@jbrowse/plugin-dotplot-view 3.7.0 → 4.0.0

package/dist/DotplotReadVsRef/DotplotReadVsRef.js

@@ -1,100 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.onClick = onClick;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-const { featurizeSA, getClip, getLength, getLengthSansClipping } = plugin_alignments_1.MismatchParser;
-function onClick(feature, self) {
-    var _a;
-    const session = (0, util_1.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] = (0, configuration_1.getConf)(parentTrack, 'assemblyNames');
-        const assemblyNames = [trackAssembly, readAssembly];
-        const trackId = `track-${Date.now()}`;
-        const trackName = `${readName}_vs_${trackAssembly}`;
-        const SA = (_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a.SA;
-        const SA2 = featurizeSA(SA, feature.id(), strand, readName, true);
-        const totalLength = getLength(flags & 2048 ? SA2[0].CIGAR : cigar);
-        const features = [
-            {
-                ...feature.toJSON(),
-                strand: 1,
-                mate: {
-                    refName: readName,
-                    start: clipPos,
-                    end: clipPos + getLengthSansClipping(cigar),
-                },
-            },
-            ...SA2,
-        ].sort((a, b) => a.clipPos - b.clipPos);
-        session.addView('DotplotView', {
-            type: 'DotplotView',
-            hview: {
-                offsetPx: 0,
-                bpPerPx: (0, util_1.sum)(features.map(a => a.end - a.start)) / 800,
-                displayedRegions: (0, util_1.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 ${trackAssembly}`,
-        });
-    }
-    catch (e) {
-        console.error(e);
-        session.notifyError(`${e}`, e);
-    }
-}

package/dist/DotplotReadVsRef/index.d.ts

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

package/dist/DotplotReadVsRef/index.js

@@ -1,41 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = DotplotReadVsRefMenuItem;
-const Add_1 = __importDefault(require("@mui/icons-material/Add"));
-const DotplotReadVsRef_1 = require("./DotplotReadVsRef");
-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: Add_1.default,
-                                            onClick: () => {
-                                                (0, DotplotReadVsRef_1.onClick)(feature, self);
-                                            },
-                                        },
-                                    ]
-                                    : []),
-                            ];
-                        },
-                    },
-                };
-            });
-            pluggableElement.stateModel = newStateModel;
-        }
-        return pluggableElement;
-    });
-}

package/dist/DotplotRenderer/ComparativeRenderRpc.d.ts

@@ -1,22 +0,0 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import type { RenderArgs as ComparativeRenderArgs, RenderArgsSerialized as ComparativeRenderArgsSerialized, RenderResults, ResultsSerialized } from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
-import type ComparativeRenderer from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
-interface RenderArgs extends ComparativeRenderArgs {
-    adapterConfig: Record<string, unknown>;
-    rendererType: string;
-}
-interface RenderArgsSerialized extends ComparativeRenderArgsSerialized {
-    adapterConfig: Record<string, unknown>;
-    rendererType: string;
-}
-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 & {
-        stopToken?: string;
-    }, rpcDriver: string): Promise<RenderResults | import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").ResultsSerialized>;
-    deserializeReturn(val: RenderResults | ResultsSerialized, args: RenderArgs, rpcDriver: string): Promise<unknown>;
-}
-export {};

package/dist/DotplotRenderer/ComparativeRenderRpc.js

@@ -1,53 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
-class ComparativeRender extends RpcMethodType_1.default {
-    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, stopToken } = deserializedArgs;
-        if (!sessionId) {
-            throw new Error('must pass a unique session id');
-        }
-        (0, stopToken_1.checkStopToken)(stopToken);
-        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);
-    }
-}
-exports.default = ComparativeRender;

package/dist/DotplotRenderer/DotplotRenderer.d.ts

@@ -1,65 +0,0 @@
-import ComparativeRenderer from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
-import type { Dotplot1DViewModel } from '../DotplotView/model';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { RenderArgs, RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
-import type { Region } from '@jbrowse/core/util';
-export interface DotplotRenderArgsDeserialized extends RenderArgsDeserialized {
-    adapterConfig: AnyConfigurationModel;
-    height: number;
-    width: number;
-    highResolutionScaling: number;
-    view: {
-        hview: Dotplot1DViewModel;
-        vview: Dotplot1DViewModel;
-    };
-}
-interface DotplotRenderArgs extends RenderArgs {
-    adapterConfig: AnyConfigurationModel;
-    sessionId: string;
-    view: {
-        hview: {
-            displayedRegions: Region[];
-        };
-        vview: {
-            displayedRegions: Region[];
-        };
-    };
-}
-export default class DotplotRenderer extends ComparativeRenderer {
-    supportsSVG: boolean;
-    renameRegionsIfNeeded(args: DotplotRenderArgs): Promise<DotplotRenderArgs>;
-    render(renderProps: DotplotRenderArgsDeserialized): Promise<{
-        height: number;
-        width: number;
-        offsetX: number;
-        offsetY: number;
-        bpPerPxX: number;
-        bpPerPxY: number;
-        warnings: import("./clamp").Warning[];
-        canvasRecordedData: Record<string, unknown>;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        height: number;
-        width: number;
-        offsetX: number;
-        offsetY: number;
-        bpPerPxX: number;
-        bpPerPxY: number;
-        warnings: import("./clamp").Warning[];
-        imageData: any;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        height: number;
-        width: number;
-        offsetX: number;
-        offsetY: number;
-        bpPerPxX: number;
-        bpPerPxY: number;
-        warnings: import("./clamp").Warning[];
-        reactElement: React.ReactElement;
-        html?: string;
-    }>;
-}
-export {};

package/dist/DotplotRenderer/DotplotRenderer.js

@@ -1,102 +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;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const ComparativeServerSideRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType"));
-const util_1 = require("@jbrowse/core/util");
-const model_1 = require("../DotplotView/model");
-class DotplotRenderer extends ComparativeServerSideRendererType_1.default {
-    constructor() {
-        super(...arguments);
-        this.supportsSVG = true;
-    }
-    async renameRegionsIfNeeded(args) {
-        var _a, _b;
-        const pm = this.pluginManager;
-        const assemblyManager = (_b = (_a = pm.rootModel) === null || _a === void 0 ? void 0 : _a.session) === null || _b === void 0 ? void 0 : _b.assemblyManager;
-        const { view, sessionId, adapterConfig } = args;
-        async function process(regions) {
-            if (!assemblyManager) {
-                throw new Error('No assembly manager provided');
-            }
-            const result = await (0, util_1.renameRegionsIfNeeded)(assemblyManager, {
-                sessionId,
-                adapterConfig,
-                regions,
-            });
-            return result.regions;
-        }
-        view.hview.displayedRegions = await process(view.hview.displayedRegions);
-        view.vview.displayedRegions = await process(view.vview.displayedRegions);
-        return args;
-    }
-    async render(renderProps) {
-        var _a, _b;
-        const { width, height, view: { hview, vview }, } = renderProps;
-        const dimensions = [width, height];
-        const views = [hview, vview].map((snap, idx) => {
-            const view = model_1.Dotplot1DView.create(snap);
-            view.setVolatileWidth(dimensions[idx]);
-            return view;
-        });
-        const target = views[0];
-        const feats = await this.getFeatures({
-            ...renderProps,
-            regions: target.dynamicBlocks.contentBlocks,
-        });
-        target.setFeatures(feats);
-        const { drawDotplot } = await Promise.resolve().then(() => __importStar(require('./drawDotplot')));
-        const ret = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => drawDotplot(ctx, { ...renderProps, views }));
-        const results = await super.render({
-            ...renderProps,
-            ...ret,
-            height,
-            width,
-        });
-        return {
-            ...results,
-            ...ret,
-            height,
-            width,
-            offsetX: ((_a = views[0].dynamicBlocks.blocks[0]) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0,
-            offsetY: ((_b = views[1].dynamicBlocks.blocks[0]) === null || _b === void 0 ? void 0 : _b.offsetPx) || 0,
-            bpPerPxX: views[0].bpPerPx,
-            bpPerPxY: views[1].bpPerPx,
-        };
-    }
-}
-exports.default = DotplotRenderer;

package/dist/DotplotRenderer/clamp.d.ts

@@ -1,7 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function clampWithWarnX(num: number, min: number, max: number, feature: Feature, warnings: Warning[]): number;
-export declare function clampWithWarnY(num: number, min: number, max: number, feature: Feature, warnings: Warning[]): number;
-export interface Warning {
-    message: string;
-    effect: string;
-}

package/dist/DotplotRenderer/clamp.js

@@ -1,62 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.clampWithWarnX = clampWithWarnX;
-exports.clampWithWarnY = clampWithWarnY;
-const r = 'fell outside of range due to CIGAR string';
-const lt = '(less than min coordinate of feature)';
-const gt = '(greater than max coordinate of feature)';
-const fudgeFactor = 1;
-function clampWithWarnX(num, min, max, feature, warnings) {
-    const strand = feature.get('strand') || 1;
-    if (strand === -1) {
-        ;
-        [max, min] = [min, max];
-    }
-    if (num < min - fudgeFactor) {
-        let start = feature.get('start');
-        let end = feature.get('end');
-        const refName = feature.get('refName');
-        if (strand === -1) {
-            ;
-            [end, start] = [start, end];
-        }
-        warnings.push({
-            message: `feature at (X ${refName}:${start}-${end}) ${r} ${lt}`,
-            effect: 'clipped the feature',
-        });
-        return min;
-    }
-    if (num > max + fudgeFactor) {
-        const strand = feature.get('strand') || 1;
-        const start = strand === 1 ? feature.get('start') : feature.get('end');
-        const end = strand === 1 ? feature.get('end') : feature.get('start');
-        const refName = feature.get('refName');
-        warnings.push({
-            message: `feature at (X ${refName}:${start}-${end}) ${r} ${gt}`,
-            effect: 'clipped the feature',
-        });
-        return max;
-    }
-    return num;
-}
-function clampWithWarnY(num, min, max, feature, warnings) {
-    if (num < min - fudgeFactor) {
-        const mate = feature.get('mate');
-        const { refName, start, end } = mate;
-        warnings.push({
-            message: `feature at (Y ${refName}:${start}-${end}) ${r} ${lt}`,
-            effect: 'clipped the feature',
-        });
-        return min;
-    }
-    if (num > max + fudgeFactor) {
-        const mate = feature.get('mate');
-        const { refName, start, end } = mate;
-        warnings.push({
-            message: `feature at (Y ${refName}:${start}-${end}) ${r} ${gt}`,
-            effect: 'clipped the feature',
-        });
-        return max;
-    }
-    return num;
-}

package/dist/DotplotRenderer/components/DotplotRendering.d.ts

@@ -1,3 +0,0 @@
-import type { DotplotRenderArgsDeserialized } from '../DotplotRenderer';
-declare const DotplotRendering: (props: DotplotRenderArgsDeserialized) => import("react/jsx-runtime").JSX.Element;
-export default DotplotRendering;

package/dist/DotplotRenderer/components/DotplotRendering.js

@@ -1,9 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const ui_1 = require("@jbrowse/core/ui");
-const mobx_react_1 = require("mobx-react");
-const DotplotRendering = (0, mobx_react_1.observer)(function (props) {
-    return (0, jsx_runtime_1.jsx)(ui_1.PrerenderedCanvas, { ...props });
-});
-exports.default = DotplotRendering;

package/dist/DotplotRenderer/configSchema.d.ts

@@ -1,40 +0,0 @@
-declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    color: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    posColor: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-    negColor: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-    lineWidth: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    colorBy: {
-        type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-        defaultValue: string;
-    };
-    thresholdsPalette: {
-        type: string;
-        defaultValue: string[];
-        description: string;
-    };
-    thresholds: {
-        type: string;
-        defaultValue: string[];
-        description: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default _default;

package/dist/DotplotRenderer/configSchema.js

@@ -1,57 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function x() { }
-exports.default = (0, configuration_1.ConfigurationSchema)('DotplotRenderer', {
-    color: {
-        type: 'color',
-        description: 'the color of each feature in a synteny, used with colorBy:default',
-        defaultValue: '#f0f',
-        contextVariable: ['feature'],
-    },
-    posColor: {
-        type: 'color',
-        description: 'the color for forward alignments, used with colorBy:strand',
-        defaultValue: 'blue',
-    },
-    negColor: {
-        type: 'color',
-        description: 'the color for reverse alignments, used with colorBy:strand',
-        defaultValue: 'red',
-    },
-    lineWidth: {
-        type: 'number',
-        description: 'width of the lines to be drawn',
-        defaultValue: 2.5,
-    },
-    colorBy: {
-        type: 'stringEnum',
-        model: mobx_state_tree_1.types.enumeration('colorBy', [
-            'identity',
-            'meanQueryIdentity',
-            'mappingQuality',
-            'strand',
-            'default',
-        ]),
-        description: `Color by options:<br/>
-<ul>
-  <li>"identity" - the identity of the particular hit, similar to D-GENIES, use the other config slots 'thresholds' and 'thresholdsPalette' to define colors for this setting</li>
-  <li>"meanQueryIdentity" - calculates the weighted mean identity (weighted by alignment length) of all the hits that the query maps to (e.g. if the query is split aligned to many target, uses their weighted mean. can help show patterns of more related and distant synteny after WGD)</li>
-  <li>"mappingQuality" - uses mapping quality from PAF, some adapters don't have this setting</li>
-  <li>"strand" - colors negative alignments with negColor and positive alignments with posColor</li>
-  <li>"default" - uses the 'color' config slot</li>
-</ul>`,
-        defaultValue: 'default',
-    },
-    thresholdsPalette: {
-        type: 'stringArray',
-        defaultValue: ['#094b09', '#2ebd40', '#d5670b', '#ffd84b'],
-        description: 'threshold colors, used with colorBy:identity',
-    },
-    thresholds: {
-        type: 'stringArray',
-        defaultValue: ['0.75', '0.5', '0.25', '0'],
-        description: 'threshold breakpoints, used with colorBy:identity',
-    },
-}, { explicitlyTyped: true });

package/dist/DotplotRenderer/drawDotplot.d.ts

@@ -1,22 +0,0 @@
-import { type Warning } from './clamp';
-import type { Dotplot1DViewModel } from '../DotplotView/model';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
-export interface DotplotRenderArgsDeserialized extends RenderArgsDeserialized {
-    adapterConfig: AnyConfigurationModel;
-    height: number;
-    width: number;
-    highResolutionScaling: number;
-    alpha?: number;
-    minAlignmentLength?: number;
-    colorBy?: string;
-    view: {
-        hview: Dotplot1DViewModel;
-        vview: Dotplot1DViewModel;
-    };
-}
-export declare function drawDotplot(ctx: CanvasRenderingContext2D, props: DotplotRenderArgsDeserialized & {
-    views: Dotplot1DViewModel[];
-}): Promise<{
-    warnings: Warning[];
-}>;