@jbrowse/plugin-linear-comparative-view 3.7.0 → 4.0.0

package/dist/SyntenyFeatureDetail/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/SyntenyFeatureDetail/LinkToSyntenyView.d.ts

@@ -1,7 +0,0 @@
-import type { SyntenyFeatureDetailModel } from './types';
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-declare const LinkToSyntenyView: ({ model, feat, }: {
-    model: SyntenyFeatureDetailModel;
-    feat: SimpleFeatureSerialized;
-}) => import("react/jsx-runtime").JSX.Element;
-export default LinkToSyntenyView;

package/dist/SyntenyFeatureDetail/LinkToSyntenyView.js

@@ -1,87 +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 });
-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 mobx_react_1 = require("mobx-react");
-const LaunchSyntenyViewDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../LGVSyntenyDisplay/components/LaunchSyntenyViewDialog'))));
-const LinkToSyntenyView = (0, mobx_react_1.observer)(function ({ model, feat, }) {
-    const { view, level, trackId } = model;
-    return ((0, jsx_runtime_1.jsxs)("ul", { children: [view.type === 'LinearSyntenyView' ? ((0, jsx_runtime_1.jsx)("li", { children: (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
-                        var _a, _b;
-                        event.preventDefault();
-                        const { views } = view;
-                        if (level !== undefined) {
-                            (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(feat);
-                            (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(feat.mate);
-                        }
-                        else {
-                            const f1 = feat;
-                            const f2 = feat.mate;
-                            const r1 = f1.assemblyName;
-                            const r2 = f2.assemblyName;
-                            const v1 = views.find(view => view.assemblyNames[0] === r1);
-                            const v2 = views.find(view => view.assemblyNames[0] === r2);
-                            if (!v1 || !v2) {
-                                (0, util_1.getSession)(model).notify([
-                                    v1
-                                        ? `Unable to find ${(0, util_1.assembleLocString)(f1)} in synteny view`
-                                        : '',
-                                    v2
-                                        ? `Unable to find ${(0, util_1.assembleLocString)(f2)} in synteny view`
-                                        : '',
-                                ].join(' ... '));
-                            }
-                            v1 === null || v1 === void 0 ? void 0 : v1.navTo(f1);
-                            v2 === null || v2 === void 0 ? void 0 : v2.navTo(f2);
-                        }
-                    }, children: "Center view on this feature" }) })) : null, (0, jsx_runtime_1.jsx)("li", { children: (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        const feature = new util_1.SimpleFeature(feat);
-                        const session = (0, util_1.getSession)(model);
-                        session.queueDialog(handleClose => [
-                            LaunchSyntenyViewDialog,
-                            {
-                                session,
-                                feature,
-                                trackId,
-                                handleClose,
-                            },
-                        ]);
-                    }, children: "Launch new linear synteny view on this feature" }) })] }));
-});
-exports.default = LinkToSyntenyView;

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts

@@ -1,5 +0,0 @@
-import type { SyntenyFeatureDetailModel } from './types';
-declare const SyntenyFeatureDetail: (props: {
-    model: SyntenyFeatureDetailModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default SyntenyFeatureDetail;

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -1,19 +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 jsx_runtime_1 = require("react/jsx-runtime");
-const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const Formatter_1 = __importDefault(require("./Formatter"));
-const LinkToSyntenyView_1 = __importDefault(require("./LinkToSyntenyView"));
-const SyntenyFeatureDetail = (0, mobx_react_1.observer)(function (props) {
-    const { model } = props;
-    const { featureData } = model;
-    const feat = structuredClone(featureData);
-    return feat ? ((0, jsx_runtime_1.jsxs)(material_1.Paper, { children: [(0, jsx_runtime_1.jsx)(FeatureDetails_1.default, { ...props, feature: feat, formatter: value => (0, jsx_runtime_1.jsx)(Formatter_1.default, { value: value }) }), (0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: "Link to view", children: (0, jsx_runtime_1.jsx)(LinkToSyntenyView_1.default, { model: model, feat: feat }) })] })) : ((0, jsx_runtime_1.jsx)("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" }));
-});
-exports.default = SyntenyFeatureDetail;

package/dist/SyntenyFeatureDetail/index.d.ts

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

package/dist/SyntenyFeatureDetail/index.js

@@ -1,60 +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 = SyntenyFeatureWidgetF;
-const react_1 = require("react");
-const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
-const configuration_1 = require("@jbrowse/core/configuration");
-const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
-const mobx_state_tree_1 = require("mobx-state-tree");
-const configSchema = (0, configuration_1.ConfigurationSchema)('SyntenyFeatureWidget', {});
-function stateModelF(pluginManager) {
-    return mobx_state_tree_1.types.compose((0, BaseFeatureWidget_1.stateModelFactory)(pluginManager), mobx_state_tree_1.types.model('SyntenyFeatureWidget', {
-        type: mobx_state_tree_1.types.literal('SyntenyFeatureWidget'),
-        level: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-    }));
-}
-function SyntenyFeatureWidgetF(pluginManager) {
-    pluginManager.addWidgetType(() => new WidgetType_1.default({
-        name: 'SyntenyFeatureWidget',
-        heading: 'Synteny feature details',
-        configSchema,
-        stateModel: stateModelF(pluginManager),
-        ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SyntenyFeatureDetail')))),
-    }));
-}

package/dist/SyntenyFeatureDetail/types.d.ts

@@ -1,9 +0,0 @@
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-export interface SyntenyFeatureDetailModel {
-    trackId: string;
-    featureData?: SimpleFeatureSerialized;
-    level?: number;
-    view: {
-        type: string;
-    };
-}

package/dist/SyntenyFeatureDetail/types.js

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

package/dist/SyntenyTrack/configSchema.d.ts

@@ -1,80 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    name: {
-        description: string;
-        type: string;
-        defaultValue: string;
-    };
-    assemblyNames: {
-        description: string;
-        type: string;
-        defaultValue: string[];
-    };
-    description: {
-        description: string;
-        type: string;
-        defaultValue: string;
-    };
-    category: {
-        description: string;
-        type: string;
-        defaultValue: never[];
-    };
-    metadata: {
-        type: string;
-        description: string;
-        defaultValue: {};
-    };
-    adapter: import("mobx-state-tree").IAnyModelType;
-    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        indexingAttributes: {
-            type: string;
-            description: string;
-            defaultValue: string[];
-        };
-        indexingFeatureTypesToExclude: {
-            type: string;
-            description: string;
-            defaultValue: string[];
-        };
-        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        feature: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        subfeatures: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        depth: {
-            type: string;
-            defaultValue: number;
-            description: string;
-        };
-        maxDepth: {
-            type: string;
-            defaultValue: number;
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        config: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        hideUris: {
-            type: string;
-            defaultValue: boolean;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
-export default configSchema;

package/dist/SyntenyTrack/configSchema.js

@@ -1,9 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-function x() { }
-const configSchema = (pluginManager) => (0, configuration_1.ConfigurationSchema)('SyntenyTrack', {}, {
-    baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager),
-});
-exports.default = configSchema;

package/dist/SyntenyTrack/index.d.ts

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

package/dist/SyntenyTrack/index.js

@@ -1,19 +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 = registerSyntenyTrack;
-const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-const configSchema_1 = __importDefault(require("./configSchema"));
-function registerSyntenyTrack(pluginManager) {
-    pluginManager.addTrackType(() => {
-        const configSchema = (0, configSchema_1.default)(pluginManager);
-        return new TrackType_1.default({
-            name: 'SyntenyTrack',
-            configSchema,
-            stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'SyntenyTrack', configSchema),
-        });
-    });
-}

package/dist/index.d.ts

@@ -1,7 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default class LinearComparativeViewPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-    configure(pluginManager: PluginManager): void;
-}

package/dist/index.js

@@ -1,48 +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 util_1 = require("@jbrowse/core/util");
-const CalendarViewDay_1 = __importDefault(require("@mui/icons-material/CalendarViewDay"));
-const LGVSyntenyDisplay_1 = __importDefault(require("./LGVSyntenyDisplay"));
-const LaunchLinearSyntenyView_1 = __importDefault(require("./LaunchLinearSyntenyView"));
-const LinearComparativeDisplay_1 = __importDefault(require("./LinearComparativeDisplay"));
-const LinearComparativeView_1 = __importDefault(require("./LinearComparativeView"));
-const LinearReadVsRef_1 = __importDefault(require("./LinearReadVsRef"));
-const LinearSyntenyDisplay_1 = __importDefault(require("./LinearSyntenyDisplay"));
-const LinearSyntenyView_1 = __importDefault(require("./LinearSyntenyView"));
-const LinearSyntenyViewHelper_1 = __importDefault(require("./LinearSyntenyViewHelper"));
-const SyntenyFeatureDetail_1 = __importDefault(require("./SyntenyFeatureDetail"));
-const SyntenyTrack_1 = __importDefault(require("./SyntenyTrack"));
-class LinearComparativeViewPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'LinearComparativeViewPlugin';
-    }
-    install(pluginManager) {
-        (0, LinearSyntenyViewHelper_1.default)(pluginManager);
-        (0, LinearComparativeView_1.default)(pluginManager);
-        (0, LinearSyntenyView_1.default)(pluginManager);
-        (0, LinearComparativeDisplay_1.default)(pluginManager);
-        (0, LinearSyntenyDisplay_1.default)(pluginManager);
-        (0, SyntenyFeatureDetail_1.default)(pluginManager);
-        (0, LGVSyntenyDisplay_1.default)(pluginManager);
-        (0, LaunchLinearSyntenyView_1.default)(pluginManager);
-        (0, SyntenyTrack_1.default)(pluginManager);
-        (0, LinearReadVsRef_1.default)(pluginManager);
-    }
-    configure(pluginManager) {
-        if ((0, util_1.isAbstractMenuManager)(pluginManager.rootModel)) {
-            pluginManager.rootModel.appendToSubMenu(['Add'], {
-                label: 'Linear synteny view',
-                icon: CalendarViewDay_1.default,
-                onClick: (session) => {
-                    session.addView('LinearSyntenyView', {});
-                },
-            });
-        }
-    }
-}
-exports.default = LinearComparativeViewPlugin;

package/dist/util.d.ts

@@ -1,25 +0,0 @@
-import type { Feature } from '@jbrowse/core/util/simpleFeature';
-import type { Region } from '@jbrowse/core/util/types';
-export type LayoutRecord = [number, number, number, number];
-export interface ReducedLinearGenomeView {
-    bpPerPx: number;
-    offsetPx: number;
-    staticBlocks: Region[];
-    dynamicBlocks: Region[];
-    displayedRegions: Region[];
-    headerHeight: number;
-    scaleBarHeight: number;
-    height: number;
-    features: Feature[];
-    tracks: {
-        scrollTop: number;
-        height: number;
-        configuration: string;
-        skip: number;
-    }[];
-}
-export declare function cheight(chunk: LayoutRecord): number;
-export declare function getTrackPos(view: ReducedLinearGenomeView, trackConfigId: string): number;
-export declare function getPxFromCoordinate(view: ReducedLinearGenomeView, refName: string, coord: number): number;
-export declare function overlayYPos(trackConfigId: string, level: number, views: ReducedLinearGenomeView[], c: LayoutRecord, cond: boolean): number;
-export declare function interstitialYPos(cond: boolean, height: number): number;

package/dist/util.js

@@ -1,67 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.cheight = cheight;
-exports.getTrackPos = getTrackPos;
-exports.getPxFromCoordinate = getPxFromCoordinate;
-exports.overlayYPos = overlayYPos;
-exports.interstitialYPos = interstitialYPos;
-const util_1 = require("@jbrowse/core/util");
-const [, TOP, , BOTTOM] = [0, 1, 2, 3];
-function cheight(chunk) {
-    return chunk[BOTTOM] - chunk[TOP];
-}
-function heightFromSpecificLevel(views, trackConfigId, level) {
-    const heightUpUntilThisPoint = views
-        .slice(0, level)
-        .map(v => v.height + 7)
-        .reduce((a, b) => a + b, 0);
-    const v = views[level];
-    return (heightUpUntilThisPoint +
-        v.headerHeight +
-        v.scaleBarHeight +
-        getTrackPos(v, trackConfigId) +
-        1);
-}
-function getTrackPos(view, trackConfigId) {
-    const idx = view.tracks.findIndex(t => t.configuration === trackConfigId);
-    let accum = 0;
-    for (let i = 0; i < idx; i += 1) {
-        accum += view.tracks[i].height + 3;
-    }
-    return accum;
-}
-function getPxFromCoordinate(view, refName, coord) {
-    var _a;
-    return (((_a = bpToPx(view, { refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
-}
-function overlayYPos(trackConfigId, level, views, c, cond) {
-    const track = views[level].tracks.find(t => t.configuration === trackConfigId);
-    const ypos = track
-        ? (0, util_1.clamp)(c[TOP] - (track.scrollTop || 0), 0, track.height) +
-            heightFromSpecificLevel(views, trackConfigId, level) +
-            track.skip
-        : 0;
-    return ypos + (cond ? cheight(c) : 0);
-}
-function bpToPx(view, { refName, coord }) {
-    let offsetBp = 0;
-    const index = view.displayedRegions.findIndex(r => {
-        if (refName === r.refName && coord >= r.start && coord <= r.end) {
-            offsetBp += coord - r.start;
-            return true;
-        }
-        offsetBp += r.end - r.start;
-        return false;
-    });
-    const foundRegion = view.displayedRegions[index];
-    if (foundRegion) {
-        return {
-            index,
-            offsetPx: Math.round(offsetBp / view.bpPerPx),
-        };
-    }
-    return undefined;
-}
-function interstitialYPos(cond, height) {
-    return cond ? 0 : height;
-}