@jbrowse/plugin-linear-genome-view 2.4.2 → 2.5.0

package/esm/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;
-                estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-                estimatedRegionsStats: 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";
@@ -181,26 +208,26 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 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(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-                setRegionsStatsP(arg: any): void;
-                setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-                clearRegionsStats(): 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 | undefined): 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;
             } & {
@@ -275,6 +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;
@@ -333,8 +383,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 message: string;
                 featureIdUnderMouse: string | undefined;
                 contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-                estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-                estimatedRegionsStats: 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";
@@ -353,26 +403,26 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 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(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-                setRegionsStatsP(arg: any): void;
-                setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-                clearRegionsStats(): 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 | undefined): 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;
             } & {
@@ -447,9 +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;
@@ -511,6 +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;
@@ -569,8 +666,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
             message: string;
             featureIdUnderMouse: string | undefined;
             contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-            estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-            estimatedRegionsStats: 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";
@@ -589,26 +686,26 @@ export default class LinearGenomeViewPlugin extends Plugin {
             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(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-            setRegionsStatsP(arg: any): void;
-            setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-            clearRegionsStats(): 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 | undefined): 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;
         } & {
@@ -683,15 +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: {
@@ -751,9 +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;
@@ -765,7 +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;
@@ -799,8 +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;
@@ -857,7 +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;
             } & {
@@ -943,9 +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;
@@ -957,7 +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;
@@ -991,8 +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;
@@ -1049,7 +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;
             } & {
@@ -1145,9 +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;
@@ -1159,7 +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;
@@ -1193,8 +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;
@@ -1251,7 +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;
             } & {
@@ -1337,9 +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;
@@ -1351,7 +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;
@@ -1385,8 +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;
@@ -1443,7 +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;
             } & {
@@ -1539,9 +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;
@@ -1553,7 +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;
@@ -1587,8 +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;
@@ -1645,7 +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;
             } & {
@@ -1731,9 +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;
@@ -1745,7 +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;
@@ -1779,8 +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;
@@ -1837,7 +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;
             } & {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.4.2",
+  "version": "2.5.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -49,7 +49,7 @@
     "file-saver": "^2.0.0",
     "material-ui-popup-state": "^5.0.0",
     "normalize-wheel": "^1.0.1",
-    "react-error-boundary": "^3.0.0",
+    "react-error-boundary": "^4.0.3",
     "react-popper": "^2.0.0"
   },
   "peerDependencies": {
@@ -66,5 +66,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
+  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
 }

package/src/BaseLinearDisplay/components/TooLargeMessage.tsx

@@ -1,5 +1,5 @@
 import React from 'react'
-import { Stats } from '@jbrowse/core/data_adapters/BaseAdapter'
+import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter'
 
 // locals
 import BlockMsg from '../components/BlockMsg'
@@ -9,8 +9,8 @@ function TooLargeMessage({
 }: {
   model: {
     regionTooLargeReason: string
-    estimatedRegionsStats?: Stats
-    updateStatsLimit: (s?: Stats) => void
+    featureDensityStats?: FeatureDensityStats
+    setFeatureDensityStatsLimit: (s?: FeatureDensityStats) => void
     reload: () => void
   }
 }) {
@@ -19,12 +19,16 @@ function TooLargeMessage({
     <BlockMsg
       severity="warning"
       action={() => {
-        model.updateStatsLimit(model.estimatedRegionsStats)
+        model.setFeatureDensityStatsLimit(model.featureDensityStats)
         model.reload()
       }}
       buttonText="Force load"
-      message={`${regionTooLargeReason ? `${regionTooLargeReason}. ` : ''}
-      Zoom in to see features or force load (may be slow).`}
+      message={[
+        regionTooLargeReason,
+        'Zoom in to see features or force load (may be slow)',
+      ]
+        .filter(f => !!f)
+        .join('. ')}
     />
   )
 }