@jbrowse/product-core 3.6.5 → 4.0.0

package/esm/Session/Tracks.d.ts

@@ -1,10 +1,10 @@
 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 TracksManagerSessionMixin(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 TracksManagerSessionMixin(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>;
 }, {
     selection: unknown;
     hovered: unknown;
@@ -14,8 +14,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -23,6 +23,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -46,8 +47,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -62,6 +65,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -80,8 +84,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -89,6 +93,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -112,8 +117,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -128,6 +135,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -146,17 +154,18 @@ export declare function TracksManagerSessionMixin(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;
@@ -180,8 +189,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -196,6 +207,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -214,8 +226,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -223,6 +235,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -246,8 +259,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -262,6 +277,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -280,18 +296,20 @@ export declare function TracksManagerSessionMixin(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;
@@ -315,8 +333,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -331,6 +351,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -349,8 +370,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -358,6 +379,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -381,8 +403,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -397,6 +421,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -415,20 +440,21 @@ export declare function TracksManagerSessionMixin(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: 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;
@@ -452,8 +478,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -468,6 +496,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -486,8 +515,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -495,6 +524,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -518,8 +548,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -534,6 +566,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -552,21 +585,15 @@ export declare function TracksManagerSessionMixin(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;
@@ -574,9 +601,9 @@ export declare function TracksManagerSessionMixin(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;
@@ -584,6 +611,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -607,8 +635,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -623,6 +653,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -641,17 +672,18 @@ export declare function TracksManagerSessionMixin(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;
@@ -675,8 +707,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -691,6 +725,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -709,8 +744,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -718,6 +753,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -741,8 +777,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -757,6 +795,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -775,18 +814,20 @@ export declare function TracksManagerSessionMixin(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;
@@ -810,8 +851,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -826,6 +869,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -844,8 +888,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -853,6 +897,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -876,8 +921,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -892,6 +939,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -910,20 +958,21 @@ export declare function TracksManagerSessionMixin(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: 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;
@@ -947,8 +996,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -963,6 +1014,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -981,8 +1033,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -990,6 +1042,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1013,8 +1066,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -1029,6 +1084,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -1047,21 +1103,15 @@ export declare function TracksManagerSessionMixin(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;
@@ -1069,8 +1119,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -1078,17 +1128,17 @@ export declare function TracksManagerSessionMixin(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;
@@ -1096,6 +1146,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1119,8 +1170,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -1135,6 +1188,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -1153,17 +1207,18 @@ export declare function TracksManagerSessionMixin(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;
@@ -1187,8 +1242,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -1203,6 +1260,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -1221,8 +1279,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -1230,6 +1288,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1253,8 +1312,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -1269,6 +1330,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -1287,18 +1349,20 @@ export declare function TracksManagerSessionMixin(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;
@@ -1322,8 +1386,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -1338,6 +1404,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -1356,8 +1423,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -1365,6 +1432,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1388,8 +1456,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -1404,6 +1474,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -1422,20 +1493,21 @@ export declare function TracksManagerSessionMixin(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: 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;
@@ -1459,8 +1531,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -1475,6 +1549,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -1493,8 +1568,8 @@ export declare function TracksManagerSessionMixin(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;
@@ -1502,6 +1577,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1525,8 +1601,10 @@ export declare function TracksManagerSessionMixin(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[];
@@ -1541,6 +1619,7 @@ export declare function TracksManagerSessionMixin(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>;
@@ -1559,21 +1638,15 @@ export declare function TracksManagerSessionMixin(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;
@@ -1581,7 +1654,7 @@ export declare function TracksManagerSessionMixin(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;
@@ -1590,25 +1663,21 @@ export declare function TracksManagerSessionMixin(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;
 } & {
@@ -1618,15 +1687,25 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
     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;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, {
+    id: string;
+    name: string;
+    margin: number;
+} & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type SessionWithTracksType = ReturnType<typeof TracksManagerSessionMixin>;
 export type SessionWithTracks = Instance<SessionWithTracksType>;
 export declare function isSessionWithTracks(thing: IAnyStateTreeNode): thing is SessionWithTracks;