@jbrowse/product-core 3.7.0 → 4.0.1

package/esm/Session/SessionTracks.d.ts

@@ -1,12 +1,12 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfiguration, AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-export declare function SessionTracksManagerSessionMixin(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 SessionTracksManagerSessionMixin(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>;
 } & {
-    sessionTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    sessionTracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
 }, {
     selection: unknown;
     hovered: unknown;
@@ -16,8 +16,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
         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;
@@ -25,6 +25,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -48,9 +49,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -65,6 +67,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -83,8 +86,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -92,6 +95,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -115,9 +119,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -132,6 +137,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -150,17 +156,18 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -184,9 +191,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -201,6 +209,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -219,8 +228,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -228,6 +237,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -251,9 +261,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -268,6 +279,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -286,19 +298,20 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -322,9 +335,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -339,6 +353,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -357,8 +372,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -366,6 +381,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -389,9 +405,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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 +423,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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 +442,21 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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: 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;
@@ -461,9 +480,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -478,6 +498,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -496,8 +517,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -505,6 +526,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -528,9 +550,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -545,6 +568,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -563,21 +587,15 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -585,9 +603,9 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             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;
@@ -595,6 +613,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -618,9 +637,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -635,6 +655,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -653,17 +674,18 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -687,9 +709,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -704,6 +727,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -722,8 +746,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -731,6 +755,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -754,9 +779,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -771,6 +797,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -789,19 +816,20 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -825,9 +853,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -842,6 +871,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -860,8 +890,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -869,6 +899,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -892,9 +923,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -909,6 +941,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -927,20 +960,21 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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: 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;
@@ -964,9 +998,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -981,6 +1016,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -999,8 +1035,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1008,6 +1044,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1031,9 +1068,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -1048,6 +1086,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1066,21 +1105,15 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1088,8 +1121,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             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;
@@ -1097,17 +1130,17 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
         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;
@@ -1115,6 +1148,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1138,9 +1172,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -1155,6 +1190,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1173,17 +1209,18 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1207,9 +1244,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -1224,6 +1262,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1242,8 +1281,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1251,6 +1290,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1274,9 +1314,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -1291,6 +1332,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1309,19 +1351,20 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1345,9 +1388,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -1362,6 +1406,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1380,8 +1425,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1389,6 +1434,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1412,9 +1458,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -1429,6 +1476,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1447,20 +1495,21 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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: 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;
@@ -1484,9 +1533,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -1501,6 +1551,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1519,8 +1570,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1528,6 +1579,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1551,9 +1603,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(asmName: string): string;
+                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[];
@@ -1568,6 +1621,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1586,21 +1640,15 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1608,7 +1656,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             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;
@@ -1617,25 +1665,21 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
         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;
 } & {
@@ -1645,11 +1689,17 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
     clearSelection(): void;
     setHovered(thing: unknown): void;
 } & {
-    getReferring(object: IAnyStateTreeNode): import("./ReferenceManagement").ReferringNode[];
+    getReferring(object: IAnyStateTreeNode): import("./ReferenceManagement.ts").ReferringNode[];
 } & {
-    removeReferring(referring: import("./ReferenceManagement").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
+    removeReferring(referring: import("./ReferenceManagement.ts").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
 } & {
     readonly tracks: AnyConfigurationModel[];
+    readonly assemblies: {
+        sequence: {
+            trackId: string;
+        };
+    }[];
+    readonly tracksById: Record<string, AnyConfigurationModel>;
 } & {
     addTrackConf(trackConf: AnyConfiguration): any;
     deleteTrackConf(trackConf: AnyConfigurationModel): any;
@@ -1658,7 +1708,13 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
 } & {
     addTrackConf(trackConf: AnyConfiguration): any;
     deleteTrackConf(trackConf: AnyConfigurationModel): any;
-}, 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>;
+} & {
+    sessionTracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+}>>;
 export type SessionWithSessionTracksType = ReturnType<typeof SessionTracksManagerSessionMixin>;
 export type SessionWithSessionTracks = Instance<SessionWithSessionTracksType>;
 export declare function isSessionWithSessionTracks(thing: IAnyStateTreeNode): thing is SessionWithSessionTracks;