+    trackLabels: string;
     showGridlines: boolean;
+    colorByCDS: 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;
 }>;
 export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;