@jbrowse/plugin-linear-genome-view 5.0.0-beta.11 → 5.0.0-beta.15

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>;
@@ -575,11 +602,12 @@ 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;
     /**
@@ -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
@@ -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;
@@ -1359,7 +1387,7 @@ 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
@@ -1470,6 +1498,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
@@ -1836,6 +1873,12 @@ 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 +2050,13 @@ 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 +2075,7 @@ 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 +2106,25 @@ 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 +2143,7 @@ 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 +2174,12 @@ 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 +2211,13 @@ 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 +2236,7 @@ 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 +2267,25 @@ 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 +2304,7 @@ 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>;
@@ -2289,11 +2335,12 @@ 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;
     /**
@@ -2525,6 +2572,12 @@ 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
@@ -2747,12 +2800,6 @@ 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;
@@ -3073,7 +3120,7 @@ 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
@@ -3184,6 +3231,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
@@ -3500,14 +3556,14 @@ 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>;