@jbrowse/plugin-linear-comparative-view 2.12.0 → 2.12.1

package/esm/LinearComparativeView/model.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Instance, SnapshotIn } from 'mobx-state-tree';
 import { MenuItem } from '@jbrowse/core/ui';
 import PluginManager from '@jbrowse/core/PluginManager';
@@ -52,15 +51,15 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     } & {
         volatileWidth: number | undefined;
         minimumBlockWidth: number;
-        draggingTrackId: string | undefined;
+        draggingTrackId: undefined | string;
         volatileError: unknown;
         afterDisplayedRegionsSetCallbacks: Function[];
         scaleFactor: number;
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
-        leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
-        rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
+        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
+        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
     } & {
         readonly trackLabelsSetting: any;
         readonly width: number;
@@ -109,8 +108,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
-        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
-        setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
+        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
         showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
@@ -123,30 +122,30 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         moveTrack(movingId: string, targetId: string): void;
         closeView(): void;
         toggleTrack(trackId: string): boolean;
-        setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+        setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
         setShowCenterLine(b: boolean): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
         activateTrackSelector(): import("@jbrowse/core/util").Widget;
-        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
+        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
             start: number;
             end: number;
             type: string;
-            regionNumber?: number | undefined;
-            reversed?: boolean | undefined;
+            regionNumber?: number;
+            reversed?: boolean;
             refName: string;
             assemblyName: string;
             key: string;
             offsetPx: number;
             widthPx: number;
-            variant?: string | undefined;
-            isLeftEndOfDisplayedRegion?: boolean | undefined;
+            variant?: string;
+            isLeftEndOfDisplayedRegion?: boolean;
         }[];
         afterDisplayedRegionsSet(cb: Function): void;
         horizontalScroll(distance: number): number;
         center(): void;
         showAllRegions(): void;
-        showAllRegionsInAssembly(assemblyName?: string | undefined): void;
-        setDraggingTrackId(idx?: string | undefined): void;
+        showAllRegionsInAssembly(assemblyName?: string): void;
+        setDraggingTrackId(idx?: string): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
         exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
@@ -171,141 +170,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
         afterAttach(): void;
     } & {
-        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
-        navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        navToLocString(input: string, optAssemblyName?: string): Promise<void>;
         navToSearchString({ input, assembly, }: {
             input: string;
-            assembly: {
-                configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined; /**
-                 * #property
-                 */
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-            }, {
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined; /**
-                 * #property
-                 */
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
         }): Promise<void>;
-        navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
+        navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
         navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
         navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
     } & {
@@ -313,12 +184,12 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         bpToPx({ refName, coord, regionNumber, }: {
             refName: string;
             coord: number;
-            regionNumber?: number | undefined;
+            regionNumber?: number;
         }): {
             index: number;
             offsetPx: number;
         } | undefined;
-        centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
+        centerAt(coord: number, refName: string, regionNumber?: number): void;
         pxToBp(px: number): {
             coord: number;
             index: number;
@@ -328,7 +199,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             offset: number;
             start: number;
             end: number;
-            reversed?: boolean | undefined;
+            reversed?: boolean;
         };
         readonly centerLineInfo: {
             coord: number;
@@ -339,7 +210,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             offset: number;
             start: number;
             end: number;
-            reversed?: boolean | undefined;
+            reversed?: boolean;
         } | undefined;
     } & {
         afterCreate(): void;

package/esm/LinearSyntenyDisplay/model.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
@@ -58,8 +57,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -82,19 +81,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
-    renderProps(): any; /**
-     * #getter
-     */
+    renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
-     * #getter
-     * used for synteny svg rendering
-     */
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -112,7 +106,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             configuration: {
                 [x: string]: any;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: unknown): any;
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                        [x: string]: any;
+                    } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+                } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
             } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
             height: number;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -138,8 +138,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-                onHorizontalScroll?: Function | undefined;
-                blockState?: Record<string, any> | undefined;
+                onHorizontalScroll?: Function;
+                blockState?: Record<string, any>;
             }>;
             readonly DisplayBlurb: import("react").FC<{
                 model: {
@@ -162,19 +162,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: any;
-            renderProps(): any; /**
-             * #getter
-             */
+            renderProps(): any;
             readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            readonly DisplayMessageComponent: undefined | import("react").FC<any>;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
-             * #getter
-             * used for synteny svg rendering
-             */
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
             regionCannotBeRendered(): null;
         } & {
-            setMessage(arg?: string | undefined): void;
+            setMessage(arg?: string): void;
             setError(error?: unknown): void;
             setRpcDriverName(rpcDriverName: string): void;
             reload(): void;
@@ -213,8 +208,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-                onHorizontalScroll?: Function | undefined;
-                blockState?: Record<string, any> | undefined;
+                onHorizontalScroll?: Function;
+                blockState?: Record<string, any>;
             }>;
             readonly DisplayBlurb: import("react").FC<{
                 model: {
@@ -237,19 +232,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: any;
-            renderProps(): any; /**
-             * #getter
-             */
+            renderProps(): any;
             readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            readonly DisplayMessageComponent: undefined | import("react").FC<any>;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
-             * #getter
-             * used for synteny svg rendering
-             */
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
             regionCannotBeRendered(): null;
         } & {
-            setMessage(arg?: string | undefined): void;
+            setMessage(arg?: string): void;
             setError(error?: unknown): void;
             setRpcDriverName(rpcDriverName: string): void;
             reload(): void;
@@ -265,7 +255,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setMessage(messageText: string): void;
     setRendered(args?: {
         features: Feature[];
-    } | undefined): void;
+    }): void;
     setError(error: unknown): void;
 } & {
     afterAttach(): void;