@jbrowse/plugin-gccontent 3.6.5 → 4.0.0

package/dist/LinearGCContentDisplay/shared.d.ts

@@ -1,427 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-export default function SharedModelF(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>;
-    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-} & {
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
-        key: import("mobx-state-tree").ISimpleType<string>;
-        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>;
-    }, {
-        stopToken: string | undefined;
-        filled: boolean;
-        reactElement: React.ReactElement | undefined;
-        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
-        layout: any;
-        status: string;
-        error: unknown;
-        message: string | undefined;
-        maxHeightReached: boolean;
-        ReactComponent: ({ model, }: {
-            model: {
-                error?: unknown;
-                reload: () => void;
-                message: React.ReactNode;
-                filled?: boolean;
-                status?: string;
-                reactElement?: React.ReactElement;
-            };
-        }) => import("react/jsx-runtime").JSX.Element | undefined;
-        renderProps: any;
-    } & {
-        doReload(): void;
-        afterAttach(): void;
-        setStatus(message: string): void;
-        setLoading(newStopToken: string): void;
-        setMessage(messageText: string): void;
-        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
-        setError(error: unknown): void;
-        reload(): void;
-        beforeDestroy(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    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[];
-        };
-        jexlFilters: {
-            type: string;
-            description: string;
-            defaultValue: never[];
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
-} & {
-    selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-        min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    configuration: AnyConfigurationSchemaType;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
-    invertedSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-} & {
-    windowSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    windowDelta: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-}, {
-    rendererTypeName: string;
-    error: unknown;
-    message: string | undefined;
-} & {
-    readonly RenderingComponent: React.FC<{
-        model: {
-            id: string;
-            type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<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>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }, {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: () => void;
-        blockState?: Record<string, any>;
-    }>;
-    readonly DisplayBlurb: React.FC<{
-        model: {
-            id: string;
-            type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<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>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }, {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }> | null;
-    readonly adapterConfig: any;
-    readonly parentTrack: any;
-    renderProps(): any;
-    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: undefined | React.FC<any>;
-    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-    regionCannotBeRendered(): null;
-} & {
-    setMessage(arg?: string): void;
-    setError(error?: unknown): void;
-    setRpcDriverName(rpcDriverName: string): void;
-    reload(): void;
-} & {
-    scrollTop: number;
-} & {
-    readonly height: number;
-} & {
-    setScrollTop(scrollTop: number): void;
-    setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
-} & {
-    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
-    currStatsBpPerPx: number;
-} & {
-    readonly currentBytesRequested: number;
-    readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any;
-    readonly featureDensityStatsReady: boolean;
-    readonly maxAllowableBytes: number;
-} & {
-    afterAttach(): void;
-} & {
-    setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
-    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    setFeatureDensityStatsP(arg: any): void;
-    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
-    clearFeatureDensityStats(): void;
-} & {
-    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-runtime").JSX.Element | null;
-} & {
-    featureIdUnderMouse: undefined | string;
-    contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
-} & {
-    readonly DisplayMessageComponent: undefined | React.FC<any>;
-    readonly blockType: "staticBlocks" | "dynamicBlocks";
-    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
-} & {
-    readonly renderDelay: number;
-    readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
-    readonly selectedFeatureId: string | undefined;
-    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
-} & {
-    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): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
-} & {
-    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
-    deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    navToFeature(feature: import("@jbrowse/core/util").Feature): void;
-    clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string): void;
-    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
-} & {
-    reload(): Promise<void>;
-} & {
-    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    renderProps(): any;
-} & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
-    afterAttach(): void;
-} & {
-    message: undefined | string;
-    stats: {
-        currStatsBpPerPx: number;
-        scoreMin: number;
-        scoreMax: number;
-    } | undefined;
-    statsFetchInProgress: undefined | string;
-} & {
-    updateQuantitativeStats(stats: {
-        currStatsBpPerPx: number;
-        scoreMin: number;
-        scoreMax: number;
-    }): void;
-    setColor(color?: string): void;
-    setPosColor(color?: string): void;
-    setNegColor(color?: string): void;
-    setStatsLoading(arg?: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    setResolution(res: number): void;
-    setFill(fill: number): void;
-    toggleLogScale(): void;
-    setScaleType(scale?: string): void;
-    setSummaryScoreMode(val: string): void;
-    setAutoscale(val: string): void;
-    setMaxScore(val?: number): void;
-    setRendererType(val: string): void;
-    setMinScore(val?: number): void;
-    toggleCrossHatches(): void;
-    setCrossHatches(cross: boolean): void;
-} & {
-    readonly adapterTypeName: any;
-    readonly rendererTypeNameSimple: string;
-    readonly filters: undefined;
-    readonly scaleType: string;
-    readonly maxScore: number;
-    readonly minScore: number;
-} & {
-    readonly adapterCapabilities: string[];
-    readonly rendererConfig: {
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
-    readonly autoscaleType: string;
-} & {
-    readonly domain: number[] | undefined;
-} & {
-    readonly filled: boolean;
-    readonly summaryScoreModeSetting: string;
-    readonly scaleOpts: {
-        domain: number[] | undefined;
-        stats: {
-            currStatsBpPerPx: number;
-            scoreMin: number;
-            scoreMax: number;
-        } | undefined;
-        autoscaleType: string;
-        scaleType: string;
-        inverted: boolean;
-    };
-    readonly canHaveFill: boolean;
-    readonly displayCrossHatchesSetting: boolean;
-    readonly hasResolution: boolean;
-    readonly hasGlobalStats: boolean;
-} & {
-    scoreTrackMenuItems(): ({
-        label: string;
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-        onClick?: undefined;
-    } | {
-        label: string;
-        subMenu: {
-            label: string;
-            type: string;
-            checked: boolean;
-            onClick: () => void;
-        }[];
-        onClick?: undefined;
-    } | {
-        label: string;
-        onClick: () => void;
-        subMenu?: undefined;
-    })[];
-} & {
-    reload(): Promise<void>;
-} & {
-    setInverted(arg: boolean): void;
-} & {
-    readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
-    readonly rendererTypeName: string;
-    readonly quantitativeStatsRelevantToCurrentZoom: boolean;
-    readonly graphType: boolean;
-    readonly inverted: boolean;
-} & {
-    adapterProps(): any;
-    readonly ticks: {
-        range: number[];
-        values: number[];
-        format: (d: import("d3-scale").NumberValue) => string;
-        position: import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
-    } | undefined;
-} & {
-    renderProps(): any;
-    readonly fillSetting: 1 | 2 | 0;
-    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 | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        subMenu: ({
-            label: string;
-            subMenu: {
-                label: string;
-                onClick: () => void;
-            }[];
-            onClick?: undefined;
-        } | {
-            label: string;
-            subMenu: {
-                label: string;
-                type: string;
-                checked: boolean;
-                onClick: () => void;
-            }[];
-            onClick?: undefined;
-        } | {
-            label: string;
-            onClick: () => void;
-            subMenu?: undefined;
-        })[];
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-    } | {
-        label: string;
-        type: string;
-        checked: boolean;
-        onClick: () => void;
-        icon?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        subMenu: {
-            label: string;
-            type: string;
-            checked: boolean;
-            onClick: () => void;
-        }[];
-        icon?: undefined;
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-        subMenu?: undefined;
-        type?: undefined;
-        checked?: undefined;
-    } | {
-        type: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        label: string;
-        checked: boolean;
-        onClick: () => void;
-        subMenu?: undefined;
-    })[];
-} & {
-    afterAttach(): void;
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
-} & {
-    setGCContentParams({ windowSize, windowDelta, }: {
-        windowSize: number;
-        windowDelta: number;
-    }): void;
-} & {
-    readonly windowSizeSetting: any;
-    readonly windowDeltaSetting: any;
-} & {
-    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    adapterProps(): any;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/LinearGCContentDisplay/shared.js

@@ -1,96 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-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 EditGCContentParamsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/EditGCContentParams'))));
-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({
-        windowSize: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        windowDelta: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-    }))
-        .actions(self => ({
-        setGCContentParams({ windowSize, windowDelta, }) {
-            self.windowSize = windowSize;
-            self.windowDelta = windowDelta;
-        },
-    }))
-        .views(self => ({
-        get windowSizeSetting() {
-            var _a;
-            return (_a = self.windowSize) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'windowSize');
-        },
-        get windowDeltaSetting() {
-            var _a;
-            return (_a = self.windowDelta) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'windowDelta');
-        },
-    }))
-        .views(self => {
-        const { trackMenuItems: superTrackMenuItems, adapterProps: superAdapterProps, } = self;
-        return {
-            trackMenuItems() {
-                return [
-                    ...superTrackMenuItems(),
-                    {
-                        label: 'Change GC parameters',
-                        onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                EditGCContentParamsDialog,
-                                { model: self, handleClose },
-                            ]);
-                        },
-                    },
-                ];
-            },
-            adapterProps() {
-                const sequenceAdapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
-                return {
-                    ...superAdapterProps(),
-                    adapterConfig: {
-                        type: 'GCContentAdapter',
-                        sequenceAdapter,
-                        windowSize: self.windowSizeSetting,
-                        windowDelta: self.windowDeltaSetting,
-                    },
-                };
-            },
-        };
-    });
-}