@jbrowse/react-circular-genome-view2 3.6.5 → 4.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (55) hide show
  1. package/esm/JBrowseCircularGenomeView/JBrowseCircularGenomeView.d.ts +1 -1
  2. package/esm/JBrowseCircularGenomeView/JBrowseCircularGenomeView.js +1 -1
  3. package/esm/JBrowseCircularGenomeView/index.d.ts +1 -1
  4. package/esm/JBrowseCircularGenomeView/index.js +1 -1
  5. package/esm/corePlugins.d.ts +2 -2
  6. package/esm/createModel/createConfigModel.d.ts +25 -29
  7. package/esm/createModel/createConfigModel.js +1 -1
  8. package/esm/createModel/createModel.d.ts +524 -629
  9. package/esm/createModel/createModel.js +5 -5
  10. package/esm/createModel/createSessionModel.d.ts +250 -305
  11. package/esm/createModel/createSessionModel.js +5 -4
  12. package/esm/createModel/index.d.ts +3 -3
  13. package/esm/createModel/index.js +3 -3
  14. package/esm/createViewState.d.ts +1323 -1625
  15. package/esm/createViewState.js +3 -4
  16. package/esm/index.d.ts +4 -4
  17. package/esm/index.js +4 -4
  18. package/esm/loadPlugins.js +1 -1
  19. package/esm/types.d.ts +1 -1
  20. package/esm/version.d.ts +1 -1
  21. package/esm/version.js +1 -1
  22. package/esm/webpack.d.ts +4 -4
  23. package/esm/webpack.js +4 -4
  24. package/package.json +38 -40
  25. package/dist/JBrowseCircularGenomeView/JBrowseCircularGenomeView.d.ts +0 -5
  26. package/dist/JBrowseCircularGenomeView/JBrowseCircularGenomeView.js +0 -23
  27. package/dist/JBrowseCircularGenomeView/index.d.ts +0 -1
  28. package/dist/JBrowseCircularGenomeView/index.js +0 -8
  29. package/dist/corePlugins.d.ts +0 -3
  30. package/dist/corePlugins.js +0 -22
  31. package/dist/createModel/AboutDialog.d.ts +0 -1
  32. package/dist/createModel/AboutDialog.js +0 -5
  33. package/dist/createModel/createConfigModel.d.ts +0 -104
  34. package/dist/createModel/createConfigModel.js +0 -43
  35. package/dist/createModel/createModel.d.ts +0 -4530
  36. package/dist/createModel/createModel.js +0 -117
  37. package/dist/createModel/createSessionModel.d.ts +0 -1845
  38. package/dist/createModel/createSessionModel.js +0 -115
  39. package/dist/createModel/index.d.ts +0 -3
  40. package/dist/createModel/index.js +0 -12
  41. package/dist/createViewState.d.ts +0 -11620
  42. package/dist/createViewState.js +0 -64
  43. package/dist/index.d.ts +0 -4
  44. package/dist/index.js +0 -14
  45. package/dist/loadPlugins.d.ts +0 -13
  46. package/dist/loadPlugins.js +0 -12
  47. package/dist/react-circular-genome-view.umd.production.min.js +0 -229
  48. package/dist/react-circular-genome-view.umd.production.min.js.LICENSE.txt +0 -135
  49. package/dist/react-circular-genome-view.umd.production.min.js.map +0 -1
  50. package/dist/types.d.ts +0 -5
  51. package/dist/types.js +0 -2
  52. package/dist/version.d.ts +0 -1
  53. package/dist/version.js +0 -4
  54. package/dist/webpack.d.ts +0 -7
  55. package/dist/webpack.js +0 -53
package/esm/createModel/createModel.d.ts CHANGED
@@ -3,24 +3,24 @@ import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
3
3
  import RpcManager from '@jbrowse/core/rpc/RpcManager';
4
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  import type { PluginConstructor } from '@jbrowse/core/Plugin';
5
5
  import type { UriLocation } from '@jbrowse/core/util';
6
- import type { Instance, SnapshotIn } from 'mobx-state-tree';
6
+ import type { Instance, SnapshotIn } from '@jbrowse/mobx-state-tree';
7
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  export default function createModel(runtimePlugins: PluginConstructor[], makeWorkerInstance?: () => Worker): {
8
- model: import("mobx-state-tree").IModelType<{
9
- config: import("mobx-state-tree").IModelType<{
10
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
11
- rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
8
+ model: import("@jbrowse/mobx-state-tree").IModelType<{
9
+ config: import("@jbrowse/mobx-state-tree").IModelType<{
10
+ configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
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+ rpc: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
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  defaultDriver: {
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  type: string;
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  description: string;
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  defaultValue: string;
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  };
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- drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
18
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
17
+ drivers: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
18
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
19
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  highResolutionScaling: {
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  type: string;
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  defaultValue: number;
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  };
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- formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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+ formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
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24
  feature: {
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  type: string;
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  description: string;
@@ -43,8 +43,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
43
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  defaultValue: number;
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  description: string;
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45
  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
47
- formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
46
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
47
+ formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
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  config: {
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  type: string;
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  description: string;
@@ -55,9 +55,9 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
55
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  type: string;
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  defaultValue: boolean;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
59
- hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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- sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
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+ hierarchical: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
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+ sort: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
61
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  trackNames: {
62
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  type: string;
63
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  defaultValue: boolean;
@@ -66,8 +66,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
66
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  type: string;
67
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  defaultValue: boolean;
68
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  };
69
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
70
- defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
70
+ defaultCollapsed: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
71
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  categoryNames: {
72
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  type: string;
73
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  defaultValue: never[];
@@ -80,91 +80,44 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
80
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  type: string;
81
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  defaultValue: boolean;
82
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  };
83
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
84
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
83
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
84
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
85
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  theme: {
86
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  type: string;
87
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  defaultValue: {};
88
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  };
89
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
89
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
90
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  assembly: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
91
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
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- internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
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- connections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
94
- aggregateTextSearchAdapters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
95
- plugins: import("mobx-state-tree").IType<any, any, any>;
91
+ tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
92
+ internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
93
+ connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
94
+ aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
95
+ plugins: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
96
96
  }, {
97
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  readonly assemblies: ({
98
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  [x: string]: any;
99
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
99
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
100
100
  setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
101
101
  [x: string]: any;
102
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
103
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
104
- [x: string]: any;
105
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
106
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
107
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
102
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
103
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
108
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  readonly assemblyName: string;
109
105
  readonly rpcManager: any;
110
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
111
- session: import("mobx-state-tree").IModelType<{
112
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
113
- name: import("mobx-state-tree").ISimpleType<string>;
114
- margin: import("mobx-state-tree").IType<number | undefined, number, number>;
106
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
107
+ session: import("@jbrowse/mobx-state-tree").IModelType<{
108
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
109
+ name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
110
+ margin: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
115
111
  } & {
116
- drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
117
- drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
118
- widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
119
- activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
120
- minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
112
+ drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
113
+ drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
114
+ widgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>;
115
+ activeWidgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>;
116
+ minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
121
117
  } & {
122
- connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
123
- name: import("mobx-state-tree").ISimpleType<string>;
124
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
125
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
126
- name: {
127
- type: string;
128
- defaultValue: string;
129
- description: string;
130
- };
131
- assemblyNames: {
132
- type: string;
133
- defaultValue: never[];
134
- description: string;
135
- };
136
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
137
- }, {
138
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
139
- } & {
140
- afterAttach(): void;
141
- addTrackConf(trackConf: Record<string, unknown> | ({
142
- [x: string]: any;
143
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
144
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
145
- [x: string]: any;
146
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
147
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
148
- [x: string]: any;
149
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
150
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
151
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
152
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
153
- [x: string]: any;
154
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
155
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
156
- [x: string]: any;
157
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
158
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
159
- [x: string]: any;
160
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
161
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
162
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
163
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
164
- clear(): void;
165
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
118
+ connectionInstances: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
166
119
  } & {
167
- view: import("mobx-state-tree").IAnyModelType;
120
+ view: import("@jbrowse/mobx-state-tree").IAnyModelType;
168
121
  }, {
169
122
  selection: unknown;
170
123
  hovered: unknown;
@@ -174,8 +127,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
174
127
  session: any;
175
128
  sessionPath: string;
176
129
  assemblyManager: {
177
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
178
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
130
+ assemblies: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IModelType<{
131
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
179
132
  }, {
180
133
  error: unknown;
181
134
  loadingP: Promise<void> | undefined;
@@ -183,6 +136,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
183
136
  refNameAliases: {
184
137
  [x: string]: string;
185
138
  } | undefined;
139
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
186
140
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
187
141
  } & {
188
142
  getConf(arg: string): any;
@@ -206,8 +160,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
206
160
  readonly refNames: string[] | undefined;
207
161
  } & {
208
162
  getCanonicalRefName(refName: string): string | undefined;
163
+ getCanonicalRefName2(refName: string): string;
209
164
  getRefNameColor(refName: string): string | undefined;
210
165
  isValidRefName(refName: string): boolean;
166
+ getSeqAdapterRefName(canonicalRefName: string): string;
211
167
  } & {
212
168
  setLoaded({ regions, refNameAliases, cytobands, }: {
213
169
  regions: import("@jbrowse/core/util").Region[];
@@ -222,6 +178,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
222
178
  [x: string]: string;
223
179
  }): void;
224
180
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
181
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
225
182
  setLoadingP(p?: Promise<void>): void;
226
183
  load(): Promise<void>;
227
184
  loadPre(): Promise<void>;
@@ -240,8 +197,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
240
197
  [x: string]: string;
241
198
  }>;
242
199
  afterCreate(): void;
243
- }, 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<{
244
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
200
+ }, 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<{
201
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
245
202
  }, {
246
203
  error: unknown;
247
204
  loadingP: Promise<void> | undefined;
@@ -249,6 +206,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
249
206
  refNameAliases: {
250
207
  [x: string]: string;
251
208
  } | undefined;
209
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
252
210
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
253
211
  } & {
254
212
  getConf(arg: string): any;
@@ -272,8 +230,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
272
230
  readonly refNames: string[] | undefined;
273
231
  } & {
274
232
  getCanonicalRefName(refName: string): string | undefined;
233
+ getCanonicalRefName2(refName: string): string;
275
234
  getRefNameColor(refName: string): string | undefined;
276
235
  isValidRefName(refName: string): boolean;
236
+ getSeqAdapterRefName(canonicalRefName: string): string;
277
237
  } & {
278
238
  setLoaded({ regions, refNameAliases, cytobands, }: {
279
239
  regions: import("@jbrowse/core/util").Region[];
@@ -288,6 +248,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
288
248
  [x: string]: string;
289
249
  }): void;
290
250
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
251
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
291
252
  setLoadingP(p?: Promise<void>): void;
292
253
  load(): Promise<void>;
293
254
  loadPre(): Promise<void>;
@@ -306,17 +267,18 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
306
267
  [x: string]: string;
307
268
  }>;
308
269
  afterCreate(): void;
309
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
310
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
270
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
271
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
311
272
  readonly assemblyNameMap: Record<string, {
312
273
  configuration: any;
313
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
274
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
314
275
  error: unknown;
315
276
  loadingP: Promise<void> | undefined;
316
277
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
317
278
  refNameAliases: {
318
279
  [x: string]: string;
319
280
  } | undefined;
281
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
320
282
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
321
283
  } & {
322
284
  getConf(arg: string): any;
@@ -340,8 +302,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
340
302
  readonly refNames: string[] | undefined;
341
303
  } & {
342
304
  getCanonicalRefName(refName: string): string | undefined;
305
+ getCanonicalRefName2(refName: string): string;
343
306
  getRefNameColor(refName: string): string | undefined;
344
307
  isValidRefName(refName: string): boolean;
308
+ getSeqAdapterRefName(canonicalRefName: string): string;
345
309
  } & {
346
310
  setLoaded({ regions, refNameAliases, cytobands, }: {
347
311
  regions: import("@jbrowse/core/util").Region[];
@@ -356,6 +320,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
356
320
  [x: string]: string;
357
321
  }): void;
358
322
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
323
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
359
324
  setLoadingP(p?: Promise<void>): void;
360
325
  load(): Promise<void>;
361
326
  loadPre(): Promise<void>;
@@ -374,8 +339,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
374
339
  [x: string]: string;
375
340
  }>;
376
341
  afterCreate(): void;
377
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
378
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
342
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
343
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
379
344
  }, {
380
345
  error: unknown;
381
346
  loadingP: Promise<void> | undefined;
@@ -383,6 +348,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
383
348
  refNameAliases: {
384
349
  [x: string]: string;
385
350
  } | undefined;
351
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
386
352
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
387
353
  } & {
388
354
  getConf(arg: string): any;
@@ -406,8 +372,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
406
372
  readonly refNames: string[] | undefined;
407
373
  } & {
408
374
  getCanonicalRefName(refName: string): string | undefined;
375
+ getCanonicalRefName2(refName: string): string;
409
376
  getRefNameColor(refName: string): string | undefined;
410
377
  isValidRefName(refName: string): boolean;
378
+ getSeqAdapterRefName(canonicalRefName: string): string;
411
379
  } & {
412
380
  setLoaded({ regions, refNameAliases, cytobands, }: {
413
381
  regions: import("@jbrowse/core/util").Region[];
@@ -422,6 +390,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
422
390
  [x: string]: string;
423
391
  }): void;
424
392
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
393
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
425
394
  setLoadingP(p?: Promise<void>): void;
426
395
  load(): Promise<void>;
427
396
  loadPre(): Promise<void>;
@@ -440,18 +409,20 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
440
409
  [x: string]: string;
441
410
  }>;
442
411
  afterCreate(): void;
443
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
412
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
444
413
  } & {
445
414
  getCanonicalAssemblyName(asmName: string): string | undefined;
415
+ getCanonicalAssemblyName2(asmName: string): string;
446
416
  get(asmName: string): ({
447
417
  configuration: any;
448
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
418
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
449
419
  error: unknown;
450
420
  loadingP: Promise<void> | undefined;
451
421
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
452
422
  refNameAliases: {
453
423
  [x: string]: string;
454
424
  } | undefined;
425
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
455
426
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
456
427
  } & {
457
428
  getConf(arg: string): any;
@@ -475,8 +446,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
475
446
  readonly refNames: string[] | undefined;
476
447
  } & {
477
448
  getCanonicalRefName(refName: string): string | undefined;
449
+ getCanonicalRefName2(refName: string): string;
478
450
  getRefNameColor(refName: string): string | undefined;
479
451
  isValidRefName(refName: string): boolean;
452
+ getSeqAdapterRefName(canonicalRefName: string): string;
480
453
  } & {
481
454
  setLoaded({ regions, refNameAliases, cytobands, }: {
482
455
  regions: import("@jbrowse/core/util").Region[];
@@ -491,6 +464,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
491
464
  [x: string]: string;
492
465
  }): void;
493
466
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
467
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
494
468
  setLoadingP(p?: Promise<void>): void;
495
469
  load(): Promise<void>;
496
470
  loadPre(): Promise<void>;
@@ -509,8 +483,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
509
483
  [x: string]: string;
510
484
  }>;
511
485
  afterCreate(): void;
512
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
513
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
486
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
487
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
514
488
  }, {
515
489
  error: unknown;
516
490
  loadingP: Promise<void> | undefined;
@@ -518,6 +492,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
518
492
  refNameAliases: {
519
493
  [x: string]: string;
520
494
  } | undefined;
495
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
521
496
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
522
497
  } & {
523
498
  getConf(arg: string): any;
@@ -541,8 +516,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
541
516
  readonly refNames: string[] | undefined;
542
517
  } & {
543
518
  getCanonicalRefName(refName: string): string | undefined;
519
+ getCanonicalRefName2(refName: string): string;
544
520
  getRefNameColor(refName: string): string | undefined;
545
521
  isValidRefName(refName: string): boolean;
522
+ getSeqAdapterRefName(canonicalRefName: string): string;
546
523
  } & {
547
524
  setLoaded({ regions, refNameAliases, cytobands, }: {
548
525
  regions: import("@jbrowse/core/util").Region[];
@@ -557,6 +534,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
557
534
  [x: string]: string;
558
535
  }): void;
559
536
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
537
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
560
538
  setLoadingP(p?: Promise<void>): void;
561
539
  load(): Promise<void>;
562
540
  loadPre(): Promise<void>;
@@ -575,20 +553,21 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
575
553
  [x: string]: string;
576
554
  }>;
577
555
  afterCreate(): void;
578
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
556
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
579
557
  readonly assemblyNamesList: any[];
580
558
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
581
559
  readonly rpcManager: RpcManager;
582
560
  } & {
583
561
  waitForAssembly(assemblyName: string): Promise<({
584
562
  configuration: any;
585
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
563
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
586
564
  error: unknown;
587
565
  loadingP: Promise<void> | undefined;
588
566
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
589
567
  refNameAliases: {
590
568
  [x: string]: string;
591
569
  } | undefined;
570
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
592
571
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
593
572
  } & {
594
573
  getConf(arg: string): any;
@@ -612,8 +591,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
612
591
  readonly refNames: string[] | undefined;
613
592
  } & {
614
593
  getCanonicalRefName(refName: string): string | undefined;
594
+ getCanonicalRefName2(refName: string): string;
615
595
  getRefNameColor(refName: string): string | undefined;
616
596
  isValidRefName(refName: string): boolean;
597
+ getSeqAdapterRefName(canonicalRefName: string): string;
617
598
  } & {
618
599
  setLoaded({ regions, refNameAliases, cytobands, }: {
619
600
  regions: import("@jbrowse/core/util").Region[];
@@ -628,6 +609,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
628
609
  [x: string]: string;
629
610
  }): void;
630
611
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
612
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
631
613
  setLoadingP(p?: Promise<void>): void;
632
614
  load(): Promise<void>;
633
615
  loadPre(): Promise<void>;
@@ -646,8 +628,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
646
628
  [x: string]: string;
647
629
  }>;
648
630
  afterCreate(): void;
649
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
650
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
631
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
632
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
651
633
  }, {
652
634
  error: unknown;
653
635
  loadingP: Promise<void> | undefined;
@@ -655,6 +637,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
655
637
  refNameAliases: {
656
638
  [x: string]: string;
657
639
  } | undefined;
640
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
658
641
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
659
642
  } & {
660
643
  getConf(arg: string): any;
@@ -678,8 +661,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
678
661
  readonly refNames: string[] | undefined;
679
662
  } & {
680
663
  getCanonicalRefName(refName: string): string | undefined;
664
+ getCanonicalRefName2(refName: string): string;
681
665
  getRefNameColor(refName: string): string | undefined;
682
666
  isValidRefName(refName: string): boolean;
667
+ getSeqAdapterRefName(canonicalRefName: string): string;
683
668
  } & {
684
669
  setLoaded({ regions, refNameAliases, cytobands, }: {
685
670
  regions: import("@jbrowse/core/util").Region[];
@@ -694,6 +679,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
694
679
  [x: string]: string;
695
680
  }): void;
696
681
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
682
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
697
683
  setLoadingP(p?: Promise<void>): void;
698
684
  load(): Promise<void>;
699
685
  loadPre(): Promise<void>;
@@ -712,21 +698,15 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
712
698
  [x: string]: string;
713
699
  }>;
714
700
  afterCreate(): void;
715
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
701
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
716
702
  getRefNameMapForAdapter(adapterConf: {
717
703
  [x: string]: unknown;
718
- }, assemblyName: string | undefined, opts: {
719
- stopToken?: string;
720
- sessionId: string;
721
- }): Promise<{
704
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
722
705
  [x: string]: string;
723
706
  } | undefined>;
724
707
  getReverseRefNameMapForAdapter(adapterConf: {
725
708
  [x: string]: unknown;
726
- }, assemblyName: string | undefined, opts: {
727
- stopToken?: string;
728
- sessionId: string;
729
- }): Promise<{
709
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
730
710
  [x: string]: string;
731
711
  } | undefined>;
732
712
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -734,9 +714,9 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
734
714
  afterAttach(): void;
735
715
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
736
716
  addAssembly(configuration: any): void;
737
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
738
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
739
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
717
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
718
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
719
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
740
720
  }, {
741
721
  error: unknown;
742
722
  loadingP: Promise<void> | undefined;
@@ -744,6 +724,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
744
724
  refNameAliases: {
745
725
  [x: string]: string;
746
726
  } | undefined;
727
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
747
728
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
748
729
  } & {
749
730
  getConf(arg: string): any;
@@ -767,8 +748,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
767
748
  readonly refNames: string[] | undefined;
768
749
  } & {
769
750
  getCanonicalRefName(refName: string): string | undefined;
751
+ getCanonicalRefName2(refName: string): string;
770
752
  getRefNameColor(refName: string): string | undefined;
771
753
  isValidRefName(refName: string): boolean;
754
+ getSeqAdapterRefName(canonicalRefName: string): string;
772
755
  } & {
773
756
  setLoaded({ regions, refNameAliases, cytobands, }: {
774
757
  regions: import("@jbrowse/core/util").Region[];
@@ -783,6 +766,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
783
766
  [x: string]: string;
784
767
  }): void;
785
768
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
769
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
786
770
  setLoadingP(p?: Promise<void>): void;
787
771
  load(): Promise<void>;
788
772
  loadPre(): Promise<void>;
@@ -801,17 +785,18 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
801
785
  [x: string]: string;
802
786
  }>;
803
787
  afterCreate(): void;
804
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
788
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
805
789
  }, {
806
790
  readonly assemblyNameMap: Record<string, {
807
791
  configuration: any;
808
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
792
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
809
793
  error: unknown;
810
794
  loadingP: Promise<void> | undefined;
811
795
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
812
796
  refNameAliases: {
813
797
  [x: string]: string;
814
798
  } | undefined;
799
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
815
800
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
816
801
  } & {
817
802
  getConf(arg: string): any;
@@ -835,8 +820,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
835
820
  readonly refNames: string[] | undefined;
836
821
  } & {
837
822
  getCanonicalRefName(refName: string): string | undefined;
823
+ getCanonicalRefName2(refName: string): string;
838
824
  getRefNameColor(refName: string): string | undefined;
839
825
  isValidRefName(refName: string): boolean;
826
+ getSeqAdapterRefName(canonicalRefName: string): string;
840
827
  } & {
841
828
  setLoaded({ regions, refNameAliases, cytobands, }: {
842
829
  regions: import("@jbrowse/core/util").Region[];
@@ -851,6 +838,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
851
838
  [x: string]: string;
852
839
  }): void;
853
840
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
841
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
854
842
  setLoadingP(p?: Promise<void>): void;
855
843
  load(): Promise<void>;
856
844
  loadPre(): Promise<void>;
@@ -869,8 +857,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
869
857
  [x: string]: string;
870
858
  }>;
871
859
  afterCreate(): void;
872
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
873
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
860
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
861
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
874
862
  }, {
875
863
  error: unknown;
876
864
  loadingP: Promise<void> | undefined;
@@ -878,6 +866,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
878
866
  refNameAliases: {
879
867
  [x: string]: string;
880
868
  } | undefined;
869
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
881
870
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
882
871
  } & {
883
872
  getConf(arg: string): any;
@@ -901,8 +890,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
901
890
  readonly refNames: string[] | undefined;
902
891
  } & {
903
892
  getCanonicalRefName(refName: string): string | undefined;
893
+ getCanonicalRefName2(refName: string): string;
904
894
  getRefNameColor(refName: string): string | undefined;
905
895
  isValidRefName(refName: string): boolean;
896
+ getSeqAdapterRefName(canonicalRefName: string): string;
906
897
  } & {
907
898
  setLoaded({ regions, refNameAliases, cytobands, }: {
908
899
  regions: import("@jbrowse/core/util").Region[];
@@ -917,6 +908,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
917
908
  [x: string]: string;
918
909
  }): void;
919
910
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
911
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
920
912
  setLoadingP(p?: Promise<void>): void;
921
913
  load(): Promise<void>;
922
914
  loadPre(): Promise<void>;
@@ -935,18 +927,20 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
935
927
  [x: string]: string;
936
928
  }>;
937
929
  afterCreate(): void;
938
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
930
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
939
931
  } & {
940
932
  getCanonicalAssemblyName(asmName: string): string | undefined;
933
+ getCanonicalAssemblyName2(asmName: string): string;
941
934
  get(asmName: string): ({
942
935
  configuration: any;
943
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
936
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
944
937
  error: unknown;
945
938
  loadingP: Promise<void> | undefined;
946
939
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
947
940
  refNameAliases: {
948
941
  [x: string]: string;
949
942
  } | undefined;
943
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
950
944
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
951
945
  } & {
952
946
  getConf(arg: string): any;
@@ -970,8 +964,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
970
964
  readonly refNames: string[] | undefined;
971
965
  } & {
972
966
  getCanonicalRefName(refName: string): string | undefined;
967
+ getCanonicalRefName2(refName: string): string;
973
968
  getRefNameColor(refName: string): string | undefined;
974
969
  isValidRefName(refName: string): boolean;
970
+ getSeqAdapterRefName(canonicalRefName: string): string;
975
971
  } & {
976
972
  setLoaded({ regions, refNameAliases, cytobands, }: {
977
973
  regions: import("@jbrowse/core/util").Region[];
@@ -986,6 +982,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
986
982
  [x: string]: string;
987
983
  }): void;
988
984
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
985
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
989
986
  setLoadingP(p?: Promise<void>): void;
990
987
  load(): Promise<void>;
991
988
  loadPre(): Promise<void>;
@@ -1004,8 +1001,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1004
1001
  [x: string]: string;
1005
1002
  }>;
1006
1003
  afterCreate(): void;
1007
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1008
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1004
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1005
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1009
1006
  }, {
1010
1007
  error: unknown;
1011
1008
  loadingP: Promise<void> | undefined;
@@ -1013,6 +1010,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1013
1010
  refNameAliases: {
1014
1011
  [x: string]: string;
1015
1012
  } | undefined;
1013
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1016
1014
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1017
1015
  } & {
1018
1016
  getConf(arg: string): any;
@@ -1036,8 +1034,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1036
1034
  readonly refNames: string[] | undefined;
1037
1035
  } & {
1038
1036
  getCanonicalRefName(refName: string): string | undefined;
1037
+ getCanonicalRefName2(refName: string): string;
1039
1038
  getRefNameColor(refName: string): string | undefined;
1040
1039
  isValidRefName(refName: string): boolean;
1040
+ getSeqAdapterRefName(canonicalRefName: string): string;
1041
1041
  } & {
1042
1042
  setLoaded({ regions, refNameAliases, cytobands, }: {
1043
1043
  regions: import("@jbrowse/core/util").Region[];
@@ -1052,6 +1052,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1052
1052
  [x: string]: string;
1053
1053
  }): void;
1054
1054
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1055
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1055
1056
  setLoadingP(p?: Promise<void>): void;
1056
1057
  load(): Promise<void>;
1057
1058
  loadPre(): Promise<void>;
@@ -1070,20 +1071,21 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1070
1071
  [x: string]: string;
1071
1072
  }>;
1072
1073
  afterCreate(): void;
1073
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1074
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1074
1075
  readonly assemblyNamesList: any[];
1075
1076
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1076
1077
  readonly rpcManager: RpcManager;
1077
1078
  } & {
1078
1079
  waitForAssembly(assemblyName: string): Promise<({
1079
1080
  configuration: any;
1080
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1081
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1081
1082
  error: unknown;
1082
1083
  loadingP: Promise<void> | undefined;
1083
1084
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1084
1085
  refNameAliases: {
1085
1086
  [x: string]: string;
1086
1087
  } | undefined;
1088
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1087
1089
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1088
1090
  } & {
1089
1091
  getConf(arg: string): any;
@@ -1107,8 +1109,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1107
1109
  readonly refNames: string[] | undefined;
1108
1110
  } & {
1109
1111
  getCanonicalRefName(refName: string): string | undefined;
1112
+ getCanonicalRefName2(refName: string): string;
1110
1113
  getRefNameColor(refName: string): string | undefined;
1111
1114
  isValidRefName(refName: string): boolean;
1115
+ getSeqAdapterRefName(canonicalRefName: string): string;
1112
1116
  } & {
1113
1117
  setLoaded({ regions, refNameAliases, cytobands, }: {
1114
1118
  regions: import("@jbrowse/core/util").Region[];
@@ -1123,6 +1127,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1123
1127
  [x: string]: string;
1124
1128
  }): void;
1125
1129
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1130
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1126
1131
  setLoadingP(p?: Promise<void>): void;
1127
1132
  load(): Promise<void>;
1128
1133
  loadPre(): Promise<void>;
@@ -1141,8 +1146,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1141
1146
  [x: string]: string;
1142
1147
  }>;
1143
1148
  afterCreate(): void;
1144
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1145
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1149
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1150
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1146
1151
  }, {
1147
1152
  error: unknown;
1148
1153
  loadingP: Promise<void> | undefined;
@@ -1150,6 +1155,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1150
1155
  refNameAliases: {
1151
1156
  [x: string]: string;
1152
1157
  } | undefined;
1158
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1153
1159
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1154
1160
  } & {
1155
1161
  getConf(arg: string): any;
@@ -1173,8 +1179,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1173
1179
  readonly refNames: string[] | undefined;
1174
1180
  } & {
1175
1181
  getCanonicalRefName(refName: string): string | undefined;
1182
+ getCanonicalRefName2(refName: string): string;
1176
1183
  getRefNameColor(refName: string): string | undefined;
1177
1184
  isValidRefName(refName: string): boolean;
1185
+ getSeqAdapterRefName(canonicalRefName: string): string;
1178
1186
  } & {
1179
1187
  setLoaded({ regions, refNameAliases, cytobands, }: {
1180
1188
  regions: import("@jbrowse/core/util").Region[];
@@ -1189,6 +1197,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1189
1197
  [x: string]: string;
1190
1198
  }): void;
1191
1199
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1200
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1192
1201
  setLoadingP(p?: Promise<void>): void;
1193
1202
  load(): Promise<void>;
1194
1203
  loadPre(): Promise<void>;
@@ -1207,21 +1216,15 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1207
1216
  [x: string]: string;
1208
1217
  }>;
1209
1218
  afterCreate(): void;
1210
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1219
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1211
1220
  getRefNameMapForAdapter(adapterConf: {
1212
1221
  [x: string]: unknown;
1213
- }, assemblyName: string | undefined, opts: {
1214
- stopToken?: string;
1215
- sessionId: string;
1216
- }): Promise<{
1222
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1217
1223
  [x: string]: string;
1218
1224
  } | undefined>;
1219
1225
  getReverseRefNameMapForAdapter(adapterConf: {
1220
1226
  [x: string]: unknown;
1221
- }, assemblyName: string | undefined, opts: {
1222
- stopToken?: string;
1223
- sessionId: string;
1224
- }): Promise<{
1227
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1225
1228
  [x: string]: string;
1226
1229
  } | undefined>;
1227
1230
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -1229,8 +1232,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1229
1232
  afterAttach(): void;
1230
1233
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1231
1234
  addAssembly(configuration: any): void;
1232
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1233
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1235
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>>;
1236
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1234
1237
  rpcManager: RpcManager;
1235
1238
  adminMode: boolean;
1236
1239
  error: unknown;
@@ -1238,17 +1241,17 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1238
1241
  pluginManager: PluginManager;
1239
1242
  } & {
1240
1243
  setError(error: unknown): void;
1241
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1244
+ setSession(sessionSnapshot?: SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1242
1245
  setDefaultSession(): void;
1243
1246
  setSessionPath(path: string): void;
1244
1247
  renameCurrentSession(newName: string): void;
1245
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1246
- jbrowse: import("mobx-state-tree").IAnyType;
1247
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1248
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1249
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1250
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1251
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1248
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1249
+ jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
1250
+ session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
1251
+ sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
1252
+ assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
1253
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
1254
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1252
1255
  }, {
1253
1256
  error: unknown;
1254
1257
  loadingP: Promise<void> | undefined;
@@ -1256,6 +1259,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1256
1259
  refNameAliases: {
1257
1260
  [x: string]: string;
1258
1261
  } | undefined;
1262
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1259
1263
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1260
1264
  } & {
1261
1265
  getConf(arg: string): any;
@@ -1279,8 +1283,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1279
1283
  readonly refNames: string[] | undefined;
1280
1284
  } & {
1281
1285
  getCanonicalRefName(refName: string): string | undefined;
1286
+ getCanonicalRefName2(refName: string): string;
1282
1287
  getRefNameColor(refName: string): string | undefined;
1283
1288
  isValidRefName(refName: string): boolean;
1289
+ getSeqAdapterRefName(canonicalRefName: string): string;
1284
1290
  } & {
1285
1291
  setLoaded({ regions, refNameAliases, cytobands, }: {
1286
1292
  regions: import("@jbrowse/core/util").Region[];
@@ -1295,6 +1301,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1295
1301
  [x: string]: string;
1296
1302
  }): void;
1297
1303
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1304
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1298
1305
  setLoadingP(p?: Promise<void>): void;
1299
1306
  load(): Promise<void>;
1300
1307
  loadPre(): Promise<void>;
@@ -1313,17 +1320,18 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1313
1320
  [x: string]: string;
1314
1321
  }>;
1315
1322
  afterCreate(): void;
1316
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1323
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1317
1324
  }, {
1318
1325
  readonly assemblyNameMap: Record<string, {
1319
1326
  configuration: any;
1320
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1327
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1321
1328
  error: unknown;
1322
1329
  loadingP: Promise<void> | undefined;
1323
1330
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1324
1331
  refNameAliases: {
1325
1332
  [x: string]: string;
1326
1333
  } | undefined;
1334
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1327
1335
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1328
1336
  } & {
1329
1337
  getConf(arg: string): any;
@@ -1347,8 +1355,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1347
1355
  readonly refNames: string[] | undefined;
1348
1356
  } & {
1349
1357
  getCanonicalRefName(refName: string): string | undefined;
1358
+ getCanonicalRefName2(refName: string): string;
1350
1359
  getRefNameColor(refName: string): string | undefined;
1351
1360
  isValidRefName(refName: string): boolean;
1361
+ getSeqAdapterRefName(canonicalRefName: string): string;
1352
1362
  } & {
1353
1363
  setLoaded({ regions, refNameAliases, cytobands, }: {
1354
1364
  regions: import("@jbrowse/core/util").Region[];
@@ -1363,6 +1373,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1363
1373
  [x: string]: string;
1364
1374
  }): void;
1365
1375
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1376
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1366
1377
  setLoadingP(p?: Promise<void>): void;
1367
1378
  load(): Promise<void>;
1368
1379
  loadPre(): Promise<void>;
@@ -1381,8 +1392,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1381
1392
  [x: string]: string;
1382
1393
  }>;
1383
1394
  afterCreate(): void;
1384
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1385
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1395
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1396
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1386
1397
  }, {
1387
1398
  error: unknown;
1388
1399
  loadingP: Promise<void> | undefined;
@@ -1390,6 +1401,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1390
1401
  refNameAliases: {
1391
1402
  [x: string]: string;
1392
1403
  } | undefined;
1404
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1393
1405
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1394
1406
  } & {
1395
1407
  getConf(arg: string): any;
@@ -1413,8 +1425,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1413
1425
  readonly refNames: string[] | undefined;
1414
1426
  } & {
1415
1427
  getCanonicalRefName(refName: string): string | undefined;
1428
+ getCanonicalRefName2(refName: string): string;
1416
1429
  getRefNameColor(refName: string): string | undefined;
1417
1430
  isValidRefName(refName: string): boolean;
1431
+ getSeqAdapterRefName(canonicalRefName: string): string;
1418
1432
  } & {
1419
1433
  setLoaded({ regions, refNameAliases, cytobands, }: {
1420
1434
  regions: import("@jbrowse/core/util").Region[];
@@ -1429,6 +1443,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1429
1443
  [x: string]: string;
1430
1444
  }): void;
1431
1445
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1446
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1432
1447
  setLoadingP(p?: Promise<void>): void;
1433
1448
  load(): Promise<void>;
1434
1449
  loadPre(): Promise<void>;
@@ -1447,18 +1462,20 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1447
1462
  [x: string]: string;
1448
1463
  }>;
1449
1464
  afterCreate(): void;
1450
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1465
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1451
1466
  } & {
1452
1467
  getCanonicalAssemblyName(asmName: string): string | undefined;
1468
+ getCanonicalAssemblyName2(asmName: string): string;
1453
1469
  get(asmName: string): ({
1454
1470
  configuration: any;
1455
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1471
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1456
1472
  error: unknown;
1457
1473
  loadingP: Promise<void> | undefined;
1458
1474
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1459
1475
  refNameAliases: {
1460
1476
  [x: string]: string;
1461
1477
  } | undefined;
1478
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1462
1479
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1463
1480
  } & {
1464
1481
  getConf(arg: string): any;
@@ -1482,8 +1499,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1482
1499
  readonly refNames: string[] | undefined;
1483
1500
  } & {
1484
1501
  getCanonicalRefName(refName: string): string | undefined;
1502
+ getCanonicalRefName2(refName: string): string;
1485
1503
  getRefNameColor(refName: string): string | undefined;
1486
1504
  isValidRefName(refName: string): boolean;
1505
+ getSeqAdapterRefName(canonicalRefName: string): string;
1487
1506
  } & {
1488
1507
  setLoaded({ regions, refNameAliases, cytobands, }: {
1489
1508
  regions: import("@jbrowse/core/util").Region[];
@@ -1498,6 +1517,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1498
1517
  [x: string]: string;
1499
1518
  }): void;
1500
1519
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1520
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1501
1521
  setLoadingP(p?: Promise<void>): void;
1502
1522
  load(): Promise<void>;
1503
1523
  loadPre(): Promise<void>;
@@ -1516,8 +1536,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1516
1536
  [x: string]: string;
1517
1537
  }>;
1518
1538
  afterCreate(): void;
1519
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1520
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1539
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1540
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1521
1541
  }, {
1522
1542
  error: unknown;
1523
1543
  loadingP: Promise<void> | undefined;
@@ -1525,6 +1545,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1525
1545
  refNameAliases: {
1526
1546
  [x: string]: string;
1527
1547
  } | undefined;
1548
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1528
1549
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1529
1550
  } & {
1530
1551
  getConf(arg: string): any;
@@ -1548,8 +1569,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1548
1569
  readonly refNames: string[] | undefined;
1549
1570
  } & {
1550
1571
  getCanonicalRefName(refName: string): string | undefined;
1572
+ getCanonicalRefName2(refName: string): string;
1551
1573
  getRefNameColor(refName: string): string | undefined;
1552
1574
  isValidRefName(refName: string): boolean;
1575
+ getSeqAdapterRefName(canonicalRefName: string): string;
1553
1576
  } & {
1554
1577
  setLoaded({ regions, refNameAliases, cytobands, }: {
1555
1578
  regions: import("@jbrowse/core/util").Region[];
@@ -1564,6 +1587,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1564
1587
  [x: string]: string;
1565
1588
  }): void;
1566
1589
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1590
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1567
1591
  setLoadingP(p?: Promise<void>): void;
1568
1592
  load(): Promise<void>;
1569
1593
  loadPre(): Promise<void>;
@@ -1582,20 +1606,21 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1582
1606
  [x: string]: string;
1583
1607
  }>;
1584
1608
  afterCreate(): void;
1585
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1609
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1586
1610
  readonly assemblyNamesList: any[];
1587
1611
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1588
1612
  readonly rpcManager: RpcManager;
1589
1613
  } & {
1590
1614
  waitForAssembly(assemblyName: string): Promise<({
1591
1615
  configuration: any;
1592
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1616
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1593
1617
  error: unknown;
1594
1618
  loadingP: Promise<void> | undefined;
1595
1619
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1596
1620
  refNameAliases: {
1597
1621
  [x: string]: string;
1598
1622
  } | undefined;
1623
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1599
1624
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1600
1625
  } & {
1601
1626
  getConf(arg: string): any;
@@ -1619,8 +1644,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1619
1644
  readonly refNames: string[] | undefined;
1620
1645
  } & {
1621
1646
  getCanonicalRefName(refName: string): string | undefined;
1647
+ getCanonicalRefName2(refName: string): string;
1622
1648
  getRefNameColor(refName: string): string | undefined;
1623
1649
  isValidRefName(refName: string): boolean;
1650
+ getSeqAdapterRefName(canonicalRefName: string): string;
1624
1651
  } & {
1625
1652
  setLoaded({ regions, refNameAliases, cytobands, }: {
1626
1653
  regions: import("@jbrowse/core/util").Region[];
@@ -1635,6 +1662,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1635
1662
  [x: string]: string;
1636
1663
  }): void;
1637
1664
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1665
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1638
1666
  setLoadingP(p?: Promise<void>): void;
1639
1667
  load(): Promise<void>;
1640
1668
  loadPre(): Promise<void>;
@@ -1653,8 +1681,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1653
1681
  [x: string]: string;
1654
1682
  }>;
1655
1683
  afterCreate(): void;
1656
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1657
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1684
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1685
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1658
1686
  }, {
1659
1687
  error: unknown;
1660
1688
  loadingP: Promise<void> | undefined;
@@ -1662,6 +1690,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1662
1690
  refNameAliases: {
1663
1691
  [x: string]: string;
1664
1692
  } | undefined;
1693
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1665
1694
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1666
1695
  } & {
1667
1696
  getConf(arg: string): any;
@@ -1685,8 +1714,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1685
1714
  readonly refNames: string[] | undefined;
1686
1715
  } & {
1687
1716
  getCanonicalRefName(refName: string): string | undefined;
1717
+ getCanonicalRefName2(refName: string): string;
1688
1718
  getRefNameColor(refName: string): string | undefined;
1689
1719
  isValidRefName(refName: string): boolean;
1720
+ getSeqAdapterRefName(canonicalRefName: string): string;
1690
1721
  } & {
1691
1722
  setLoaded({ regions, refNameAliases, cytobands, }: {
1692
1723
  regions: import("@jbrowse/core/util").Region[];
@@ -1701,6 +1732,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1701
1732
  [x: string]: string;
1702
1733
  }): void;
1703
1734
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1735
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1704
1736
  setLoadingP(p?: Promise<void>): void;
1705
1737
  load(): Promise<void>;
1706
1738
  loadPre(): Promise<void>;
@@ -1719,21 +1751,15 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1719
1751
  [x: string]: string;
1720
1752
  }>;
1721
1753
  afterCreate(): void;
1722
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1754
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1723
1755
  getRefNameMapForAdapter(adapterConf: {
1724
1756
  [x: string]: unknown;
1725
- }, assemblyName: string | undefined, opts: {
1726
- stopToken?: string;
1727
- sessionId: string;
1728
- }): Promise<{
1757
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1729
1758
  [x: string]: string;
1730
1759
  } | undefined>;
1731
1760
  getReverseRefNameMapForAdapter(adapterConf: {
1732
1761
  [x: string]: unknown;
1733
- }, assemblyName: string | undefined, opts: {
1734
- stopToken?: string;
1735
- sessionId: string;
1736
- }): Promise<{
1762
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1737
1763
  [x: string]: string;
1738
1764
  } | undefined>;
1739
1765
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -1741,7 +1767,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1741
1767
  afterAttach(): void;
1742
1768
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1743
1769
  addAssembly(configuration: any): void;
1744
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1770
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
1745
1771
  }, {
1746
1772
  rpcManager: RpcManager;
1747
1773
  adminMode: boolean;
@@ -1750,25 +1776,21 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1750
1776
  pluginManager: PluginManager;
1751
1777
  } & {
1752
1778
  setError(error: unknown): void;
1753
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1779
+ setSession(sessionSnapshot?: SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1754
1780
  setDefaultSession(): void;
1755
1781
  setSessionPath(path: string): void;
1756
1782
  renameCurrentSession(newName: string): void;
1757
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1783
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1758
1784
  } & {
1759
1785
  readonly jbrowse: any;
1760
1786
  readonly rpcManager: RpcManager;
1761
1787
  readonly configuration: {
1762
1788
  [x: string]: any;
1763
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1789
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1764
1790
  setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1765
1791
  [x: string]: any;
1766
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1767
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1768
- [x: string]: any;
1769
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1770
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1771
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1792
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1793
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1772
1794
  readonly adminMode: boolean;
1773
1795
  readonly textSearchManager: TextSearchManager;
1774
1796
  } & {
@@ -1790,108 +1812,14 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1790
1812
  minimizeWidgetDrawer(): void;
1791
1813
  showWidgetDrawer(): void;
1792
1814
  hideAllWidgets(): void;
1793
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1815
+ editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel | {
1816
+ trackId: string;
1817
+ }): void;
1794
1818
  afterAttach(): void;
1795
1819
  } & {
1796
1820
  readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
1797
1821
  } & {
1798
- makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
1799
- name: string;
1800
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
1801
- configuration: {
1802
- [x: string]: any;
1803
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1804
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1805
- [x: string]: any;
1806
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1807
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1808
- [x: string]: any;
1809
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1810
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1811
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1812
- name: {
1813
- type: string;
1814
- defaultValue: string;
1815
- description: string;
1816
- };
1817
- assemblyNames: {
1818
- type: string;
1819
- defaultValue: never[];
1820
- description: string;
1821
- };
1822
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
1823
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1824
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1825
- } & {
1826
- afterAttach(): void;
1827
- addTrackConf(trackConf: Record<string, unknown> | ({
1828
- [x: string]: any;
1829
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1830
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1831
- [x: string]: any;
1832
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1833
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1834
- [x: string]: any;
1835
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1836
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1837
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
1838
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
1839
- [x: string]: any;
1840
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1841
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1842
- [x: string]: any;
1843
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1844
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1845
- [x: string]: any;
1846
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1847
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1848
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
1849
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1850
- clear(): void;
1851
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1852
- name: import("mobx-state-tree").ISimpleType<string>;
1853
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
1854
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1855
- name: {
1856
- type: string;
1857
- defaultValue: string;
1858
- description: string;
1859
- };
1860
- assemblyNames: {
1861
- type: string;
1862
- defaultValue: never[];
1863
- description: string;
1864
- };
1865
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
1866
- }, {
1867
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1868
- } & {
1869
- afterAttach(): void;
1870
- addTrackConf(trackConf: Record<string, unknown> | ({
1871
- [x: string]: any;
1872
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1873
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1874
- [x: string]: any;
1875
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1876
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1877
- [x: string]: any;
1878
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1879
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1880
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
1881
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
1882
- [x: string]: any;
1883
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1884
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1885
- [x: string]: any;
1886
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1887
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1888
- [x: string]: any;
1889
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1890
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1891
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
1892
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1893
- clear(): void;
1894
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1822
+ makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): any;
1895
1823
  prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
1896
1824
  breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1897
1825
  deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
@@ -1906,11 +1834,17 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1906
1834
  removeActiveDialog(): void;
1907
1835
  queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
1908
1836
  } & {
1909
- getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
1837
+ getReferring(object: import("@jbrowse/mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
1910
1838
  } & {
1911
1839
  removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1912
1840
  } & {
1913
1841
  readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1842
+ readonly assemblies: {
1843
+ sequence: {
1844
+ trackId: string;
1845
+ };
1846
+ }[];
1847
+ readonly tracksById: Record<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
1914
1848
  } & {
1915
1849
  addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1916
1850
  deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
@@ -1941,17 +1875,23 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1941
1875
  addView(typeName: string, initialState?: {}): any;
1942
1876
  removeView(): void;
1943
1877
  } & {
1944
- getTrackActionMenuItems(config: any): {
1945
- label: string;
1946
- onClick: () => void;
1947
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
1948
- muiName: string;
1949
- };
1950
- }[];
1951
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
1952
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1953
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1954
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1878
+ getTrackActionMenuItems(config: any, extraTrackActions?: import("@jbrowse/core/ui").MenuItem[]): import("@jbrowse/core/ui").MenuItem[];
1879
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
1880
+ id: string;
1881
+ name: string;
1882
+ margin: number;
1883
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1884
+ drawerPosition: string;
1885
+ drawerWidth: number;
1886
+ widgets: import("mobx").IKeyValueMap<any>;
1887
+ activeWidgets: import("mobx").IKeyValueMap<import("@jbrowse/mobx-state-tree").ReferenceIdentifier | undefined>;
1888
+ minimized: boolean;
1889
+ } & {
1890
+ connectionInstances: any[];
1891
+ } & import("@jbrowse/mobx-state-tree")._NotCustomized>;
1892
+ assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
1893
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
1894
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1955
1895
  }, {
1956
1896
  error: unknown;
1957
1897
  loadingP: Promise<void> | undefined;
@@ -1959,6 +1899,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1959
1899
  refNameAliases: {
1960
1900
  [x: string]: string;
1961
1901
  } | undefined;
1902
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1962
1903
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1963
1904
  } & {
1964
1905
  getConf(arg: string): any;
@@ -1982,8 +1923,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1982
1923
  readonly refNames: string[] | undefined;
1983
1924
  } & {
1984
1925
  getCanonicalRefName(refName: string): string | undefined;
1926
+ getCanonicalRefName2(refName: string): string;
1985
1927
  getRefNameColor(refName: string): string | undefined;
1986
1928
  isValidRefName(refName: string): boolean;
1929
+ getSeqAdapterRefName(canonicalRefName: string): string;
1987
1930
  } & {
1988
1931
  setLoaded({ regions, refNameAliases, cytobands, }: {
1989
1932
  regions: import("@jbrowse/core/util").Region[];
@@ -1998,6 +1941,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
1998
1941
  [x: string]: string;
1999
1942
  }): void;
2000
1943
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1944
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2001
1945
  setLoadingP(p?: Promise<void>): void;
2002
1946
  load(): Promise<void>;
2003
1947
  loadPre(): Promise<void>;
@@ -2016,17 +1960,18 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2016
1960
  [x: string]: string;
2017
1961
  }>;
2018
1962
  afterCreate(): void;
2019
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1963
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
2020
1964
  }, {
2021
1965
  readonly assemblyNameMap: Record<string, {
2022
1966
  configuration: any;
2023
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1967
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
2024
1968
  error: unknown;
2025
1969
  loadingP: Promise<void> | undefined;
2026
1970
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2027
1971
  refNameAliases: {
2028
1972
  [x: string]: string;
2029
1973
  } | undefined;
1974
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2030
1975
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2031
1976
  } & {
2032
1977
  getConf(arg: string): any;
@@ -2050,8 +1995,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2050
1995
  readonly refNames: string[] | undefined;
2051
1996
  } & {
2052
1997
  getCanonicalRefName(refName: string): string | undefined;
1998
+ getCanonicalRefName2(refName: string): string;
2053
1999
  getRefNameColor(refName: string): string | undefined;
2054
2000
  isValidRefName(refName: string): boolean;
2001
+ getSeqAdapterRefName(canonicalRefName: string): string;
2055
2002
  } & {
2056
2003
  setLoaded({ regions, refNameAliases, cytobands, }: {
2057
2004
  regions: import("@jbrowse/core/util").Region[];
@@ -2066,6 +2013,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2066
2013
  [x: string]: string;
2067
2014
  }): void;
2068
2015
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2016
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2069
2017
  setLoadingP(p?: Promise<void>): void;
2070
2018
  load(): Promise<void>;
2071
2019
  loadPre(): Promise<void>;
@@ -2084,8 +2032,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2084
2032
  [x: string]: string;
2085
2033
  }>;
2086
2034
  afterCreate(): void;
2087
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2088
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2035
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2036
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2089
2037
  }, {
2090
2038
  error: unknown;
2091
2039
  loadingP: Promise<void> | undefined;
@@ -2093,6 +2041,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2093
2041
  refNameAliases: {
2094
2042
  [x: string]: string;
2095
2043
  } | undefined;
2044
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2096
2045
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2097
2046
  } & {
2098
2047
  getConf(arg: string): any;
@@ -2116,8 +2065,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2116
2065
  readonly refNames: string[] | undefined;
2117
2066
  } & {
2118
2067
  getCanonicalRefName(refName: string): string | undefined;
2068
+ getCanonicalRefName2(refName: string): string;
2119
2069
  getRefNameColor(refName: string): string | undefined;
2120
2070
  isValidRefName(refName: string): boolean;
2071
+ getSeqAdapterRefName(canonicalRefName: string): string;
2121
2072
  } & {
2122
2073
  setLoaded({ regions, refNameAliases, cytobands, }: {
2123
2074
  regions: import("@jbrowse/core/util").Region[];
@@ -2132,6 +2083,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2132
2083
  [x: string]: string;
2133
2084
  }): void;
2134
2085
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2086
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2135
2087
  setLoadingP(p?: Promise<void>): void;
2136
2088
  load(): Promise<void>;
2137
2089
  loadPre(): Promise<void>;
@@ -2150,18 +2102,20 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2150
2102
  [x: string]: string;
2151
2103
  }>;
2152
2104
  afterCreate(): void;
2153
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
2105
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
2154
2106
  } & {
2155
2107
  getCanonicalAssemblyName(asmName: string): string | undefined;
2108
+ getCanonicalAssemblyName2(asmName: string): string;
2156
2109
  get(asmName: string): ({
2157
2110
  configuration: any;
2158
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2111
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
2159
2112
  error: unknown;
2160
2113
  loadingP: Promise<void> | undefined;
2161
2114
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2162
2115
  refNameAliases: {
2163
2116
  [x: string]: string;
2164
2117
  } | undefined;
2118
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2165
2119
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2166
2120
  } & {
2167
2121
  getConf(arg: string): any;
@@ -2185,8 +2139,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2185
2139
  readonly refNames: string[] | undefined;
2186
2140
  } & {
2187
2141
  getCanonicalRefName(refName: string): string | undefined;
2142
+ getCanonicalRefName2(refName: string): string;
2188
2143
  getRefNameColor(refName: string): string | undefined;
2189
2144
  isValidRefName(refName: string): boolean;
2145
+ getSeqAdapterRefName(canonicalRefName: string): string;
2190
2146
  } & {
2191
2147
  setLoaded({ regions, refNameAliases, cytobands, }: {
2192
2148
  regions: import("@jbrowse/core/util").Region[];
@@ -2201,6 +2157,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2201
2157
  [x: string]: string;
2202
2158
  }): void;
2203
2159
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2160
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2204
2161
  setLoadingP(p?: Promise<void>): void;
2205
2162
  load(): Promise<void>;
2206
2163
  loadPre(): Promise<void>;
@@ -2219,8 +2176,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2219
2176
  [x: string]: string;
2220
2177
  }>;
2221
2178
  afterCreate(): void;
2222
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2223
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2179
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2180
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2224
2181
  }, {
2225
2182
  error: unknown;
2226
2183
  loadingP: Promise<void> | undefined;
@@ -2228,6 +2185,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2228
2185
  refNameAliases: {
2229
2186
  [x: string]: string;
2230
2187
  } | undefined;
2188
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2231
2189
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2232
2190
  } & {
2233
2191
  getConf(arg: string): any;
@@ -2251,8 +2209,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2251
2209
  readonly refNames: string[] | undefined;
2252
2210
  } & {
2253
2211
  getCanonicalRefName(refName: string): string | undefined;
2212
+ getCanonicalRefName2(refName: string): string;
2254
2213
  getRefNameColor(refName: string): string | undefined;
2255
2214
  isValidRefName(refName: string): boolean;
2215
+ getSeqAdapterRefName(canonicalRefName: string): string;
2256
2216
  } & {
2257
2217
  setLoaded({ regions, refNameAliases, cytobands, }: {
2258
2218
  regions: import("@jbrowse/core/util").Region[];
@@ -2267,6 +2227,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2267
2227
  [x: string]: string;
2268
2228
  }): void;
2269
2229
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2230
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2270
2231
  setLoadingP(p?: Promise<void>): void;
2271
2232
  load(): Promise<void>;
2272
2233
  loadPre(): Promise<void>;
@@ -2285,20 +2246,21 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2285
2246
  [x: string]: string;
2286
2247
  }>;
2287
2248
  afterCreate(): void;
2288
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
2249
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
2289
2250
  readonly assemblyNamesList: any[];
2290
2251
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
2291
2252
  readonly rpcManager: RpcManager;
2292
2253
  } & {
2293
2254
  waitForAssembly(assemblyName: string): Promise<({
2294
2255
  configuration: any;
2295
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2256
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
2296
2257
  error: unknown;
2297
2258
  loadingP: Promise<void> | undefined;
2298
2259
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2299
2260
  refNameAliases: {
2300
2261
  [x: string]: string;
2301
2262
  } | undefined;
2263
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2302
2264
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2303
2265
  } & {
2304
2266
  getConf(arg: string): any;
@@ -2322,8 +2284,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2322
2284
  readonly refNames: string[] | undefined;
2323
2285
  } & {
2324
2286
  getCanonicalRefName(refName: string): string | undefined;
2287
+ getCanonicalRefName2(refName: string): string;
2325
2288
  getRefNameColor(refName: string): string | undefined;
2326
2289
  isValidRefName(refName: string): boolean;
2290
+ getSeqAdapterRefName(canonicalRefName: string): string;
2327
2291
  } & {
2328
2292
  setLoaded({ regions, refNameAliases, cytobands, }: {
2329
2293
  regions: import("@jbrowse/core/util").Region[];
@@ -2338,6 +2302,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2338
2302
  [x: string]: string;
2339
2303
  }): void;
2340
2304
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2305
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2341
2306
  setLoadingP(p?: Promise<void>): void;
2342
2307
  load(): Promise<void>;
2343
2308
  loadPre(): Promise<void>;
@@ -2356,8 +2321,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2356
2321
  [x: string]: string;
2357
2322
  }>;
2358
2323
  afterCreate(): void;
2359
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2360
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2324
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2325
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2361
2326
  }, {
2362
2327
  error: unknown;
2363
2328
  loadingP: Promise<void> | undefined;
@@ -2365,6 +2330,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2365
2330
  refNameAliases: {
2366
2331
  [x: string]: string;
2367
2332
  } | undefined;
2333
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2368
2334
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2369
2335
  } & {
2370
2336
  getConf(arg: string): any;
@@ -2388,8 +2354,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2388
2354
  readonly refNames: string[] | undefined;
2389
2355
  } & {
2390
2356
  getCanonicalRefName(refName: string): string | undefined;
2357
+ getCanonicalRefName2(refName: string): string;
2391
2358
  getRefNameColor(refName: string): string | undefined;
2392
2359
  isValidRefName(refName: string): boolean;
2360
+ getSeqAdapterRefName(canonicalRefName: string): string;
2393
2361
  } & {
2394
2362
  setLoaded({ regions, refNameAliases, cytobands, }: {
2395
2363
  regions: import("@jbrowse/core/util").Region[];
@@ -2404,6 +2372,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2404
2372
  [x: string]: string;
2405
2373
  }): void;
2406
2374
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2375
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2407
2376
  setLoadingP(p?: Promise<void>): void;
2408
2377
  load(): Promise<void>;
2409
2378
  loadPre(): Promise<void>;
@@ -2422,21 +2391,15 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2422
2391
  [x: string]: string;
2423
2392
  }>;
2424
2393
  afterCreate(): void;
2425
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
2394
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
2426
2395
  getRefNameMapForAdapter(adapterConf: {
2427
2396
  [x: string]: unknown;
2428
- }, assemblyName: string | undefined, opts: {
2429
- stopToken?: string;
2430
- sessionId: string;
2431
- }): Promise<{
2397
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
2432
2398
  [x: string]: string;
2433
2399
  } | undefined>;
2434
2400
  getReverseRefNameMapForAdapter(adapterConf: {
2435
2401
  [x: string]: unknown;
2436
- }, assemblyName: string | undefined, opts: {
2437
- stopToken?: string;
2438
- sessionId: string;
2439
- }): Promise<{
2402
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
2440
2403
  [x: string]: string;
2441
2404
  } | undefined>;
2442
2405
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -2444,8 +2407,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2444
2407
  afterAttach(): void;
2445
2408
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
2446
2409
  addAssembly(configuration: any): void;
2447
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
2448
- internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2410
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
2411
+ internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
2449
2412
  }, {
2450
2413
  error: unknown;
2451
2414
  adminMode: boolean;
@@ -2453,63 +2416,20 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2453
2416
  rpcManager: RpcManager;
2454
2417
  textSearchManager: TextSearchManager;
2455
2418
  } & {
2456
- setSession(sessionSnapshot: SnapshotIn<import("mobx-state-tree").IModelType<{
2457
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2458
- name: import("mobx-state-tree").ISimpleType<string>;
2459
- margin: import("mobx-state-tree").IType<number | undefined, number, number>;
2419
+ setSession(sessionSnapshot: SnapshotIn<import("@jbrowse/mobx-state-tree").IModelType<{
2420
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
2421
+ name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
2422
+ margin: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
2460
2423
  } & {
2461
- drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2462
- drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
2463
- widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
2464
- activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
2465
- minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2424
+ drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
2425
+ drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
2426
+ widgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>;
2427
+ activeWidgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>;
2428
+ minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2466
2429
  } & {
2467
- connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
2468
- name: import("mobx-state-tree").ISimpleType<string>;
2469
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
2470
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2471
- name: {
2472
- type: string;
2473
- defaultValue: string;
2474
- description: string;
2475
- };
2476
- assemblyNames: {
2477
- type: string;
2478
- defaultValue: never[];
2479
- description: string;
2480
- };
2481
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
2482
- }, {
2483
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
2484
- } & {
2485
- afterAttach(): void;
2486
- addTrackConf(trackConf: Record<string, unknown> | ({
2487
- [x: string]: any;
2488
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2489
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2490
- [x: string]: any;
2491
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2492
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2493
- [x: string]: any;
2494
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2495
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2496
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
2497
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
2498
- [x: string]: any;
2499
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2500
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2501
- [x: string]: any;
2502
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2503
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2504
- [x: string]: any;
2505
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2506
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2507
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
2508
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
2509
- clear(): void;
2510
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
2430
+ connectionInstances: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
2511
2431
  } & {
2512
- view: import("mobx-state-tree").IAnyModelType;
2432
+ view: import("@jbrowse/mobx-state-tree").IAnyModelType;
2513
2433
  }, {
2514
2434
  selection: unknown;
2515
2435
  hovered: unknown;
@@ -2519,8 +2439,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2519
2439
  session: any;
2520
2440
  sessionPath: string;
2521
2441
  assemblyManager: {
2522
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
2523
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2442
+ assemblies: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IModelType<{
2443
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2524
2444
  }, {
2525
2445
  error: unknown;
2526
2446
  loadingP: Promise<void> | undefined;
@@ -2528,6 +2448,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2528
2448
  refNameAliases: {
2529
2449
  [x: string]: string;
2530
2450
  } | undefined;
2451
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2531
2452
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2532
2453
  } & {
2533
2454
  getConf(arg: string): any;
@@ -2551,8 +2472,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2551
2472
  readonly refNames: string[] | undefined;
2552
2473
  } & {
2553
2474
  getCanonicalRefName(refName: string): string | undefined;
2475
+ getCanonicalRefName2(refName: string): string;
2554
2476
  getRefNameColor(refName: string): string | undefined;
2555
2477
  isValidRefName(refName: string): boolean;
2478
+ getSeqAdapterRefName(canonicalRefName: string): string;
2556
2479
  } & {
2557
2480
  setLoaded({ regions, refNameAliases, cytobands, }: {
2558
2481
  regions: import("@jbrowse/core/util").Region[];
@@ -2567,6 +2490,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2567
2490
  [x: string]: string;
2568
2491
  }): void;
2569
2492
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2493
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2570
2494
  setLoadingP(p?: Promise<void>): void;
2571
2495
  load(): Promise<void>;
2572
2496
  loadPre(): Promise<void>;
@@ -2585,8 +2509,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2585
2509
  [x: string]: string;
2586
2510
  }>;
2587
2511
  afterCreate(): void;
2588
- }, 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<{
2589
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2512
+ }, 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<{
2513
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2590
2514
  }, {
2591
2515
  error: unknown;
2592
2516
  loadingP: Promise<void> | undefined;
@@ -2594,6 +2518,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2594
2518
  refNameAliases: {
2595
2519
  [x: string]: string;
2596
2520
  } | undefined;
2521
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2597
2522
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2598
2523
  } & {
2599
2524
  getConf(arg: string): any;
@@ -2617,8 +2542,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2617
2542
  readonly refNames: string[] | undefined;
2618
2543
  } & {
2619
2544
  getCanonicalRefName(refName: string): string | undefined;
2545
+ getCanonicalRefName2(refName: string): string;
2620
2546
  getRefNameColor(refName: string): string | undefined;
2621
2547
  isValidRefName(refName: string): boolean;
2548
+ getSeqAdapterRefName(canonicalRefName: string): string;
2622
2549
  } & {
2623
2550
  setLoaded({ regions, refNameAliases, cytobands, }: {
2624
2551
  regions: import("@jbrowse/core/util").Region[];
@@ -2633,6 +2560,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2633
2560
  [x: string]: string;
2634
2561
  }): void;
2635
2562
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2563
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2636
2564
  setLoadingP(p?: Promise<void>): void;
2637
2565
  load(): Promise<void>;
2638
2566
  loadPre(): Promise<void>;
@@ -2651,17 +2579,18 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2651
2579
  [x: string]: string;
2652
2580
  }>;
2653
2581
  afterCreate(): void;
2654
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
2655
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2582
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
2583
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
2656
2584
  readonly assemblyNameMap: Record<string, {
2657
2585
  configuration: any;
2658
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2586
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
2659
2587
  error: unknown;
2660
2588
  loadingP: Promise<void> | undefined;
2661
2589
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2662
2590
  refNameAliases: {
2663
2591
  [x: string]: string;
2664
2592
  } | undefined;
2593
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2665
2594
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2666
2595
  } & {
2667
2596
  getConf(arg: string): any;
@@ -2685,8 +2614,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2685
2614
  readonly refNames: string[] | undefined;
2686
2615
  } & {
2687
2616
  getCanonicalRefName(refName: string): string | undefined;
2617
+ getCanonicalRefName2(refName: string): string;
2688
2618
  getRefNameColor(refName: string): string | undefined;
2689
2619
  isValidRefName(refName: string): boolean;
2620
+ getSeqAdapterRefName(canonicalRefName: string): string;
2690
2621
  } & {
2691
2622
  setLoaded({ regions, refNameAliases, cytobands, }: {
2692
2623
  regions: import("@jbrowse/core/util").Region[];
@@ -2701,6 +2632,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2701
2632
  [x: string]: string;
2702
2633
  }): void;
2703
2634
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2635
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2704
2636
  setLoadingP(p?: Promise<void>): void;
2705
2637
  load(): Promise<void>;
2706
2638
  loadPre(): Promise<void>;
@@ -2719,8 +2651,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2719
2651
  [x: string]: string;
2720
2652
  }>;
2721
2653
  afterCreate(): void;
2722
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2723
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2654
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2655
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2724
2656
  }, {
2725
2657
  error: unknown;
2726
2658
  loadingP: Promise<void> | undefined;
@@ -2728,6 +2660,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2728
2660
  refNameAliases: {
2729
2661
  [x: string]: string;
2730
2662
  } | undefined;
2663
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2731
2664
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2732
2665
  } & {
2733
2666
  getConf(arg: string): any;
@@ -2751,8 +2684,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2751
2684
  readonly refNames: string[] | undefined;
2752
2685
  } & {
2753
2686
  getCanonicalRefName(refName: string): string | undefined;
2687
+ getCanonicalRefName2(refName: string): string;
2754
2688
  getRefNameColor(refName: string): string | undefined;
2755
2689
  isValidRefName(refName: string): boolean;
2690
+ getSeqAdapterRefName(canonicalRefName: string): string;
2756
2691
  } & {
2757
2692
  setLoaded({ regions, refNameAliases, cytobands, }: {
2758
2693
  regions: import("@jbrowse/core/util").Region[];
@@ -2767,6 +2702,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2767
2702
  [x: string]: string;
2768
2703
  }): void;
2769
2704
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2705
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2770
2706
  setLoadingP(p?: Promise<void>): void;
2771
2707
  load(): Promise<void>;
2772
2708
  loadPre(): Promise<void>;
@@ -2785,18 +2721,20 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2785
2721
  [x: string]: string;
2786
2722
  }>;
2787
2723
  afterCreate(): void;
2788
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
2724
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
2789
2725
  } & {
2790
2726
  getCanonicalAssemblyName(asmName: string): string | undefined;
2727
+ getCanonicalAssemblyName2(asmName: string): string;
2791
2728
  get(asmName: string): ({
2792
2729
  configuration: any;
2793
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2730
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
2794
2731
  error: unknown;
2795
2732
  loadingP: Promise<void> | undefined;
2796
2733
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2797
2734
  refNameAliases: {
2798
2735
  [x: string]: string;
2799
2736
  } | undefined;
2737
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2800
2738
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2801
2739
  } & {
2802
2740
  getConf(arg: string): any;
@@ -2820,8 +2758,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2820
2758
  readonly refNames: string[] | undefined;
2821
2759
  } & {
2822
2760
  getCanonicalRefName(refName: string): string | undefined;
2761
+ getCanonicalRefName2(refName: string): string;
2823
2762
  getRefNameColor(refName: string): string | undefined;
2824
2763
  isValidRefName(refName: string): boolean;
2764
+ getSeqAdapterRefName(canonicalRefName: string): string;
2825
2765
  } & {
2826
2766
  setLoaded({ regions, refNameAliases, cytobands, }: {
2827
2767
  regions: import("@jbrowse/core/util").Region[];
@@ -2836,6 +2776,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2836
2776
  [x: string]: string;
2837
2777
  }): void;
2838
2778
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2779
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2839
2780
  setLoadingP(p?: Promise<void>): void;
2840
2781
  load(): Promise<void>;
2841
2782
  loadPre(): Promise<void>;
@@ -2854,8 +2795,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2854
2795
  [x: string]: string;
2855
2796
  }>;
2856
2797
  afterCreate(): void;
2857
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2858
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2798
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2799
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2859
2800
  }, {
2860
2801
  error: unknown;
2861
2802
  loadingP: Promise<void> | undefined;
@@ -2863,6 +2804,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2863
2804
  refNameAliases: {
2864
2805
  [x: string]: string;
2865
2806
  } | undefined;
2807
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2866
2808
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2867
2809
  } & {
2868
2810
  getConf(arg: string): any;
@@ -2886,8 +2828,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2886
2828
  readonly refNames: string[] | undefined;
2887
2829
  } & {
2888
2830
  getCanonicalRefName(refName: string): string | undefined;
2831
+ getCanonicalRefName2(refName: string): string;
2889
2832
  getRefNameColor(refName: string): string | undefined;
2890
2833
  isValidRefName(refName: string): boolean;
2834
+ getSeqAdapterRefName(canonicalRefName: string): string;
2891
2835
  } & {
2892
2836
  setLoaded({ regions, refNameAliases, cytobands, }: {
2893
2837
  regions: import("@jbrowse/core/util").Region[];
@@ -2902,6 +2846,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2902
2846
  [x: string]: string;
2903
2847
  }): void;
2904
2848
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2849
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2905
2850
  setLoadingP(p?: Promise<void>): void;
2906
2851
  load(): Promise<void>;
2907
2852
  loadPre(): Promise<void>;
@@ -2920,20 +2865,21 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2920
2865
  [x: string]: string;
2921
2866
  }>;
2922
2867
  afterCreate(): void;
2923
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
2868
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
2924
2869
  readonly assemblyNamesList: any[];
2925
2870
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
2926
2871
  readonly rpcManager: RpcManager;
2927
2872
  } & {
2928
2873
  waitForAssembly(assemblyName: string): Promise<({
2929
2874
  configuration: any;
2930
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2875
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
2931
2876
  error: unknown;
2932
2877
  loadingP: Promise<void> | undefined;
2933
2878
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2934
2879
  refNameAliases: {
2935
2880
  [x: string]: string;
2936
2881
  } | undefined;
2882
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2937
2883
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2938
2884
  } & {
2939
2885
  getConf(arg: string): any;
@@ -2957,8 +2903,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2957
2903
  readonly refNames: string[] | undefined;
2958
2904
  } & {
2959
2905
  getCanonicalRefName(refName: string): string | undefined;
2906
+ getCanonicalRefName2(refName: string): string;
2960
2907
  getRefNameColor(refName: string): string | undefined;
2961
2908
  isValidRefName(refName: string): boolean;
2909
+ getSeqAdapterRefName(canonicalRefName: string): string;
2962
2910
  } & {
2963
2911
  setLoaded({ regions, refNameAliases, cytobands, }: {
2964
2912
  regions: import("@jbrowse/core/util").Region[];
@@ -2973,6 +2921,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2973
2921
  [x: string]: string;
2974
2922
  }): void;
2975
2923
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2924
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
2976
2925
  setLoadingP(p?: Promise<void>): void;
2977
2926
  load(): Promise<void>;
2978
2927
  loadPre(): Promise<void>;
@@ -2991,8 +2940,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
2991
2940
  [x: string]: string;
2992
2941
  }>;
2993
2942
  afterCreate(): void;
2994
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2995
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2943
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2944
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2996
2945
  }, {
2997
2946
  error: unknown;
2998
2947
  loadingP: Promise<void> | undefined;
@@ -3000,6 +2949,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3000
2949
  refNameAliases: {
3001
2950
  [x: string]: string;
3002
2951
  } | undefined;
2952
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3003
2953
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3004
2954
  } & {
3005
2955
  getConf(arg: string): any;
@@ -3023,8 +2973,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3023
2973
  readonly refNames: string[] | undefined;
3024
2974
  } & {
3025
2975
  getCanonicalRefName(refName: string): string | undefined;
2976
+ getCanonicalRefName2(refName: string): string;
3026
2977
  getRefNameColor(refName: string): string | undefined;
3027
2978
  isValidRefName(refName: string): boolean;
2979
+ getSeqAdapterRefName(canonicalRefName: string): string;
3028
2980
  } & {
3029
2981
  setLoaded({ regions, refNameAliases, cytobands, }: {
3030
2982
  regions: import("@jbrowse/core/util").Region[];
@@ -3039,6 +2991,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3039
2991
  [x: string]: string;
3040
2992
  }): void;
3041
2993
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2994
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3042
2995
  setLoadingP(p?: Promise<void>): void;
3043
2996
  load(): Promise<void>;
3044
2997
  loadPre(): Promise<void>;
@@ -3057,21 +3010,15 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3057
3010
  [x: string]: string;
3058
3011
  }>;
3059
3012
  afterCreate(): void;
3060
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
3013
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
3061
3014
  getRefNameMapForAdapter(adapterConf: {
3062
3015
  [x: string]: unknown;
3063
- }, assemblyName: string | undefined, opts: {
3064
- stopToken?: string;
3065
- sessionId: string;
3066
- }): Promise<{
3016
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
3067
3017
  [x: string]: string;
3068
3018
  } | undefined>;
3069
3019
  getReverseRefNameMapForAdapter(adapterConf: {
3070
3020
  [x: string]: unknown;
3071
- }, assemblyName: string | undefined, opts: {
3072
- stopToken?: string;
3073
- sessionId: string;
3074
- }): Promise<{
3021
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
3075
3022
  [x: string]: string;
3076
3023
  } | undefined>;
3077
3024
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -3079,9 +3026,9 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3079
3026
  afterAttach(): void;
3080
3027
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
3081
3028
  addAssembly(configuration: any): void;
3082
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
3083
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
3084
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3029
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
3030
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
3031
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
3085
3032
  }, {
3086
3033
  error: unknown;
3087
3034
  loadingP: Promise<void> | undefined;
@@ -3089,6 +3036,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3089
3036
  refNameAliases: {
3090
3037
  [x: string]: string;
3091
3038
  } | undefined;
3039
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3092
3040
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3093
3041
  } & {
3094
3042
  getConf(arg: string): any;
@@ -3112,8 +3060,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3112
3060
  readonly refNames: string[] | undefined;
3113
3061
  } & {
3114
3062
  getCanonicalRefName(refName: string): string | undefined;
3063
+ getCanonicalRefName2(refName: string): string;
3115
3064
  getRefNameColor(refName: string): string | undefined;
3116
3065
  isValidRefName(refName: string): boolean;
3066
+ getSeqAdapterRefName(canonicalRefName: string): string;
3117
3067
  } & {
3118
3068
  setLoaded({ regions, refNameAliases, cytobands, }: {
3119
3069
  regions: import("@jbrowse/core/util").Region[];
@@ -3128,6 +3078,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3128
3078
  [x: string]: string;
3129
3079
  }): void;
3130
3080
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3081
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3131
3082
  setLoadingP(p?: Promise<void>): void;
3132
3083
  load(): Promise<void>;
3133
3084
  loadPre(): Promise<void>;
@@ -3146,17 +3097,18 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3146
3097
  [x: string]: string;
3147
3098
  }>;
3148
3099
  afterCreate(): void;
3149
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
3100
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
3150
3101
  }, {
3151
3102
  readonly assemblyNameMap: Record<string, {
3152
3103
  configuration: any;
3153
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3104
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
3154
3105
  error: unknown;
3155
3106
  loadingP: Promise<void> | undefined;
3156
3107
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3157
3108
  refNameAliases: {
3158
3109
  [x: string]: string;
3159
3110
  } | undefined;
3111
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3160
3112
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3161
3113
  } & {
3162
3114
  getConf(arg: string): any;
@@ -3180,8 +3132,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3180
3132
  readonly refNames: string[] | undefined;
3181
3133
  } & {
3182
3134
  getCanonicalRefName(refName: string): string | undefined;
3135
+ getCanonicalRefName2(refName: string): string;
3183
3136
  getRefNameColor(refName: string): string | undefined;
3184
3137
  isValidRefName(refName: string): boolean;
3138
+ getSeqAdapterRefName(canonicalRefName: string): string;
3185
3139
  } & {
3186
3140
  setLoaded({ regions, refNameAliases, cytobands, }: {
3187
3141
  regions: import("@jbrowse/core/util").Region[];
@@ -3196,6 +3150,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3196
3150
  [x: string]: string;
3197
3151
  }): void;
3198
3152
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3153
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3199
3154
  setLoadingP(p?: Promise<void>): void;
3200
3155
  load(): Promise<void>;
3201
3156
  loadPre(): Promise<void>;
@@ -3214,8 +3169,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3214
3169
  [x: string]: string;
3215
3170
  }>;
3216
3171
  afterCreate(): void;
3217
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3218
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3172
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
3173
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
3219
3174
  }, {
3220
3175
  error: unknown;
3221
3176
  loadingP: Promise<void> | undefined;
@@ -3223,6 +3178,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3223
3178
  refNameAliases: {
3224
3179
  [x: string]: string;
3225
3180
  } | undefined;
3181
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3226
3182
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3227
3183
  } & {
3228
3184
  getConf(arg: string): any;
@@ -3246,8 +3202,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3246
3202
  readonly refNames: string[] | undefined;
3247
3203
  } & {
3248
3204
  getCanonicalRefName(refName: string): string | undefined;
3205
+ getCanonicalRefName2(refName: string): string;
3249
3206
  getRefNameColor(refName: string): string | undefined;
3250
3207
  isValidRefName(refName: string): boolean;
3208
+ getSeqAdapterRefName(canonicalRefName: string): string;
3251
3209
  } & {
3252
3210
  setLoaded({ regions, refNameAliases, cytobands, }: {
3253
3211
  regions: import("@jbrowse/core/util").Region[];
@@ -3262,6 +3220,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3262
3220
  [x: string]: string;
3263
3221
  }): void;
3264
3222
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3223
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3265
3224
  setLoadingP(p?: Promise<void>): void;
3266
3225
  load(): Promise<void>;
3267
3226
  loadPre(): Promise<void>;
@@ -3280,18 +3239,20 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3280
3239
  [x: string]: string;
3281
3240
  }>;
3282
3241
  afterCreate(): void;
3283
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
3242
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
3284
3243
  } & {
3285
3244
  getCanonicalAssemblyName(asmName: string): string | undefined;
3245
+ getCanonicalAssemblyName2(asmName: string): string;
3286
3246
  get(asmName: string): ({
3287
3247
  configuration: any;
3288
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3248
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
3289
3249
  error: unknown;
3290
3250
  loadingP: Promise<void> | undefined;
3291
3251
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3292
3252
  refNameAliases: {
3293
3253
  [x: string]: string;
3294
3254
  } | undefined;
3255
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3295
3256
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3296
3257
  } & {
3297
3258
  getConf(arg: string): any;
@@ -3315,8 +3276,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3315
3276
  readonly refNames: string[] | undefined;
3316
3277
  } & {
3317
3278
  getCanonicalRefName(refName: string): string | undefined;
3279
+ getCanonicalRefName2(refName: string): string;
3318
3280
  getRefNameColor(refName: string): string | undefined;
3319
3281
  isValidRefName(refName: string): boolean;
3282
+ getSeqAdapterRefName(canonicalRefName: string): string;
3320
3283
  } & {
3321
3284
  setLoaded({ regions, refNameAliases, cytobands, }: {
3322
3285
  regions: import("@jbrowse/core/util").Region[];
@@ -3331,6 +3294,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3331
3294
  [x: string]: string;
3332
3295
  }): void;
3333
3296
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3297
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3334
3298
  setLoadingP(p?: Promise<void>): void;
3335
3299
  load(): Promise<void>;
3336
3300
  loadPre(): Promise<void>;
@@ -3349,8 +3313,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3349
3313
  [x: string]: string;
3350
3314
  }>;
3351
3315
  afterCreate(): void;
3352
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3353
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3316
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
3317
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
3354
3318
  }, {
3355
3319
  error: unknown;
3356
3320
  loadingP: Promise<void> | undefined;
@@ -3358,6 +3322,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3358
3322
  refNameAliases: {
3359
3323
  [x: string]: string;
3360
3324
  } | undefined;
3325
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3361
3326
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3362
3327
  } & {
3363
3328
  getConf(arg: string): any;
@@ -3381,8 +3346,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3381
3346
  readonly refNames: string[] | undefined;
3382
3347
  } & {
3383
3348
  getCanonicalRefName(refName: string): string | undefined;
3349
+ getCanonicalRefName2(refName: string): string;
3384
3350
  getRefNameColor(refName: string): string | undefined;
3385
3351
  isValidRefName(refName: string): boolean;
3352
+ getSeqAdapterRefName(canonicalRefName: string): string;
3386
3353
  } & {
3387
3354
  setLoaded({ regions, refNameAliases, cytobands, }: {
3388
3355
  regions: import("@jbrowse/core/util").Region[];
@@ -3397,6 +3364,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3397
3364
  [x: string]: string;
3398
3365
  }): void;
3399
3366
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3367
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3400
3368
  setLoadingP(p?: Promise<void>): void;
3401
3369
  load(): Promise<void>;
3402
3370
  loadPre(): Promise<void>;
@@ -3415,20 +3383,21 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3415
3383
  [x: string]: string;
3416
3384
  }>;
3417
3385
  afterCreate(): void;
3418
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
3386
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
3419
3387
  readonly assemblyNamesList: any[];
3420
3388
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
3421
3389
  readonly rpcManager: RpcManager;
3422
3390
  } & {
3423
3391
  waitForAssembly(assemblyName: string): Promise<({
3424
3392
  configuration: any;
3425
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3393
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
3426
3394
  error: unknown;
3427
3395
  loadingP: Promise<void> | undefined;
3428
3396
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3429
3397
  refNameAliases: {
3430
3398
  [x: string]: string;
3431
3399
  } | undefined;
3400
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3432
3401
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3433
3402
  } & {
3434
3403
  getConf(arg: string): any;
@@ -3452,8 +3421,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3452
3421
  readonly refNames: string[] | undefined;
3453
3422
  } & {
3454
3423
  getCanonicalRefName(refName: string): string | undefined;
3424
+ getCanonicalRefName2(refName: string): string;
3455
3425
  getRefNameColor(refName: string): string | undefined;
3456
3426
  isValidRefName(refName: string): boolean;
3427
+ getSeqAdapterRefName(canonicalRefName: string): string;
3457
3428
  } & {
3458
3429
  setLoaded({ regions, refNameAliases, cytobands, }: {
3459
3430
  regions: import("@jbrowse/core/util").Region[];
@@ -3468,6 +3439,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3468
3439
  [x: string]: string;
3469
3440
  }): void;
3470
3441
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3442
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3471
3443
  setLoadingP(p?: Promise<void>): void;
3472
3444
  load(): Promise<void>;
3473
3445
  loadPre(): Promise<void>;
@@ -3486,8 +3458,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3486
3458
  [x: string]: string;
3487
3459
  }>;
3488
3460
  afterCreate(): void;
3489
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3490
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3461
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
3462
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
3491
3463
  }, {
3492
3464
  error: unknown;
3493
3465
  loadingP: Promise<void> | undefined;
@@ -3495,6 +3467,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3495
3467
  refNameAliases: {
3496
3468
  [x: string]: string;
3497
3469
  } | undefined;
3470
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3498
3471
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3499
3472
  } & {
3500
3473
  getConf(arg: string): any;
@@ -3518,8 +3491,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3518
3491
  readonly refNames: string[] | undefined;
3519
3492
  } & {
3520
3493
  getCanonicalRefName(refName: string): string | undefined;
3494
+ getCanonicalRefName2(refName: string): string;
3521
3495
  getRefNameColor(refName: string): string | undefined;
3522
3496
  isValidRefName(refName: string): boolean;
3497
+ getSeqAdapterRefName(canonicalRefName: string): string;
3523
3498
  } & {
3524
3499
  setLoaded({ regions, refNameAliases, cytobands, }: {
3525
3500
  regions: import("@jbrowse/core/util").Region[];
@@ -3534,6 +3509,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3534
3509
  [x: string]: string;
3535
3510
  }): void;
3536
3511
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3512
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3537
3513
  setLoadingP(p?: Promise<void>): void;
3538
3514
  load(): Promise<void>;
3539
3515
  loadPre(): Promise<void>;
@@ -3552,21 +3528,15 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3552
3528
  [x: string]: string;
3553
3529
  }>;
3554
3530
  afterCreate(): void;
3555
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
3531
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
3556
3532
  getRefNameMapForAdapter(adapterConf: {
3557
3533
  [x: string]: unknown;
3558
- }, assemblyName: string | undefined, opts: {
3559
- stopToken?: string;
3560
- sessionId: string;
3561
- }): Promise<{
3534
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
3562
3535
  [x: string]: string;
3563
3536
  } | undefined>;
3564
3537
  getReverseRefNameMapForAdapter(adapterConf: {
3565
3538
  [x: string]: unknown;
3566
- }, assemblyName: string | undefined, opts: {
3567
- stopToken?: string;
3568
- sessionId: string;
3569
- }): Promise<{
3539
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
3570
3540
  [x: string]: string;
3571
3541
  } | undefined>;
3572
3542
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -3574,8 +3544,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3574
3544
  afterAttach(): void;
3575
3545
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
3576
3546
  addAssembly(configuration: any): void;
3577
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
3578
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3547
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>>;
3548
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
3579
3549
  rpcManager: RpcManager;
3580
3550
  adminMode: boolean;
3581
3551
  error: unknown;
@@ -3583,17 +3553,17 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3583
3553
  pluginManager: PluginManager;
3584
3554
  } & {
3585
3555
  setError(error: unknown): void;
3586
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
3556
+ setSession(sessionSnapshot?: SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
3587
3557
  setDefaultSession(): void;
3588
3558
  setSessionPath(path: string): void;
3589
3559
  renameCurrentSession(newName: string): void;
3590
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3591
- jbrowse: import("mobx-state-tree").IAnyType;
3592
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
3593
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
3594
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
3595
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
3596
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3560
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
3561
+ jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
3562
+ session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
3563
+ sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
3564
+ assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
3565
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
3566
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
3597
3567
  }, {
3598
3568
  error: unknown;
3599
3569
  loadingP: Promise<void> | undefined;
@@ -3601,6 +3571,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3601
3571
  refNameAliases: {
3602
3572
  [x: string]: string;
3603
3573
  } | undefined;
3574
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3604
3575
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3605
3576
  } & {
3606
3577
  getConf(arg: string): any;
@@ -3624,8 +3595,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3624
3595
  readonly refNames: string[] | undefined;
3625
3596
  } & {
3626
3597
  getCanonicalRefName(refName: string): string | undefined;
3598
+ getCanonicalRefName2(refName: string): string;
3627
3599
  getRefNameColor(refName: string): string | undefined;
3628
3600
  isValidRefName(refName: string): boolean;
3601
+ getSeqAdapterRefName(canonicalRefName: string): string;
3629
3602
  } & {
3630
3603
  setLoaded({ regions, refNameAliases, cytobands, }: {
3631
3604
  regions: import("@jbrowse/core/util").Region[];
@@ -3640,6 +3613,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3640
3613
  [x: string]: string;
3641
3614
  }): void;
3642
3615
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3616
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3643
3617
  setLoadingP(p?: Promise<void>): void;
3644
3618
  load(): Promise<void>;
3645
3619
  loadPre(): Promise<void>;
@@ -3658,17 +3632,18 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3658
3632
  [x: string]: string;
3659
3633
  }>;
3660
3634
  afterCreate(): void;
3661
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
3635
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
3662
3636
  }, {
3663
3637
  readonly assemblyNameMap: Record<string, {
3664
3638
  configuration: any;
3665
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3639
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
3666
3640
  error: unknown;
3667
3641
  loadingP: Promise<void> | undefined;
3668
3642
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3669
3643
  refNameAliases: {
3670
3644
  [x: string]: string;
3671
3645
  } | undefined;
3646
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3672
3647
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3673
3648
  } & {
3674
3649
  getConf(arg: string): any;
@@ -3692,8 +3667,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3692
3667
  readonly refNames: string[] | undefined;
3693
3668
  } & {
3694
3669
  getCanonicalRefName(refName: string): string | undefined;
3670
+ getCanonicalRefName2(refName: string): string;
3695
3671
  getRefNameColor(refName: string): string | undefined;
3696
3672
  isValidRefName(refName: string): boolean;
3673
+ getSeqAdapterRefName(canonicalRefName: string): string;
3697
3674
  } & {
3698
3675
  setLoaded({ regions, refNameAliases, cytobands, }: {
3699
3676
  regions: import("@jbrowse/core/util").Region[];
@@ -3708,6 +3685,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3708
3685
  [x: string]: string;
3709
3686
  }): void;
3710
3687
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3688
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3711
3689
  setLoadingP(p?: Promise<void>): void;
3712
3690
  load(): Promise<void>;
3713
3691
  loadPre(): Promise<void>;
@@ -3726,8 +3704,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3726
3704
  [x: string]: string;
3727
3705
  }>;
3728
3706
  afterCreate(): void;
3729
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3730
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3707
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
3708
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
3731
3709
  }, {
3732
3710
  error: unknown;
3733
3711
  loadingP: Promise<void> | undefined;
@@ -3735,6 +3713,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3735
3713
  refNameAliases: {
3736
3714
  [x: string]: string;
3737
3715
  } | undefined;
3716
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3738
3717
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3739
3718
  } & {
3740
3719
  getConf(arg: string): any;
@@ -3758,8 +3737,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3758
3737
  readonly refNames: string[] | undefined;
3759
3738
  } & {
3760
3739
  getCanonicalRefName(refName: string): string | undefined;
3740
+ getCanonicalRefName2(refName: string): string;
3761
3741
  getRefNameColor(refName: string): string | undefined;
3762
3742
  isValidRefName(refName: string): boolean;
3743
+ getSeqAdapterRefName(canonicalRefName: string): string;
3763
3744
  } & {
3764
3745
  setLoaded({ regions, refNameAliases, cytobands, }: {
3765
3746
  regions: import("@jbrowse/core/util").Region[];
@@ -3774,6 +3755,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3774
3755
  [x: string]: string;
3775
3756
  }): void;
3776
3757
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3758
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3777
3759
  setLoadingP(p?: Promise<void>): void;
3778
3760
  load(): Promise<void>;
3779
3761
  loadPre(): Promise<void>;
@@ -3792,18 +3774,20 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3792
3774
  [x: string]: string;
3793
3775
  }>;
3794
3776
  afterCreate(): void;
3795
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
3777
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
3796
3778
  } & {
3797
3779
  getCanonicalAssemblyName(asmName: string): string | undefined;
3780
+ getCanonicalAssemblyName2(asmName: string): string;
3798
3781
  get(asmName: string): ({
3799
3782
  configuration: any;
3800
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3783
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
3801
3784
  error: unknown;
3802
3785
  loadingP: Promise<void> | undefined;
3803
3786
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3804
3787
  refNameAliases: {
3805
3788
  [x: string]: string;
3806
3789
  } | undefined;
3790
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3807
3791
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3808
3792
  } & {
3809
3793
  getConf(arg: string): any;
@@ -3827,8 +3811,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3827
3811
  readonly refNames: string[] | undefined;
3828
3812
  } & {
3829
3813
  getCanonicalRefName(refName: string): string | undefined;
3814
+ getCanonicalRefName2(refName: string): string;
3830
3815
  getRefNameColor(refName: string): string | undefined;
3831
3816
  isValidRefName(refName: string): boolean;
3817
+ getSeqAdapterRefName(canonicalRefName: string): string;
3832
3818
  } & {
3833
3819
  setLoaded({ regions, refNameAliases, cytobands, }: {
3834
3820
  regions: import("@jbrowse/core/util").Region[];
@@ -3843,6 +3829,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3843
3829
  [x: string]: string;
3844
3830
  }): void;
3845
3831
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3832
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3846
3833
  setLoadingP(p?: Promise<void>): void;
3847
3834
  load(): Promise<void>;
3848
3835
  loadPre(): Promise<void>;
@@ -3861,8 +3848,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3861
3848
  [x: string]: string;
3862
3849
  }>;
3863
3850
  afterCreate(): void;
3864
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3865
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3851
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
3852
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
3866
3853
  }, {
3867
3854
  error: unknown;
3868
3855
  loadingP: Promise<void> | undefined;
@@ -3870,6 +3857,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3870
3857
  refNameAliases: {
3871
3858
  [x: string]: string;
3872
3859
  } | undefined;
3860
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3873
3861
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3874
3862
  } & {
3875
3863
  getConf(arg: string): any;
@@ -3893,8 +3881,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3893
3881
  readonly refNames: string[] | undefined;
3894
3882
  } & {
3895
3883
  getCanonicalRefName(refName: string): string | undefined;
3884
+ getCanonicalRefName2(refName: string): string;
3896
3885
  getRefNameColor(refName: string): string | undefined;
3897
3886
  isValidRefName(refName: string): boolean;
3887
+ getSeqAdapterRefName(canonicalRefName: string): string;
3898
3888
  } & {
3899
3889
  setLoaded({ regions, refNameAliases, cytobands, }: {
3900
3890
  regions: import("@jbrowse/core/util").Region[];
@@ -3909,6 +3899,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3909
3899
  [x: string]: string;
3910
3900
  }): void;
3911
3901
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3902
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3912
3903
  setLoadingP(p?: Promise<void>): void;
3913
3904
  load(): Promise<void>;
3914
3905
  loadPre(): Promise<void>;
@@ -3927,20 +3918,21 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3927
3918
  [x: string]: string;
3928
3919
  }>;
3929
3920
  afterCreate(): void;
3930
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
3921
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
3931
3922
  readonly assemblyNamesList: any[];
3932
3923
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
3933
3924
  readonly rpcManager: RpcManager;
3934
3925
  } & {
3935
3926
  waitForAssembly(assemblyName: string): Promise<({
3936
3927
  configuration: any;
3937
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3928
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
3938
3929
  error: unknown;
3939
3930
  loadingP: Promise<void> | undefined;
3940
3931
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3941
3932
  refNameAliases: {
3942
3933
  [x: string]: string;
3943
3934
  } | undefined;
3935
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3944
3936
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3945
3937
  } & {
3946
3938
  getConf(arg: string): any;
@@ -3964,8 +3956,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3964
3956
  readonly refNames: string[] | undefined;
3965
3957
  } & {
3966
3958
  getCanonicalRefName(refName: string): string | undefined;
3959
+ getCanonicalRefName2(refName: string): string;
3967
3960
  getRefNameColor(refName: string): string | undefined;
3968
3961
  isValidRefName(refName: string): boolean;
3962
+ getSeqAdapterRefName(canonicalRefName: string): string;
3969
3963
  } & {
3970
3964
  setLoaded({ regions, refNameAliases, cytobands, }: {
3971
3965
  regions: import("@jbrowse/core/util").Region[];
@@ -3980,6 +3974,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3980
3974
  [x: string]: string;
3981
3975
  }): void;
3982
3976
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3977
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
3983
3978
  setLoadingP(p?: Promise<void>): void;
3984
3979
  load(): Promise<void>;
3985
3980
  loadPre(): Promise<void>;
@@ -3998,8 +3993,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
3998
3993
  [x: string]: string;
3999
3994
  }>;
4000
3995
  afterCreate(): void;
4001
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
4002
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3996
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
3997
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
4003
3998
  }, {
4004
3999
  error: unknown;
4005
4000
  loadingP: Promise<void> | undefined;
@@ -4007,6 +4002,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4007
4002
  refNameAliases: {
4008
4003
  [x: string]: string;
4009
4004
  } | undefined;
4005
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
4010
4006
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
4011
4007
  } & {
4012
4008
  getConf(arg: string): any;
@@ -4030,8 +4026,10 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4030
4026
  readonly refNames: string[] | undefined;
4031
4027
  } & {
4032
4028
  getCanonicalRefName(refName: string): string | undefined;
4029
+ getCanonicalRefName2(refName: string): string;
4033
4030
  getRefNameColor(refName: string): string | undefined;
4034
4031
  isValidRefName(refName: string): boolean;
4032
+ getSeqAdapterRefName(canonicalRefName: string): string;
4035
4033
  } & {
4036
4034
  setLoaded({ regions, refNameAliases, cytobands, }: {
4037
4035
  regions: import("@jbrowse/core/util").Region[];
@@ -4046,6 +4044,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4046
4044
  [x: string]: string;
4047
4045
  }): void;
4048
4046
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
4047
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
4049
4048
  setLoadingP(p?: Promise<void>): void;
4050
4049
  load(): Promise<void>;
4051
4050
  loadPre(): Promise<void>;
@@ -4064,21 +4063,15 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4064
4063
  [x: string]: string;
4065
4064
  }>;
4066
4065
  afterCreate(): void;
4067
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
4066
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
4068
4067
  getRefNameMapForAdapter(adapterConf: {
4069
4068
  [x: string]: unknown;
4070
- }, assemblyName: string | undefined, opts: {
4071
- stopToken?: string;
4072
- sessionId: string;
4073
- }): Promise<{
4069
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
4074
4070
  [x: string]: string;
4075
4071
  } | undefined>;
4076
4072
  getReverseRefNameMapForAdapter(adapterConf: {
4077
4073
  [x: string]: unknown;
4078
- }, assemblyName: string | undefined, opts: {
4079
- stopToken?: string;
4080
- sessionId: string;
4081
- }): Promise<{
4074
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
4082
4075
  [x: string]: string;
4083
4076
  } | undefined>;
4084
4077
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -4086,7 +4079,7 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4086
4079
  afterAttach(): void;
4087
4080
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
4088
4081
  addAssembly(configuration: any): void;
4089
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
4082
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
4090
4083
  }, {
4091
4084
  rpcManager: RpcManager;
4092
4085
  adminMode: boolean;
@@ -4095,25 +4088,21 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4095
4088
  pluginManager: PluginManager;
4096
4089
  } & {
4097
4090
  setError(error: unknown): void;
4098
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
4091
+ setSession(sessionSnapshot?: SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
4099
4092
  setDefaultSession(): void;
4100
4093
  setSessionPath(path: string): void;
4101
4094
  renameCurrentSession(newName: string): void;
4102
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
4095
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
4103
4096
  } & {
4104
4097
  readonly jbrowse: any;
4105
4098
  readonly rpcManager: RpcManager;
4106
4099
  readonly configuration: {
4107
4100
  [x: string]: any;
4108
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4101
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
4109
4102
  setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4110
4103
  [x: string]: any;
4111
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4112
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4113
- [x: string]: any;
4114
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4115
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4116
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
4104
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4105
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
4117
4106
  readonly adminMode: boolean;
4118
4107
  readonly textSearchManager: TextSearchManager;
4119
4108
  } & {
@@ -4135,108 +4124,14 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4135
4124
  minimizeWidgetDrawer(): void;
4136
4125
  showWidgetDrawer(): void;
4137
4126
  hideAllWidgets(): void;
4138
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4127
+ editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel | {
4128
+ trackId: string;
4129
+ }): void;
4139
4130
  afterAttach(): void;
4140
4131
  } & {
4141
4132
  readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
4142
4133
  } & {
4143
- makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
4144
- name: string;
4145
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
4146
- configuration: {
4147
- [x: string]: any;
4148
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4149
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4150
- [x: string]: any;
4151
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4152
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4153
- [x: string]: any;
4154
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4155
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4156
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4157
- name: {
4158
- type: string;
4159
- defaultValue: string;
4160
- description: string;
4161
- };
4162
- assemblyNames: {
4163
- type: string;
4164
- defaultValue: never[];
4165
- description: string;
4166
- };
4167
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
4168
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4169
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4170
- } & {
4171
- afterAttach(): void;
4172
- addTrackConf(trackConf: Record<string, unknown> | ({
4173
- [x: string]: any;
4174
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4175
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4176
- [x: string]: any;
4177
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4178
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4179
- [x: string]: any;
4180
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4181
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4182
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
4183
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
4184
- [x: string]: any;
4185
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4186
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4187
- [x: string]: any;
4188
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4189
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4190
- [x: string]: any;
4191
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4192
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4193
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
4194
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
4195
- clear(): void;
4196
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
4197
- name: import("mobx-state-tree").ISimpleType<string>;
4198
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4199
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4200
- name: {
4201
- type: string;
4202
- defaultValue: string;
4203
- description: string;
4204
- };
4205
- assemblyNames: {
4206
- type: string;
4207
- defaultValue: never[];
4208
- description: string;
4209
- };
4210
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
4211
- }, {
4212
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4213
- } & {
4214
- afterAttach(): void;
4215
- addTrackConf(trackConf: Record<string, unknown> | ({
4216
- [x: string]: any;
4217
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4218
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4219
- [x: string]: any;
4220
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4221
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4222
- [x: string]: any;
4223
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4224
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4225
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
4226
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
4227
- [x: string]: any;
4228
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4229
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4230
- [x: string]: any;
4231
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4232
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4233
- [x: string]: any;
4234
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4235
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4236
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
4237
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
4238
- clear(): void;
4239
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
4134
+ makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): any;
4240
4135
  prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
4241
4136
  breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4242
4137
  deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
@@ -4251,11 +4146,17 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4251
4146
  removeActiveDialog(): void;
4252
4147
  queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
4253
4148
  } & {
4254
- getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
4149
+ getReferring(object: import("@jbrowse/mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
4255
4150
  } & {
4256
4151
  removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
4257
4152
  } & {
4258
4153
  readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
4154
+ readonly assemblies: {
4155
+ sequence: {
4156
+ trackId: string;
4157
+ };
4158
+ }[];
4159
+ readonly tracksById: Record<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
4259
4160
  } & {
4260
4161
  addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
4261
4162
  deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
@@ -4286,14 +4187,20 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4286
4187
  addView(typeName: string, initialState?: {}): any;
4287
4188
  removeView(): void;
4288
4189
  } & {
4289
- getTrackActionMenuItems(config: any): {
4290
- label: string;
4291
- onClick: () => void;
4292
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
4293
- muiName: string;
4294
- };
4295
- }[];
4296
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
4190
+ getTrackActionMenuItems(config: any, extraTrackActions?: import("@jbrowse/core/ui").MenuItem[]): import("@jbrowse/core/ui").MenuItem[];
4191
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
4192
+ id: string;
4193
+ name: string;
4194
+ margin: number;
4195
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
4196
+ drawerPosition: string;
4197
+ drawerWidth: number;
4198
+ widgets: import("mobx").IKeyValueMap<any>;
4199
+ activeWidgets: import("mobx").IKeyValueMap<import("@jbrowse/mobx-state-tree").ReferenceIdentifier | undefined>;
4200
+ minimized: boolean;
4201
+ } & {
4202
+ connectionInstances: any[];
4203
+ } & import("@jbrowse/mobx-state-tree")._NotCustomized>>): void;
4297
4204
  renameCurrentSession(sessionName: string): void;
4298
4205
  setError(error: unknown): void;
4299
4206
  addInternetAccount(internetAccount: SnapshotIn<any>): void;
@@ -4302,28 +4209,28 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4302
4209
  readonly jbrowse: {
4303
4210
  configuration: {
4304
4211
  [x: string]: any;
4305
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4212
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
4306
4213
  setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4307
4214
  [x: string]: any;
4308
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4215
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
4309
4216
  setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4310
4217
  [x: string]: any;
4311
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4312
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4313
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4314
- rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4218
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4219
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4220
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4221
+ rpc: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4315
4222
  defaultDriver: {
4316
4223
  type: string;
4317
4224
  description: string;
4318
4225
  defaultValue: string;
4319
4226
  };
4320
- drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
4321
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4227
+ drivers: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
4228
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4322
4229
  highResolutionScaling: {
4323
4230
  type: string;
4324
4231
  defaultValue: number;
4325
4232
  };
4326
- formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4233
+ formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4327
4234
  feature: {
4328
4235
  type: string;
4329
4236
  description: string;
@@ -4346,8 +4253,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4346
4253
  defaultValue: number;
4347
4254
  description: string;
4348
4255
  };
4349
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4350
- formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4256
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4257
+ formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4351
4258
  config: {
4352
4259
  type: string;
4353
4260
  description: string;
@@ -4358,9 +4265,9 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4358
4265
  type: string;
4359
4266
  defaultValue: boolean;
4360
4267
  };
4361
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4362
- hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4363
- sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4268
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4269
+ hierarchical: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4270
+ sort: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4364
4271
  trackNames: {
4365
4272
  type: string;
4366
4273
  defaultValue: boolean;
@@ -4369,8 +4276,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4369
4276
  type: string;
4370
4277
  defaultValue: boolean;
4371
4278
  };
4372
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4373
- defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4279
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4280
+ defaultCollapsed: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4374
4281
  categoryNames: {
4375
4282
  type: string;
4376
4283
  defaultValue: never[];
@@ -4383,58 +4290,50 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4383
4290
  type: string;
4384
4291
  defaultValue: boolean;
4385
4292
  };
4386
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4387
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4293
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4294
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4388
4295
  theme: {
4389
4296
  type: string;
4390
4297
  defaultValue: {};
4391
4298
  };
4392
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>>;
4299
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>>;
4393
4300
  assembly: {
4394
4301
  [x: string]: any;
4395
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4302
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
4396
4303
  setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4397
4304
  [x: string]: any;
4398
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4399
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4400
- [x: string]: any;
4401
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4402
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4403
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
4404
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
4405
- internetAccounts: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
4406
- connections: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
4407
- aggregateTextSearchAdapters: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
4305
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4306
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
4307
+ tracks: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IAnyModelType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>>;
4308
+ internetAccounts: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IAnyModelType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>>;
4309
+ connections: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IAnyModelType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>>;
4310
+ aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IAnyModelType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>>;
4408
4311
  plugins: any;
4409
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4312
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
4410
4313
  readonly assemblies: ({
4411
4314
  [x: string]: any;
4412
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4315
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
4413
4316
  setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4414
4317
  [x: string]: any;
4415
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4416
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4417
- [x: string]: any;
4418
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4419
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4420
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
4318
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4319
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
4421
4320
  readonly assemblyName: string;
4422
4321
  readonly rpcManager: any;
4423
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
4424
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4425
- rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4322
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
4323
+ configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4324
+ rpc: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4426
4325
  defaultDriver: {
4427
4326
  type: string;
4428
4327
  description: string;
4429
4328
  defaultValue: string;
4430
4329
  };
4431
- drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
4432
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4330
+ drivers: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
4331
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4433
4332
  highResolutionScaling: {
4434
4333
  type: string;
4435
4334
  defaultValue: number;
4436
4335
  };
4437
- formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4336
+ formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4438
4337
  feature: {
4439
4338
  type: string;
4440
4339
  description: string;
@@ -4457,8 +4356,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4457
4356
  defaultValue: number;
4458
4357
  description: string;
4459
4358
  };
4460
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4461
- formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4359
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4360
+ formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4462
4361
  config: {
4463
4362
  type: string;
4464
4363
  description: string;
@@ -4469,9 +4368,9 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4469
4368
  type: string;
4470
4369
  defaultValue: boolean;
4471
4370
  };
4472
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4473
- hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4474
- sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4371
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4372
+ hierarchical: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4373
+ sort: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4475
4374
  trackNames: {
4476
4375
  type: string;
4477
4376
  defaultValue: boolean;
@@ -4480,8 +4379,8 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4480
4379
  type: string;
4481
4380
  defaultValue: boolean;
4482
4381
  };
4483
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4484
- defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4382
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4383
+ defaultCollapsed: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
4485
4384
  categoryNames: {
4486
4385
  type: string;
4487
4386
  defaultValue: never[];
@@ -4494,36 +4393,32 @@ export default function createModel(runtimePlugins: PluginConstructor[], makeWor
4494
4393
  type: string;
4495
4394
  defaultValue: boolean;
4496
4395
  };
4497
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4498
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4396
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4397
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4499
4398
  theme: {
4500
4399
  type: string;
4501
4400
  defaultValue: {};
4502
4401
  };
4503
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4402
+ }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
4504
4403
  assembly: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
4505
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4506
- internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4507
- connections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4508
- aggregateTextSearchAdapters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4509
- plugins: import("mobx-state-tree").IType<any, any, any>;
4404
+ tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
4405
+ internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
4406
+ connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
4407
+ aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
4408
+ plugins: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
4510
4409
  }, {
4511
4410
  readonly assemblies: ({
4512
4411
  [x: string]: any;
4513
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4412
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
4514
4413
  setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4515
4414
  [x: string]: any;
4516
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4517
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4518
- [x: string]: any;
4519
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4520
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4521
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
4415
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4416
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
4522
4417
  readonly assemblyName: string;
4523
4418
  readonly rpcManager: any;
4524
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
4419
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
4525
4420
  readonly pluginManager: PluginManager;
4526
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
4421
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
4527
4422
  pluginManager: PluginManager;
4528
4423
  };
4529
4424
  export type ViewStateModel = ReturnType<typeof createModel>['model'];