@jbrowse/plugin-gccontent 2.10.3 → 2.11.1

package/esm/LinearGCContentDisplay/stateModel2.d.ts

@@ -0,0 +1,408 @@
+/// <reference types="react" />
+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)
+ */
+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>;
+    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").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>;
+        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;
+        filled: boolean;
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | 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: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | 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[];
+        };
+    }, 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">;
+} & {
+    windowSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    windowDelta: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearGCContentTrackDisplay">;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+    message: string | undefined;
+} & {
+    readonly RenderingComponent: import("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?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("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: import("react").FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): null;
+} & {
+    setMessage(arg?: string | undefined): 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: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    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 | undefined): 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;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+} & {
+    featureIdUnderMouse: string | undefined;
+    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
+} & {
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: import("react").FC<any>;
+    readonly selectedFeatureId: string | undefined;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+} & {
+    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;
+    clearFeatureSelection(): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): 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.Element>;
+    afterAttach(): void;
+} & {
+    message: string | undefined;
+    stats: {
+        scoreMin: number;
+        scoreMax: number;
+    } | undefined;
+    statsFetchInProgress: AbortController | undefined;
+} & {
+    updateQuantitativeStats(stats: {
+        scoreMin: number;
+        scoreMax: number;
+    }): void;
+    setColor(color?: string | undefined): void;
+    setPosColor(color?: string | undefined): void;
+    setNegColor(color?: string | undefined): void;
+    setLoading(aborter: AbortController): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    setResolution(res: number): void;
+    setFill(fill: number): void;
+    toggleLogScale(): void;
+    setScaleType(scale?: string | undefined): void;
+    setSummaryScoreMode(val: string): void;
+    setAutoscale(val: string): void;
+    setMaxScore(val?: number | undefined): void;
+    setRendererType(val: string): void;
+    setMinScore(val?: number | undefined): void;
+    toggleCrossHatches(): void;
+    setCrossHatches(cross: boolean): void;
+} & {
+    readonly adapterTypeName: any;
+    readonly rendererTypeNameSimple: any;
+    readonly filters: undefined;
+    readonly scaleType: any;
+    readonly maxScore: any;
+    readonly minScore: any;
+} & {
+    readonly adapterCapabilities: string[];
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+    readonly autoscaleType: any;
+} & {
+    readonly domain: number[] | undefined;
+} & {
+    readonly filled: boolean;
+    readonly summaryScoreModeSetting: string;
+    readonly scaleOpts: {
+        domain: number[] | undefined;
+        stats: {
+            scoreMin: number;
+            scoreMax: number;
+        } | undefined;
+        autoscaleType: any;
+        scaleType: any;
+        inverted: any;
+    };
+    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>;
+} & {
+    readonly TooltipComponent: import("react").FC<{}>;
+    readonly rendererTypeName: string;
+} & {
+    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 needsScalebar: boolean;
+    readonly fillSetting: 1 | 2 | 0;
+} & {
+    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;
+        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;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+    } | {
+        type: string;
+        label: string;
+        checked: boolean;
+        onClick: () => void;
+        subMenu?: undefined;
+    })[];
+} & {
+    afterAttach(): void;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+} & {
+    setGCContentParams({ windowSize, windowDelta, }: {
+        windowSize: number;
+        windowDelta: number;
+    }): void;
+} & {
+    readonly windowSizeSetting: any;
+    readonly windowDeltaSetting: any;
+} & {
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    renderProps(): any;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/LinearGCContentDisplay/stateModel2.js

@@ -0,0 +1,18 @@
+import { types } from 'mobx-state-tree';
+// locals
+import SharedModelF from './shared';
+/**
+ * #stateModel LinearGCContentTrackDisplay
+ * #category display
+ *
+ * used on GCContentTrack, separately from the display type on the
+ * ReferenceSequenceTrack
+ *
+ * extends
+ * - [SharedGCContentModel](../sharedgccontentmodel)
+ */
+export default function stateModelF(pluginManager, configSchema) {
+    return types.compose('LinearGCContentTrackDisplay', SharedModelF(pluginManager, configSchema), types.model({
+        type: types.literal('LinearGCContentTrackDisplay'),
+    }));
+}

package/esm/index.js

@@ -1,6 +1,7 @@
 import Plugin from '@jbrowse/core/Plugin';
 // locals
 import GCContentAdapterF from './GCContentAdapter';
+import GCContentTrackF from './GCContentTrack';
 import LinearGCContentDisplayF from './LinearGCContentDisplay';
 export default class GCContentPlugin extends Plugin {
     constructor() {
@@ -9,6 +10,7 @@ export default class GCContentPlugin extends Plugin {
     }
     install(pluginManager) {
         GCContentAdapterF(pluginManager);
+        GCContentTrackF(pluginManager);
         LinearGCContentDisplayF(pluginManager);
     }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gccontent",
-  "version": "2.10.3",
+  "version": "2.11.1",
   "description": "JBrowse 2 gccontent concepts",
   "keywords": [
     "jbrowse",
@@ -53,5 +53,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
+  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
 }