@jbrowse/plugin-variants 2.1.0 → 2.1.2

package/dist/VariantFeatureWidget/AnnotGrid.js

@@ -0,0 +1,22 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable @typescript-eslint/no-explicit-any */
+const react_1 = __importDefault(require("react"));
+const x_data_grid_1 = require("@mui/x-data-grid");
+function VariantAnnotPanel({ rows, columns, }) {
+    const rowHeight = 25;
+    const hideFooter = rows.length < 100;
+    const headerHeight = 80;
+    return rows.length ? (react_1.default.createElement("div", { style: {
+            height: Math.min(rows.length, 100) * rowHeight +
+                headerHeight +
+                (hideFooter ? 0 : 50),
+            width: '100%',
+        } },
+        react_1.default.createElement(x_data_grid_1.DataGrid, { rowHeight: rowHeight, rows: rows, columns: columns }))) : null;
+}
+exports.default = VariantAnnotPanel;
+//# sourceMappingURL=AnnotGrid.js.map

package/dist/VariantFeatureWidget/AnnotGrid.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"AnnotGrid.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/AnnotGrid.tsx"],"names":[],"mappings":";;;;;AAAA,uDAAuD;AACvD,kDAAyB;AACzB,kDAA2C;AAE3C,SAAwB,iBAAiB,CAAC,EACxC,IAAI,EACJ,OAAO,GAIR;IACC,MAAM,SAAS,GAAG,EAAE,CAAA;IACpB,MAAM,UAAU,GAAG,IAAI,CAAC,MAAM,GAAG,GAAG,CAAA;IACpC,MAAM,YAAY,GAAG,EAAE,CAAA;IACvB,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CACnB,uCACE,KAAK,EAAE;YACL,MAAM,EACJ,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,CAAC,GAAG,SAAS;gBACtC,YAAY;gBACZ,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YACvB,KAAK,EAAE,MAAM;SACd;QAED,8BAAC,sBAAQ,IAAC,SAAS,EAAE,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,OAAO,EAAE,OAAO,GAAI,CAC5D,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AAvBD,oCAuBC"}

package/dist/VariantFeatureWidget/BreakendOptionDialog.js

@@ -22,35 +22,19 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 /* eslint-disable @typescript-eslint/no-explicit-any */
-var react_1 = __importStar(require("react"));
-var mobx_react_1 = require("mobx-react");
-var material_1 = require("@mui/material");
-var mui_1 = require("tss-react/mui");
-var Close_1 = __importDefault(require("@mui/icons-material/Close"));
-var mobx_state_tree_1 = require("mobx-state-tree");
-var util_1 = require("@jbrowse/core/util");
-var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
+const react_1 = __importStar(require("react"));
+const mobx_react_1 = require("mobx-react");
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_1 = require("@jbrowse/core/util");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     closeButton: {
         position: 'absolute',
         right: theme.spacing(1),
@@ -60,31 +44,30 @@ var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
     block: {
         display: 'block',
     },
-}); });
-function BreakendOptionDialog(_a) {
-    var model = _a.model, handleClose = _a.handleClose, feature = _a.feature, viewType = _a.viewType;
-    var classes = useStyles().classes;
-    var _b = __read((0, react_1.useState)(true), 2), copyTracks = _b[0], setCopyTracks = _b[1];
-    var _c = __read((0, react_1.useState)(true), 2), mirrorTracks = _c[0], setMirrorTracks = _c[1];
+}));
+function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
+    const { classes } = useStyles();
+    const [copyTracks, setCopyTracks] = (0, react_1.useState)(true);
+    const [mirrorTracks, setMirrorTracks] = (0, react_1.useState)(true);
     return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
         react_1.default.createElement(material_1.DialogTitle, null,
             "Breakpoint split view options",
-            handleClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: function () { return handleClose(); } },
+            handleClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => handleClose() },
                 react_1.default.createElement(Close_1.default, null))) : null),
         react_1.default.createElement(material_1.Divider, null),
         react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: copyTracks, onChange: function () { return setCopyTracks(function (val) { return !val; }); } }), label: "Copy tracks into the new view" }),
-            react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: mirrorTracks, onChange: function () { return setMirrorTracks(function (val) { return !val; }); } }), label: "Mirror tracks vertically in vertically stacked view" })),
+            react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: copyTracks, onChange: () => setCopyTracks(val => !val) }), label: "Copy tracks into the new view" }),
+            react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: mirrorTracks, onChange: () => setMirrorTracks(val => !val) }), label: "Mirror tracks vertically in vertically stacked view" })),
         react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { onClick: function () {
-                    var view = model.view;
-                    var session = (0, util_1.getSession)(model);
+            react_1.default.createElement(material_1.Button, { onClick: () => {
+                    const { view } = model;
+                    const session = (0, util_1.getSession)(model);
                     try {
-                        var viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view);
+                        const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view);
                         viewSnapshot.views[0].offsetPx -= view.width / 2 + 100;
                         viewSnapshot.views[1].offsetPx -= view.width / 2 + 100;
                         viewSnapshot.featureData = feature;
-                        var viewTracks = (0, mobx_state_tree_1.getSnapshot)(view.tracks);
+                        const viewTracks = (0, mobx_state_tree_1.getSnapshot)(view.tracks);
                         viewSnapshot.views[0].tracks = viewTracks;
                         viewSnapshot.views[1].tracks = mirrorTracks
                             ? viewTracks.slice().reverse()
@@ -93,11 +76,11 @@ function BreakendOptionDialog(_a) {
                     }
                     catch (e) {
                         console.error(e);
-                        session.notify("".concat(e));
+                        session.notify(`${e}`);
                     }
                     handleClose();
                 }, variant: "contained", color: "primary", autoFocus: true }, "OK"),
-            react_1.default.createElement(material_1.Button, { onClick: function () { return handleClose(); }, color: "secondary", variant: "contained" }, "Cancel"))));
+            react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), color: "secondary", variant: "contained" }, "Cancel"))));
 }
 exports.default = (0, mobx_react_1.observer)(BreakendOptionDialog);
 //# sourceMappingURL=BreakendOptionDialog.js.map

package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map

@@ -1 +1 @@
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package/dist/VariantFeatureWidget/BreakendPanel.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+export default function BreakendPanel(props: {
+    locStrings: string[];
+    model: any;
+    feature: SimpleFeatureSerialized;
+}): JSX.Element;

package/dist/VariantFeatureWidget/BreakendPanel.js

@@ -0,0 +1,82 @@
+"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 });
+/* eslint-disable @typescript-eslint/no-explicit-any */
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+const util_1 = require("@jbrowse/core/util");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const BreakendOptionDialog_1 = __importDefault(require("./BreakendOptionDialog"));
+function BreakendPanel(props) {
+    const { model, locStrings, feature } = props;
+    const session = (0, util_1.getSession)(model);
+    const { pluginManager } = (0, mobx_state_tree_1.getEnv)(session);
+    const [breakpointDialog, setBreakpointDialog] = (0, react_1.useState)(false);
+    let viewType;
+    try {
+        viewType = pluginManager.getViewType('BreakpointSplitView');
+    }
+    catch (e) {
+        // ignore
+    }
+    const simpleFeature = new simpleFeature_1.default(feature);
+    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Breakends" },
+        react_1.default.createElement(material_1.Typography, null, "Link to linear view of breakend endpoints"),
+        react_1.default.createElement("ul", null, locStrings.map(locString => (react_1.default.createElement("li", { key: `${JSON.stringify(locString)}` },
+            react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+                    var _a;
+                    event.preventDefault();
+                    const { view } = model;
+                    try {
+                        if (view) {
+                            (_a = view.navToLocString) === null || _a === void 0 ? void 0 : _a.call(view, locString);
+                        }
+                        else {
+                            throw new Error('No view associated with this feature detail panel anymore');
+                        }
+                    }
+                    catch (e) {
+                        console.error(e);
+                        session.notify(`${e}`);
+                    }
+                } }, `LGV - ${locString}`))))),
+        viewType ? (react_1.default.createElement("div", null,
+            react_1.default.createElement(material_1.Typography, null, "Launch split views with breakend source and target"),
+            react_1.default.createElement("ul", null, locStrings.map(locString => (react_1.default.createElement("li", { key: `${JSON.stringify(locString)}` },
+                react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+                        event.preventDefault();
+                        setBreakpointDialog(true);
+                    } }, `${feature.refName}:${feature.start} // ${locString} (split view)`))))),
+            breakpointDialog ? (react_1.default.createElement(BreakendOptionDialog_1.default, { model: model, feature: simpleFeature, viewType: viewType, handleClose: () => {
+                    setBreakpointDialog(false);
+                } })) : null)) : null));
+}
+exports.default = BreakendPanel;
+//# sourceMappingURL=BreakendPanel.js.map

package/dist/VariantFeatureWidget/BreakendPanel.js.map

@@ -0,0 +1 @@
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package/dist/VariantFeatureWidget/VariantAnnPanel.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+export default function VariantAnnPanel({ feature, descriptions, }: {
+    feature: any;
+    descriptions: any;
+}): JSX.Element | null;

package/dist/VariantFeatureWidget/VariantAnnPanel.js

@@ -0,0 +1,25 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable @typescript-eslint/no-explicit-any */
+const react_1 = __importDefault(require("react"));
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const AnnotGrid_1 = __importDefault(require("./AnnotGrid"));
+function VariantAnnPanel({ feature, descriptions, }) {
+    var _a, _b, _c, _d;
+    const annFields = (((_d = (_c = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.ANN) === null || _b === void 0 ? void 0 : _b.Description) === null || _c === void 0 ? void 0 : _c.match(/.*Functional annotations:'(.*)'$/)) === null || _d === void 0 ? void 0 : _d[1].split('|')) || []);
+    const ann = (feature.INFO.ANN || []);
+    const rows = ann.map((elt, id) => ({
+        id,
+        ...Object.fromEntries(elt.split('|').map((e, i) => [annFields[i], e])),
+    })) || [];
+    const columns = annFields.map(c => ({
+        field: c,
+    }));
+    return ann.length ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "ANN table" },
+        react_1.default.createElement(AnnotGrid_1.default, { rows: rows, columns: columns }))) : null;
+}
+exports.default = VariantAnnPanel;
+//# sourceMappingURL=VariantAnnPanel.js.map

package/dist/VariantFeatureWidget/VariantAnnPanel.js.map

@@ -0,0 +1 @@
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package/dist/VariantFeatureWidget/VariantCsqPanel.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+export default function VariantCsqPanel({ feature, descriptions, }: {
+    feature: any;
+    descriptions: any;
+}): JSX.Element | null;

package/dist/VariantFeatureWidget/VariantCsqPanel.js

@@ -0,0 +1,25 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable @typescript-eslint/no-explicit-any */
+const react_1 = __importDefault(require("react"));
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const AnnotGrid_1 = __importDefault(require("./AnnotGrid"));
+function VariantCsqPanel({ feature, descriptions, }) {
+    var _a, _b, _c, _d;
+    const csqFields = (((_d = (_c = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.CSQ) === null || _b === void 0 ? void 0 : _b.Description) === null || _c === void 0 ? void 0 : _c.match(/.*Format: (.*)/)) === null || _d === void 0 ? void 0 : _d[1].split('|')) || []);
+    const csq = (feature.INFO.CSQ || []);
+    const rows = csq.map((elt, id) => ({
+        id,
+        ...Object.fromEntries(elt.split('|').map((e, i) => [csqFields[i], e])),
+    })) || [];
+    const columns = csqFields.map(c => ({
+        field: c,
+    }));
+    return csq.length ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "CSQ table" },
+        react_1.default.createElement(AnnotGrid_1.default, { rows: rows, columns: columns }))) : null;
+}
+exports.default = VariantCsqPanel;
+//# sourceMappingURL=VariantCsqPanel.js.map

package/dist/VariantFeatureWidget/VariantCsqPanel.js.map

@@ -0,0 +1 @@
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package/dist/VariantFeatureWidget/VariantFeatureWidget.js

@@ -1,190 +1,25 @@
 "use strict";
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
-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 __rest = (this && this.__rest) || function (s, e) {
-    var t = {};
-    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
-        t[p] = s[p];
-    if (s != null && typeof Object.getOwnPropertySymbols === "function")
-        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
-            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
-                t[p[i]] = s[p[i]];
-        }
-    return t;
-};
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
-var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
-    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
-        if (ar || !(i in from)) {
-            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
-            ar[i] = from[i];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 /* eslint-disable @typescript-eslint/no-explicit-any */
-var react_1 = __importStar(require("react"));
-var material_1 = require("@mui/material");
-var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-var x_data_grid_1 = require("@mui/x-data-grid");
-var mobx_react_1 = require("mobx-react");
-var util_1 = require("@jbrowse/core/util");
-var mobx_state_tree_1 = require("mobx-state-tree");
-var BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
-var BreakendOptionDialog_1 = __importDefault(require("./BreakendOptionDialog"));
-var vcf_1 = require("@gmod/vcf");
-function VariantSamples(props) {
-    var _a = __read((0, react_1.useState)({}), 2), filter = _a[0], setFilter = _a[1];
-    var _b = __read((0, react_1.useState)(false), 2), showFilters = _b[0], setShowFilters = _b[1];
-    var feature = props.feature;
-    var _c = feature.samples, samples = _c === void 0 ? {} : _c;
-    var preFilteredRows = Object.entries(samples);
-    if (!preFilteredRows.length) {
-        return null;
-    }
-    var infoFields = __spreadArray(['sample'], __read(Object.keys(preFilteredRows[0][1])), false).map(function (field) { return ({
-        field: field,
-    }); });
-    var error;
-    var rows = [];
-    var filters = Object.keys(filter);
-    // catch some error thrown from regex
-    // note: maps all values into a string, if this is not done rows are not
-    // sortable by the data-grid
-    try {
-        rows = preFilteredRows
-            .map(function (row) { return (__assign(__assign({}, Object.fromEntries(Object.entries(row[1]).map(function (entry) { return [entry[0], String(entry[1])]; }))), { sample: row[0], id: row[0] })); })
-            .filter(function (row) {
-            return filters.length
-                ? filters.every(function (key) {
-                    var val = row[key];
-                    var currFilter = filter[key];
-                    return currFilter ? val.match(new RegExp(currFilter, 'i')) : true;
-                })
-                : true;
-        });
-    }
-    catch (e) {
-        error = e;
-    }
-    // disableSelectionOnClick helps avoid
-    // https://github.com/mui-org/material-ui-x/issues/1197
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, __assign({}, props, { title: "Samples" }),
-        error ? react_1.default.createElement(material_1.Typography, { color: "error" }, "".concat(error)) : null,
-        react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: showFilters, onChange: function () { return setShowFilters(function (f) { return !f; }); } }), label: "Show sample filters" }),
-        showFilters ? (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement(material_1.Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
-            infoFields.map(function (_a) {
-                var field = _a.field;
-                return (react_1.default.createElement(material_1.TextField, { key: "filter-".concat(field), placeholder: "Filter ".concat(field), value: filter[field] || '', onChange: function (event) {
-                        var _a;
-                        return setFilter(__assign(__assign({}, filter), (_a = {}, _a[field] = event.target.value, _a)));
-                    } }));
-            }))) : null,
-        react_1.default.createElement("div", { style: { height: 600, width: '100%', overflow: 'auto' } },
-            react_1.default.createElement(x_data_grid_1.DataGrid, { rows: rows, columns: infoFields, disableSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true }))));
-}
-function BreakendPanel(props) {
-    var model = props.model, locStrings = props.locStrings, feature = props.feature;
-    var session = (0, util_1.getSession)(model);
-    var pluginManager = (0, mobx_state_tree_1.getEnv)(session).pluginManager;
-    var _a = __read((0, react_1.useState)(false), 2), breakpointDialog = _a[0], setBreakpointDialog = _a[1];
-    var viewType;
-    try {
-        viewType = pluginManager.getViewType('BreakpointSplitView');
-    }
-    catch (e) {
-        // ignore
-    }
-    var simpleFeature = new simpleFeature_1.default(feature);
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, __assign({}, props, { title: "Breakends" }),
-        react_1.default.createElement(material_1.Typography, null, "Link to linear view of breakend endpoints"),
-        react_1.default.createElement("ul", null, locStrings.map(function (locString) { return (react_1.default.createElement("li", { key: "".concat(JSON.stringify(locString)) },
-            react_1.default.createElement(material_1.Link, { href: "#", onClick: function (event) {
-                    var _a;
-                    event.preventDefault();
-                    var view = model.view;
-                    try {
-                        if (view) {
-                            (_a = view.navToLocString) === null || _a === void 0 ? void 0 : _a.call(view, locString);
-                        }
-                        else {
-                            throw new Error('No view associated with this feature detail panel anymore');
-                        }
-                    }
-                    catch (e) {
-                        console.error(e);
-                        session.notify("".concat(e));
-                    }
-                } }, "LGV - ".concat(locString)))); })),
-        viewType ? (react_1.default.createElement("div", null,
-            react_1.default.createElement(material_1.Typography, null, "Launch split views with breakend source and target"),
-            react_1.default.createElement("ul", null, locStrings.map(function (locString) { return (react_1.default.createElement("li", { key: "".concat(JSON.stringify(locString)) },
-                react_1.default.createElement(material_1.Link, { href: "#", onClick: function (event) {
-                        event.preventDefault();
-                        setBreakpointDialog(true);
-                    } }, "".concat(feature.refName, ":").concat(feature.start, " // ").concat(locString, " (split view)")))); })),
-            breakpointDialog ? (react_1.default.createElement(BreakendOptionDialog_1.default, { model: model, feature: simpleFeature, viewType: viewType, handleClose: function () {
-                    setBreakpointDialog(false);
-                } })) : null)) : null));
-}
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+const material_1 = require("@mui/material");
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const vcf_1 = require("@gmod/vcf");
+// locals
+const VariantSampleGrid_1 = __importDefault(require("./VariantSampleGrid"));
+const VariantCsqPanel_1 = __importDefault(require("./VariantCsqPanel"));
+const VariantAnnPanel_1 = __importDefault(require("./VariantAnnPanel"));
+const BreakendPanel_1 = __importDefault(require("./BreakendPanel"));
 function VariantFeatureDetails(props) {
-    var model = props.model;
-    var featureData = model.featureData, descriptions = model.descriptions;
-    var feat = JSON.parse(JSON.stringify(featureData));
-    var samples = feat.samples, rest = __rest(feat, ["samples"]);
-    var basicDescriptions = {
+    const { model } = props;
+    const { featureData, descriptions } = model;
+    const feat = JSON.parse(JSON.stringify(featureData));
+    const { samples, ...rest } = feat;
+    const basicDescriptions = {
         CHROM: 'chromosome: An identifier from the reference genome',
         POS: 'position: The reference position, with the 1st base having position 1',
         ID: 'identifier: Semi-colon separated list of unique identifiers where available',
@@ -194,11 +29,15 @@ function VariantFeatureDetails(props) {
         FILTER: 'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
     };
     return (react_1.default.createElement(material_1.Paper, { "data-testid": "variant-side-drawer" },
-        react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, __assign({ feature: rest, descriptions: __assign(__assign({}, basicDescriptions), descriptions) }, props)),
+        react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, { feature: rest, descriptions: { ...basicDescriptions, ...descriptions }, ...props }),
+        react_1.default.createElement(material_1.Divider, null),
+        react_1.default.createElement(VariantCsqPanel_1.default, { feature: rest, descriptions: descriptions }),
+        react_1.default.createElement(material_1.Divider, null),
+        react_1.default.createElement(VariantAnnPanel_1.default, { feature: rest, descriptions: descriptions }),
         react_1.default.createElement(material_1.Divider, null),
-        feat.type === 'breakend' ? (react_1.default.createElement(BreakendPanel, { feature: feat, locStrings: feat.ALT.map(function (alt) { var _a; return ((_a = (0, vcf_1.parseBreakend)(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : null,
-        feat.type === 'translocation' ? (react_1.default.createElement(BreakendPanel, { feature: feat, model: model, locStrings: ["".concat(feat.INFO.CHR2[0], ":").concat(feat.INFO.END)] })) : null,
-        react_1.default.createElement(VariantSamples, __assign({ feature: feat }, props))));
+        feat.type === 'breakend' ? (react_1.default.createElement(BreakendPanel_1.default, { feature: feat, locStrings: feat.ALT.map((alt) => { var _a; return ((_a = (0, vcf_1.parseBreakend)(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : null,
+        feat.type === 'translocation' ? (react_1.default.createElement(BreakendPanel_1.default, { feature: feat, model: model, locStrings: [`${feat.INFO.CHR2[0]}:${feat.INFO.END}`] })) : null,
+        react_1.default.createElement(VariantSampleGrid_1.default, { feature: feat, ...props })));
 }
 exports.default = (0, mobx_react_1.observer)(VariantFeatureDetails);
 //# sourceMappingURL=VariantFeatureWidget.js.map

package/dist/VariantFeatureWidget/VariantFeatureWidget.js.map

@@ -1 +1 @@
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package/dist/VariantFeatureWidget/VariantSampleGrid.d.ts

@@ -0,0 +1,2 @@
+/// <reference types="react" />
+export default function VariantSamples(props: any): JSX.Element | null;