@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/dist/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.d.ts

@@ -1 +0,0 @@
-export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';

package/dist/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js

@@ -1,5 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = void 0;
-var sv_core_1 = require("@jbrowse/sv-core");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendSingleLevelOptionDialog; } });

package/dist/AlignmentsFeatureDetail/Flags.d.ts

@@ -1,3 +0,0 @@
-export default function AlignmentFlags(props: {
-    flags: number;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/Flags.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 = AlignmentFlags;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-const SimpleField_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()({
-    compact: {
-        paddingRight: 0,
-        paddingTop: 0,
-        paddingBottom: 0,
-    },
-});
-const flagNames = [
-    'read paired',
-    'read mapped in proper pair',
-    'read unmapped',
-    'mate unmapped',
-    'read reverse strand',
-    'mate reverse strand',
-    'first in pair',
-    'second in pair',
-    'not primary alignment',
-    'read fails platform/vendor quality checks',
-    'read is PCR or optical duplicate',
-    'supplementary alignment',
-];
-function AlignmentFlags(props) {
-    const { classes } = useStyles();
-    const { flags } = props;
-    return ((0, jsx_runtime_1.jsxs)(BaseCard_1.default, { ...props, title: "Flags", children: [(0, jsx_runtime_1.jsx)(SimpleField_1.default, { name: "Flag", value: flags }), (0, jsx_runtime_1.jsx)(material_1.FormGroup, { children: flagNames.map((name, idx) => {
-                    const val = flags & (1 << idx);
-                    const key = `${name}_${val}`;
-                    return ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { className: classes.compact, checked: Boolean(val), name: name, readOnly: true }), label: name }, key));
-                }) })] }));
-}

package/dist/AlignmentsFeatureDetail/Formatter.d.ts

@@ -1,3 +0,0 @@
-export default function Formatter({ value }: {
-    value: unknown;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/Formatter.js

@@ -1,23 +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 = Formatter;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-function Formatter({ value }) {
-    const [show, setShow] = (0, react_1.useState)(false);
-    const [copied, setCopied] = (0, react_1.useState)(false);
-    const display = String(value);
-    return display.length > 100 ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
-                    (0, copy_to_clipboard_1.default)(display);
-                    setCopied(true);
-                    setTimeout(() => {
-                        setCopied(false);
-                    }, 700);
-                }, children: copied ? 'Copied to clipboard' : 'Copy' }), (0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
-                    setShow(val => !val);
-                }, children: show ? 'Show less' : 'Show more' }), (0, jsx_runtime_1.jsx)("div", { children: show ? display : `${display.slice(0, 100)}...` })] })) : ((0, jsx_runtime_1.jsx)("div", { children: display }));
-}

package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts

@@ -1,6 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }: {
-    model: AlignmentFeatureWidgetModel;
-    feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js

@@ -1,84 +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;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = LaunchPairedEndBreakpointSplitViewPanel;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const BreakendMultiLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendMultiLevelOptionDialog'))));
-const BreakendSingleLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendSingleLevelOptionDialog'))));
-function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }) {
-    const session = (0, util_1.getSession)(model);
-    const f1 = {
-        uniqueId: feature.uniqueId,
-        refName: feature.refName,
-        start: feature.start,
-        end: feature.end,
-        strand: feature.strand,
-    };
-    const f2 = {
-        uniqueId: `${feature.id}-mate`,
-        refName: feature.next_ref,
-        start: feature.next_pos,
-        end: feature.next_pos + 1,
-        strand: feature.strand,
-    };
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Launch split view" }), (0, jsx_runtime_1.jsx)("ul", { children: (0, jsx_runtime_1.jsxs)("li", { children: [f1.refName, ":", (0, util_1.toLocale)(f1.start), " -> ", f2.refName, ":", (0, util_1.toLocale)(f2.start), ' ', (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
-                                event.preventDefault();
-                                session.queueDialog(handleClose => [
-                                    BreakendMultiLevelOptionDialog,
-                                    {
-                                        handleClose,
-                                        session,
-                                        feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                        view: model.view,
-                                        assemblyName: model.view.displayedRegions[0].assemblyName,
-                                    },
-                                ]);
-                            }, children: "(top/bottom)" }), ' ', (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
-                                event.preventDefault();
-                                session.queueDialog(handleClose => [
-                                    BreakendSingleLevelOptionDialog,
-                                    {
-                                        handleClose,
-                                        session,
-                                        feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                        view: model.view,
-                                        assemblyName: model.view.displayedRegions[0].assemblyName,
-                                    },
-                                ]);
-                            }, children: "(single row)" })] }) })] }));
-}

package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.d.ts

@@ -1,6 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-export default function LaunchBreakpointSplitViewPanel({ model, feature, }: {
-    model: AlignmentFeatureWidgetModel;
-    feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element | null;

package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js

@@ -1,107 +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;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = LaunchBreakpointSplitViewPanel;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const getSAFeatures_1 = require("./getSAFeatures");
-const BreakendMultiLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendMultiLevelOptionDialog'))));
-const BreakendSingleLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendSingleLevelOptionDialog'))));
-function LaunchBreakpointSplitViewPanel({ model, feature, }) {
-    const { view } = model;
-    const [res, setRes] = (0, react_1.useState)();
-    const [error, setError] = (0, react_1.useState)();
-    (0, react_1.useEffect)(() => {
-        ;
-        (async () => {
-            try {
-                const feats = await (0, getSAFeatures_1.getSAFeatures)({
-                    view,
-                    feature: new util_1.SimpleFeature(feature),
-                });
-                setRes(feats);
-            }
-            catch (e) {
-                setError(e);
-                console.error(e);
-            }
-        })();
-    }, [feature, view]);
-    const ret = [];
-    if (res) {
-        for (let i = 0; i < res.length - 1; i++) {
-            ret.push([res[i], res[i + 1]]);
-        }
-    }
-    return ret.length ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Launch split view" }), error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsx)("ul", { children: ret.map((arg, index) => {
-                    const [f1, f2] = arg;
-                    return ((0, jsx_runtime_1.jsxs)("li", { children: [f1.refName, ":", (0, util_1.toLocale)(f1.strand === 1 ? f1.end : f1.start), " ->", ' ', f2.refName, ":", (0, util_1.toLocale)(f2.strand === 1 ? f2.start : f2.end), ' ', (0, jsx_runtime_1.jsx)(TopBottomSplitViewLink, { model: model, f1: f1, f2: f2 }), ' ', (0, jsx_runtime_1.jsx)(SideBySideViewLink, { model: model, f1: f1, f2: f2 })] }, `${JSON.stringify(arg)}-${index}`));
-                }) })] })) : null;
-}
-function TopBottomSplitViewLink({ model, f1, f2, }) {
-    return ((0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
-            event.preventDefault();
-            const session = (0, util_1.getSession)(model);
-            session.queueDialog(handleClose => [
-                BreakendMultiLevelOptionDialog,
-                {
-                    handleClose,
-                    session,
-                    feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                    view: model.view,
-                    assemblyName: model.view.displayedRegions[0].assemblyName,
-                },
-            ]);
-        }, children: "(top/bottom)" }));
-}
-function SideBySideViewLink({ model, f1, f2, }) {
-    return ((0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
-            event.preventDefault();
-            const session = (0, util_1.getSession)(model);
-            session.queueDialog(handleClose => [
-                BreakendSingleLevelOptionDialog,
-                {
-                    handleClose,
-                    session,
-                    feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                    view: model.view,
-                    assemblyName: model.view.displayedRegions[0].assemblyName,
-                },
-            ]);
-        }, children: "(single row)" }));
-}

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts

@@ -1,6 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-export default function SuppAlignments(props: {
-    model: AlignmentFeatureWidgetModel;
-    feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element | null;

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -1,22 +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 = SuppAlignments;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-const util_1 = require("@jbrowse/core/util");
-const LaunchPairedEndBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchPairedEndBreakpointSplitViewPanel"));
-function SuppAlignments(props) {
-    const { model, feature } = props;
-    const session = (0, util_1.getSession)(model);
-    const { pluginManager } = (0, util_1.getEnv)(session);
-    let hasBreakendSplitView = false;
-    try {
-        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
-    }
-    catch (e) {
-    }
-    return hasBreakendSplitView ? ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { ...props, title: "Paired alignments", children: (0, jsx_runtime_1.jsx)(LaunchPairedEndBreakpointSplitViewPanel_1.default, { model: model, feature: feature }) })) : null;
-}

package/dist/AlignmentsFeatureDetail/PairLink.d.ts

@@ -1,5 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function PairLink({ locString, model, }: {
-    locString: string;
-    model: AlignmentFeatureWidgetModel;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/PairLink.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = PairLink;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const material_1 = require("@mui/material");
-const util_1 = require("./util");
-function PairLink({ locString, model, }) {
-    return ((0, jsx_runtime_1.jsx)(material_1.Link, { onClick: event => {
-            event.preventDefault();
-            (0, util_1.navToLoc)(locString, model);
-        }, href: "#", children: locString }));
-}

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts

@@ -1,7 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-export default function SupplementaryAlignments(props: {
-    tag: string;
-    model: AlignmentFeatureWidgetModel;
-    feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.js

@@ -1,23 +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 = SupplementaryAlignments;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-const util_1 = require("@jbrowse/core/util");
-const LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchSupplementaryAlignmentBreakpointSplitViewPanel"));
-const SupplementaryAlignmentsLocStrings_1 = __importDefault(require("./SupplementaryAlignmentsLocStrings"));
-function SupplementaryAlignments(props) {
-    const { model, tag, feature } = props;
-    const session = (0, util_1.getSession)(model);
-    const { pluginManager } = (0, util_1.getEnv)(session);
-    let hasBreakendSplitView = false;
-    try {
-        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
-    }
-    catch (e) {
-    }
-    return ((0, jsx_runtime_1.jsxs)(BaseCard_1.default, { ...props, title: "Supplementary alignments", children: [(0, jsx_runtime_1.jsx)(SupplementaryAlignmentsLocStrings_1.default, { model: model, tag: tag }), hasBreakendSplitView ? ((0, jsx_runtime_1.jsx)(LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1.default, { model: model, feature: feature })) : null] }));
-}

package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts

@@ -1,5 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function SupplementaryAlignmentsLocStrings({ tag, model, }: {
-    tag: string;
-    model: AlignmentFeatureWidgetModel;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js

@@ -1,29 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SupplementaryAlignmentsLocStrings;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const material_1 = require("@mui/material");
-const MismatchParser_1 = require("../MismatchParser");
-const util_1 = require("./util");
-function SupplementaryAlignmentsLocStrings({ tag, model, }) {
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "List of supplementary alignment locations" }), (0, jsx_runtime_1.jsx)("ul", { children: tag
-                    .split(';')
-                    .filter(SA => !!SA)
-                    .map((SA, idx) => {
-                    const [saRef, saStart, saStrand, saCigar] = SA.split(',');
-                    const saLength = (0, MismatchParser_1.getLengthOnRef)(saCigar);
-                    const extra = Math.floor(saLength / 5);
-                    const start = +saStart;
-                    const end = +saStart + saLength;
-                    const sp = start - extra;
-                    const ep = end + extra;
-                    const locString = `${saRef}:${Math.max(1, sp)}-${ep}`;
-                    const displayStart = start.toLocaleString('en-US');
-                    const displayEnd = end.toLocaleString('en-US');
-                    const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
-                    return ((0, jsx_runtime_1.jsx)("li", { children: (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: async (event) => {
-                                event.preventDefault();
-                                (0, util_1.navToLoc)(locString, model);
-                            }, children: displayString }) }, `${locString}-${idx}`));
-                }) })] }));
-}

package/dist/AlignmentsFeatureDetail/configSchema.d.ts

@@ -1 +0,0 @@
-export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/dist/AlignmentsFeatureDetail/configSchema.js

@@ -1,5 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = void 0;
-const configuration_1 = require("@jbrowse/core/configuration");
-exports.configSchema = (0, configuration_1.ConfigurationSchema)('AlignmentsFeatureWidget', {});

package/dist/AlignmentsFeatureDetail/getSAFeatures.d.ts

@@ -1,23 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export interface ReducedFeature {
-    refName: string;
-    start: number;
-    clipPos: number;
-    end: number;
-    strand: number;
-    seqLength: number;
-    syntenyId?: number;
-    uniqueId: string;
-    mate: {
-        refName: string;
-        start: number;
-        end: number;
-        syntenyId?: number;
-        uniqueId?: string;
-    };
-}
-export declare function getSAFeatures({ view, feature, }: {
-    view: LinearGenomeViewModel;
-    feature: Feature;
-}): Promise<ReducedFeature[]>;

package/dist/AlignmentsFeatureDetail/getSAFeatures.js

@@ -1,36 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getSAFeatures = getSAFeatures;
-const util_1 = require("@jbrowse/core/util");
-const MismatchParser_1 = require("../MismatchParser");
-async function getSAFeatures({ view, feature, }) {
-    var _a;
-    const { assemblyManager } = (0, util_1.getSession)(view);
-    const cigar = feature.get('CIGAR');
-    const origStrand = feature.get('strand');
-    const SA = ((_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a.SA) || '';
-    const readName = feature.get('name');
-    const clipPos = (0, MismatchParser_1.getClip)(cigar, 1);
-    const assembly = await assemblyManager.waitForAssembly(view.assemblyNames[0]);
-    if (!assembly) {
-        throw new Error('assembly not found');
-    }
-    const suppAlns = (0, MismatchParser_1.featurizeSA)(SA, feature.id(), origStrand, readName, true);
-    const feat = feature.toJSON();
-    feat.clipPos = clipPos;
-    feat.strand = 1;
-    feat.mate = {
-        refName: readName,
-        start: clipPos,
-        end: clipPos + (0, MismatchParser_1.getLengthSansClipping)(cigar),
-    };
-    const features = [feat, ...suppAlns];
-    for (const [idx, f] of features.entries()) {
-        f.refName = assembly.getCanonicalRefName(f.refName) || f.refName;
-        f.syntenyId = idx;
-        f.mate.syntenyId = idx;
-        f.mate.uniqueId = `${f.uniqueId}_mate`;
-    }
-    features.sort((a, b) => a.clipPos - b.clipPos);
-    return features;
-}

package/dist/AlignmentsFeatureDetail/index.d.ts

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

package/dist/AlignmentsFeatureDetail/index.js

@@ -1,52 +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.default = AlignmentFeatureDetailsF;
-const react_1 = require("react");
-const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
-const configSchema_1 = require("./configSchema");
-const stateModelFactory_1 = require("./stateModelFactory");
-function AlignmentFeatureDetailsF(pluginManager) {
-    pluginManager.addWidgetType(() => new WidgetType_1.default({
-        name: 'AlignmentsFeatureWidget',
-        heading: 'Feature details',
-        configSchema: configSchema_1.configSchema,
-        stateModel: (0, stateModelFactory_1.stateModelFactory)(pluginManager),
-        ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AlignmentsFeatureDetail')))),
-    }));
-}

package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts

@@ -1,22 +0,0 @@
-import type { ReducedFeature } from './getSAFeatures';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function getBreakpointSplitView({ f1, f2, view, }: {
-    f1: ReducedFeature;
-    f2: ReducedFeature;
-    view: LinearGenomeViewModel;
-}): {
-    type: string;
-    views: {
-        type: string;
-        displayedRegions: {
-            start: number;
-            end: number;
-            refName: string;
-            assemblyName: string;
-        }[];
-        hideHeader: boolean;
-        bpPerPx: number;
-        offsetPx: number;
-    }[];
-    displayName: string;
-};

package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.js

@@ -1,49 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getBreakpointSplitView = getBreakpointSplitView;
-const util_1 = require("@jbrowse/core/util");
-function getBreakpointSplitView({ f1, f2, view, }) {
-    const { assemblyName } = view.displayedRegions[0];
-    const { assemblyManager } = (0, util_1.getSession)(view);
-    const assembly = assemblyManager.get(assemblyName);
-    if (!assembly) {
-        throw new Error(`assembly ${assemblyName} not found`);
-    }
-    if (!assembly.regions) {
-        throw new Error(`assembly ${assemblyName} regions not loaded`);
-    }
-    const topRegion = assembly.regions.find(f => f.refName === f1.refName);
-    const bottomRegion = assembly.regions.find(f => f.refName === f2.refName);
-    if (!topRegion || !bottomRegion) {
-        throw new Error('unable to find the refName for the top or bottom of the breakpoint view');
-    }
-    const topMarkedRegion = [{ ...topRegion }, { ...topRegion }];
-    const bottomMarkedRegion = [{ ...bottomRegion }, { ...bottomRegion }];
-    const s = f1.strand === 1 ? f1.end : f1.start;
-    const e = f2.strand === 1 ? f2.start : f2.end;
-    topMarkedRegion[0].end = s;
-    topMarkedRegion[1].start = s + 1;
-    bottomMarkedRegion[0].end = e;
-    bottomMarkedRegion[1].start = e + 1;
-    const bpPerPx = 10;
-    return {
-        type: 'BreakpointSplitView',
-        views: [
-            {
-                type: 'LinearGenomeView',
-                displayedRegions: topMarkedRegion,
-                hideHeader: true,
-                bpPerPx,
-                offsetPx: (topRegion.start + s) / bpPerPx,
-            },
-            {
-                type: 'LinearGenomeView',
-                displayedRegions: bottomMarkedRegion,
-                hideHeader: true,
-                bpPerPx,
-                offsetPx: (bottomRegion.start + e) / bpPerPx,
-            },
-        ],
-        displayName: 'breakend split detail',
-    };
-}