@jbrowse/plugin-linear-genome-view 5.0.0-beta.17 → 5.0.0-beta.19

package/esm/LinearGenomeView/model.d.ts

@@ -1,4 +1,4 @@
-import type { BpOffset, ExportSvgOptions, HighlightType, InitState, NavLocation, ViewTrackLabelMode, VolatileGuide } from './types.ts';
+import type { BpOffset, ExportSvgOptions, HighlightInput, HighlightType, InitState, NavLocation, ViewTrackLabelMode, VolatileGuide } from './types.ts';
 import type { RegionEdit } from './util.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type BaseResult from '@jbrowse/core/TextSearch/BaseResults';
@@ -9,6 +9,7 @@ import type { BlockSet, ContentBlock } from '@jbrowse/core/util/blockTypes';
 import type { Region } from '@jbrowse/core/util/types';
 import type { ViewStatus } from '@jbrowse/core/util/viewStatus';
 import type { LaunchInput } from '@jbrowse/core/util/withLaunchInput';
+import type { LinearDisplayModel } from '@jbrowse/display-kit/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 /** One place a name search points at, as a picker lists it. */
 export interface SearchPickerRow {
@@ -20,18 +21,24 @@ export interface SearchPickerRow {
     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.
+ * A name search's hits as a host lists them: what `view.search` returns, and
+ * what the picker holds.
  */
-export interface SearchPickerState {
+export interface SearchHits {
     query: string;
     assemblyName: string;
-    /** one row per place, hits in a track the view already shows first */
+    /** one row per hit, hits in a track the view already shows first */
     rows: SearchPickerRow[];
-    /** navigates to the row's place, reports a failure and closes the picker */
+    /** lands on the row's place and reports a failure */
     pick: (id: string) => Promise<unknown>;
 }
+/**
+ * The hits of a name search that point at more than one place, waiting for the
+ * user to choose; its `pick` also closes the picker. A host draws them however
+ * it likes: the Material view shows a dialog, and `SearchPicker` in
+ * `@jbrowse/display-ui/embed` a plain list.
+ */
+export type SearchPickerState = SearchHits;
 export type { PaddingSpan } from './util.ts';
 export interface HighlightRegion {
     assemblyName?: string;
@@ -87,11 +94,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     windowWidthBp: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     legacyBpPerPx: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     displayedRegions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Region[], Region[], Region[]>, [undefined]>;
-    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>;
     hideHeader: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     hideHeaderOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     hideNoTracksActive: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    trackSelectorType: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"hierarchical">, [undefined]>;
+    trackSelectorType: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showCenterLine: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showCytobands: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -172,6 +179,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #volatile
      */
     coarseBpPerPx: number;
+    /**
+     * #volatile
+     * the scroll offset the coarse blocks were laid out at, in px at
+     * `coarseBpPerPx`: the settled viewport's left edge, which the first
+     * coarse block is not while the view is scrolled before the first region
+     */
+    coarseOffsetPx: number;
     /**
      * #volatile
      */
@@ -236,11 +250,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      */
-    readonly pinnedTracks: any[];
+    readonly pinnedTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      */
-    readonly unpinnedTracks: any[];
+    readonly unpinnedTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      * the effective track labels setting, resolving the stored `trackLabels`
@@ -287,7 +301,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * The census entry for this view: the tracks it holds itself. Declared
      * rather than derived — see `BaseViewModel.ownTracks`.
      */
-    readonly ownTracks: any[];
+    readonly ownTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      * See `BaseViewModel.rendersDisplays`.
@@ -324,7 +338,48 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * and error checks resolve it directly through here.
      */
     readonly initAssembly: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
@@ -339,6 +394,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -352,6 +408,7 @@ 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;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
         setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
@@ -391,8 +448,50 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
             [x: string]: unknown;
         }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | undefined;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }, {
         error: unknown;
         loadingP: Promise<void> | undefined;
@@ -407,6 +506,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -420,6 +520,7 @@ 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;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
         setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
@@ -459,6 +560,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
             [x: string]: unknown;
         }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | undefined;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
      * #getter
@@ -485,7 +587,48 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * displayed assemblies that hasn't finished loading.
      */
     readonly loadingAssembly: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
@@ -500,6 +643,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -513,6 +657,7 @@ 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;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
         setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
@@ -552,8 +697,50 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
             [x: string]: unknown;
         }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | undefined;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }, {
         error: unknown;
         loadingP: Promise<void> | undefined;
@@ -568,6 +755,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -581,6 +769,7 @@ 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;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
         setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
@@ -620,6 +809,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
             [x: string]: unknown;
         }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | undefined;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
      * #getter
@@ -727,13 +917,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * mounts — rather than re-picking `displays[0]`, so the view's height math
      * can't diverge from what is on screen.
      */
-    trackHeight(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IAnyType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>>)[number]): any;
+    trackHeight(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>)[number]): number;
     /**
      * #method
      * the measured in-flow label band above a track's rendering container,
      * 0 until TrackContainer has measured one or when no label is in flow
      */
-    trackLabelBand(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IAnyType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>>)[number]): number;
+    trackLabelBand(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>)[number]): number;
     /**
      * #getter
      */
@@ -751,7 +941,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * The display height of each track a whole-stack resize moves, by track
      * instance id: every shown track that is not minimized.
      */
-    readonly resizableTrackHeights: Map<any, any>;
+    readonly resizableTrackHeights: Map<string, number>;
     /**
      * #method
      * Y offset (in pixels, from the top of the view) where a track's
@@ -771,7 +961,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * up/down/top/bottom reorder inside this section rather than the full
      * `tracks` array, since the two sections lay out independently
      */
-    trackSection(id: string): any[];
+    trackSection(id: string): (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      */
@@ -838,11 +1028,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      */
-    readonly trackMap: Map<string, any>;
+    readonly trackMap: Map<string, import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>;
     /**
      * #method
      */
-    getTrack(id: string): any;
+    getTrack(id: string): (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>) | undefined;
     /**
      * #method
      * displayId of the active (shown) display for a track in this view, used
@@ -967,6 +1157,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * there and shows the track its index came from
      */
     setSearchResults(searchResults: BaseResult[], searchQuery: string, assemblyName: string, onPick?: (result: BaseResult) => Promise<unknown>): void;
+    /**
+     * #action
+     * Search the view's assembly by name, for a host listing the hits
+     * itself. A row's `pick` lands as the search box does: it navigates
+     * there and shows the track the hit's index came from.
+     */
+    search(query: string, opts?: {
+        signal?: AbortSignal;
+    }): Promise<SearchHits>;
     /**
      * #action
      */
@@ -988,6 +1187,22 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * loaded: loads it, then shows
      */
     launchTrack(trackId: string, initialSnapshot?: any, displayInitialSnapshot?: any, inlineConf?: Record<string, unknown>): Promise<any>;
+    /**
+     * #action
+     * Replace the highlights `highlights` reads, each written as the launch
+     * spec's `highlight` writes one: a locstring, or an object whose
+     * `assemblyName` defaults to the view's. Throws on one that names no
+     * region, writing none.
+     */
+    setHighlights(highlights: readonly (string | HighlightInput)[]): void;
+    /**
+     * #action
+     * Show files from the user's disk as session tracks: one per data file,
+     * beside the index among them that names it, its type guessed from its
+     * name. Adds nothing when one file has no known type. Resolves the new
+     * tracks' ids.
+     */
+    showFiles(files: readonly File[]): Promise<string[]>;
 } & {
     /**
      * #method
@@ -996,7 +1211,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * both name one shown track. Answers the model id, or the argument
      * unchanged when nothing shown matches, so the move reports it.
      */
-    trackModelId(idOrTrackId: string): any;
+    trackModelId(idOrTrackId: string): string;
 } & {
     moveTrack: (moving: string, target: string) => void;
     /**
@@ -1482,7 +1697,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *
      * The coarse blocks are a 500ms throttle, and every consumer trades
      * freshness for not recomputing per animation frame — the location box,
-     * canvas's on-screen feature set, and the two per-bp scans behind
+     * the feature display's on-screen feature set, and the two per-bp scans behind
      * `settledDynamicBlocks`. That trade is only sound while the answer is a
      * few frames old. **A jump makes it unrelated instead**, because there is
      * nothing to coalesce: the viewport left behind is not an approximation of
@@ -1708,10 +1923,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * adds the region in view to the session's highlights
      */
     highlightCurrentRegion(): void;
+    /**
+     * #action
+     * navigates to a highlight, zoomed out a little for context. Goes through
+     * a locstring so it reaches a refName the view is not displaying
+     */
+    navToHighlight(highlight: HighlightType): Promise<boolean>;
+} & {
     /**
      * #action
      * navigates to the most recently added highlight on this view's
-     * assemblies, zoomed out a little for context
+     * assemblies
      */
     navigateNewestHighlight(): Promise<void>;
 } & {
@@ -1748,7 +1970,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     nonGenomicTrackBands(): {
         top: number;
-        height: any;
+        height: number;
     }[];
     /**
      * #method
@@ -1792,8 +2014,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     rubberbandClickMenuItems(clickOffset: BpOffset): MenuItem[];
     /**
      * #method
-     * returns menu items for a highlight context menu. plugins can extend
-     * this via Core-extendPluggableElement to add items
+     * a highlight chip's menu rows after Dismiss; extend this to add one
      */
     highlightMenuItems(_highlight: HighlightType): MenuItem[];
 } & {
@@ -1826,11 +2047,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     windowWidthBp: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     legacyBpPerPx: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     displayedRegions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Region[], Region[], Region[]>, [undefined]>;
-    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>;
     hideHeader: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     hideHeaderOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     hideNoTracksActive: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    trackSelectorType: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"hierarchical">, [undefined]>;
+    trackSelectorType: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showCenterLine: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showCytobands: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -1911,6 +2132,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #volatile
      */
     coarseBpPerPx: number;
+    /**
+     * #volatile
+     * the scroll offset the coarse blocks were laid out at, in px at
+     * `coarseBpPerPx`: the settled viewport's left edge, which the first
+     * coarse block is not while the view is scrolled before the first region
+     */
+    coarseOffsetPx: number;
     /**
      * #volatile
      */
@@ -1975,11 +2203,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      */
-    readonly pinnedTracks: any[];
+    readonly pinnedTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      */
-    readonly unpinnedTracks: any[];
+    readonly unpinnedTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      * the effective track labels setting, resolving the stored `trackLabels`
@@ -2026,7 +2254,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * The census entry for this view: the tracks it holds itself. Declared
      * rather than derived — see `BaseViewModel.ownTracks`.
      */
-    readonly ownTracks: any[];
+    readonly ownTracks: (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      * See `BaseViewModel.rendersDisplays`.
@@ -2063,7 +2291,48 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * and error checks resolve it directly through here.
      */
     readonly initAssembly: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
@@ -2078,6 +2347,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -2091,6 +2361,7 @@ 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;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
         setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
@@ -2130,8 +2401,50 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
             [x: string]: unknown;
         }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | undefined;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }, {
         error: unknown;
         loadingP: Promise<void> | undefined;
@@ -2146,6 +2459,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -2159,6 +2473,7 @@ 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;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
         setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
@@ -2198,6 +2513,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
             [x: string]: unknown;
         }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | undefined;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
      * #getter
@@ -2224,7 +2540,48 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * displayed assemblies that hasn't finished loading.
      */
     readonly loadingAssembly: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
@@ -2239,6 +2596,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -2252,6 +2610,7 @@ 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;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
         setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
@@ -2291,8 +2650,50 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
             [x: string]: unknown;
         }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | undefined;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            readonly aliases: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+            readonly refNameColors: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodes: {
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly circularRefNames: {
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
+            };
+            readonly geneticCodesLocation: {
+                type: "maybeFileLocation";
+            };
+            readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+            readonly displayName: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+            name: {
+                type: "string";
+            } & {
+                defaultValue: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>>;
     }, {
         error: unknown;
         loadingP: Promise<void> | undefined;
@@ -2307,6 +2708,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         statusProgress: number | undefined;
         statusSource: string | undefined;
         refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        contigLengthMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch>;
     } & {
         getConf(arg: string): any;
     } & {
@@ -2320,6 +2722,7 @@ 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;
+        setContigLengthMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch): void;
     } & {
         setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
             regions: import("@jbrowse/core/util").Region[];
@@ -2359,6 +2762,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
             [x: string]: unknown;
         }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        getContigLengthMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").ContigLengthMismatch | undefined;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
      * #getter
@@ -2466,13 +2870,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * mounts — rather than re-picking `displays[0]`, so the view's height math
      * can't diverge from what is on screen.
      */
-    trackHeight(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IAnyType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>>)[number]): any;
+    trackHeight(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>)[number]): number;
     /**
      * #method
      * the measured in-flow label band above a track's rendering container,
      * 0 until TrackContainer has measured one or when no label is in flow
      */
-    trackLabelBand(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IAnyType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>>)[number]): number;
+    trackLabelBand(track: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>)[number]): number;
     /**
      * #getter
      */
@@ -2490,7 +2894,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * The display height of each track a whole-stack resize moves, by track
      * instance id: every shown track that is not minimized.
      */
-    readonly resizableTrackHeights: Map<any, any>;
+    readonly resizableTrackHeights: Map<string, number>;
     /**
      * #method
      * Y offset (in pixels, from the top of the view) where a track's
@@ -2510,7 +2914,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * up/down/top/bottom reorder inside this section rather than the full
      * `tracks` array, since the two sections lay out independently
      */
-    trackSection(id: string): any[];
+    trackSection(id: string): (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>)[];
     /**
      * #getter
      */
@@ -2577,11 +2981,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      */
-    readonly trackMap: Map<string, any>;
+    readonly trackMap: Map<string, import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>>;
     /**
      * #method
      */
-    getTrack(id: string): any;
+    getTrack(id: string): (import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableStateModelUnion<import("@jbrowse/core/pluggableElementTypes/models").TrackModelOf<LinearDisplayModel>, import("@jbrowse/core/util/tracks").TrackSnapshot>>) | undefined;
     /**
      * #method
      * displayId of the active (shown) display for a track in this view, used
@@ -2706,6 +3110,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * there and shows the track its index came from
      */
     setSearchResults(searchResults: BaseResult[], searchQuery: string, assemblyName: string, onPick?: (result: BaseResult) => Promise<unknown>): void;
+    /**
+     * #action
+     * Search the view's assembly by name, for a host listing the hits
+     * itself. A row's `pick` lands as the search box does: it navigates
+     * there and shows the track the hit's index came from.
+     */
+    search(query: string, opts?: {
+        signal?: AbortSignal;
+    }): Promise<SearchHits>;
     /**
      * #action
      */
@@ -2727,6 +3140,22 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * loaded: loads it, then shows
      */
     launchTrack(trackId: string, initialSnapshot?: any, displayInitialSnapshot?: any, inlineConf?: Record<string, unknown>): Promise<any>;
+    /**
+     * #action
+     * Replace the highlights `highlights` reads, each written as the launch
+     * spec's `highlight` writes one: a locstring, or an object whose
+     * `assemblyName` defaults to the view's. Throws on one that names no
+     * region, writing none.
+     */
+    setHighlights(highlights: readonly (string | HighlightInput)[]): void;
+    /**
+     * #action
+     * Show files from the user's disk as session tracks: one per data file,
+     * beside the index among them that names it, its type guessed from its
+     * name. Adds nothing when one file has no known type. Resolves the new
+     * tracks' ids.
+     */
+    showFiles(files: readonly File[]): Promise<string[]>;
 } & {
     /**
      * #method
@@ -2735,7 +3164,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * both name one shown track. Answers the model id, or the argument
      * unchanged when nothing shown matches, so the move reports it.
      */
-    trackModelId(idOrTrackId: string): any;
+    trackModelId(idOrTrackId: string): string;
 } & {
     moveTrack: (moving: string, target: string) => void;
     /**
@@ -3221,7 +3650,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *
      * The coarse blocks are a 500ms throttle, and every consumer trades
      * freshness for not recomputing per animation frame — the location box,
-     * canvas's on-screen feature set, and the two per-bp scans behind
+     * the feature display's on-screen feature set, and the two per-bp scans behind
      * `settledDynamicBlocks`. That trade is only sound while the answer is a
      * few frames old. **A jump makes it unrelated instead**, because there is
      * nothing to coalesce: the viewport left behind is not an approximation of
@@ -3447,10 +3876,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * adds the region in view to the session's highlights
      */
     highlightCurrentRegion(): void;
+    /**
+     * #action
+     * navigates to a highlight, zoomed out a little for context. Goes through
+     * a locstring so it reaches a refName the view is not displaying
+     */
+    navToHighlight(highlight: HighlightType): Promise<boolean>;
+} & {
     /**
      * #action
      * navigates to the most recently added highlight on this view's
-     * assemblies, zoomed out a little for context
+     * assemblies
      */
     navigateNewestHighlight(): Promise<void>;
 } & {
@@ -3487,7 +3923,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     nonGenomicTrackBands(): {
         top: number;
-        height: any;
+        height: number;
     }[];
     /**
      * #method
@@ -3531,8 +3967,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     rubberbandClickMenuItems(clickOffset: BpOffset): MenuItem[];
     /**
      * #method
-     * returns menu items for a highlight context menu. plugins can extend
-     * this via Core-extendPluggableElement to add items
+     * a highlight chip's menu rows after Dismiss; extend this to add one
      */
     highlightMenuItems(_highlight: HighlightType): MenuItem[];
 } & {
@@ -3563,11 +3998,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     windowWidthBp: number;
     legacyBpPerPx: number;
     displayedRegions: Region[];
-    tracks: any[];
+    tracks: import("@jbrowse/core/util/tracks").TrackSnapshot[];
     hideHeader: boolean;
     hideHeaderOverview: boolean;
     hideNoTracksActive: boolean;
-    trackSelectorType: "hierarchical";
+    trackSelectorType: string;
     showCytobands: boolean;
     trackLabels: string;
     axis: import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, any>>;
@@ -3577,8 +4012,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     scalebarOnly: boolean;
     launch: LaunchInput<InitState> | undefined;
 }>;
-export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
+export interface LinearGenomeViewStateModel extends ReturnType<typeof stateModelFactory> {
+}
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
+export type LinearGenomeViewTrack = LinearGenomeViewModel['tracks'][number];
 declare module '@jbrowse/core/PluginManager' {
     interface ViewTypeRegistry {
         LinearGenomeView: LinearGenomeViewStateModel;