@jbrowse/plugin-linear-comparative-view 2.6.1

package/dist/LinearSyntenyView/components/ImportForm.js

@@ -0,0 +1,127 @@
+"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 mui_1 = require("tss-react/mui");
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("@jbrowse/core/util");
+const ui_1 = require("@jbrowse/core/ui");
+const ImportCustomTrack_1 = __importDefault(require("./ImportCustomTrack"));
+const ImportSyntenyTrackSelector_1 = __importDefault(require("./ImportSyntenyTrackSelector"));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    importFormContainer: {
+        padding: theme.spacing(4),
+        margin: '0 auto',
+    },
+    assemblySelector: {
+        width: '75%',
+        margin: '0 auto',
+    },
+}));
+function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData, assembly1, assembly2, model, }) {
+    const [choice, setChoice] = (0, react_1.useState)('none');
+    (0, react_1.useEffect)(() => {
+        if (choice === 'none') {
+            setSessionTrackData(undefined);
+            setShowTrackId(undefined);
+        }
+    }, [choice, setSessionTrackData, setShowTrackId]);
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(material_1.FormControl, null,
+            react_1.default.createElement(material_1.FormLabel, { id: "group-label" }, "(Optional) Select or add a synteny track"),
+            react_1.default.createElement(material_1.RadioGroup, { row: true, value: choice, onChange: event => setChoice(event.target.value), "aria-labelledby": "group-label" },
+                react_1.default.createElement(material_1.FormControlLabel, { value: "none", control: react_1.default.createElement(material_1.Radio, null), label: "None" }),
+                react_1.default.createElement(material_1.FormControlLabel, { value: "tracklist", control: react_1.default.createElement(material_1.Radio, null), label: "Existing track" }),
+                react_1.default.createElement(material_1.FormControlLabel, { value: "custom", control: react_1.default.createElement(material_1.Radio, null), label: "New track" }))),
+        choice === 'custom' ? (react_1.default.createElement(ImportCustomTrack_1.default, { setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, assembly2: assembly2, assembly1: assembly1 })) : null,
+        choice === 'tracklist' ? (react_1.default.createElement(ImportSyntenyTrackSelector_1.default, { model: model, assembly1: assembly1, assembly2: assembly2, setShowTrackId: setShowTrackId })) : null));
+}
+exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
+    const { classes } = useStyles();
+    const session = (0, util_1.getSession)(model);
+    const { assemblyNames } = session;
+    const [assembly2, setAssembly2] = (0, react_1.useState)(assemblyNames[0] || '');
+    const [assembly1, setAssembly1] = (0, react_1.useState)(assemblyNames[0] || '');
+    const [error, setError] = (0, react_1.useState)();
+    const [sessionTrackData, setSessionTrackData] = (0, react_1.useState)();
+    const [showTrackId, setShowTrackId] = (0, react_1.useState)();
+    async function onOpenClick() {
+        try {
+            if (!(0, util_1.isSessionWithAddTracks)(session)) {
+                return;
+            }
+            setError(undefined);
+            const { assemblyManager } = session;
+            const assemblies = [assembly1, assembly2];
+            model.setViews(await Promise.all(assemblies.map(async (sel) => {
+                const asm = await assemblyManager.waitForAssembly(sel);
+                if (!asm) {
+                    throw new Error(`Assembly ${sel} failed to load`);
+                }
+                return {
+                    type: 'LinearGenomeView',
+                    bpPerPx: 1,
+                    offsetPx: 0,
+                    hideHeader: true,
+                    displayedRegions: asm.regions,
+                };
+            })));
+            model.views.forEach(view => view.setWidth(model.width));
+            if (sessionTrackData) {
+                session.addTrackConf(sessionTrackData);
+                model.toggleTrack(sessionTrackData.trackId);
+            }
+            else if (showTrackId) {
+                model.showTrack(showTrackId);
+            }
+        }
+        catch (e) {
+            console.error(e);
+            setError(e);
+        }
+    }
+    // this is a combination of any displayed error message we have
+    const displayError = error;
+    return (react_1.default.createElement(material_1.Container, { className: classes.importFormContainer },
+        displayError ? react_1.default.createElement(ui_1.ErrorMessage, { error: displayError }) : null,
+        react_1.default.createElement(material_1.Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center", className: classes.assemblySelector },
+            react_1.default.createElement(material_1.Grid, { item: true },
+                react_1.default.createElement(material_1.Paper, { style: { padding: 12 } },
+                    react_1.default.createElement("p", { style: { textAlign: 'center' } }, "Select assemblies for linear synteny view"),
+                    react_1.default.createElement(material_1.Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
+                        react_1.default.createElement(material_1.Grid, { item: true },
+                            react_1.default.createElement(ui_1.AssemblySelector, { selected: assembly1, onChange: val => setAssembly1(val), session: session })),
+                        react_1.default.createElement(material_1.Grid, { item: true },
+                            react_1.default.createElement(ui_1.AssemblySelector, { selected: assembly2, onChange: val => setAssembly2(val), session: session })),
+                        react_1.default.createElement(material_1.Grid, { item: true },
+                            react_1.default.createElement(material_1.FormControl, null,
+                                react_1.default.createElement(material_1.Button, { onClick: onOpenClick, variant: "contained", color: "primary" }, "Launch"))))),
+                react_1.default.createElement(TrackSelector, { setShowTrackId: setShowTrackId, assembly2: assembly2, assembly1: assembly1, setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, model: model })))));
+});
+//# sourceMappingURL=ImportForm.js.map

package/dist/LinearSyntenyView/components/ImportForm.js.map

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package/dist/LinearSyntenyView/components/ImportSyntenyTrackSelector.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { LinearSyntenyViewModel } from '../model';
+declare const Selector: ({ model, assembly1, assembly2, setShowTrackId, }: {
+    model: LinearSyntenyViewModel;
+    assembly1: string;
+    assembly2: string;
+    setShowTrackId: (arg: string) => void;
+}) => React.JSX.Element;
+export default Selector;

package/dist/LinearSyntenyView/components/ImportSyntenyTrackSelector.js

@@ -0,0 +1,63 @@
+"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;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const ui_1 = require("@jbrowse/core/ui");
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_react_1 = require("mobx-react");
+function f(track, assembly1, assembly2) {
+    const assemblyNames = (0, configuration_1.readConfObject)(track, 'assemblyNames');
+    return (assemblyNames.includes(assembly1) &&
+        assemblyNames.includes(assembly2) &&
+        track.type.includes('Synteny'));
+}
+const Selector = (0, mobx_react_1.observer)(({ model, assembly1, assembly2, setShowTrackId, }) => {
+    var _a;
+    const session = (0, util_1.getSession)(model);
+    const { tracks = [], sessionTracks = [] } = session;
+    const allTracks = [...tracks, ...sessionTracks];
+    const filteredTracks = allTracks.filter(t => f(t, assembly2, assembly1));
+    const resetTrack = ((_a = filteredTracks[0]) === null || _a === void 0 ? void 0 : _a.trackId) || '';
+    const [value, setValue] = (0, react_1.useState)(resetTrack);
+    (0, react_1.useEffect)(() => {
+        // if assembly1/assembly2 changes, then we will want to use this effect to
+        // change the state of the useState because it otherwise gets locked to a
+        // stale value
+        setValue(resetTrack);
+    }, [resetTrack]);
+    (0, react_1.useEffect)(() => {
+        // sets track data in a useEffect because the initial load is needed as well
+        // as onChange's to the select box
+        setShowTrackId(value);
+    }, [value, setShowTrackId]);
+    return (react_1.default.createElement(material_1.Paper, { style: { padding: 12 } },
+        react_1.default.createElement(material_1.Typography, { paragraph: true }, "Select a track from the select box below, the track will be shown when you hit \"Launch\"."),
+        filteredTracks.length ? (react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, filteredTracks.map(track => (react_1.default.createElement(material_1.MenuItem, { key: track.trackId, value: track.trackId }, (0, tracks_1.getTrackName)(track, session)))))) : (react_1.default.createElement(ui_1.ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
+});
+exports.default = Selector;
+//# sourceMappingURL=ImportSyntenyTrackSelector.js.map

package/dist/LinearSyntenyView/components/ImportSyntenyTrackSelector.js.map

@@ -0,0 +1 @@
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package/dist/LinearSyntenyView/components/LinearSyntenyView.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { LinearSyntenyViewModel } from '../model';
+type LSV = LinearSyntenyViewModel;
+declare const LinearSyntenyView: ({ model }: {
+    model: LSV;
+}) => React.JSX.Element;
+export default LinearSyntenyView;

package/dist/LinearSyntenyView/components/LinearSyntenyView.js

@@ -0,0 +1,38 @@
+"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 mobx_react_1 = require("mobx-react");
+// locals
+const LinearComparativeView_1 = __importDefault(require("../../LinearComparativeView/components/LinearComparativeView"));
+const ImportForm = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./ImportForm'))));
+const LinearSyntenyView = (0, mobx_react_1.observer)(({ model }) => {
+    return !model.initialized ? (react_1.default.createElement(ImportForm, { model: model })) : (react_1.default.createElement(LinearComparativeView_1.default, { model: model }));
+});
+exports.default = LinearSyntenyView;
+//# sourceMappingURL=LinearSyntenyView.js.map

package/dist/LinearSyntenyView/components/LinearSyntenyView.js.map

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package/dist/LinearSyntenyView/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/LinearSyntenyView/index.js

@@ -0,0 +1,42 @@
+"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 = require("react");
+const model_1 = __importDefault(require("./model"));
+const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
+exports.default = (pluginManager) => {
+    pluginManager.addViewType(() => {
+        return new ViewType_1.default({
+            name: 'LinearSyntenyView',
+            displayName: 'Linear synteny view',
+            stateModel: (0, model_1.default)(pluginManager),
+            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/LinearSyntenyView')))),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/dist/LinearSyntenyView/index.js.map

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