jbrowse-plugin-mafviewer 1.0.6 → 1.0.8

package/dist/LinearMafDisplay/stateModel.d.ts

@@ -0,0 +1,364 @@
+import { Instance } from 'mobx-state-tree';
+import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
+/**
+ * #stateModel LinearMafDisplay
+ * extends LinearBasicDisplay
+ */
+export default function stateModelFactory(configSchema: AnyConfigurationSchemaType, pluginManager: PluginManager): 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.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/dist/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">>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearMafDisplay">;
+    configuration: AnyConfigurationSchemaType;
+    rowHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
+    rowProportion: import("mobx-state-tree").IType<number | undefined, number, number>;
+    showAllLetters: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    mismatchRendering: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+}, {
+    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.Element | null;
+} & {
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
+} & {
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
+    readonly selectedFeatureId: string | 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;
+    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/dist/BaseLinearDisplay").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    afterAttach(): void;
+} & {
+    /**
+     * #volatile
+     */
+    prefersOffset: boolean;
+} & {
+    /**
+     * #action
+     */
+    setRowHeight(n: number): void;
+    /**
+     * #action
+     */
+    setRowProportion(n: number): void;
+    /**
+     * #action
+     */
+    setShowAllLetters(f: boolean): void;
+    /**
+     * #action
+     */
+    setMismatchRendering(f: boolean): void;
+} & {
+    /**
+     * #getter
+     */
+    readonly samples: {
+        id: string;
+        label: string;
+        color?: string;
+    }[];
+    /**
+     * #getter
+     */
+    readonly rendererTypeName: string;
+    /**
+     * #getter
+     */
+    readonly rendererConfig: AnyConfigurationModel;
+} & {
+    /**
+     * #method
+     */
+    renderProps(): any;
+    /**
+     * #method
+     */
+    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;
+        type: string;
+        checked: boolean;
+        onClick: () => void;
+    })[];
+} & {
+    /**
+     * #action
+     */
+    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+}, {
+    type: string;
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    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.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/dist/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">>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
+    type: string;
+    id: string;
+    configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
+    rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
+    userBpPerPxLimit: number | undefined;
+    userByteSizeLimit: number | undefined;
+} & import("mobx-state-tree")._NotCustomized>;
+export type LinearMafDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type LinearMafDisplayModel = Instance<LinearMafDisplayStateModel>;

package/dist/LinearMafDisplay/stateModel.js

@@ -0,0 +1,176 @@
+import { types } from 'mobx-state-tree';
+import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
+import { getEnv, getSession } from '@jbrowse/core/util';
+import SetRowHeightDialog from './components/SetRowHeight';
+function isStrs(array) {
+    return typeof array[0] === 'string';
+}
+/**
+ * #stateModel LinearMafDisplay
+ * extends LinearBasicDisplay
+ */
+export default function stateModelFactory(configSchema, pluginManager) {
+    const LinearGenomePlugin = pluginManager.getPlugin('LinearGenomeViewPlugin');
+    const { BaseLinearDisplay } = LinearGenomePlugin.exports;
+    return types
+        .compose('LinearMafDisplay', BaseLinearDisplay, types.model({
+        /**
+         * #property
+         */
+        type: types.literal('LinearMafDisplay'),
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(configSchema),
+        /**
+         * #property
+         */
+        rowHeight: 15,
+        /**
+         * #property
+         */
+        rowProportion: 0.8,
+        /**
+         * #property
+         */
+        showAllLetters: false,
+        /**
+         * #property
+         */
+        mismatchRendering: true,
+    }))
+        .volatile(() => ({
+        /**
+         * #volatile
+         */
+        prefersOffset: true,
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setRowHeight(n) {
+            self.rowHeight = n;
+        },
+        /**
+         * #action
+         */
+        setRowProportion(n) {
+            self.rowProportion = n;
+        },
+        /**
+         * #action
+         */
+        setShowAllLetters(f) {
+            self.showAllLetters = f;
+        },
+        /**
+         * #action
+         */
+        setMismatchRendering(f) {
+            self.mismatchRendering = f;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get samples() {
+            const r = self.adapterConfig.samples;
+            return isStrs(r)
+                ? r.map(elt => ({ id: elt, label: elt, color: undefined }))
+                : r;
+        },
+        /**
+         * #getter
+         */
+        get rendererTypeName() {
+            return 'LinearMafRenderer';
+        },
+        /**
+         * #getter
+         */
+        get rendererConfig() {
+            const configBlob = getConf(self, ['renderer']) || {};
+            const config = configBlob;
+            return self.rendererType.configSchema.create({
+                ...config,
+                type: 'LinearMafRenderer',
+            }, getEnv(self));
+        },
+    }))
+        .views(self => {
+        const { 
+        // eslint-disable-next-line @typescript-eslint/unbound-method
+        trackMenuItems: superTrackMenuItems, 
+        // eslint-disable-next-line @typescript-eslint/unbound-method
+        renderProps: superRenderProps, } = self;
+        return {
+            /**
+             * #method
+             */
+            renderProps() {
+                const { showAllLetters, rendererConfig, samples, rowHeight, rowProportion, mismatchRendering, } = self;
+                return {
+                    ...superRenderProps(),
+                    config: rendererConfig,
+                    samples,
+                    rowHeight,
+                    rowProportion,
+                    showAllLetters,
+                    mismatchRendering,
+                };
+            },
+            /**
+             * #method
+             */
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Set row height',
+                        onClick: () => {
+                            getSession(self).queueDialog(handleClose => [
+                                SetRowHeightDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
+                    {
+                        label: 'Show all letters',
+                        type: 'checkbox',
+                        checked: self.showAllLetters,
+                        onClick: () => {
+                            self.setShowAllLetters(!self.showAllLetters);
+                        },
+                    },
+                    {
+                        label: 'Draw mismatches as single color',
+                        type: 'checkbox',
+                        checked: !self.mismatchRendering,
+                        onClick: () => {
+                            self.setMismatchRendering(!self.mismatchRendering);
+                        },
+                    },
+                ];
+            },
+        };
+    })
+        .actions(self => {
+        // eslint-disable-next-line @typescript-eslint/unbound-method
+        const { renderSvg: superRenderSvg } = self;
+        return {
+            /**
+             * #action
+             */
+            async renderSvg(opts) {
+                const { renderSvg } = await import('./renderSvg');
+                return renderSvg(self, opts, superRenderSvg);
+            },
+        };
+    });
+}
+//# sourceMappingURL=stateModel.js.map

package/dist/LinearMafDisplay/stateModel.js.map

@@ -0,0 +1 @@
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package/dist/LinearMafRenderer/LinearMafRenderer.d.ts

@@ -0,0 +1,45 @@
+import { FeatureRendererType } from '@jbrowse/core/pluggableElementTypes';
+import { RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { Feature, Region } from '@jbrowse/core/util';
+interface Sample {
+    id: string;
+    color?: string;
+}
+interface RenderArgs extends RenderArgsDeserialized {
+    samples: Sample[];
+    rowHeight: number;
+    rowProportion: number;
+    showAllLetters: boolean;
+    mismatchRendering: boolean;
+}
+export default class LinearMafRenderer extends FeatureRendererType {
+    getExpandedRegion(region: Region): {
+        start: number;
+        end: number;
+        refName: string;
+        reversed?: boolean | undefined;
+        assemblyName: string;
+    };
+    render(renderProps: RenderArgs): Promise<{
+        width: number;
+        height: number;
+        canvasRecordedData: any;
+        features: Map<string, Feature>;
+        reactElement?: import("react").ReactElement;
+        html?: string;
+    } | {
+        width: number;
+        height: number;
+        reactElement: React.JSX.Element;
+        features: Map<string, Feature>;
+        html?: string;
+    } | {
+        width: number;
+        height: number;
+        imageData: any;
+        features: Map<string, Feature>;
+        reactElement?: import("react").ReactElement;
+        html?: string;
+    }>;
+}
+export {};