@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/dist/SNPCoverageRenderer/configSchema.js

@@ -1,37 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const SNPCoverageRenderer = (0, configuration_1.ConfigurationSchema)('SNPCoverageRenderer', {
-    clipColor: {
-        type: 'color',
-        description: 'the color of the clipping marker',
-        defaultValue: 'red',
-    },
-    indicatorThreshold: {
-        type: 'number',
-        description: 'the proportion of reads containing a insertion/clip indicator',
-        defaultValue: 0.4,
-    },
-    showArcs: {
-        type: 'boolean',
-        description: 'Draw sashimi-style arcs for intron features',
-        defaultValue: true,
-    },
-    showInterbaseCounts: {
-        type: 'boolean',
-        description: 'draw count "upsidedown histogram" of the interbase events that don\'t contribute to the coverage count so are not drawn in the normal histogram',
-        defaultValue: true,
-    },
-    showInterbaseIndicators: {
-        type: 'boolean',
-        description: 'draw a triangular indicator where an event has been detected',
-        defaultValue: true,
-    },
-    color: {
-        type: 'color',
-        description: 'Background color for the SNPCoverage renderer',
-        defaultValue: '#d3d3d3',
-    },
-}, { explicitlyTyped: true });
-exports.default = SNPCoverageRenderer;

package/dist/SNPCoverageRenderer/index.d.ts

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

package/dist/SNPCoverageRenderer/index.js

@@ -1,17 +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 = register;
-const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function register(pluginManager) {
-    pluginManager.addRendererType(() => new SNPCoverageRenderer_1.default({
-        name: 'SNPCoverageRenderer',
-        ReactComponent: plugin_wiggle_1.WiggleRendering,
-        configSchema: configSchema_1.default,
-        pluginManager,
-    }));
-}

package/dist/SNPCoverageRenderer/makeImage.d.ts

@@ -1,2 +0,0 @@
-import type { RenderArgsDeserializedWithFeatures } from './types';
-export declare function makeImage(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;

package/dist/SNPCoverageRenderer/makeImage.js

@@ -1,259 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.makeImage = makeImage;
-const configuration_1 = require("@jbrowse/core/configuration");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const util_2 = require("../shared/util");
-const INTERBASE_INDICATOR_WIDTH = 7;
-const INTERBASE_INDICATOR_HEIGHT = 4.5;
-const MINIMUM_INTERBASE_INDICATOR_READ_DEPTH = 7;
-const complementBase = {
-    C: 'G',
-    G: 'C',
-    A: 'T',
-    T: 'A',
-};
-const fudgeFactor = 0.6;
-async function makeImage(ctx, props) {
-    var _a;
-    const { features, regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, stopToken, } = props;
-    const theme = (0, ui_1.createJBrowseTheme)(configTheme);
-    const region = regions[0];
-    const width = (region.end - region.start) / bpPerPx;
-    const offset = plugin_wiggle_1.YSCALEBAR_LABEL_OFFSET;
-    const height = unadjustedHeight - offset * 2;
-    const opts = { ...scaleOpts, range: [0, height] };
-    const viewScale = (0, plugin_wiggle_1.getScale)(opts);
-    const indicatorViewScale = (0, plugin_wiggle_1.getScale)({
-        ...opts,
-        range: [0, height / 2],
-        scaleType: 'linear',
-    });
-    const originY = (0, plugin_wiggle_1.getOrigin)(scaleOpts.scaleType);
-    const originLinear = (0, plugin_wiggle_1.getOrigin)('linear');
-    const indicatorThreshold = (0, configuration_1.readConfObject)(cfg, 'indicatorThreshold');
-    const showInterbaseCounts = (0, configuration_1.readConfObject)(cfg, 'showInterbaseCounts');
-    const showArcs = (0, configuration_1.readConfObject)(cfg, 'showArcs');
-    const showInterbaseIndicators = (0, configuration_1.readConfObject)(cfg, 'showInterbaseIndicators');
-    const toY = (n) => height - (viewScale(n) || 0) + offset;
-    const toHeight = (n) => toY(originY) - toY(n);
-    const toY2 = (n) => height - (indicatorViewScale(n) || 0) + offset;
-    const toHeight2 = (n) => toY2(originLinear) - toY2(n);
-    const { bases, softclip, hardclip, insertion } = theme.palette;
-    const colorMap = {
-        A: bases.A.main,
-        C: bases.C.main,
-        G: bases.G.main,
-        T: bases.T.main,
-        insertion,
-        softclip,
-        hardclip,
-        total: (0, configuration_1.readConfObject)(cfg, 'color'),
-        mod_NONE: 'blue',
-        cpg_meth: 'red',
-        cpg_unmeth: 'blue',
-    };
-    ctx.fillStyle = colorMap.total;
-    (0, util_1.forEachWithStopTokenCheck)(features.values(), stopToken, feature => {
-        if (feature.get('type') === 'skip') {
-            return;
-        }
-        const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-        const w = rightPx - leftPx + fudgeFactor;
-        const score = feature.get('score');
-        ctx.fillRect(leftPx, toY(score), w, toHeight(score));
-    });
-    let prevTotal = 0;
-    const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0;
-    const drawingModifications = colorBy.type === 'modifications';
-    const drawingMethylation = colorBy.type === 'methylation';
-    const isolatedModification = (_a = colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
-    (0, util_1.forEachWithStopTokenCheck)(features.values(), stopToken, feature => {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
-        if (feature.get('type') === 'skip') {
-            return;
-        }
-        const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-        const snpinfo = feature.get('snpinfo');
-        const w = Math.max(rightPx - leftPx, 1);
-        const score0 = feature.get('score');
-        if (drawingModifications) {
-            let curr = 0;
-            const refbase = (_a = snpinfo.refbase) === null || _a === void 0 ? void 0 : _a.toUpperCase();
-            const { nonmods, mods, snps, ref } = snpinfo;
-            for (const m of Object.keys(nonmods).sort().reverse()) {
-                const mod = visibleModifications[m.replace('nonmod_', '')] ||
-                    visibleModifications[m.replace('mod_', '')];
-                if (!mod) {
-                    console.warn(`${m} not known yet`);
-                    continue;
-                }
-                if (isolatedModification && mod.type !== isolatedModification) {
-                    continue;
-                }
-                const cmp = complementBase[mod.base];
-                const detectable = mod.base === 'N'
-                    ? score0
-                    : (((_b = snps[mod.base]) === null || _b === void 0 ? void 0 : _b.entryDepth) || 0) +
-                        (((_c = snps[cmp]) === null || _c === void 0 ? void 0 : _c.entryDepth) || 0) +
-                        (refbase === mod.base ? ref['1'] : 0) +
-                        (refbase === cmp ? ref['-1'] : 0);
-                const modifiable = mod.base === 'N'
-                    ? score0
-                    : (((_d = snps[mod.base]) === null || _d === void 0 ? void 0 : _d.entryDepth) || 0) +
-                        (((_e = snps[cmp]) === null || _e === void 0 ? void 0 : _e.entryDepth) || 0) +
-                        (refbase === mod.base ? ref.entryDepth : 0) +
-                        (refbase === cmp ? ref.entryDepth : 0);
-                const { entryDepth, avgProbability = 0 } = snpinfo.nonmods[m];
-                const modFraction = (modifiable / score0) * (entryDepth / detectable);
-                const nonModColor = 'blue';
-                const c = (0, util_2.alphaColor)(nonModColor, avgProbability);
-                const height = toHeight(score0);
-                const bottom = toY(score0) + height;
-                ctx.fillStyle = c;
-                ctx.fillRect(Math.round(leftPx), bottom - (curr + modFraction * height), w, modFraction * height);
-                curr += modFraction * height;
-            }
-            for (const m of Object.keys(mods).sort().reverse()) {
-                const mod = visibleModifications[m.replace('mod_', '')];
-                if (!mod) {
-                    console.warn(`${m} not known yet`);
-                    continue;
-                }
-                if (isolatedModification && mod.type !== isolatedModification) {
-                    continue;
-                }
-                const cmp = complementBase[mod.base];
-                const detectable = mod.base === 'N'
-                    ? score0
-                    : (((_f = snps[mod.base]) === null || _f === void 0 ? void 0 : _f.entryDepth) || 0) +
-                        (((_g = snps[cmp]) === null || _g === void 0 ? void 0 : _g.entryDepth) || 0) +
-                        (refbase === mod.base ? ref['1'] : 0) +
-                        (refbase === cmp ? ref['-1'] : 0);
-                const modifiable = mod.base === 'N'
-                    ? score0
-                    : (((_h = snps[mod.base]) === null || _h === void 0 ? void 0 : _h.entryDepth) || 0) +
-                        (((_j = snps[cmp]) === null || _j === void 0 ? void 0 : _j.entryDepth) || 0) +
-                        (refbase === mod.base ? ref.entryDepth : 0) +
-                        (refbase === cmp ? ref.entryDepth : 0);
-                const { entryDepth, avgProbability = 0 } = mods[m];
-                const modFraction = (modifiable / score0) * (entryDepth / detectable);
-                const baseColor = mod.color || 'black';
-                const c = (0, util_2.alphaColor)(baseColor, avgProbability);
-                const height = toHeight(score0);
-                const bottom = toY(score0) + height;
-                ctx.fillStyle = c;
-                ctx.fillRect(Math.round(leftPx), bottom - (curr + modFraction * height), w, modFraction * height);
-                curr += modFraction * height;
-            }
-        }
-        else if (drawingMethylation) {
-            const { depth, nonmods, mods } = snpinfo;
-            let curr = 0;
-            for (const base of Object.keys(mods).sort().reverse()) {
-                const { entryDepth } = mods[base];
-                const height = toHeight(score0);
-                const bottom = toY(score0) + height;
-                ctx.fillStyle = colorMap[base] || 'black';
-                ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
-                curr += entryDepth;
-            }
-            for (const base of Object.keys(nonmods).sort().reverse()) {
-                const { entryDepth } = nonmods[base];
-                const height = toHeight(score0);
-                const bottom = toY(score0) + height;
-                ctx.fillStyle = colorMap[base] || 'black';
-                ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
-                curr += entryDepth;
-            }
-        }
-        else {
-            const { depth, snps } = snpinfo;
-            let curr = 0;
-            for (const base of Object.keys(snps).sort().reverse()) {
-                const { entryDepth } = snps[base];
-                const height = toHeight(score0);
-                const bottom = toY(score0) + height;
-                ctx.fillStyle = colorMap[base] || 'black';
-                ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
-                curr += entryDepth;
-            }
-        }
-        const interbaseEvents = Object.keys(snpinfo.noncov);
-        if (showInterbaseCounts) {
-            let curr = 0;
-            for (const base of interbaseEvents) {
-                const { entryDepth } = snpinfo.noncov[base];
-                const r = 0.6;
-                ctx.fillStyle = colorMap[base];
-                ctx.fillRect(leftPx - r + extraHorizontallyFlippedOffset, INTERBASE_INDICATOR_HEIGHT + toHeight2(curr), r * 2, toHeight2(entryDepth));
-                curr += entryDepth;
-            }
-        }
-        if (showInterbaseIndicators) {
-            let accum = 0;
-            let max = 0;
-            let maxBase = '';
-            for (const base of interbaseEvents) {
-                const { entryDepth } = snpinfo.noncov[base];
-                accum += entryDepth;
-                if (entryDepth > max) {
-                    max = entryDepth;
-                    maxBase = base;
-                }
-            }
-            const indicatorComparatorScore = Math.max(score0, prevTotal);
-            if (accum > indicatorComparatorScore * indicatorThreshold &&
-                indicatorComparatorScore > MINIMUM_INTERBASE_INDICATOR_READ_DEPTH) {
-                ctx.fillStyle = colorMap[maxBase];
-                ctx.beginPath();
-                const l = leftPx + extraHorizontallyFlippedOffset;
-                ctx.moveTo(l - INTERBASE_INDICATOR_WIDTH / 2, 0);
-                ctx.lineTo(l + INTERBASE_INDICATOR_WIDTH / 2, 0);
-                ctx.lineTo(l, INTERBASE_INDICATOR_HEIGHT);
-                ctx.fill();
-            }
-        }
-        prevTotal = score0;
-    });
-    if (showArcs) {
-        (0, util_1.forEachWithStopTokenCheck)(features.values(), stopToken, feature => {
-            if (feature.get('type') !== 'skip') {
-                return;
-            }
-            const s = feature.get('start');
-            const e = feature.get('end');
-            const [left, right] = (0, util_1.bpSpanPx)(s, e, region, bpPerPx);
-            ctx.beginPath();
-            const effectiveStrand = feature.get('effectiveStrand');
-            const pos = 'rgba(255,200,200,0.7)';
-            const neg = 'rgba(200,200,255,0.7)';
-            const neutral = 'rgba(200,200,200,0.7)';
-            if (effectiveStrand === 1) {
-                ctx.strokeStyle = pos;
-            }
-            else if (effectiveStrand === -1) {
-                ctx.strokeStyle = neg;
-            }
-            else {
-                ctx.strokeStyle = neutral;
-            }
-            ctx.lineWidth = Math.log(feature.get('score') + 1);
-            ctx.moveTo(left, height - offset * 2);
-            ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2);
-            ctx.stroke();
-        });
-    }
-    if (displayCrossHatches) {
-        ctx.lineWidth = 1;
-        ctx.strokeStyle = 'rgba(140,140,140,0.8)';
-        for (const tick of ticks.values) {
-            ctx.beginPath();
-            ctx.moveTo(0, Math.round(toY(tick)));
-            ctx.lineTo(width, Math.round(toY(tick)));
-            ctx.stroke();
-        }
-    }
-}

package/dist/SNPCoverageRenderer/types.d.ts

@@ -1,20 +0,0 @@
-import type { ColorBy, ModificationTypeWithColor } from '../shared/types';
-import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import type { Feature } from '@jbrowse/core/util';
-import type { ScaleOpts } from '@jbrowse/plugin-wiggle';
-export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
-    bpPerPx: number;
-    height: number;
-    highResolutionScaling: number;
-    scaleOpts: ScaleOpts;
-}
-export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
-    features: Map<string, Feature>;
-    ticks: {
-        values: number[];
-    };
-    displayCrossHatches: boolean;
-    visibleModifications?: Record<string, ModificationTypeWithColor>;
-    statusCallback?: (arg: string) => void;
-    colorBy: ColorBy;
-}

package/dist/SNPCoverageRenderer/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/index.d.ts

@@ -1,9 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default class AlignmentsPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}
-export { SharedLinearPileupDisplayMixin, linearPileupDisplayConfigSchemaFactory, linearPileupDisplayStateModelFactory, } from './LinearPileupDisplay';
-export { type LinearPileupDisplayModel } from './LinearPileupDisplay/model';
-export * as MismatchParser from './MismatchParser';

package/dist/index.js

@@ -1,89 +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 });
-exports.MismatchParser = exports.linearPileupDisplayStateModelFactory = exports.linearPileupDisplayConfigSchemaFactory = exports.SharedLinearPileupDisplayMixin = void 0;
-const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const AlignmentsFeatureDetail_1 = __importDefault(require("./AlignmentsFeatureDetail"));
-const AlignmentsTrack_1 = __importDefault(require("./AlignmentsTrack"));
-const BamAdapter_1 = __importDefault(require("./BamAdapter"));
-const CramAdapter_1 = __importDefault(require("./CramAdapter"));
-const GuessAlignmentsTypes_1 = __importDefault(require("./GuessAlignmentsTypes"));
-const HtsgetBamAdapter_1 = __importDefault(require("./HtsgetBamAdapter"));
-const LinearAlignmentsDisplay_1 = __importDefault(require("./LinearAlignmentsDisplay"));
-const LinearPileupDisplay_1 = __importDefault(require("./LinearPileupDisplay"));
-const LinearReadArcsDisplay_1 = __importDefault(require("./LinearReadArcsDisplay"));
-const LinearReadCloudDisplay_1 = __importDefault(require("./LinearReadCloudDisplay"));
-const LinearSNPCoverageDisplay_1 = __importDefault(require("./LinearSNPCoverageDisplay"));
-const PileupRPC_1 = __importDefault(require("./PileupRPC"));
-const PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
-const SNPCoverageAdapter_1 = __importDefault(require("./SNPCoverageAdapter"));
-const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
-class AlignmentsPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'AlignmentsPlugin';
-    }
-    install(pluginManager) {
-        ;
-        [
-            BamAdapter_1.default,
-            CramAdapter_1.default,
-            LinearPileupDisplay_1.default,
-            LinearSNPCoverageDisplay_1.default,
-            AlignmentsTrack_1.default,
-            SNPCoverageAdapter_1.default,
-            HtsgetBamAdapter_1.default,
-            PileupRenderer_1.default,
-            PileupRPC_1.default,
-            SNPCoverageRenderer_1.default,
-            LinearReadArcsDisplay_1.default,
-            LinearReadCloudDisplay_1.default,
-            LinearAlignmentsDisplay_1.default,
-            AlignmentsFeatureDetail_1.default,
-            GuessAlignmentsTypes_1.default,
-        ].map(f => {
-            f(pluginManager);
-        });
-    }
-}
-exports.default = AlignmentsPlugin;
-var LinearPileupDisplay_2 = require("./LinearPileupDisplay");
-Object.defineProperty(exports, "SharedLinearPileupDisplayMixin", { enumerable: true, get: function () { return LinearPileupDisplay_2.SharedLinearPileupDisplayMixin; } });
-Object.defineProperty(exports, "linearPileupDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearPileupDisplay_2.linearPileupDisplayConfigSchemaFactory; } });
-Object.defineProperty(exports, "linearPileupDisplayStateModelFactory", { enumerable: true, get: function () { return LinearPileupDisplay_2.linearPileupDisplayStateModelFactory; } });
-exports.MismatchParser = __importStar(require("./MismatchParser"));

package/dist/shared/afterAttach.d.ts

@@ -1,2 +0,0 @@
-import type { IAnyStateTreeNode } from 'mobx-state-tree';
-export declare function doAfterAttach<T extends IAnyStateTreeNode>(self: T, cb: (self: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): void;

package/dist/shared/afterAttach.js

@@ -1,40 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.doAfterAttach = doAfterAttach;
-const util_1 = require("@jbrowse/core/util");
-const util_2 = require("../util");
-const fetchChains_1 = require("./fetchChains");
-function doAfterAttach(self, cb) {
-    (0, util_2.createAutorun)(self, async () => {
-        await (0, fetchChains_1.fetchChains)(self);
-    }, { delay: 1000 });
-    function draw(view) {
-        const canvas = self.ref;
-        if (!canvas) {
-            return;
-        }
-        const ctx = canvas.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        if (!self.chainData) {
-            return;
-        }
-        ctx.clearRect(0, 0, canvas.width, self.height * 2);
-        ctx.resetTransform();
-        ctx.scale(2, 2);
-        cb(self, ctx, canvas.width, self.height);
-        self.setLastDrawnOffsetPx(view.offsetPx);
-        self.setLastDrawnBpPerPx(view.bpPerPx);
-    }
-    (0, util_2.createAutorun)(self, async () => {
-        const view = (0, util_1.getContainingView)(self);
-        if (view.bpPerPx !== self.lastDrawnBpPerPx) {
-            draw(view);
-        }
-    });
-    (0, util_2.createAutorun)(self, async () => {
-        const view = (0, util_1.getContainingView)(self);
-        draw(view);
-    }, { delay: 1000 });
-}

package/dist/shared/color.d.ts

@@ -1,58 +0,0 @@
-import type { ChainStats } from './fetchChains';
-export declare const fillColor: {
-    color_fwd_strand_not_proper: string;
-    color_rev_strand_not_proper: string;
-    color_fwd_strand: string;
-    color_rev_strand: string;
-    color_fwd_missing_mate: string;
-    color_rev_missing_mate: string;
-    color_fwd_diff_chr: string;
-    color_rev_diff_chr: string;
-    color_pair_lr: string;
-    color_pair_rr: string;
-    color_pair_rl: string;
-    color_pair_ll: string;
-    color_nostrand: string;
-    color_interchrom: string;
-    color_longinsert: string;
-    color_shortinsert: string;
-    color_unknown: string;
-};
-export declare const strokeColor: {
-    color_fwd_strand_not_proper: string;
-    color_rev_strand_not_proper: string;
-    color_fwd_strand: string;
-    color_rev_strand: string;
-    color_fwd_missing_mate: string;
-    color_rev_missing_mate: string;
-    color_fwd_diff_chr: string;
-    color_rev_diff_chr: string;
-    color_pair_lr: string;
-    color_pair_rr: string;
-    color_pair_rl: string;
-    color_pair_ll: string;
-    color_nostrand: string;
-    color_interchrom: string;
-    color_longinsert: string;
-    color_shortinsert: string;
-    color_unknown: string;
-};
-export declare function getPairedInsertSizeColor(f1: {
-    refName: string;
-    tlen?: number;
-}, f2: {
-    refName: string;
-}, stats?: ChainStats): readonly [string, string] | undefined;
-export declare function getPairedInsertSizeAndOrientationColor(f1: {
-    refName: string;
-    pair_orientation?: string;
-    tlen?: number;
-}, f2: {
-    refName: string;
-}, stats?: ChainStats): readonly [string, string];
-export declare function getPairedOrientationColorOrDefault(f: {
-    pair_orientation?: string;
-}): readonly [string, string] | undefined;
-export declare function getPairedOrientationColor(f: {
-    pair_orientation?: string;
-}): readonly [string, string];

package/dist/shared/color.js

@@ -1,79 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.strokeColor = exports.fillColor = void 0;
-exports.getPairedInsertSizeColor = getPairedInsertSizeColor;
-exports.getPairedInsertSizeAndOrientationColor = getPairedInsertSizeAndOrientationColor;
-exports.getPairedOrientationColorOrDefault = getPairedOrientationColorOrDefault;
-exports.getPairedOrientationColor = getPairedOrientationColor;
-const util_1 = require("../util");
-exports.fillColor = {
-    color_fwd_strand_not_proper: '#ECC8C8',
-    color_rev_strand_not_proper: '#BEBED8',
-    color_fwd_strand: '#EC8B8B',
-    color_rev_strand: '#8F8FD8',
-    color_fwd_missing_mate: '#D11919',
-    color_rev_missing_mate: '#1919D1',
-    color_fwd_diff_chr: '#000',
-    color_rev_diff_chr: '#969696',
-    color_pair_lr: '#c8c8c8',
-    color_pair_rr: 'navy',
-    color_pair_rl: 'teal',
-    color_pair_ll: 'green',
-    color_nostrand: '#c8c8c8',
-    color_interchrom: 'purple',
-    color_longinsert: 'red',
-    color_shortinsert: 'pink',
-    color_unknown: 'grey',
-};
-exports.strokeColor = {
-    color_fwd_strand_not_proper: '#CA6767',
-    color_rev_strand_not_proper: '#7272AA',
-    color_fwd_strand: '#DC2A2A',
-    color_rev_strand: '#4141BA',
-    color_fwd_missing_mate: '#921111',
-    color_rev_missing_mate: '#111192',
-    color_fwd_diff_chr: '#000000',
-    color_rev_diff_chr: '#696969',
-    color_pair_lr: '#8C8C8C',
-    color_pair_rr: '#00005A',
-    color_pair_rl: '#005A5A',
-    color_pair_ll: '#005A00',
-    color_nostrand: '#8C8C8C',
-    color_interchrom: '#5A005A',
-    color_longinsert: '#B30000',
-    color_shortinsert: '#FF3A5C',
-    color_unknown: 'grey',
-};
-function getPairedInsertSizeColor(f1, f2, stats) {
-    const sameRef = f1.refName === f2.refName;
-    const tlen = Math.abs(f1.tlen || 0);
-    if (sameRef && tlen > ((stats === null || stats === void 0 ? void 0 : stats.upper) || 0)) {
-        return [exports.fillColor.color_longinsert, exports.strokeColor.color_longinsert];
-    }
-    else if (sameRef && tlen < ((stats === null || stats === void 0 ? void 0 : stats.lower) || 0)) {
-        return [exports.fillColor.color_shortinsert, exports.strokeColor.color_shortinsert];
-    }
-    else if (!sameRef) {
-        return [exports.fillColor.color_interchrom, exports.strokeColor.color_interchrom];
-    }
-    else {
-        return undefined;
-    }
-}
-const defaultColor = [exports.fillColor.color_unknown, exports.fillColor.color_unknown];
-function getPairedInsertSizeAndOrientationColor(f1, f2, stats) {
-    return (getPairedOrientationColorOrDefault(f1) ||
-        getPairedInsertSizeColor(f1, f2, stats) ||
-        defaultColor);
-}
-function getPairedOrientationColorOrDefault(f) {
-    const type = util_1.orientationTypes.fr;
-    const r = type[f.pair_orientation || ''];
-    const type2 = util_1.pairMap[r];
-    return r === 'LR'
-        ? undefined
-        : [exports.fillColor[type2], exports.strokeColor[type2]];
-}
-function getPairedOrientationColor(f) {
-    return getPairedOrientationColorOrDefault(f) || defaultColor;
-}

package/dist/shared/components/BaseDisplayComponent.d.ts

@@ -1,7 +0,0 @@
-import type { LinearReadArcsDisplayModel } from '../../LinearReadArcsDisplay/model';
-import type { LinearReadCloudDisplayModel } from '../../LinearReadCloudDisplay/model';
-declare const BaseDisplayComponent: ({ model, children, }: {
-    model: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel;
-    children?: React.ReactNode;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default BaseDisplayComponent;