@jbrowse/plugin-linear-genome-view 2.4.1 → 2.5.0

package/dist/index.d.ts

@@ -103,6 +103,33 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
                 userBpPerPxLimit: number | undefined;
                 userByteSizeLimit: number | undefined;
+                configuration: {
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    setSubschema(slotName: string, data: unknown): any;
+                } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                    maxFeatureScreenDensity: {
+                        type: string;
+                        description: string;
+                        defaultValue: number;
+                    };
+                    fetchSizeLimit: {
+                        type: string;
+                        defaultValue: number;
+                        description: string;
+                    };
+                    height: {
+                        type: string;
+                        defaultValue: number;
+                        description: string;
+                    };
+                    mouseover: {
+                        type: string;
+                        description: string;
+                        defaultValue: string;
+                        contextVariable: string[];
+                    };
+                }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 rendererTypeName: string;
                 error: unknown;
@@ -161,8 +188,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 message: string;
                 featureIdUnderMouse: string | undefined;
                 contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-                estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-                estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+                featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+                featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
             } & {
                 readonly height: number;
                 readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -175,35 +202,32 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
                 readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
-                getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+                getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
                 getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
                 searchFeatureByID(id: string): [number, number, number, number] | undefined;
                 readonly currentBytesRequested: number;
                 readonly currentFeatureScreenDensity: number;
                 readonly maxFeatureScreenDensity: any;
-                readonly estimatedStatsReady: boolean;
+                readonly featureDensityStatsReady: boolean;
                 readonly maxAllowableBytes: number;
             } & {
                 setMessage(message: string): void;
+            } & {
                 afterAttach(): void;
-                estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-                    headers?: Record<string, string> | undefined;
-                    signal?: AbortSignal | undefined;
-                    filters?: string[] | undefined;
-                }): Promise<{}>;
-                setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-                setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-                clearRegionStats(): void;
+                getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+                setFeatureDensityStatsP(arg: any): void;
+                setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+                clearFeatureDensityStats(): void;
                 setHeight(displayHeight: number): number;
                 resizeHeight(distance: number): number;
                 setScrollTop(scrollTop: number): void;
-                updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+                setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
                 addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
                 setCurrBpPerPx(n: number): void;
                 deleteBlock(key: string): void;
                 selectFeature(feature: import("@jbrowse/core/util").Feature): void;
                 clearFeatureSelection(): void;
-                setFeatureIdUnderMouse(feature: string | undefined): void;
+                setFeatureIdUnderMouse(feature?: string | undefined): void;
                 reload(): void;
                 setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
             } & {
@@ -211,18 +235,13 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly regionTooLargeReason: string;
             } & {
                 reload(): Promise<void>;
+            } & {
                 afterAttach(): void;
             } & {
                 regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
                 regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
                 trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-                contextMenuItems(): {
-                    label: string;
-                    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-                        muiName: string;
-                    };
-                    onClick: () => void;
-                }[];
+                contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
                 renderProps(): any;
             } & {
                 renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
@@ -283,6 +302,29 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
                 userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
                 userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+                configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                    maxFeatureScreenDensity: {
+                        type: string;
+                        description: string;
+                        defaultValue: number;
+                    };
+                    fetchSizeLimit: {
+                        type: string;
+                        defaultValue: number;
+                        description: string;
+                    };
+                    height: {
+                        type: string;
+                        defaultValue: number;
+                        description: string;
+                    };
+                    mouseover: {
+                        type: string;
+                        description: string;
+                        defaultValue: string;
+                        contextVariable: string[];
+                    };
+                }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             }, {
                 rendererTypeName: string;
                 error: unknown;
@@ -341,8 +383,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 message: string;
                 featureIdUnderMouse: string | undefined;
                 contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-                estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-                estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+                featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+                featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
             } & {
                 readonly height: number;
                 readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -355,35 +397,32 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
                 readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
-                getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+                getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
                 getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
                 searchFeatureByID(id: string): [number, number, number, number] | undefined;
                 readonly currentBytesRequested: number;
                 readonly currentFeatureScreenDensity: number;
                 readonly maxFeatureScreenDensity: any;
-                readonly estimatedStatsReady: boolean;
+                readonly featureDensityStatsReady: boolean;
                 readonly maxAllowableBytes: number;
             } & {
                 setMessage(message: string): void;
+            } & {
                 afterAttach(): void;
-                estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-                    headers?: Record<string, string> | undefined;
-                    signal?: AbortSignal | undefined;
-                    filters?: string[] | undefined;
-                }): Promise<{}>;
-                setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-                setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-                clearRegionStats(): void;
+                getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+                setFeatureDensityStatsP(arg: any): void;
+                setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+                clearFeatureDensityStats(): void;
                 setHeight(displayHeight: number): number;
                 resizeHeight(distance: number): number;
                 setScrollTop(scrollTop: number): void;
-                updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+                setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
                 addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
                 setCurrBpPerPx(n: number): void;
                 deleteBlock(key: string): void;
                 selectFeature(feature: import("@jbrowse/core/util").Feature): void;
                 clearFeatureSelection(): void;
-                setFeatureIdUnderMouse(feature: string | undefined): void;
+                setFeatureIdUnderMouse(feature?: string | undefined): void;
                 reload(): void;
                 setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
             } & {
@@ -391,18 +430,13 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly regionTooLargeReason: string;
             } & {
                 reload(): Promise<void>;
+            } & {
                 afterAttach(): void;
             } & {
                 regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
                 regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
                 trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-                contextMenuItems(): {
-                    label: string;
-                    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-                        muiName: string;
-                    };
-                    onClick: () => void;
-                }[];
+                contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
                 renderProps(): any;
             } & {
                 renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
@@ -463,9 +497,33 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
                 userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
                 userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+                configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                    maxFeatureScreenDensity: {
+                        type: string;
+                        description: string;
+                        defaultValue: number;
+                    };
+                    fetchSizeLimit: {
+                        type: string;
+                        defaultValue: number;
+                        description: string;
+                    };
+                    height: {
+                        type: string;
+                        defaultValue: number;
+                        description: string;
+                    };
+                    mouseover: {
+                        type: string;
+                        description: string;
+                        defaultValue: string;
+                        contextVariable: string[];
+                    };
+                }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             }>>, {
                 type: string;
                 id: string;
+                configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
                 rpcDriverName: string | undefined;
                 heightPreConfig: number | undefined;
                 userBpPerPxLimit: number | undefined;
@@ -527,6 +585,29 @@ export default class LinearGenomeViewPlugin extends Plugin {
             }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
             userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
             userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+            configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                maxFeatureScreenDensity: {
+                    type: string;
+                    description: string;
+                    defaultValue: number;
+                };
+                fetchSizeLimit: {
+                    type: string;
+                    defaultValue: number;
+                    description: string;
+                };
+                height: {
+                    type: string;
+                    defaultValue: number;
+                    description: string;
+                };
+                mouseover: {
+                    type: string;
+                    description: string;
+                    defaultValue: string;
+                    contextVariable: string[];
+                };
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
         }, {
             rendererTypeName: string;
             error: unknown;
@@ -585,8 +666,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
             message: string;
             featureIdUnderMouse: string | undefined;
             contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-            estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-            estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+            featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+            featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
         } & {
             readonly height: number;
             readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -599,35 +680,32 @@ export default class LinearGenomeViewPlugin extends Plugin {
         } & {
             readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
             readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
-            getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+            getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
             getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
             searchFeatureByID(id: string): [number, number, number, number] | undefined;
             readonly currentBytesRequested: number;
             readonly currentFeatureScreenDensity: number;
             readonly maxFeatureScreenDensity: any;
-            readonly estimatedStatsReady: boolean;
+            readonly featureDensityStatsReady: boolean;
             readonly maxAllowableBytes: number;
         } & {
             setMessage(message: string): void;
+        } & {
             afterAttach(): void;
-            estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-                headers?: Record<string, string> | undefined;
-                signal?: AbortSignal | undefined;
-                filters?: string[] | undefined;
-            }): Promise<{}>;
-            setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-            setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-            clearRegionStats(): void;
+            getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+            setFeatureDensityStatsP(arg: any): void;
+            setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+            clearFeatureDensityStats(): void;
             setHeight(displayHeight: number): number;
             resizeHeight(distance: number): number;
             setScrollTop(scrollTop: number): void;
-            updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+            setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
             addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
             setCurrBpPerPx(n: number): void;
             deleteBlock(key: string): void;
             selectFeature(feature: import("@jbrowse/core/util").Feature): void;
             clearFeatureSelection(): void;
-            setFeatureIdUnderMouse(feature: string | undefined): void;
+            setFeatureIdUnderMouse(feature?: string | undefined): void;
             reload(): void;
             setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
         } & {
@@ -635,18 +713,13 @@ export default class LinearGenomeViewPlugin extends Plugin {
             readonly regionTooLargeReason: string;
         } & {
             reload(): Promise<void>;
+        } & {
             afterAttach(): void;
         } & {
             regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
             regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            contextMenuItems(): {
-                label: string;
-                icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-                    muiName: string;
-                };
-                onClick: () => void;
-            }[];
+            contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
             renderProps(): any;
         } & {
             renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
@@ -707,15 +780,61 @@ export default class LinearGenomeViewPlugin extends Plugin {
             }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
             userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
             userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+            configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                maxFeatureScreenDensity: {
+                    type: string;
+                    description: string;
+                    defaultValue: number;
+                };
+                fetchSizeLimit: {
+                    type: string;
+                    defaultValue: number;
+                    description: string;
+                };
+                height: {
+                    type: string;
+                    defaultValue: number;
+                    description: string;
+                };
+                mouseover: {
+                    type: string;
+                    description: string;
+                    defaultValue: string;
+                    contextVariable: string[];
+                };
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
         }>>, {
             type: string;
             id: string;
+            configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
             rpcDriverName: string | undefined;
             heightPreConfig: number | undefined;
             userBpPerPxLimit: number | undefined;
             userByteSizeLimit: number | undefined;
         }>;
-        baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            maxFeatureScreenDensity: {
+                type: string;
+                description: string;
+                defaultValue: number;
+            };
+            fetchSizeLimit: {
+                type: string;
+                defaultValue: number;
+                description: string;
+            };
+            height: {
+                type: string;
+                defaultValue: number;
+                description: string;
+            };
+            mouseover: {
+                type: string;
+                description: string;
+                defaultValue: string;
+                contextVariable: string[];
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
         SearchBox: ({ model, showHelp, }: {
             showHelp?: boolean | undefined;
             model: {
@@ -775,9 +894,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 coarseTotalBp: number;
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
-                searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined;
-                searchQuery: string | undefined;
-                seqDialogDisplayed: boolean;
             } & {
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
@@ -789,7 +905,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly assembliesInitialized: boolean;
                 readonly initialized: boolean;
                 readonly hasDisplayedRegions: boolean;
-                readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
                 readonly trackHeights: number;
@@ -823,8 +938,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
-                setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
-                setGetSequenceDialogOpen(open: boolean): void;
+                setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
                 setNewView(bpPerPx: number, offsetPx: number): void;
                 horizontallyFlip(): void;
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
@@ -881,7 +995,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 afterAttach(): void;
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
-                navToLocString(locString: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
             } & {
@@ -967,9 +1082,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 coarseTotalBp: number;
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
-                searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined;
-                searchQuery: string | undefined;
-                seqDialogDisplayed: boolean;
             } & {
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
@@ -981,7 +1093,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly assembliesInitialized: boolean;
                 readonly initialized: boolean;
                 readonly hasDisplayedRegions: boolean;
-                readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
                 readonly trackHeights: number;
@@ -1015,8 +1126,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
-                setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
-                setGetSequenceDialogOpen(open: boolean): void;
+                setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
                 setNewView(bpPerPx: number, offsetPx: number): void;
                 horizontallyFlip(): void;
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
@@ -1073,7 +1183,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 afterAttach(): void;
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
-                navToLocString(locString: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
             } & {
@@ -1169,9 +1280,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 coarseTotalBp: number;
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
-                searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined;
-                searchQuery: string | undefined;
-                seqDialogDisplayed: boolean;
             } & {
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
@@ -1183,7 +1291,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly assembliesInitialized: boolean;
                 readonly initialized: boolean;
                 readonly hasDisplayedRegions: boolean;
-                readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
                 readonly trackHeights: number;
@@ -1217,8 +1324,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
-                setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
-                setGetSequenceDialogOpen(open: boolean): void;
+                setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
                 setNewView(bpPerPx: number, offsetPx: number): void;
                 horizontallyFlip(): void;
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
@@ -1275,7 +1381,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 afterAttach(): void;
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
-                navToLocString(locString: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
             } & {
@@ -1361,9 +1468,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 coarseTotalBp: number;
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
-                searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined;
-                searchQuery: string | undefined;
-                seqDialogDisplayed: boolean;
             } & {
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
@@ -1375,7 +1479,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly assembliesInitialized: boolean;
                 readonly initialized: boolean;
                 readonly hasDisplayedRegions: boolean;
-                readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
                 readonly trackHeights: number;
@@ -1409,8 +1512,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
-                setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
-                setGetSequenceDialogOpen(open: boolean): void;
+                setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
                 setNewView(bpPerPx: number, offsetPx: number): void;
                 horizontallyFlip(): void;
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
@@ -1467,7 +1569,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 afterAttach(): void;
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
-                navToLocString(locString: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
             } & {
@@ -1563,9 +1666,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 coarseTotalBp: number;
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
-                searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined;
-                searchQuery: string | undefined;
-                seqDialogDisplayed: boolean;
             } & {
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
@@ -1577,7 +1677,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly assembliesInitialized: boolean;
                 readonly initialized: boolean;
                 readonly hasDisplayedRegions: boolean;
-                readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
                 readonly trackHeights: number;
@@ -1611,8 +1710,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
-                setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
-                setGetSequenceDialogOpen(open: boolean): void;
+                setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
                 setNewView(bpPerPx: number, offsetPx: number): void;
                 horizontallyFlip(): void;
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
@@ -1669,7 +1767,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 afterAttach(): void;
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
-                navToLocString(locString: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
             } & {
@@ -1755,9 +1854,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 coarseTotalBp: number;
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
-                searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined;
-                searchQuery: string | undefined;
-                seqDialogDisplayed: boolean;
             } & {
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
@@ -1769,7 +1865,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly assembliesInitialized: boolean;
                 readonly initialized: boolean;
                 readonly hasDisplayedRegions: boolean;
-                readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
                 readonly trackHeights: number;
@@ -1803,8 +1898,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
-                setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
-                setGetSequenceDialogOpen(open: boolean): void;
+                setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
                 setNewView(bpPerPx: number, offsetPx: number): void;
                 horizontallyFlip(): void;
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
@@ -1861,7 +1955,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 afterAttach(): void;
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
-                navToLocString(locString: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
             } & {