@jbrowse/plugin-gccontent 2.17.0 → 3.0.0

package/dist/LinearGCContentDisplay/shared.js

@@ -15,37 +15,35 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SharedModelF;
+const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
 const mobx_state_tree_1 = require("mobx-state-tree");
-const react_1 = require("react");
 const EditGCContentParamsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/EditGCContentParams'))));
-/**
- * #stateModel SharedGCContentModel
- * #category display
- * extends
- * - [LinearWiggleDisplay](../linearwiggledisplay)
- */
 function SharedModelF(pluginManager, configSchema) {
     return mobx_state_tree_1.types
         .compose('SharedGCContentModel', (0, plugin_wiggle_1.linearWiggleDisplayModelFactory)(pluginManager, configSchema), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         windowSize: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        /**
-         * #property
-         */
         windowDelta: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
     }))
         .actions(self => ({
@@ -65,7 +63,7 @@ function SharedModelF(pluginManager, configSchema) {
         },
     }))
         .views(self => {
-        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
+        const { trackMenuItems: superTrackMenuItems, adapterProps: superAdapterProps, } = self;
         return {
             trackMenuItems() {
                 return [
@@ -81,15 +79,10 @@ function SharedModelF(pluginManager, configSchema) {
                     },
                 ];
             },
-            /**
-             * #method
-             * retrieves the sequence adapter from parent track, and puts it as a
-             * subadapter on a GCContentAdapter
-             */
-            renderProps() {
+            adapterProps() {
                 const sequenceAdapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
                 return {
-                    ...superRenderProps(),
+                    ...superAdapterProps(),
                     adapterConfig: {
                         type: 'GCContentAdapter',
                         sequenceAdapter,

package/dist/LinearGCContentDisplay/stateModel1.d.ts

@@ -1,10 +1,5 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #stateModel LinearGCContentDisplay
- * #category display
- * base model `SharedGCContentModel`
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export default function stateModelF(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -17,21 +12,12 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -49,21 +35,15 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -210,14 +190,15 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -244,7 +225,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     message: undefined | string;
@@ -253,7 +234,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: undefined | AbortController;
+    statsFetchInProgress: undefined | string;
 } & {
     updateQuantitativeStats(stats: {
         currStatsBpPerPx: number;
@@ -263,7 +244,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setStatsLoading(aborter: AbortController): void;
+    setStatsLoading(arg?: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -360,7 +341,17 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly quantitativeStatsReady: boolean;
 } & {
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        type: string;
+        label?: undefined;
+        icon?: undefined;
+        subMenu?: undefined;
+        onClick?: undefined;
+        checked?: undefined;
+    } | {
         label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         subMenu: ({
             label: string;
             subMenu: {
@@ -383,8 +374,8 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
             subMenu?: undefined;
         })[];
         type?: undefined;
-        checked?: undefined;
         onClick?: undefined;
+        checked?: undefined;
     } | {
         label: string;
         subMenu: {
@@ -394,10 +385,23 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
             onClick: () => void;
         }[];
         type?: undefined;
-        checked?: undefined;
+        icon?: undefined;
         onClick?: undefined;
+        checked?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+        type?: undefined;
+        subMenu?: undefined;
+        checked?: undefined;
     } | {
         type: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         label: string;
         checked: boolean;
         onClick: () => void;
@@ -405,7 +409,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     })[];
 } & {
     afterAttach(): void;
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
 } & {
     setGCContentParams({ windowSize, windowDelta, }: {
         windowSize: number;
@@ -416,5 +420,5 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly windowDeltaSetting: any;
 } & {
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    renderProps(): any;
+    adapterProps(): any;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/LinearGCContentDisplay/stateModel1.js

@@ -5,13 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = stateModelF;
 const mobx_state_tree_1 = require("mobx-state-tree");
-// locals
 const shared_1 = __importDefault(require("./shared"));
-/**
- * #stateModel LinearGCContentDisplay
- * #category display
- * base model `SharedGCContentModel`
- */
 function stateModelF(pluginManager, configSchema) {
     return mobx_state_tree_1.types.compose('LinearGCContentDisplay', (0, shared_1.default)(pluginManager, configSchema), mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('LinearGCContentDisplay'),

package/dist/LinearGCContentDisplay/stateModel2.d.ts

@@ -1,15 +1,5 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #stateModel LinearGCContentTrackDisplay
- * #category display
- *
- * used on GCContentTrack, separately from the display type on the
- * ReferenceSequenceTrack
- *
- * extends
- * - [SharedGCContentModel](../sharedgccontentmodel)
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export default function stateModelF(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -22,21 +12,12 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -54,21 +35,15 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -215,14 +190,15 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -249,7 +225,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     message: undefined | string;
@@ -258,7 +234,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: undefined | AbortController;
+    statsFetchInProgress: undefined | string;
 } & {
     updateQuantitativeStats(stats: {
         currStatsBpPerPx: number;
@@ -268,7 +244,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setStatsLoading(aborter: AbortController): void;
+    setStatsLoading(arg?: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -365,7 +341,17 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly quantitativeStatsReady: boolean;
 } & {
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        type: string;
+        label?: undefined;
+        icon?: undefined;
+        subMenu?: undefined;
+        onClick?: undefined;
+        checked?: undefined;
+    } | {
         label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         subMenu: ({
             label: string;
             subMenu: {
@@ -388,8 +374,8 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
             subMenu?: undefined;
         })[];
         type?: undefined;
-        checked?: undefined;
         onClick?: undefined;
+        checked?: undefined;
     } | {
         label: string;
         subMenu: {
@@ -399,10 +385,23 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
             onClick: () => void;
         }[];
         type?: undefined;
-        checked?: undefined;
+        icon?: undefined;
         onClick?: undefined;
+        checked?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+        type?: undefined;
+        subMenu?: undefined;
+        checked?: undefined;
     } | {
         type: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         label: string;
         checked: boolean;
         onClick: () => void;
@@ -410,7 +409,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     })[];
 } & {
     afterAttach(): void;
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
 } & {
     setGCContentParams({ windowSize, windowDelta, }: {
         windowSize: number;
@@ -421,5 +420,5 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly windowDeltaSetting: any;
 } & {
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    renderProps(): any;
+    adapterProps(): any;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/LinearGCContentDisplay/stateModel2.js

@@ -5,18 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = stateModelF;
 const mobx_state_tree_1 = require("mobx-state-tree");
-// locals
 const shared_1 = __importDefault(require("./shared"));
-/**
- * #stateModel LinearGCContentTrackDisplay
- * #category display
- *
- * used on GCContentTrack, separately from the display type on the
- * ReferenceSequenceTrack
- *
- * extends
- * - [SharedGCContentModel](../sharedgccontentmodel)
- */
 function stateModelF(pluginManager, configSchema) {
     return mobx_state_tree_1.types.compose('LinearGCContentTrackDisplay', (0, shared_1.default)(pluginManager, configSchema), mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('LinearGCContentTrackDisplay'),

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class GCContentPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -4,7 +4,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-// locals
 const GCContentAdapter_1 = __importDefault(require("./GCContentAdapter"));
 const GCContentTrack_1 = __importDefault(require("./GCContentTrack"));
 const LinearGCContentDisplay_1 = __importDefault(require("./LinearGCContentDisplay"));

package/esm/GCContentAdapter/GCContentAdapter.d.ts

@@ -1,15 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, Region } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 export default class GCContentAdapter extends BaseFeatureDataAdapter {
     private gcMode;
     static capabilities: string[];
     configure(): Promise<BaseFeatureDataAdapter>;
-    getRefNames(): Promise<string[]>;
-    getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/esm/GCContentAdapter/GCContentAdapter.js

@@ -1,7 +1,8 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { firstValueFrom } from 'rxjs';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, updateStatus } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature } from '@jbrowse/core/util';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
 class GCContentAdapter extends BaseFeatureDataAdapter {
     constructor() {
@@ -16,71 +17,76 @@ class GCContentAdapter extends BaseFeatureDataAdapter {
         }
         return adapter.dataAdapter;
     }
-    async getRefNames() {
+    async getRefNames(opts) {
         const adapter = await this.configure();
-        return adapter.getRefNames();
+        return adapter.getRefNames(opts);
     }
     getFeatures(query, opts) {
+        const { statusCallback = () => { }, stopToken } = opts || {};
         return ObservableCreate(async (observer) => {
             var _a;
             const sequenceAdapter = await this.configure();
             const windowSize = this.getConf('windowSize');
             const windowDelta = this.getConf('windowDelta');
-            const hw = windowSize === 1 ? 1 : windowSize / 2; // Half the window size
-            const f = windowSize === 1;
-            let { start: queryStart, end: queryEnd } = query;
-            queryStart = Math.max(0, queryStart - hw);
-            queryEnd += hw;
-            if (queryEnd < 0 || queryStart > queryEnd) {
+            const halfWindowSize = windowSize === 1 ? 1 : Math.ceil(windowSize / 2);
+            const isWindowSizeOneBp = windowSize === 1;
+            const qs = Math.max(0, Math.floor((query.start - halfWindowSize) / windowSize) * windowSize);
+            const qe = Math.ceil((query.end + halfWindowSize) / windowSize) * windowSize;
+            if (qe < 0 || qs > qe) {
                 observer.complete();
                 return;
             }
-            const ret = sequenceAdapter.getFeatures({
+            const feats = await firstValueFrom(sequenceAdapter
+                .getFeatures({
                 ...query,
-                start: queryStart,
-                end: queryEnd,
-            }, opts);
-            const feats = await firstValueFrom(ret.pipe(toArray()));
+                start: qs,
+                end: qe,
+            }, opts)
+                .pipe(toArray()));
             const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
-            for (let i = hw; i < residues.length - hw; i += windowDelta) {
-                const r = f ? residues[i] : residues.slice(i - hw, i + hw);
-                let nc = 0;
-                let ng = 0;
-                let len = 0;
-                for (const letter of r) {
-                    if (letter === 'c' || letter === 'C') {
-                        nc++;
+            let start = performance.now();
+            await updateStatus('Calculating GC', statusCallback, () => {
+                for (let i = halfWindowSize; i < residues.length - halfWindowSize; i += windowDelta) {
+                    if (performance.now() - start > 400) {
+                        checkStopToken(stopToken);
+                        start = performance.now();
                     }
-                    else if (letter === 'g' || letter === 'G') {
-                        ng++;
-                    }
-                    if (letter !== 'N') {
-                        len++;
+                    const r = isWindowSizeOneBp
+                        ? residues[i]
+                        : residues.slice(i - halfWindowSize, i + halfWindowSize);
+                    let nc = 0;
+                    let ng = 0;
+                    let len = 0;
+                    for (const letter of r) {
+                        if (letter === 'c' || letter === 'C') {
+                            nc++;
+                        }
+                        else if (letter === 'g' || letter === 'G') {
+                            ng++;
+                        }
+                        if (letter !== 'N') {
+                            len++;
+                        }
                     }
+                    const pos = qs;
+                    const score = this.gcMode === 'content'
+                        ? (ng + nc) / (len || 1)
+                        : this.gcMode === 'skew'
+                            ? (ng - nc) / (ng + nc || 1)
+                            : 0;
+                    observer.next(new SimpleFeature({
+                        uniqueId: `${this.id}_${pos + i}`,
+                        refName: query.refName,
+                        start: pos + i,
+                        end: pos + i + windowDelta,
+                        score,
+                    }));
                 }
-                const pos = queryStart;
-                const score = this.gcMode === 'content'
-                    ? (ng + nc) / (len || 1)
-                    : this.gcMode === 'skew'
-                        ? (ng - nc) / (ng + nc || 1)
-                        : 0;
-                observer.next(new SimpleFeature({
-                    uniqueId: `${this.id}_${pos + i}`,
-                    refName: query.refName,
-                    start: pos + i,
-                    end: pos + i + windowDelta,
-                    score,
-                }));
-            }
+            });
             observer.complete();
         });
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 GCContentAdapter.capabilities = ['hasLocalStats'];
 export default GCContentAdapter;