@jbrowse/product-core 2.6.1

package/dist/Session/Tracks.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isSessionWithTracks = exports.TracksManagerSessionMixin = void 0;
+const mobx_state_tree_1 = require("mobx-state-tree");
+const BaseSession_1 = require("./BaseSession");
+const ReferenceManagement_1 = require("./ReferenceManagement");
+/**
+ * #stateModel TracksManagerSessionMixin
+ * composed of
+ * - BaseSessionModel
+ * - ReferenceManagementSessionMixin
+ */
+function TracksManagerSessionMixin(pluginManager) {
+    return mobx_state_tree_1.types
+        .compose('TracksManagerSessionMixin', (0, BaseSession_1.BaseSessionModel)(pluginManager), (0, ReferenceManagement_1.ReferenceManagementSessionMixin)(pluginManager))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get tracks() {
+            return self.jbrowse.tracks;
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        addTrackConf(trackConf) {
+            return self.jbrowse.addTrackConf(trackConf);
+        },
+        /**
+         * #action
+         */
+        deleteTrackConf(trackConf) {
+            const callbacksToDereferenceTrack = [];
+            const dereferenceTypeCount = {};
+            const referring = self.getReferring(trackConf);
+            self.removeReferring(referring, trackConf, callbacksToDereferenceTrack, dereferenceTypeCount);
+            callbacksToDereferenceTrack.forEach(cb => cb());
+            if (self.adminMode) {
+                return self.jbrowse.deleteTrackConf(trackConf);
+            }
+        },
+    }));
+}
+exports.TracksManagerSessionMixin = TracksManagerSessionMixin;
+/** Type guard for SessionWithTracks */
+function isSessionWithTracks(thing) {
+    return (0, BaseSession_1.isBaseSession)(thing) && 'tracks' in thing;
+}
+exports.isSessionWithTracks = isSessionWithTracks;

package/dist/Session/index.d.ts

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+export * from './ReferenceManagement';
+export * from './Connections';
+export * from './DrawerWidgets';
+export * from './DialogQueue';
+export * from './Themes';
+export * from './Tracks';
+export * from './MultipleViews';
+export * from './BaseSession';
+export * from './SessionTracks';
+export * from './BaseSession';

package/dist/Session/index.js

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+"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 __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./ReferenceManagement"), exports);
+__exportStar(require("./Connections"), exports);
+__exportStar(require("./DrawerWidgets"), exports);
+__exportStar(require("./DialogQueue"), exports);
+__exportStar(require("./Themes"), exports);
+__exportStar(require("./Tracks"), exports);
+__exportStar(require("./MultipleViews"), exports);
+__exportStar(require("./BaseSession"), exports);
+__exportStar(require("./SessionTracks"), exports);
+__exportStar(require("./BaseSession"), exports);

package/dist/index.d.ts

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+export * from './RootModel';
+export * from './Session';
+export * from './ui';

package/dist/index.js

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+"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 __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./RootModel"), exports);
+__exportStar(require("./Session"), exports);
+__exportStar(require("./ui"), exports);

package/dist/ui/AboutDialog.d.ts

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+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function AboutDialog({ config, handleClose, }: {
+    config: AnyConfigurationModel;
+    handleClose: () => void;
+}): React.JSX.Element;

package/dist/ui/AboutDialog.js

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+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AboutDialog = void 0;
+const react_1 = __importDefault(require("react"));
+const Dialog_1 = __importDefault(require("@jbrowse/core/ui/Dialog"));
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const AboutDialogContents_1 = __importDefault(require("./AboutDialogContents"));
+function AboutDialog({ config, handleClose, }) {
+    const session = (0, util_1.getSession)(config);
+    const trackName = (0, tracks_1.getTrackName)(config, session);
+    const { pluginManager } = (0, util_1.getEnv)(session);
+    const AboutComponent = pluginManager.evaluateExtensionPoint('Core-replaceAbout', AboutDialogContents_1.default, { session, config });
+    return (react_1.default.createElement(Dialog_1.default, { open: true, onClose: handleClose, title: trackName, maxWidth: "xl" },
+        react_1.default.createElement(AboutComponent, { config: config })));
+}
+exports.AboutDialog = AboutDialog;

package/dist/ui/AboutDialogContents.d.ts

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+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export default function AboutContents({ config, }: {
+    config: AnyConfigurationModel;
+}): React.JSX.Element;

package/dist/ui/AboutDialogContents.js

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+"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 (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __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 react_1 = __importStar(require("react"));
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const FileInfoPanel_1 = __importDefault(require("./FileInfoPanel"));
+const useStyles = (0, mui_1.makeStyles)()({
+    content: {
+        minWidth: 800,
+    },
+});
+function AboutContents({ config, }) {
+    const [copied, setCopied] = (0, react_1.useState)(false);
+    const conf = (0, configuration_1.readConfObject)(config);
+    const session = (0, util_1.getSession)(config);
+    const { classes } = useStyles();
+    const hideUris = (0, configuration_1.getConf)(session, ['formatAbout', 'hideUris']) ||
+        (0, configuration_1.readConfObject)(config, ['formatAbout', 'hideUris']);
+    const { pluginManager } = (0, util_1.getEnv)(session);
+    const confPostExt = pluginManager.evaluateExtensionPoint('Core-customizeAbout', {
+        config: {
+            ...conf,
+            ...(0, configuration_1.getConf)(session, ['formatAbout', 'config'], { config: conf }),
+            ...(0, configuration_1.readConfObject)(config, ['formatAbout', 'config'], { config: conf }),
+        },
+    }, { session, config });
+    const ExtraPanel = pluginManager.evaluateExtensionPoint('Core-extraAboutPanel', null, { session, config });
+    return (react_1.default.createElement("div", { className: classes.content },
+        react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "Configuration" },
+            !hideUris ? (react_1.default.createElement(material_1.Button, { variant: "contained", style: { float: 'right' }, onClick: () => {
+                    (0, copy_to_clipboard_1.default)(JSON.stringify(conf, null, 2));
+                    setCopied(true);
+                    setTimeout(() => setCopied(false), 1000);
+                } }, copied ? 'Copied to clipboard!' : 'Copy config')) : null,
+            react_1.default.createElement(BaseFeatureDetail_1.Attributes, { attributes: confPostExt, omit: ['displays', 'baseUri', 'refNames', 'formatAbout'], hideUris: hideUris })),
+        ExtraPanel ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: ExtraPanel.name },
+            react_1.default.createElement(ExtraPanel.Component, { config: config }))) : null,
+        react_1.default.createElement(FileInfoPanel_1.default, { config: config })));
+}
+exports.default = AboutContents;

package/dist/ui/FileInfoPanel.d.ts

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+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export default function FileInfoPanel({ config, }: {
+    config: AnyConfigurationModel;
+}): React.JSX.Element | null;

package/dist/ui/FileInfoPanel.js

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+"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 (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __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 react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const configuration_1 = require("@jbrowse/core/configuration");
+const LoadingEllipses_1 = __importDefault(require("@jbrowse/core/ui/LoadingEllipses"));
+const util_1 = require("@jbrowse/core/util");
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+function FileInfoPanel({ config, }) {
+    const [error, setError] = (0, react_1.useState)();
+    const [info, setInfo] = (0, react_1.useState)();
+    const session = (0, util_1.getSession)(config);
+    const { rpcManager } = session;
+    (0, react_1.useEffect)(() => {
+        const aborter = new AbortController();
+        const { signal } = aborter;
+        let cancelled = false;
+        (async () => {
+            try {
+                const adapterConfig = (0, configuration_1.readConfObject)(config, 'adapter');
+                const result = await rpcManager.call(config.trackId, 'CoreGetInfo', {
+                    adapterConfig,
+                    signal,
+                });
+                if (!cancelled) {
+                    setInfo(result);
+                }
+            }
+            catch (e) {
+                if (!cancelled) {
+                    console.error(e);
+                    setError(e);
+                }
+            }
+        })();
+        return () => {
+            aborter.abort();
+            cancelled = true;
+        };
+    }, [config, rpcManager]);
+    const details = typeof info === 'string'
+        ? {
+            header: `<pre>${info
+                .replaceAll('<', '&lt;')
+                .replaceAll('>', '&gt;')}</pre>`,
+        }
+        : info || {};
+    return info !== null ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "File info" }, error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : info === undefined ? (react_1.default.createElement(LoadingEllipses_1.default, { message: "Loading file data" })) : (react_1.default.createElement(BaseFeatureDetail_1.Attributes, { attributes: details })))) : null;
+}
+exports.default = FileInfoPanel;

package/dist/ui/index.d.ts

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+export * from './AboutDialog';

package/dist/ui/index.js

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+"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 __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./AboutDialog"), exports);