@jbrowse/plugin-sv-inspector 3.7.0 → 4.0.0

package/esm/SvInspectorView/model.js

@@ -2,9 +2,9 @@ import { readConfObject } from '@jbrowse/core/configuration';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { getSession } from '@jbrowse/core/util';
 import { ElementId } from '@jbrowse/core/util/types/mst';
+import { addDisposer, types } from '@jbrowse/mobx-state-tree';
 import FolderOpenIcon from '@mui/icons-material/FolderOpen';
 import { autorun, reaction } from 'mobx';
-import { addDisposer, types } from 'mobx-state-tree';
 function SvInspectorViewF(pluginManager) {
     const SpreadsheetViewType = pluginManager.getViewType('SpreadsheetView');
     const CircularViewType = pluginManager.getViewType('CircularView');
@@ -30,6 +30,7 @@ function SvInspectorViewF(pluginManager) {
             hideTrackSelectorButton: true,
             disableImportForm: true,
         })),
+        init: types.frozen(),
     }))
         .volatile(() => ({
         width: 800,
@@ -45,12 +46,12 @@ function SvInspectorViewF(pluginManager) {
                 : undefined;
         },
         get showCircularView() {
-            var _a;
-            return !!((_a = self.spreadsheetView.spreadsheet) === null || _a === void 0 ? void 0 : _a.rowSet);
+            return !!self.spreadsheetView.spreadsheet?.rowSet;
         },
         get features() {
-            var _a, _b;
-            return (((_b = structuredClone((_a = self.spreadsheetView.spreadsheet) === null || _a === void 0 ? void 0 : _a.visibleRows)) === null || _b === void 0 ? void 0 : _b.map(row => row.feature).filter(f => !!f)) || []);
+            return (structuredClone(self.spreadsheetView.spreadsheet?.visibleRows)
+                ?.map(row => row.feature)
+                .filter(f => !!f) || []);
         },
         get featuresAdapterConfigSnapshot() {
             return {
@@ -62,8 +63,8 @@ function SvInspectorViewF(pluginManager) {
             return [
                 ...new Set([
                     ...this.features.map(r => r.refName),
-                    ...this.features.flatMap(r => { var _a; return (_a = r.INFO) === null || _a === void 0 ? void 0 : _a.CHR2; }),
-                    ...this.features.flatMap(r => { var _a; return (_a = r.mate) === null || _a === void 0 ? void 0 : _a.refName; }),
+                    ...this.features.flatMap(r => r.INFO?.CHR2),
+                    ...this.features.flatMap(r => r.mate?.refName),
                 ].filter(f => !!f)),
             ];
         },
@@ -75,7 +76,7 @@ function SvInspectorViewF(pluginManager) {
         },
         get canonicalFeatureRefNameSet() {
             const asm = this.currentAssembly;
-            return new Set((asm === null || asm === void 0 ? void 0 : asm.initialized)
+            return new Set(asm?.initialized
                 ? this.featureRefNames.map(r => asm.getCanonicalRefName(r) || r)
                 : []);
         },
@@ -113,6 +114,9 @@ function SvInspectorViewF(pluginManager) {
         setOnlyDisplayRelevantRegionsInCircularView(val) {
             self.onlyDisplayRelevantRegionsInCircularView = val;
         },
+        setInit(init) {
+            self.init = init;
+        },
     }))
         .views(self => ({
         menuItems() {
@@ -134,6 +138,33 @@ function SvInspectorViewF(pluginManager) {
             return newHeight - oldHeight;
         },
         afterAttach() {
+            addDisposer(self, autorun(async function svInspectorViewInitAutorun() {
+                const { init, width } = self;
+                if (!width || !init) {
+                    return;
+                }
+                const session = getSession(self);
+                try {
+                    const exts = init.uri.split('.');
+                    let ext = exts.pop()?.toUpperCase();
+                    if (ext === 'GZ') {
+                        ext = exts.pop()?.toUpperCase();
+                    }
+                    self.spreadsheetView.importWizard.setFileType(init.fileType || ext || '');
+                    self.spreadsheetView.importWizard.setSelectedAssemblyName(init.assembly);
+                    self.spreadsheetView.importWizard.setFileSource({
+                        uri: init.uri,
+                        locationType: 'UriLocation',
+                    });
+                    await self.spreadsheetView.importWizard.import(init.assembly);
+                    self.setInit(undefined);
+                }
+                catch (e) {
+                    console.error(e);
+                    session.notifyError(`${e}`, e);
+                    self.setInit(undefined);
+                }
+            }, { name: 'SvInspectorViewInit' }));
             addDisposer(self, autorun(() => {
                 const borderWidth = 1;
                 if (self.showCircularView) {
@@ -154,7 +185,7 @@ function SvInspectorViewF(pluginManager) {
             }));
             addDisposer(self, autorun(async () => {
                 const { onlyDisplayRelevantRegionsInCircularView, circularView, canonicalFeatureRefNameSet, currentAssembly, } = self;
-                if (!circularView.initialized || !(currentAssembly === null || currentAssembly === void 0 ? void 0 : currentAssembly.regions)) {
+                if (!circularView.initialized || !currentAssembly?.regions) {
                     return;
                 }
                 else if (onlyDisplayRelevantRegionsInCircularView) {
@@ -196,7 +227,7 @@ function SvInspectorViewF(pluginManager) {
         },
     }))
         .postProcessSnapshot(snap => {
-        const { circularView, ...rest } = snap;
+        const { init, circularView, ...rest } = snap;
         return rest;
     });
 }

package/esm/index.js

@@ -1,13 +1,10 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { isAbstractMenuManager } from '@jbrowse/core/util/types';
 import TableChartIcon from '@mui/icons-material/TableChart';
-import LaunchSvInspectorViewF from './LaunchSvInspectorView';
-import SvInspectorViewF from './SvInspectorView';
+import LaunchSvInspectorViewF from "./LaunchSvInspectorView/index.js";
+import SvInspectorViewF from "./SvInspectorView/index.js";
 export default class SvInspectorViewPlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'SvInspectorViewPlugin';
-    }
+    name = 'SvInspectorViewPlugin';
     install(pluginManager) {
         SvInspectorViewF(pluginManager);
         LaunchSvInspectorViewF(pluginManager);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sv-inspector",
-  "version": "3.7.0",
+  "version": "4.0.0",
   "description": "JBrowse 2 SV inspector view",
   "keywords": [
     "jbrowse",
@@ -15,47 +15,41 @@
     "directory": "plugins/sv-inspector"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/sv-inspector",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@jbrowse/core": "^3.7.0",
-    "@jbrowse/plugin-circular-view": "^3.7.0",
-    "@jbrowse/plugin-spreadsheet-view": "^3.7.0",
-    "@jbrowse/sv-core": "^3.7.0",
-    "@mui/icons-material": "^7.0.0",
-    "@mui/material": "^7.0.0",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "tss-react": "^4.0.0"
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/icons-material": "^7.3.6",
+    "@mui/material": "^7.3.6",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "@jbrowse/core": "^4.0.0",
+    "@jbrowse/sv-core": "^4.0.0",
+    "@jbrowse/plugin-circular-view": "^4.0.0",
+    "@jbrowse/plugin-spreadsheet-view": "^4.0.0"
   },
   "peerDependencies": {
     "react": ">=18.0.0",
     "react-dom": ">=18.0.0"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/sv-inspector",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/LaunchSvInspectorView/index.d.ts

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

package/dist/LaunchSvInspectorView/index.js

@@ -1,21 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = LaunchSvInspectorViewF;
-function LaunchSvInspectorViewF(pluginManager) {
-    pluginManager.addToExtensionPoint('LaunchView-SvInspectorView', async ({ session, assembly, uri, fileType, }) => {
-        var _a, _b;
-        const view = session.addView('SvInspectorView');
-        const exts = uri.split('.');
-        let ext = (_a = exts.pop()) === null || _a === void 0 ? void 0 : _a.toUpperCase();
-        if (ext === 'GZ') {
-            ext = (_b = exts.pop()) === null || _b === void 0 ? void 0 : _b.toUpperCase();
-        }
-        view.spreadsheetView.importWizard.setFileType(fileType || ext || '');
-        view.spreadsheetView.importWizard.setSelectedAssemblyName(assembly);
-        view.spreadsheetView.importWizard.setFileSource({
-            uri,
-            locationType: 'UriLocation',
-        });
-        await view.spreadsheetView.importWizard.import(assembly);
-    });
-}

package/dist/SvInspectorView/components/CircularViewOptions.d.ts

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

package/dist/SvInspectorView/components/CircularViewOptions.js

@@ -1,18 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    circularViewOptions: {
-        padding: theme.spacing(1),
-    },
-}));
-const CircularViewOptions = (0, mobx_react_1.observer)(function ({ svInspector, }) {
-    const { classes } = useStyles();
-    return ((0, jsx_runtime_1.jsx)("div", { className: classes.circularViewOptions, style: { height: svInspector.circularViewOptionsBarHeight }, children: (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: svInspector.onlyDisplayRelevantRegionsInCircularView, onChange: e => {
-                    svInspector.setOnlyDisplayRelevantRegionsInCircularView(e.target.checked);
-                } }), label: "show only regions with data" }) }));
-});
-exports.default = CircularViewOptions;

package/dist/SvInspectorView/components/SvInspectorView.d.ts

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

package/dist/SvInspectorView/components/SvInspectorView.js

@@ -1,44 +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 ui_1 = require("@jbrowse/core/ui");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const CircularViewOptions_1 = __importDefault(require("./CircularViewOptions"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    resizeHandleVert: {
-        background: theme.palette.action.selected,
-        width: 4,
-        boxSizing: 'border-box',
-        borderTop: '1px solid #fafafa',
-    },
-    resizeHandleHoriz: {
-        background: theme.palette.action.selected,
-        height: 4,
-        boxSizing: 'border-box',
-        borderTop: '1px solid #fafafa',
-    },
-    viewControls: {
-        margin: 0,
-    },
-    viewsContainer: {
-        display: 'flex',
-    },
-    container: {
-        overflow: 'hidden',
-    },
-}));
-const SvInspectorView = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes } = useStyles();
-    const { SpreadsheetViewReactComponent, CircularViewReactComponent, showCircularView, } = model;
-    return ((0, jsx_runtime_1.jsxs)("div", { className: classes.container, children: [(0, jsx_runtime_1.jsxs)("div", { className: classes.viewsContainer, children: [(0, jsx_runtime_1.jsx)("div", { style: {
-                            width: model.spreadsheetView.width,
-                        }, className: classes.container, children: (0, jsx_runtime_1.jsx)(SpreadsheetViewReactComponent, { model: model.spreadsheetView }) }), showCircularView ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(ui_1.ResizeHandle, { onDrag: distance => {
-                                    const ret1 = model.circularView.resizeWidth(-distance);
-                                    return model.spreadsheetView.resizeWidth(-ret1);
-                                }, vertical: true, flexbox: true, className: classes.resizeHandleVert }), (0, jsx_runtime_1.jsxs)("div", { style: { width: model.circularView.width }, children: [(0, jsx_runtime_1.jsx)(CircularViewOptions_1.default, { svInspector: model }), (0, jsx_runtime_1.jsx)(CircularViewReactComponent, { model: model.circularView })] })] })) : null] }), (0, jsx_runtime_1.jsx)(ui_1.ResizeHandle, { onDrag: model.resizeHeight, className: classes.resizeHandleHoriz })] }));
-});
-exports.default = SvInspectorView;

package/dist/SvInspectorView/index.d.ts

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

package/dist/SvInspectorView/index.js

@@ -1,79 +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 = SvInspectorViewF;
-const react_1 = require("react");
-const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
-const util_1 = require("@jbrowse/core/util");
-const sv_core_1 = require("@jbrowse/sv-core");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const model_1 = __importDefault(require("./model"));
-function defaultOnChordClick(feature, chordTrack) {
-    ;
-    (async () => {
-        const session = (0, util_1.getSession)(chordTrack);
-        try {
-            session.setSelection(feature);
-            const view = (0, util_1.getContainingView)(chordTrack);
-            const parentView = (0, mobx_state_tree_1.getParent)(view);
-            const stableViewId = `${parentView.id}_spawned`;
-            await (0, sv_core_1.navToMultiLevelBreak)({
-                assemblyName: view.assemblyNames[0],
-                session,
-                stableViewId,
-                feature,
-            });
-        }
-        catch (e) {
-            console.error(e);
-            session.notifyError(`${e}`, e);
-        }
-    })();
-}
-function SvInspectorViewF(pluginManager) {
-    pluginManager.jexl.addFunction('defaultOnChordClick', defaultOnChordClick);
-    pluginManager.addViewType(() => {
-        const stateModel = (0, model_1.default)(pluginManager);
-        return new ViewType_1.default({
-            name: 'SvInspectorView',
-            displayName: 'SV inspector',
-            stateModel,
-            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SvInspectorView')))),
-        });
-    });
-}