@jbrowse/plugin-linear-genome-view 1.5.7 → 1.6.1

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -1,10 +1,11 @@
+import React from 'react';
 import { MenuItem } from '@jbrowse/core/ui';
+import { Stats } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { BaseBlock } from '@jbrowse/core/util/blockTypes';
 import { Region } from '@jbrowse/core/util/types';
 import CompositeMap from '@jbrowse/core/util/compositeMap';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { Instance } from 'mobx-state-tree';
-import React from 'react';
 import { ExportSvgOptions } from '../../LinearGenomeView';
 export interface Layout {
     minX: number;
@@ -53,27 +54,24 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void; /**
-         * returns a string feature ID if the globally-selected object
-         * is probably a feature
-         */
+        setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: React.ReactElement<any, string | ((props: any) => React.ReactElement<any, any> | null) | (new (props: any) => React.Component<any, any, any>)>;
             features: Map<string, Feature>;
             layout: any;
-            /**
-             * a CompositeMap of `featureId -> feature obj` that
-             * just looks in all the block data for that feature
-             */
             maxHeightReached: boolean;
             renderProps: any;
-        } | undefined): void;
+        } | undefined): void; /**
+         * a CompositeMap of `featureId -> feature obj` that
+         * just looks in all the block data for that feature
+         */
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
     }, 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>>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -127,18 +125,17 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
+    currBpPerPx: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
     scrollTop: number;
+    estimatedRegionStatsP: Promise<Stats> | undefined;
+    estimatedRegionStats: Stats | undefined;
 } & {
     readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
-    /**
-     * set limit to config amount, or user amount if they force load,
-     */
-    readonly maxViewBpPerPx: any;
     /**
      * how many milliseconds to wait for the display to
      * "settle" before re-rendering a block
@@ -165,14 +162,28 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     getFeatureOverlapping(blockKey: string, x: number, y: number): any;
     getFeatureByID(blockKey: string, id: string): LayoutRecord | undefined;
     searchFeatureByID(id: string): LayoutRecord | undefined;
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly estimatedStatsReady: boolean;
+    readonly maxAllowableBytes: number;
 } & {
+    setMessage(message: string): void;
     afterAttach(): void;
+    estimateRegionsStats(regions: Region[], opts: {
+        headers?: Record<string, string>;
+        signal?: AbortSignal;
+        filters?: string[];
+    }): Promise<Stats>;
+    setRegionStatsP(p?: Promise<Stats> | undefined): void;
+    setRegionStats(estimatedRegionStats?: Stats | undefined): void;
+    clearRegionStats(): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    setUserBpPerPxLimit(limit: number): void;
-    setMessage(message: string): void;
+    updateStatsLimit(stats: Stats): void;
     addBlock(key: string, block: BaseBlock): void;
+    setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
@@ -180,7 +191,13 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
 } & {
-    regionCannotBeRenderedText(_region: Region): "" | "Zoom in to see features";
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    reload(): Promise<void>;
+    afterAttach(): void;
+} & {
+    regionCannotBeRenderedText(_region: Region): "" | "Force load to see features";
     /**
      * @param region -
      * @returns falsy if the region is fine to try rendering. Otherwise,
@@ -206,6 +223,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     rpcDriverName: string | undefined;
     height: number;
     userBpPerPxLimit: number | undefined;
+    userByteSizeLimit: number | undefined;
 }>;
 export declare type BaseLinearDisplayStateModel = typeof BaseLinearDisplay;
 export declare type BaseLinearDisplayModel = Instance<BaseLinearDisplayStateModel>;

package/dist/LinearBareDisplay/model.d.ts

@@ -53,6 +53,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         beforeDestroy(): void;
     }, 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>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearBareDisplay">;
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
@@ -109,15 +110,17 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
+    currBpPerPx: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util/simpleFeature").Feature | undefined;
     scrollTop: number;
+    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
     readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
-    readonly maxViewBpPerPx: any;
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
@@ -128,14 +131,28 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     getFeatureOverlapping(blockKey: string, x: number, y: number): any;
     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 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<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    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;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    setUserBpPerPxLimit(limit: number): void;
-    setMessage(message: string): void;
+    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): 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/simpleFeature").Feature): void;
     clearFeatureSelection(): void;
@@ -143,7 +160,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     reload(): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util/simpleFeature").Feature | undefined): void;
 } & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Zoom in to see features";
+    readonly regionTooLarge: boolean;
+    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 | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
@@ -165,4 +188,5 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     rpcDriverName: string | undefined;
     height: number;
     userBpPerPxLimit: number | undefined;
+    userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;

package/dist/LinearBasicDisplay/model.d.ts

@@ -55,6 +55,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
         beforeDestroy(): void;
     }, 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>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
     trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
@@ -115,15 +116,17 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
+    currBpPerPx: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util/simpleFeature").Feature | undefined;
     scrollTop: number;
+    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
     readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
-    readonly maxViewBpPerPx: any;
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
@@ -134,14 +137,28 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     getFeatureOverlapping(blockKey: string, x: number, y: number): any;
     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 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<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    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;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    setUserBpPerPxLimit(limit: number): void;
-    setMessage(message: string): void;
+    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): 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/simpleFeature").Feature): void;
     clearFeatureSelection(): void;
@@ -149,7 +166,13 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     reload(): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util/simpleFeature").Feature | undefined): void;
 } & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Zoom in to see features";
+    readonly regionTooLarge: boolean;
+    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 | undefined;
     trackMenuItems(): MenuItem[];
     contextMenuItems(): {
@@ -183,6 +206,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     rpcDriverName: string | undefined;
     height: number;
     userBpPerPxLimit: number | undefined;
+    userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;
 export declare type FeatureTrackStateModel = ReturnType<typeof stateModelFactory>;
 export declare type FeatureTrackModel = Instance<FeatureTrackStateModel>;

package/dist/LinearGenomeView/components/Header.d.ts

@@ -1,6 +1,7 @@
 /// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
+declare type LGV = LinearGenomeViewModel;
 declare const LinearGenomeViewHeader: ({ model }: {
-    model: LinearGenomeViewModel;
+    model: LGV;
 }) => JSX.Element;
 export default LinearGenomeViewHeader;

package/dist/LinearGenomeView/components/RefNameAutocomplete.d.ts

@@ -6,7 +6,7 @@ export interface Option {
     group?: string;
     result: BaseResult;
 }
-declare function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, value, minWidth, TextFieldProps, }: {
+declare function RefNameAutocomplete({ model, showHelp, onSelect, assemblyName, style, fetchResults, value, minWidth, TextFieldProps, }: {
     model: LinearGenomeViewModel;
     onSelect: (region: BaseResult) => void;
     assemblyName?: string;
@@ -14,6 +14,7 @@ declare function RefNameAutocomplete({ model, onSelect, assemblyName, style, fet
     fetchResults: (query: string) => Promise<BaseResult[]>;
     style?: React.CSSProperties;
     minWidth?: number;
+    showHelp?: boolean;
     TextFieldProps?: TFP;
 }): JSX.Element;
 declare const _default: typeof RefNameAutocomplete;

package/dist/LinearGenomeView/components/ScaleBar.d.ts

@@ -22,9 +22,9 @@ declare const _default: React.ForwardRefExoticComponent<{
         hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<"hierarchical">, [undefined]>;
-        trackLabels: import("mobx-state-tree").IType<string | undefined, string, string>;
-        showCenterLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        showCytobandsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }> & {
         width: number;
     } & {
@@ -130,7 +130,7 @@ declare const _default: React.ForwardRefExoticComponent<{
         moveTrack(movingTrackId: string, targetTrackId: string): void;
         closeView(): void;
         toggleTrack(trackId: string): void;
-        setTrackLabels(setting: "overlapping" | "hidden" | "offset"): void;
+        setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
         toggleCenterLine(): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
         activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -218,9 +218,9 @@ declare const _default: React.ForwardRefExoticComponent<{
         hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<"hierarchical">, [undefined]>;
-        trackLabels: import("mobx-state-tree").IType<string | undefined, string, string>;
-        showCenterLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        showCytobandsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
         width: number;
     } & {
@@ -326,7 +326,7 @@ declare const _default: React.ForwardRefExoticComponent<{
         moveTrack(movingTrackId: string, targetTrackId: string): void;
         closeView(): void;
         toggleTrack(trackId: string): void;
-        setTrackLabels(setting: "overlapping" | "hidden" | "offset"): void;
+        setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
         toggleCenterLine(): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
         activateTrackSelector(): import("@jbrowse/core/util").Widget;

package/dist/LinearGenomeView/components/SearchBox.d.ts

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+import { LinearGenomeViewModel } from '..';
+declare function SearchBox({ model, showHelp, }: {
+    showHelp?: boolean;
+    model: LinearGenomeViewModel;
+}): JSX.Element;
+declare const _default: typeof SearchBox;
+export default _default;

package/dist/LinearGenomeView/index.d.ts

@@ -6,6 +6,7 @@ import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { renderToSvg } from './components/LinearGenomeViewSvg';
 import RefNameAutocomplete from './components/RefNameAutocomplete';
+import SearchBox from './components/SearchBox';
 export interface BpOffset {
     refName?: string;
     index: number;
@@ -31,6 +32,8 @@ export declare const HEADER_OVERVIEW_HEIGHT = 20;
 export declare const SCALE_BAR_HEIGHT = 17;
 export declare const RESIZE_HANDLE_HEIGHT = 3;
 export declare const INTER_REGION_PADDING_WIDTH = 2;
+export declare const WIDGET_HEIGHT = 32;
+export declare const SPACING = 7;
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -53,9 +56,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<"hierarchical">, [undefined]>;
-    trackLabels: import("mobx-state-tree").IType<string | undefined, string, string>;
-    showCenterLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    showCytobandsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
     width: number;
 } & {
@@ -282,7 +285,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     rubberBandMenuItems(): MenuItem[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export { renderToSvg, RefNameAutocomplete };
+export { renderToSvg, RefNameAutocomplete, SearchBox };
 export declare type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export declare type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
 export { default as ReactComponent } from './components/LinearGenomeView';