@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/esm/NestedFrequencyTable.js

@@ -0,0 +1,101 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+// see perf results on object.keys vs for-in loop
+// https://jsperf.com/object-keys-vs-hasownproperty/55
+export default class NestedFrequencyTable {
+    constructor(initialData = {}) {
+        this.categories = { ...initialData };
+    }
+    // get the sum of all the category counts
+    total() {
+        // calculate total if necessary
+        let t = 0;
+        for (const k in this.categories) {
+            const v = this.categories[k];
+            t += v.total ? v.total() : v;
+        }
+        return t;
+    }
+    // decrement the count for the given category
+    decrement(slotName, amount) {
+        if (!amount) {
+            amount = 1;
+        }
+        if (!slotName) {
+            slotName = 'default';
+        }
+        else {
+            slotName = slotName.toString();
+        }
+        if (this.categories[slotName]) {
+            this.categories[slotName] = Math.max(0, this.categories[slotName] - amount);
+            return this.categories[slotName];
+        }
+        return 0;
+    }
+    // increment the count for the given category
+    increment(slotName, amount) {
+        if (!amount) {
+            amount = 1;
+        }
+        if (!slotName) {
+            slotName = 'default';
+        }
+        else {
+            slotName = slotName.toString();
+        }
+        this.categories[slotName] = (this.categories[slotName] || 0) + amount;
+        return this.categories[slotName];
+    }
+    // get the value of the given category.  may be a number or a
+    // frequency table.
+    get(slotName) {
+        return this.categories[slotName] || 0;
+    }
+    // get a given category as a frequency table
+    getNested(path) {
+        if (typeof path === 'string') {
+            path = path.split('/');
+        }
+        if (!path.length) {
+            return this;
+        }
+        const slotName = path[0].toString();
+        let slot = this.categories[slotName];
+        if (!slot || !slot.categories) {
+            this.categories[slotName] = new NestedFrequencyTable(slot ? { default: slot + 0 } : {});
+        }
+        slot = this.categories[slotName];
+        if (path.length > 1) {
+            return slot.getNested(path.slice(1));
+        }
+        return slot;
+    }
+    toString() {
+        return this.total()
+            .toPrecision(6)
+            .toString()
+            .replace(/\.?0+$/, '');
+    }
+    valueOf() {
+        return this.total();
+    }
+    // iterate through the categories and counts, call like:
+    //
+    //   tbl.forEach( function( count, categoryName ) {
+    //      // do something
+    //   }, this );
+    //
+    forEach(func, ctx) {
+        if (ctx) {
+            for (const slotName in this.categories) {
+                func.call(ctx, this.categories[slotName], slotName);
+            }
+        }
+        else {
+            for (const slotName in this.categories) {
+                func(this.categories[slotName], slotName);
+            }
+        }
+    }
+}
+//# sourceMappingURL=NestedFrequencyTable.js.map

package/esm/NestedFrequencyTable.js.map

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

@@ -0,0 +1,34 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
+import { Region } from '@jbrowse/core/util/types';
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+export declare class PileupGetGlobalValueForTag extends RpcMethodType {
+    name: string;
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: Function;
+    }, rpcDriverClassName: string): Promise<{}>;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sessionId: string;
+        tag: string;
+    }, rpcDriverClassName: string): Promise<string[]>;
+}
+export declare class PileupGetVisibleModifications extends RpcMethodType {
+    name: string;
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: Function;
+    }, rpcDriverClassName: string): Promise<{}>;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sessionId: string;
+        tag: string;
+    }, rpcDriverClassName: string): Promise<string[]>;
+}

package/esm/PileupRPC/rpcMethods.js

@@ -0,0 +1,70 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { renameRegionsIfNeeded } from '@jbrowse/core/util';
+import { toArray } from 'rxjs/operators';
+import { getTagAlt } from '../util';
+import { getModificationTypes } from '../BamAdapter/MismatchParser';
+export class PileupGetGlobalValueForTag extends RpcMethodType {
+    constructor() {
+        super(...arguments);
+        this.name = 'PileupGetGlobalValueForTag';
+    }
+    async serializeArguments(args, rpcDriverClassName) {
+        var _a;
+        const { rootModel } = this.pluginManager;
+        const assemblyManager = (_a = rootModel === null || rootModel === void 0 ? void 0 : rootModel.session) === null || _a === void 0 ? void 0 : _a.assemblyManager;
+        if (!assemblyManager) {
+            throw new Error('no assembly manager available');
+        }
+        const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args);
+        return super.serializeArguments(renamedArgs, rpcDriverClassName);
+    }
+    async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { adapterConfig, sessionId, regions, tag } = deserializedArgs;
+        const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
+        const features = dataAdapter.getFeaturesInMultipleRegions(regions);
+        const featuresArray = await features.pipe(toArray()).toPromise();
+        const uniqueValues = new Set();
+        featuresArray.forEach(feature => {
+            const tags = feature.get('tags');
+            const val = tags ? tags[tag] : feature.get(tag);
+            if (val !== undefined) {
+                uniqueValues.add(`${val}`);
+            }
+        });
+        return [...uniqueValues];
+    }
+}
+export class PileupGetVisibleModifications extends RpcMethodType {
+    constructor() {
+        super(...arguments);
+        this.name = 'PileupGetVisibleModifications';
+    }
+    async serializeArguments(args, rpcDriverClassName) {
+        var _a;
+        const { rootModel } = this.pluginManager;
+        const assemblyManager = (_a = rootModel === null || rootModel === void 0 ? void 0 : rootModel.session) === null || _a === void 0 ? void 0 : _a.assemblyManager;
+        if (!assemblyManager) {
+            throw new Error('no assembly manager available');
+        }
+        const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args);
+        return super.serializeArguments(renamedArgs, rpcDriverClassName);
+    }
+    async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { adapterConfig, sessionId, regions } = deserializedArgs;
+        const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
+        const features = dataAdapter.getFeaturesInMultipleRegions(regions);
+        const featuresArray = await features.pipe(toArray()).toPromise();
+        const uniqueValues = new Set();
+        featuresArray.forEach(feature => {
+            const val = getTagAlt(feature, 'MM', 'Mm') || '';
+            if (val !== undefined) {
+                getModificationTypes(val).forEach(t => uniqueValues.add(t));
+            }
+        });
+        return [...uniqueValues];
+    }
+}
+//# sourceMappingURL=rpcMethods.js.map

package/esm/PileupRPC/rpcMethods.js.map

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

@@ -0,0 +1,32 @@
+import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
+import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
+import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
+export interface PileupLayoutSessionProps {
+    config: AnyConfigurationModel;
+    bpPerPx: number;
+    filters: SerializableFilterChain;
+    filterBy: unknown;
+    sortedBy: unknown;
+    showSoftClip: unknown;
+}
+declare type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
+interface CachedPileupLayout {
+    layout: MyMultiLayout;
+    config: AnyConfigurationModel;
+    filters: SerializableFilterChain;
+    filterBy: unknown;
+    sortedBy: unknown;
+    showSoftClip: boolean;
+}
+export declare class PileupLayoutSession extends LayoutSession {
+    sortedBy: unknown;
+    filterBy: unknown;
+    showSoftClip: boolean;
+    constructor(args: PileupLayoutSessionProps);
+    cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
+    cachedLayout: CachedPileupLayout | undefined;
+    get layout(): MyMultiLayout;
+}
+export {};

package/esm/PileupRenderer/PileupLayoutSession.js

@@ -0,0 +1,32 @@
+import deepEqual from 'fast-deep-equal';
+import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { readConfObject } from '@jbrowse/core/configuration';
+// Sorting and revealing soft clip changes the layout of Pileup renderer
+// Adds extra conditions to see if cached layout is valid
+export class PileupLayoutSession extends LayoutSession {
+    constructor(args) {
+        super(args);
+        this.showSoftClip = false;
+        this.config = args.config;
+    }
+    cachedLayoutIsValid(cachedLayout) {
+        return (super.cachedLayoutIsValid(cachedLayout) &&
+            this.showSoftClip === cachedLayout.showSoftClip &&
+            deepEqual(this.sortedBy, cachedLayout.sortedBy) &&
+            deepEqual(this.filterBy, cachedLayout.filterBy));
+    }
+    get layout() {
+        if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
+            this.cachedLayout = {
+                layout: this.makeLayout(),
+                config: readConfObject(this.config),
+                filters: this.filters,
+                filterBy: this.filterBy,
+                sortedBy: this.sortedBy,
+                showSoftClip: this.showSoftClip,
+            };
+        }
+        return this.cachedLayout.layout;
+    }
+}
+//# sourceMappingURL=PileupLayoutSession.js.map

package/esm/PileupRenderer/PileupLayoutSession.js.map

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

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+/// <reference types="react" />
+import { Theme } from '@mui/material/styles';
+import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { Region, Feature } from '@jbrowse/core/util';
+import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { PileupLayoutSession, PileupLayoutSessionProps } from './PileupLayoutSession';
+export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
+    colorBy?: {
+        type: string;
+        tag?: string;
+    };
+    colorTagMap?: Record<string, string>;
+    modificationTagMap?: Record<string, string>;
+    sortedBy?: {
+        type: string;
+        pos: number;
+        refName: string;
+        assemblyName: string;
+        tag?: string;
+    };
+    showSoftClip: boolean;
+    highResolutionScaling: number;
+}
+export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+    layout: BaseLayout<Feature>;
+    regionSequence?: string;
+}
+interface LayoutRecord {
+    feature: Feature;
+    leftPx: number;
+    rightPx: number;
+    topPx: number;
+    heightPx: number;
+}
+interface LayoutFeature {
+    heightPx: number;
+    topPx: number;
+    feature: Feature;
+}
+export default class PileupRenderer extends BoxRendererType {
+    supportsSVG: boolean;
+    getCharWidthHeight(ctx: CanvasRenderingContext2D): {
+        charWidth: number;
+        charHeight: number;
+    };
+    layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }: {
+        feature: Feature;
+        layout: BaseLayout<Feature>;
+        bpPerPx: number;
+        region: Region;
+        showSoftClip?: boolean;
+        heightPx: number;
+        displayMode: string;
+    }): LayoutRecord | null;
+    getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
+        start: number;
+        end: number;
+        reversed?: boolean | undefined;
+        refName: string;
+        assemblyName: string;
+    };
+    colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;
+    getOrientation(feature: Feature, config: AnyConfigurationModel): string;
+    colorByInsertSize(feature: Feature, _config: AnyConfigurationModel): string;
+    colorByStranded(feature: Feature, _config: AnyConfigurationModel): "color_rev_strand" | "color_fwd_strand" | "color_rev_missing_mate" | "color_fwd_missing_mate" | "color_rev_strand_not_proper" | "color_fwd_strand_not_proper" | "color_fwd_diff_chr" | "color_rev_diff_chr";
+    colorByPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        region: Region;
+        bpPerPx: number;
+        colorForBase: Record<string, string>;
+        contrastForBase: Record<string, string>;
+        charWidth: number;
+        charHeight: number;
+        canvasWidth: number;
+    }): void;
+    colorByPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        region: Region;
+        bpPerPx: number;
+        canvasWidth: number;
+    }): void;
+    colorByModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        region: Region;
+        bpPerPx: number;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+        canvasWidth: number;
+    }): void;
+    colorByMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        region: Region;
+        bpPerPx: number;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+        canvasWidth: number;
+    }): void;
+    drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
+    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+        colorForBase: Record<string, string>;
+        contrastForBase: Record<string, string>;
+        charWidth: number;
+        charHeight: number;
+        defaultColor: boolean;
+        canvasWidth: number;
+    }): void;
+    drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+        colorForBase: {
+            [key: string]: string;
+        };
+        contrastForBase: {
+            [key: string]: string;
+        };
+        mismatchAlpha?: boolean;
+        drawIndels?: boolean;
+        drawSNPsMuted?: boolean;
+        minSubfeatureWidth: number;
+        largeInsertionIndicatorScale: number;
+        charWidth: number;
+        charHeight: number;
+        canvasWidth: number;
+    }): void;
+    drawSoftClipping({ ctx, feat, renderArgs, config, theme, canvasWidth, }: {
+        ctx: CanvasRenderingContext2D;
+        feat: LayoutFeature;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+        config: AnyConfigurationModel;
+        theme: Theme;
+        canvasWidth: number;
+    }): void;
+    makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }: {
+        ctx: CanvasRenderingContext2D;
+        canvasWidth: number;
+        layoutRecords: (LayoutFeature | null)[];
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+    }): void;
+    layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
+    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
+    render(renderProps: RenderArgsDeserialized): Promise<{
+        features: Map<any, any>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
+        height: number;
+        width: number;
+        maxHeightReached: boolean;
+        canvasRecordedData: any;
+        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        imageData?: undefined;
+        html?: string | undefined;
+    } | {
+        features: Map<any, any>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
+        height: number;
+        width: number;
+        maxHeightReached: boolean;
+        reactElement: JSX.Element;
+        canvasRecordedData?: undefined;
+        imageData?: undefined;
+        html?: string | undefined;
+    } | {
+        features: Map<any, any>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
+        height: number;
+        width: number;
+        maxHeightReached: boolean;
+        imageData: any;
+        canvasRecordedData?: undefined;
+        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        html?: string | undefined;
+    }>;
+    createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
+}
+export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };