@jbrowse/product-core 3.6.5 → 4.0.0

package/esm/Session/MultipleViews.d.ts

@@ -1,19 +1,20 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { IBaseViewModel } from '@jbrowse/core/pluggableElementTypes';
-import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-export declare function MultipleViewsSessionMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    name: import("mobx-state-tree").ISimpleType<string>;
-    margin: import("mobx-state-tree").IType<number | undefined, number, number>;
+import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
+export declare function MultipleViewsSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    margin: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
 } & {
-    drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
-    activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
-    minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    widgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    activeWidgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>;
+    minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 } & {
-    views: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
-    stickyViewHeaders: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    views: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    stickyViewHeaders: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    useWorkspaces: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
     selection: unknown;
     hovered: unknown;
@@ -23,8 +24,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
         session: any;
         sessionPath: string;
         assemblyManager: {
-            assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            assemblies: import("@jbrowse/mobx-state-tree").IMSTArray<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;
@@ -32,6 +33,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -55,8 +57,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -71,6 +75,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -89,8 +94,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<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;
@@ -98,6 +103,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -121,8 +127,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -137,6 +145,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -155,17 +164,18 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             readonly assemblyNameMap: Record<string, {
                 configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -189,8 +199,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -205,6 +217,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -223,8 +236,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            } & 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;
@@ -232,6 +245,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -255,8 +269,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -271,6 +287,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -289,18 +306,20 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
         } & {
             getCanonicalAssemblyName(asmName: string): string | undefined;
+            getCanonicalAssemblyName2(asmName: string): string;
             get(asmName: string): ({
                 configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -324,8 +343,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -340,6 +361,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -358,8 +380,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            } & 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;
@@ -367,6 +389,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -390,8 +413,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -406,6 +431,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -424,20 +450,21 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: any[];
             readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             waitForAssembly(assemblyName: string): Promise<({
                 configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -461,8 +488,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -477,6 +506,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -495,8 +525,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            } & 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;
@@ -504,6 +534,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -527,8 +558,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -543,6 +576,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -561,21 +595,15 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, assemblyName: string | undefined, opts: {
-                stopToken?: string;
-                sessionId: string;
-            }): Promise<{
+            }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
                 [x: string]: string;
             } | undefined>;
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, assemblyName: string | undefined, opts: {
-                stopToken?: string;
-                sessionId: string;
-            }): Promise<{
+            }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
                 [x: string]: string;
             } | undefined>;
             isValidRefName(refName: string, assemblyName: string): boolean;
@@ -583,9 +611,9 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
             afterAttach(): void;
             removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
             addAssembly(configuration: any): void;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-            assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+            assemblies: import("@jbrowse/mobx-state-tree").IArrayType<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;
@@ -593,6 +621,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -616,8 +645,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -632,6 +663,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -650,17 +682,18 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
         }, {
             readonly assemblyNameMap: Record<string, {
                 configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -684,8 +717,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -700,6 +735,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -718,8 +754,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            } & 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;
@@ -727,6 +763,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -750,8 +787,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -766,6 +805,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -784,18 +824,20 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
         } & {
             getCanonicalAssemblyName(asmName: string): string | undefined;
+            getCanonicalAssemblyName2(asmName: string): string;
             get(asmName: string): ({
                 configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -819,8 +861,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -835,6 +879,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -853,8 +898,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            } & 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;
@@ -862,6 +907,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -885,8 +931,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -901,6 +949,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -919,20 +968,21 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: any[];
             readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             waitForAssembly(assemblyName: string): Promise<({
                 configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -956,8 +1006,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -972,6 +1024,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -990,8 +1043,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            } & 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;
@@ -999,6 +1052,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1022,8 +1076,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -1038,6 +1094,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -1056,21 +1113,15 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, assemblyName: string | undefined, opts: {
-                stopToken?: string;
-                sessionId: string;
-            }): Promise<{
+            }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
                 [x: string]: string;
             } | undefined>;
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, assemblyName: string | undefined, opts: {
-                stopToken?: string;
-                sessionId: string;
-            }): Promise<{
+            }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
                 [x: string]: string;
             } | undefined>;
             isValidRefName(refName: string, assemblyName: string): boolean;
@@ -1078,8 +1129,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
             afterAttach(): void;
             removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
             addAssembly(configuration: any): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>>;
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
         rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         adminMode: boolean;
         error: unknown;
@@ -1087,17 +1138,17 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
         pluginManager: PluginManager;
     } & {
         setError(error: unknown): void;
-        setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
+        setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
         setDefaultSession(): void;
         setSessionPath(path: string): void;
         renameCurrentSession(newName: string): void;
-    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-        jbrowse: import("mobx-state-tree").IAnyType;
-        session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
-        sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-        assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-            assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+        jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
+        session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
+        sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+            assemblies: import("@jbrowse/mobx-state-tree").IArrayType<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;
@@ -1105,6 +1156,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1128,8 +1180,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -1144,6 +1198,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -1162,17 +1217,18 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
         }, {
             readonly assemblyNameMap: Record<string, {
                 configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1196,8 +1252,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -1212,6 +1270,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -1230,8 +1289,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            } & 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;
@@ -1239,6 +1298,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1262,8 +1322,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -1278,6 +1340,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -1296,18 +1359,20 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
         } & {
             getCanonicalAssemblyName(asmName: string): string | undefined;
+            getCanonicalAssemblyName2(asmName: string): string;
             get(asmName: string): ({
                 configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1331,8 +1396,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -1347,6 +1414,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -1365,8 +1433,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            } & 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;
@@ -1374,6 +1442,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1397,8 +1466,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -1413,6 +1484,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -1431,20 +1503,21 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: any[];
             readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             waitForAssembly(assemblyName: string): Promise<({
                 configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1468,8 +1541,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -1484,6 +1559,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -1502,8 +1578,8 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            } & 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;
@@ -1511,6 +1587,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1534,8 +1611,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                getCanonicalRefName2(refName: string): string;
                 getRefNameColor(refName: string): string | undefined;
                 isValidRefName(refName: string): boolean;
+                getSeqAdapterRefName(canonicalRefName: string): string;
             } & {
                 setLoaded({ regions, refNameAliases, cytobands, }: {
                     regions: import("@jbrowse/core/util").Region[];
@@ -1550,6 +1629,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
                 setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
@@ -1568,21 +1648,15 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
                     [x: string]: string;
                 }>;
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, assemblyName: string | undefined, opts: {
-                stopToken?: string;
-                sessionId: string;
-            }): Promise<{
+            }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
                 [x: string]: string;
             } | undefined>;
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, assemblyName: string | undefined, opts: {
-                stopToken?: string;
-                sessionId: string;
-            }): Promise<{
+            }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
                 [x: string]: string;
             } | undefined>;
             isValidRefName(refName: string, assemblyName: string): boolean;
@@ -1590,7 +1664,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
             afterAttach(): void;
             removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
             addAssembly(configuration: any): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
     }, {
         rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         adminMode: boolean;
@@ -1599,25 +1673,21 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
         pluginManager: PluginManager;
     } & {
         setError(error: unknown): void;
-        setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
+        setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
         setDefaultSession(): void;
         setSessionPath(path: string): void;
         renameCurrentSession(newName: string): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
 } & {
     readonly jbrowse: any;
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
     readonly configuration: {
         [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
             [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     readonly adminMode: boolean;
     readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
 } & {
@@ -1639,7 +1709,9 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     minimizeWidgetDrawer(): void;
     showWidgetDrawer(): void;
     hideAllWidgets(): void;
-    editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
+    editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel | {
+        trackId: string;
+    }): void;
     afterAttach(): void;
 } & {
     moveViewDown(id: string): void;
@@ -1649,8 +1721,23 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     addView(typeName: string, initialState?: {}): any;
     removeView(view: IBaseViewModel): void;
     setStickyViewHeaders(sticky: boolean): void;
+    setUseWorkspaces(useWorkspaces: boolean): void;
     afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    margin: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+} & {
+    drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    widgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    activeWidgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>;
+    minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+} & {
+    views: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    stickyViewHeaders: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    useWorkspaces: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}>>;
 export type SessionWithMultipleViewsType = ReturnType<typeof MultipleViewsSessionMixin>;
 export type SessionWithMultipleViews = Instance<SessionWithMultipleViewsType>;
 export declare function isSessionWithMultipleViews(session: IAnyStateTreeNode): session is SessionWithMultipleViews;