@jbrowse/plugin-arc 3.7.0 → 4.0.0

package/dist/LinearPairedArcDisplay/util.js

@@ -1,119 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.modificationColors = exports.pairMap = exports.orientationTypes = void 0;
-exports.getTag = getTag;
-exports.getTagAlt = getTagAlt;
-exports.getColorWGBS = getColorWGBS;
-exports.fetchSequence = fetchSequence;
-exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
-exports.createAutorun = createAutorun;
-exports.randomColor = randomColor;
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const rxjs_1 = require("rxjs");
-const operators_1 = require("rxjs/operators");
-function getTag(feature, tag) {
-    return feature.get('tags')[tag];
-}
-function getTagAlt(feature, tag, alt) {
-    var _a;
-    return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
-}
-exports.orientationTypes = {
-    fr: {
-        F1R2: 'LR',
-        F2R1: 'LR',
-        F1F2: 'LL',
-        F2F1: 'LL',
-        R1R2: 'RR',
-        R2R1: 'RR',
-        R1F2: 'RL',
-        R2F1: 'RL',
-    },
-    rf: {
-        R1F2: 'LR',
-        R2F1: 'LR',
-        R1R2: 'LL',
-        R2R1: 'LL',
-        F1F2: 'RR',
-        F2F1: 'RR',
-        F1R2: 'RL',
-        F2R1: 'RL',
-    },
-    ff: {
-        F2F1: 'LR',
-        R1R2: 'LR',
-        F2R1: 'LL',
-        R1F2: 'LL',
-        R2F1: 'RR',
-        F1R2: 'RR',
-        R2R1: 'RL',
-        F1F2: 'RL',
-    },
-};
-exports.pairMap = {
-    LR: 'color_pair_lr',
-    LL: 'color_pair_ll',
-    RR: 'color_pair_rr',
-    RL: 'color_pair_rl',
-};
-function getColorWGBS(strand, base) {
-    if (strand === 1) {
-        if (base === 'C') {
-            return '#f00';
-        }
-        if (base === 'T') {
-            return '#00f';
-        }
-    }
-    else if (strand === -1) {
-        if (base === 'G') {
-            return '#f00';
-        }
-        if (base === 'A') {
-            return '#00f';
-        }
-    }
-    return '#888';
-}
-async function fetchSequence(region, adapter) {
-    var _a;
-    const { start, end, originalRefName, refName } = region;
-    const feats = await (0, rxjs_1.firstValueFrom)(adapter
-        .getFeatures({
-        ...region,
-        refName: originalRefName || refName,
-        end: end + 1,
-        start: Math.max(0, start - 1),
-    })
-        .pipe((0, operators_1.toArray)()));
-    return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
-}
-function shouldFetchReferenceSequence(type) {
-    return type === 'methylation';
-}
-exports.modificationColors = {
-    m: 'rgb(255,0,0)',
-    h: 'rgb(11, 132, 165)',
-    o: 'rgb(111, 78, 129)',
-    f: 'rgb(246, 200, 95)',
-    c: 'rgb(157, 216, 102)',
-    g: 'rgb(255, 160, 86)',
-    e: 'rgb(141, 221, 208)',
-    b: 'rgb(202, 71, 47)',
-};
-function createAutorun(self, cb, opts) {
-    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-        try {
-            await cb();
-        }
-        catch (e) {
-            if ((0, mobx_state_tree_1.isAlive)(self)) {
-                self.setError(e);
-            }
-        }
-    }, opts));
-}
-function randomColor() {
-    return `hsl(${Math.random() * 200}, 50%, 50%)`;
-}

package/dist/index.d.ts

@@ -1,6 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default class ArcPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}

package/dist/index.js

@@ -1,43 +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 Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const colors_1 = require("@jbrowse/core/ui/colors");
-const ArcRenderer_1 = __importDefault(require("./ArcRenderer"));
-const LinearArcDisplay_1 = __importDefault(require("./LinearArcDisplay"));
-const LinearPairedArcDisplay_1 = __importDefault(require("./LinearPairedArcDisplay"));
-class ArcPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'ArcRenderer';
-    }
-    install(pluginManager) {
-        (0, ArcRenderer_1.default)(pluginManager);
-        (0, LinearArcDisplay_1.default)(pluginManager);
-        (0, LinearPairedArcDisplay_1.default)(pluginManager);
-        pluginManager.jexl.addFunction('logThickness', (feature, attributeName) => Math.log(feature.get(attributeName) + 1));
-        pluginManager.jexl.addFunction('defaultPairedArcColor', (_feature, alt) => {
-            if (alt === null || alt === void 0 ? void 0 : alt.startsWith('<DEL')) {
-                return colors_1.set1[0];
-            }
-            else if (alt === null || alt === void 0 ? void 0 : alt.startsWith('<DUP')) {
-                return colors_1.set1[1];
-            }
-            else if (alt === null || alt === void 0 ? void 0 : alt.startsWith('<INV')) {
-                return colors_1.set1[2];
-            }
-            else if (alt === null || alt === void 0 ? void 0 : alt.startsWith('<TRA')) {
-                return colors_1.set1[3];
-            }
-            else if (alt === null || alt === void 0 ? void 0 : alt.startsWith('<CNV')) {
-                return colors_1.set1[4];
-            }
-            else {
-                return colors_1.set1[6];
-            }
-        });
-    }
-}
-exports.default = ArcPlugin;