@jbrowse/plugin-dotplot-view 2.6.1

package/esm/DotplotDisplay/renderDotplotBlock.js

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+import clone from 'clone';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { getSnapshot } from 'mobx-state-tree';
+import { getContainingView, getSession } from '@jbrowse/core/util';
+export function renderBlockData(self) {
+    const { rpcManager } = getSession(self);
+    const { rendererType } = self;
+    const { adapterConfig } = self;
+    const parent = getContainingView(self);
+    // Alternative to readConfObject(config) is below used because renderProps is
+    // something under our control.  Compare to serverSideRenderedBlock
+    readConfObject(self.configuration);
+    getSnapshot(parent);
+    if (parent.initialized) {
+        const { viewWidth, viewHeight, borderSize, borderX, borderY } = parent;
+        return {
+            rendererType,
+            rpcManager,
+            renderProps: {
+                ...self.renderProps(),
+                view: clone(getSnapshot(parent)),
+                width: viewWidth,
+                height: viewHeight,
+                borderSize,
+                borderX,
+                borderY,
+                adapterConfig,
+                rendererType: rendererType.name,
+                sessionId: getRpcSessionId(self),
+                timeout: 1000000, // 10000,
+            },
+        };
+    }
+    return undefined;
+}
+export async function renderBlockEffect(props) {
+    if (!props) {
+        return;
+    }
+    const { rendererType, rpcManager, renderProps } = props;
+    const { reactElement, ...data } = await rendererType.renderInClient(rpcManager, renderProps);
+    return {
+        reactElement,
+        data,
+        renderingComponent: rendererType.ReactComponent,
+    };
+}
+//# sourceMappingURL=renderDotplotBlock.js.map

package/esm/DotplotDisplay/renderDotplotBlock.js.map

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package/esm/DotplotDisplay/stateModelFactory.d.ts

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+import React from 'react';
+import { ThemeOptions } from '@mui/material';
+import { Instance } from 'mobx-state-tree';
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { ExportSvgOptions } from '../DotplotView/model';
+/**
+ * #stateModel DotplotDisplay
+ * #category display
+ */
+export declare function stateModelFactory(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>>;
+} & {
+    /**
+     * #property
+     */
+    type: import("mobx-state-tree").ISimpleType<"DotplotDisplay">;
+    /**
+     * #property
+     */
+    configuration: AnyConfigurationSchemaType;
+}, {
+    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; /**
+             * #property
+             */
+        } & 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: 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: React.FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[]; /**
+     * #action
+     */
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): null;
+} & {
+    setMessage(arg?: string | undefined): void;
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    warnings: {
+        message: string;
+        effect: string;
+    }[];
+    renderInProgress: AbortController | undefined;
+    filled: boolean;
+    data: any;
+    reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+    message: string | undefined;
+    renderingComponent: any;
+    ReactComponent2: React.FC<any>;
+} & {
+    readonly shouldDisplay: boolean;
+    /**
+     * #getter
+     */
+    readonly rendererTypeName: any;
+    /**
+     * #method
+     */
+    renderProps(): any;
+} & {
+    /**
+     * #method
+     */
+    renderSvg(opts: ExportSvgOptions & {
+        theme: ThemeOptions;
+    }): Promise<React.JSX.Element | null>;
+} & {
+    afterAttach(): void;
+    /**
+     * #action
+     */
+    setLoading(abortController: AbortController): void;
+    /**
+     * #action
+     */
+    setMessage(messageText: string): void;
+    /**
+     * #action
+     */
+    setRendered(args?: {
+        data: any;
+        reactElement: React.ReactElement;
+        renderingComponent: React.Component;
+    }): void;
+    /**
+     * #action
+     */
+    setError(error: unknown): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type DotplotDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type DotplotDisplayModel = Instance<DotplotDisplayStateModel>;

package/esm/DotplotDisplay/stateModelFactory.js

@@ -0,0 +1,158 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React from 'react';
+import { types } from 'mobx-state-tree';
+import { getConf, ConfigurationReference, } from '@jbrowse/core/configuration';
+import { getParentRenderProps } from '@jbrowse/core/util/tracks';
+import { getContainingView, makeAbortableReaction, ReactRendering, } from '@jbrowse/core/util';
+import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
+// locals
+import ServerSideRenderedBlockContent from '../ServerSideRenderedBlockContent';
+import { renderBlockData, renderBlockEffect } from './renderDotplotBlock';
+/**
+ * #stateModel DotplotDisplay
+ * #category display
+ */
+export function stateModelFactory(configSchema) {
+    return types
+        .compose('DotplotDisplay', BaseDisplay, types
+        .model({
+        /**
+         * #property
+         */
+        type: types.literal('DotplotDisplay'),
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(configSchema),
+    })
+        .volatile(() => ({
+        warnings: [],
+        renderInProgress: undefined,
+        filled: false,
+        data: undefined,
+        reactElement: undefined,
+        message: undefined,
+        renderingComponent: undefined,
+        ReactComponent2: ServerSideRenderedBlockContent,
+    })))
+        .views(self => ({
+        get shouldDisplay() {
+            const view = getContainingView(self);
+            return (view.vview.bpPerPx === self.data.bpPerPxY &&
+                view.hview.bpPerPx === self.data.bpPerPxX);
+        },
+        /**
+         * #getter
+         */
+        get rendererTypeName() {
+            return getConf(self, ['renderer', 'type']);
+        },
+        /**
+         * #method
+         */
+        renderProps() {
+            return {
+                ...getParentRenderProps(self),
+                rpcDriverName: self.rpcDriverName,
+                displayModel: self,
+                config: self.configuration.renderer,
+            };
+        },
+    }))
+        .views(self => ({
+        /**
+         * #method
+         */
+        async renderSvg(opts) {
+            const props = renderBlockData(self);
+            if (!props) {
+                return null;
+            }
+            const { rendererType, rpcManager, renderProps } = props;
+            const rendering = await rendererType.renderInClient(rpcManager, {
+                ...renderProps,
+                exportSVG: opts,
+                theme: opts.theme || renderProps.theme,
+            });
+            const { hview, vview } = getContainingView(self);
+            const offX = -hview.offsetPx + rendering.offsetX;
+            const offY = -vview.offsetPx + rendering.offsetY;
+            return (React.createElement("g", { transform: `translate(${offX} ${-offY})` },
+                React.createElement(ReactRendering, { rendering: rendering })));
+        },
+    }))
+        .actions(self => {
+        let renderInProgress;
+        return {
+            afterAttach() {
+                makeAbortableReaction(self, () => renderBlockData(self), blockData => renderBlockEffect(blockData), {
+                    name: `${self.type} ${self.id} rendering`,
+                    delay: 500,
+                    fireImmediately: true,
+                }, this.setLoading, this.setRendered, this.setError);
+            },
+            /**
+             * #action
+             */
+            setLoading(abortController) {
+                self.filled = false;
+                self.message = undefined;
+                self.reactElement = undefined;
+                self.data = undefined;
+                self.error = undefined;
+                self.renderingComponent = undefined;
+                renderInProgress = abortController;
+            },
+            /**
+             * #action
+             */
+            setMessage(messageText) {
+                if (renderInProgress && !renderInProgress.signal.aborted) {
+                    renderInProgress.abort();
+                }
+                self.filled = false;
+                self.message = messageText;
+                self.reactElement = undefined;
+                self.data = undefined;
+                self.error = undefined;
+                self.renderingComponent = undefined;
+                renderInProgress = undefined;
+            },
+            /**
+             * #action
+             */
+            setRendered(args) {
+                if (args === undefined) {
+                    return;
+                }
+                const { data, reactElement, renderingComponent } = args;
+                self.warnings = data.warnings;
+                self.filled = true;
+                self.message = undefined;
+                self.reactElement = reactElement;
+                self.data = data;
+                self.error = undefined;
+                self.renderingComponent = renderingComponent;
+                renderInProgress = undefined;
+            },
+            /**
+             * #action
+             */
+            setError(error) {
+                console.error(error);
+                if (renderInProgress && !renderInProgress.signal.aborted) {
+                    renderInProgress.abort();
+                }
+                // the rendering failed for some reason
+                self.filled = false;
+                self.message = undefined;
+                self.reactElement = undefined;
+                self.data = undefined;
+                self.error = error;
+                self.renderingComponent = undefined;
+                renderInProgress = undefined;
+            },
+        };
+    });
+}
+//# sourceMappingURL=stateModelFactory.js.map

package/esm/DotplotDisplay/stateModelFactory.js.map

@@ -0,0 +1 @@
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package/esm/DotplotReadVsRef/DotplotReadVsRef.d.ts

@@ -0,0 +1,3 @@
+import { Feature } from '@jbrowse/core/util';
+import { LinearPileupDisplayModel } from '@jbrowse/plugin-alignments';
+export declare function onClick(feature: Feature, self: LinearPileupDisplayModel): void;

package/esm/DotplotReadVsRef/DotplotReadVsRef.js

@@ -0,0 +1,98 @@
+import { getConf } from '@jbrowse/core/configuration';
+import { getSession, gatherOverlaps } from '@jbrowse/core/util';
+import { MismatchParser, } from '@jbrowse/plugin-alignments';
+const { featurizeSA, getClip, getTag, getLength, getLengthSansClipping } = MismatchParser;
+export function onClick(feature, self) {
+    const session = getSession(self);
+    try {
+        const cigar = feature.get('CIGAR');
+        const clipPos = getClip(cigar, 1);
+        const flags = feature.get('flags');
+        const strand = feature.get('strand');
+        const readName = feature.get('name');
+        const readAssembly = `${readName}_assembly_${Date.now()}`;
+        const { parentTrack } = self;
+        const [trackAssembly] = getConf(parentTrack, 'assemblyNames');
+        const assemblyNames = [trackAssembly, readAssembly];
+        const trackId = `track-${Date.now()}`;
+        const trackName = `${readName}_vs_${trackAssembly}`;
+        const SA = getTag(feature, 'SA') || '';
+        const SA2 = featurizeSA(SA, feature.id(), strand, readName, true);
+        const feat = feature.toJSON();
+        feat.strand = 1;
+        feat.mate = {
+            refName: readName,
+            start: clipPos,
+            end: clipPos + getLengthSansClipping(cigar),
+        };
+        // if secondary alignment or supplementary, calculate length from SA[0]'s
+        // CIGAR which is the primary alignments. otherwise it is the primary
+        // alignment just use seq.length if primary alignment
+        const totalLength = getLength(flags & 2048 ? SA2[0].CIGAR : cigar);
+        const features = [feat, ...SA2];
+        features.sort((a, b) => a.clipPos - b.clipPos);
+        const refLength = features.reduce((a, f) => a + f.end - f.start, 0);
+        session.addView('DotplotView', {
+            type: 'DotplotView',
+            hview: {
+                offsetPx: 0,
+                bpPerPx: refLength / 800,
+                displayedRegions: gatherOverlaps(features.map((f, index) => {
+                    const { start, end, refName } = f;
+                    return {
+                        start,
+                        end,
+                        refName,
+                        index,
+                        assemblyName: trackAssembly,
+                    };
+                })),
+            },
+            vview: {
+                offsetPx: 0,
+                bpPerPx: totalLength / 400,
+                minimumBlockWidth: 0,
+                interRegionPaddingWidth: 0,
+                displayedRegions: [
+                    {
+                        assemblyName: readAssembly,
+                        start: 0,
+                        end: totalLength,
+                        refName: readName,
+                    },
+                ],
+            },
+            viewTrackConfigs: [
+                {
+                    type: 'SyntenyTrack',
+                    assemblyNames,
+                    adapter: {
+                        type: 'FromConfigAdapter',
+                        features,
+                    },
+                    trackId,
+                    name: trackName,
+                },
+            ],
+            assemblyNames,
+            tracks: [
+                {
+                    configuration: trackId,
+                    type: 'SyntenyTrack',
+                    displays: [
+                        {
+                            type: 'DotplotDisplay',
+                            configuration: `${trackId}-DotplotDisplay`,
+                        },
+                    ],
+                },
+            ],
+            displayName: `${readName} vs ${trackAssembly}`,
+        });
+    }
+    catch (e) {
+        console.error(e);
+        session.notify(`${e}`, 'error');
+    }
+}
+//# sourceMappingURL=DotplotReadVsRef.js.map

package/esm/DotplotReadVsRef/DotplotReadVsRef.js.map

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package/esm/DotplotReadVsRef/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function DotplotReadVsRefMenuItem(pluginManager: PluginManager): void;

package/esm/DotplotReadVsRef/index.js

@@ -0,0 +1,36 @@
+// icons
+import AddIcon from '@mui/icons-material/Add';
+// local
+import { onClick } from './DotplotReadVsRef';
+export default function DotplotReadVsRefMenuItem(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-extendPluggableElement', (pluggableElement) => {
+        if (pluggableElement.name === 'LinearPileupDisplay') {
+            const { stateModel } = pluggableElement;
+            const newStateModel = stateModel.extend((self) => {
+                const superContextMenuItems = self.contextMenuItems;
+                return {
+                    views: {
+                        contextMenuItems() {
+                            const feature = self.contextMenuFeature;
+                            return [
+                                ...superContextMenuItems(),
+                                ...(feature
+                                    ? [
+                                        {
+                                            label: 'Dotplot of read vs ref',
+                                            icon: AddIcon,
+                                            onClick: () => onClick(feature, self),
+                                        },
+                                    ]
+                                    : []),
+                            ];
+                        },
+                    },
+                };
+            });
+            pluggableElement.stateModel = newStateModel;
+        }
+        return pluggableElement;
+    });
+}
+//# sourceMappingURL=index.js.map

package/esm/DotplotReadVsRef/index.js.map

@@ -0,0 +1 @@
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package/esm/DotplotRenderer/ComparativeRenderRpc.d.ts

@@ -0,0 +1,27 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import ComparativeRenderer, { RenderArgs as ComparativeRenderArgs, RenderArgsSerialized as ComparativeRenderArgsSerialized, RenderResults, ResultsSerialized } from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+interface RenderArgs extends ComparativeRenderArgs {
+    adapterConfig: {};
+    rendererType: string;
+}
+interface RenderArgsSerialized extends ComparativeRenderArgsSerialized {
+    adapterConfig: {};
+    rendererType: string;
+}
+/**
+ * call a synteny renderer with the given args
+ * param views: a set of views that each contain a set of regions
+ * used instead of passing regions directly as in render()
+ */
+export default class ComparativeRender extends RpcMethodType {
+    name: string;
+    renameRegionsIfNeeded(args: RenderArgs, rend: ComparativeRenderer): Promise<ComparativeRenderArgs>;
+    getRenderer(rendererType: string): ComparativeRenderer;
+    serializeArguments(args: RenderArgs, rpcDriver: string): Promise<ComparativeRenderArgs | import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").RenderArgsSerialized>;
+    execute(args: RenderArgsSerialized & {
+        signal?: RemoteAbortSignal;
+    }, rpcDriver: string): Promise<RenderResults | import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").ResultsSerialized>;
+    deserializeReturn(val: RenderResults | ResultsSerialized, args: RenderArgs, rpcDriver: string): Promise<unknown>;
+}
+export {};

package/esm/DotplotRenderer/ComparativeRenderRpc.js

@@ -0,0 +1,53 @@
+import { checkAbortSignal } from '@jbrowse/core/util';
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+/**
+ * call a synteny renderer with the given args
+ * param views: a set of views that each contain a set of regions
+ * used instead of passing regions directly as in render()
+ */
+export default class ComparativeRender extends RpcMethodType {
+    constructor() {
+        super(...arguments);
+        this.name = 'ComparativeRender';
+    }
+    async renameRegionsIfNeeded(args, rend) {
+        return rend.renameRegionsIfNeeded(args);
+    }
+    getRenderer(rendererType) {
+        const pm = this.pluginManager;
+        return pm.getRendererType(rendererType);
+    }
+    async serializeArguments(args, rpcDriver) {
+        const { rendererType } = args;
+        const renderer = this.getRenderer(rendererType);
+        const n = (await super.serializeArguments(args, rpcDriver));
+        const result = await this.renameRegionsIfNeeded(n, renderer);
+        return rpcDriver === 'MainThreadRpcDriver'
+            ? result
+            : renderer.serializeArgsInClient(result);
+    }
+    async execute(args, rpcDriver) {
+        let deserializedArgs = args;
+        if (rpcDriver !== 'MainThreadRpcDriver') {
+            deserializedArgs = await this.deserializeArguments(args, rpcDriver);
+        }
+        const { sessionId, rendererType, signal } = deserializedArgs;
+        if (!sessionId) {
+            throw new Error('must pass a unique session id');
+        }
+        checkAbortSignal(signal);
+        const renderer = this.getRenderer(rendererType);
+        return rpcDriver === 'MainThreadRpcDriver'
+            ? renderer.render(deserializedArgs)
+            : renderer.renderInWorker(deserializedArgs);
+    }
+    async deserializeReturn(val, args, rpcDriver) {
+        const ret = (await super.deserializeReturn(val, args, rpcDriver));
+        if (rpcDriver === 'MainThreadRpcDriver') {
+            return ret;
+        }
+        const renderer = this.getRenderer(args.rendererType);
+        return renderer.deserializeResultsInClient(ret, args);
+    }
+}
+//# sourceMappingURL=ComparativeRenderRpc.js.map

package/esm/DotplotRenderer/ComparativeRenderRpc.js.map

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