@jbrowse/product-core 5.0.0-beta.1 → 5.0.0-beta.11

package/esm/Session/MultipleViews.d.ts

@@ -1,4 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
+import type { ViewSnapshotInput } from '@jbrowse/core/PluginManager';
 import type { IBaseViewModel } from '@jbrowse/core/pluggableElementTypes';
 import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
 /**
@@ -8,7 +9,9 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
     highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    highlightLabelsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined>, [undefined]>;
 }, never>, "activeWidgets" | "drawerPosition" | "drawerWidth" | "minimized" | "widgets"> & {
     drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("@jbrowse/core/util").DrawerPosition>, [undefined]>;
@@ -48,7 +51,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -86,7 +89,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -104,6 +106,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -119,141 +122,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 } | undefined;
             };
         } & {
-            readonly assemblyNameMap: Record<string, 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>>;
-            }> & {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-                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;
-                statusMessage: string | undefined;
-                statusProgress: number | undefined;
-                statusSource: string | undefined;
-                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly name: string;
-                readonly aliases: string[];
-                readonly displayName: string;
-                readonly refNameColors: string[];
-            } & {
-                readonly allAliases: string[];
-                hasName(name: string): boolean;
-            } & {
-                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 & {
-                    regions: import("@jbrowse/core/util").Region[];
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                    geneticCodes: Record<string, number>;
-                }): void;
-                setError(e: unknown): void;
-                setLoadingP(p?: Promise<void>): void;
-                loadPre(): Promise<void>;
-            } & {
-                load(): Promise<void>;
-            } & {
-                afterAttach(): void;
-            } & {
-                readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly allRefNames: string[] | undefined;
-                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                readonly refNameToIndex: Map<string, number> | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
-                getGeneticCodeId(refName: string): number;
-                getSeqAdapterRefName(canonicalRefName: string): string;
-            } & {
-                getCanonicalRefName2(refName: string): string;
-                isValidRefName(refName: string): boolean;
-            } & {
-                getAliasesForRefName(refName: string): string[];
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
-                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
-            } & import("@jbrowse/mobx-state-tree").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>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
-                statusMessage: string | undefined;
-                statusProgress: number | undefined;
-                statusSource: string | undefined;
-                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly name: string;
-                readonly aliases: string[];
-                readonly displayName: string;
-                readonly refNameColors: string[];
-            } & {
-                readonly allAliases: string[];
-                hasName(name: string): boolean;
-            } & {
-                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 & {
-                    regions: import("@jbrowse/core/util").Region[];
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                    geneticCodes: Record<string, number>;
-                }): void;
-                setError(e: unknown): void;
-                setLoadingP(p?: Promise<void>): void;
-                loadPre(): Promise<void>;
-            } & {
-                load(): Promise<void>;
-            } & {
-                afterAttach(): void;
-            } & {
-                readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly allRefNames: string[] | undefined;
-                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                readonly refNameToIndex: Map<string, number> | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
-                getGeneticCodeId(refName: string): number;
-                getSeqAdapterRefName(canonicalRefName: string): string;
-            } & {
-                getCanonicalRefName2(refName: string): string;
-                isValidRefName(refName: string): boolean;
-            } & {
-                getAliasesForRefName(refName: string): string[];
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
-                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
-            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+            readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
         } & {
             getCanonicalAssemblyName(asmName: string): string | undefined;
             getDisplayName(asmName: string): string;
@@ -263,7 +132,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -301,7 +170,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -319,6 +187,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -330,7 +199,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -368,7 +237,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -386,6 +254,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -399,7 +268,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -437,7 +306,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -455,6 +323,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -466,7 +335,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -504,7 +373,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -522,6 +390,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -529,11 +398,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: string[];
-            readonly configuredAssemblyNames: Set<string>;
-            readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-                setSubschema(slotName: string, data: Record<string, unknown>): any;
-                setSlot(slotName: string, value: unknown): void;
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
+            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -544,7 +410,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -582,7 +448,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -600,6 +465,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -611,7 +477,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -649,7 +515,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -667,6 +532,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -679,7 +545,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -717,7 +583,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -735,6 +600,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -746,7 +612,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -784,7 +650,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -802,6 +667,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -840,7 +706,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -878,7 +744,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -896,6 +761,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -911,141 +777,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 } | undefined;
             };
         } & {
-            readonly assemblyNameMap: Record<string, 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>>;
-            }> & {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-                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;
-                statusMessage: string | undefined;
-                statusProgress: number | undefined;
-                statusSource: string | undefined;
-                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly name: string;
-                readonly aliases: string[];
-                readonly displayName: string;
-                readonly refNameColors: string[];
-            } & {
-                readonly allAliases: string[];
-                hasName(name: string): boolean;
-            } & {
-                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 & {
-                    regions: import("@jbrowse/core/util").Region[];
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                    geneticCodes: Record<string, number>;
-                }): void;
-                setError(e: unknown): void;
-                setLoadingP(p?: Promise<void>): void;
-                loadPre(): Promise<void>;
-            } & {
-                load(): Promise<void>;
-            } & {
-                afterAttach(): void;
-            } & {
-                readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly allRefNames: string[] | undefined;
-                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                readonly refNameToIndex: Map<string, number> | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
-                getGeneticCodeId(refName: string): number;
-                getSeqAdapterRefName(canonicalRefName: string): string;
-            } & {
-                getCanonicalRefName2(refName: string): string;
-                isValidRefName(refName: string): boolean;
-            } & {
-                getAliasesForRefName(refName: string): string[];
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
-                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
-            } & import("@jbrowse/mobx-state-tree").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>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
-                statusMessage: string | undefined;
-                statusProgress: number | undefined;
-                statusSource: string | undefined;
-                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly name: string;
-                readonly aliases: string[];
-                readonly displayName: string;
-                readonly refNameColors: string[];
-            } & {
-                readonly allAliases: string[];
-                hasName(name: string): boolean;
-            } & {
-                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 & {
-                    regions: import("@jbrowse/core/util").Region[];
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                    geneticCodes: Record<string, number>;
-                }): void;
-                setError(e: unknown): void;
-                setLoadingP(p?: Promise<void>): void;
-                loadPre(): Promise<void>;
-            } & {
-                load(): Promise<void>;
-            } & {
-                afterAttach(): void;
-            } & {
-                readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly allRefNames: string[] | undefined;
-                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                readonly refNameToIndex: Map<string, number> | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
-                getGeneticCodeId(refName: string): number;
-                getSeqAdapterRefName(canonicalRefName: string): string;
-            } & {
-                getCanonicalRefName2(refName: string): string;
-                isValidRefName(refName: string): boolean;
-            } & {
-                getAliasesForRefName(refName: string): string[];
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
-                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
-            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+            readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
         } & {
             getCanonicalAssemblyName(asmName: string): string | undefined;
             getDisplayName(asmName: string): string;
@@ -1055,7 +787,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1093,7 +825,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1111,6 +842,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1122,7 +854,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1160,7 +892,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1178,6 +909,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1191,7 +923,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1229,7 +961,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1247,6 +978,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1258,7 +990,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1296,7 +1028,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1314,6 +1045,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1321,11 +1053,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: string[];
-            readonly configuredAssemblyNames: Set<string>;
-            readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-                setSubschema(slotName: string, data: Record<string, unknown>): any;
-                setSlot(slotName: string, value: unknown): void;
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
+            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1336,7 +1065,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1374,7 +1103,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1392,6 +1120,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1403,7 +1132,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1441,7 +1170,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1459,6 +1187,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1471,7 +1200,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1509,7 +1238,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1527,6 +1255,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1538,7 +1267,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1576,7 +1305,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1594,6 +1322,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1625,10 +1354,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
 } & {
     readonly jbrowse: any;
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-    readonly configuration: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-        setSubschema(slotName: string, data: Record<string, unknown>): any;
-        setSlot(slotName: string, value: unknown): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    readonly configuration: import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     readonly adminMode: boolean;
     readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
 } & {
@@ -1638,12 +1364,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
 } & {
     getPreferenceDefault(key: string): unknown;
     getPreference(key: string): unknown;
-    getDisplayTypeDefault(displayType: string, slot: string): unknown;
-    getDisplayTypeDefaults(): {
-        displayType: string;
-        slot: string;
-        value: unknown;
-    }[];
     getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
 } & {
     readonly animationMode: import("@jbrowse/core/util").AnimationMode;
@@ -1655,17 +1375,20 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     clearSelection(): void;
     setHovered(thing: unknown): void;
     setHighlightsVisible(arg: boolean): void;
-    revealHighlights(): void;
+    setHighlightLabelsVisible(arg: boolean): void;
+    addHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    removeHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    updateHighlight(old: import("@jbrowse/core/util/highlights").HighlightType, updates: Partial<import("@jbrowse/core/util/highlights").HighlightType>): void;
+    setHighlights(highlights: import("@jbrowse/core/util/highlights").HighlightType[]): void;
     setPreferenceOverride(key: string, value: unknown): void;
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
-    resetPreferenceChange(path: string[]): void;
     setScrollZoom(flag: boolean): void;
-    setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
     setName(str: string): void;
     setFocusedViewId(viewId: string | undefined): void;
     removeActiveDialog(): void;
     queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
+    removeDialog(entry: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
 } & {
     snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
     errorDialog: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined;
@@ -1678,12 +1401,16 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, actions?: import("@jbrowse/core/util").SnackAction[]): void;
     popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
     removeSnackbarMessage(message: string): void;
+} & {
+    afterAttach(): void;
 } & {
     readonly visibleWidget: import("@jbrowse/core/util").Widget | undefined;
 } & {
     poppedOut: boolean;
+    modalWidgets: boolean;
 } & {
     readonly drawerVisible: boolean;
+    readonly modalWidgetVisible: boolean;
 } & {
     setDrawerPosition(arg: import("@jbrowse/core/util").DrawerPosition): void;
     updateDrawerWidth(drawerWidth: number, availableWidth?: number): number;
@@ -1695,13 +1422,18 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     showWidgetDrawer(): void;
     popoutWidget(): void;
     returnWidgetToDrawer(): void;
+    setModalWidgets(flag: boolean): void;
     hideAllWidgets(): void;
+    afterAttach(): void;
+} & {
+    closeModalWidget(): void;
+    openWidget(typeName: string, id: string, initialState?: any, conf?: unknown): any;
+} & {
     editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel | {
         trackId: string;
     }, opts?: {
         expandedDisplayId?: string;
     }): void;
-    afterAttach(): void;
 } & {
     /**
      * #getter
@@ -1752,8 +1484,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     orderViews(ids: string[]): void;
     /**
      * #action
+     * Requires the view type's state model to be loaded; for a lazily
+     * registered type use `launchView`.
      */
-    addView(typeName: string, initialState?: any): any;
+    addView<N extends string>(typeName: N, initialState?: NoInfer<ViewSnapshotInput<N>>): any;
     /**
      * #action
      * swap `view` for a new view of `typeName`, in the slot it occupied.
@@ -1783,7 +1517,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
      * its panel, and the launch that offers a replace is a click on that
      * view's own menu.
      */
-    replaceView(view: IBaseViewModel, typeName: string, initialState?: any): any;
+    replaceView<N extends string>(view: IBaseViewModel, typeName: N, initialState?: NoInfer<ViewSnapshotInput<N>>): any;
     /**
      * #action
      */
@@ -1845,11 +1579,23 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
      */
     resetUseWorkspaces(): void;
     afterAttach(): void;
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<Omit<Omit<Omit<{
+} & {
+    /**
+     * #action
+     * `addView` for view types whose state model may be lazily loaded. The
+     * view is not in `session.views` until the promise resolves.
+     * `getViewType` first so an unknown type name fails by that name; the
+     * snapshot walk skips unregistered names and covers the displays of the
+     * tracks a launch opens with.
+     */
+    launchView<N extends string>(typeName: N, initialState?: NoInfer<ViewSnapshotInput<N>>): Promise<any>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<Omit<Omit<Omit<{
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
     highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    highlightLabelsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined>, [undefined]>;
 }, never>, "activeWidgets" | "drawerPosition" | "drawerWidth" | "minimized" | "widgets"> & {
     drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("@jbrowse/core/util").DrawerPosition>, [undefined]>;
@@ -1872,6 +1618,12 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
      * means unspecified — read `effectiveUseWorkspaces`.
      */
     useWorkspaces: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+}>, "activeWidgets" | "drawerPosition" | "drawerWidth" | "minimized" | "widgets"> & import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("@jbrowse/core/util").DrawerPosition>, [undefined]>;
+    drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    widgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
+    activeWidgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>, [undefined]>;
+    minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }>>;
 /** Session mixin MST type for a session that manages multiple views */
 export type SessionWithMultipleViewsType = ReturnType<typeof MultipleViewsSessionMixin>;