@jbrowse/plugin-data-management 2.3.3 → 2.3.4

package/dist/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.js

@@ -0,0 +1,91 @@
+"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");
+const react_vtree_1 = require("react-vtree");
+const util_1 = require("@jbrowse/core/util");
+const TrackListNode_1 = __importDefault(require("./TrackListNode"));
+function getNodeData(node, nestingLevel, extra, selection) {
+    const isLeaf = !!node.conf;
+    const selected = !!selection[node.id];
+    return {
+        data: {
+            defaultHeight: isLeaf ? 22 : 40,
+            isLeaf,
+            isOpenByDefault: true,
+            nestingLevel,
+            selected,
+            ...node,
+            ...extra,
+        },
+        nestingLevel,
+        node,
+    };
+}
+// this is the main tree component for the hierarchical track selector in note:
+// in jbrowse-web the toolbar is position="sticky" which means the autosizer
+// includes the height of the toolbar, so we subtract the given offsets
+exports.default = (0, mobx_react_1.observer)(function HierarchicalTree({ height, tree, model, }) {
+    const { filterText, selection, view } = model;
+    const treeRef = (0, react_1.useRef)(null);
+    const session = (0, util_1.getSession)(model);
+    const { drawerPosition } = session;
+    const obj = (0, react_1.useMemo)(() => Object.fromEntries(selection.map(s => [s.trackId, s])), [selection]);
+    const extra = (0, react_1.useMemo)(() => ({
+        onChange: (trackId) => view.toggleTrack(trackId),
+        toggleCollapse: (pathName) => model.toggleCategory(pathName),
+        tree,
+        model,
+        drawerPosition,
+    }), [view, model, drawerPosition, tree]);
+    const treeWalker = (0, react_1.useCallback)(function* treeWalker() {
+        for (let i = 0; i < tree.children.length; i++) {
+            const r = tree.children[i];
+            yield getNodeData(r, 0, extra, obj);
+        }
+        while (true) {
+            // @ts-ignore
+            const parentMeta = yield;
+            for (let i = 0; i < parentMeta.node.children.length; i++) {
+                const curr = parentMeta.node.children[i];
+                yield getNodeData(curr, parentMeta.nestingLevel + 1, extra, obj);
+            }
+        }
+    }, [tree, extra, obj]);
+    (0, react_1.useEffect)(() => {
+        // @ts-ignore
+        treeRef.current.recomputeTree({
+            refreshNodes: true,
+            useDefaultHeight: true,
+        });
+    }, [tree, filterText]);
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(react_vtree_1.VariableSizeTree, { ref: treeRef, treeWalker: treeWalker, height: height }, TrackListNode_1.default)));
+});
+//# sourceMappingURL=HierarchicalTree.js.map

package/dist/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.js.map

@@ -0,0 +1 @@
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package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackCategory.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { NodeData } from '../util';
+export default function Category({ isOpen, setOpen, data, }: {
+    isOpen: boolean;
+    setOpen: (arg: boolean) => void;
+    data: NodeData;
+}): JSX.Element;

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackCategory.js

@@ -0,0 +1,89 @@
+"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 Menu_1 = __importDefault(require("@jbrowse/core/ui/Menu"));
+// icons
+const ArrowDropDown_1 = __importDefault(require("@mui/icons-material/ArrowDropDown"));
+const ArrowRight_1 = __importDefault(require("@mui/icons-material/ArrowRight"));
+const MoreHoriz_1 = __importDefault(require("@mui/icons-material/MoreHoriz"));
+// locals
+const util_1 = require("../util");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    contrastColor: {
+        color: theme.palette.secondary.contrastText,
+    },
+    // margin:auto 0 to center text vertically
+    accordionText: {
+        margin: 'auto 0',
+        // width 100 so you can click anywhere on the category bar
+        width: '100%',
+    },
+}));
+function Category({ isOpen, setOpen, data, }) {
+    const { classes } = useStyles();
+    const [menuEl, setMenuEl] = (0, react_1.useState)(null);
+    const { name, model, id, tree, toggleCollapse } = data;
+    return (react_1.default.createElement("div", { className: classes.accordionText, onClick: () => {
+            if (!menuEl) {
+                toggleCollapse(id);
+                setOpen(!isOpen);
+            }
+        } },
+        react_1.default.createElement(material_1.Typography, null,
+            isOpen ? react_1.default.createElement(ArrowDropDown_1.default, null) : react_1.default.createElement(ArrowRight_1.default, null),
+            name,
+            react_1.default.createElement(material_1.IconButton, { onClick: event => {
+                    setMenuEl(event.currentTarget);
+                    event.stopPropagation();
+                }, className: classes.contrastColor },
+                react_1.default.createElement(MoreHoriz_1.default, null))),
+        menuEl ? (react_1.default.createElement(Menu_1.default, { anchorEl: menuEl, menuItems: [
+                {
+                    label: 'Add to selection',
+                    onClick: () => {
+                        const r = (0, util_1.treeToMap)(tree).get(id);
+                        model.addToSelection((0, util_1.getAllChildren)(r));
+                    },
+                },
+                {
+                    label: 'Remove from selection',
+                    onClick: () => {
+                        const r = (0, util_1.treeToMap)(tree).get(id);
+                        model.removeFromSelection((0, util_1.getAllChildren)(r));
+                    },
+                },
+            ], onMenuItemClick: (_event, callback) => {
+                callback();
+                setMenuEl(null);
+            }, open: Boolean(menuEl), onClose: () => setMenuEl(null) })) : null));
+}
+exports.default = Category;
+//# sourceMappingURL=TrackCategory.js.map

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackCategory.js.map

@@ -0,0 +1 @@
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package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.d.ts

@@ -0,0 +1,11 @@
+/// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { NodeData } from '../util';
+export interface InfoArgs {
+    target: HTMLElement;
+    id: string;
+    conf: AnyConfigurationModel;
+}
+export default function TrackLabel({ data }: {
+    data: NodeData;
+}): JSX.Element;

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js

@@ -0,0 +1,86 @@
+"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 Menu_1 = __importDefault(require("@jbrowse/core/ui/Menu"));
+const util_1 = require("@jbrowse/core/util");
+const configuration_1 = require("@jbrowse/core/configuration");
+// icons
+const MoreHoriz_1 = __importDefault(require("@mui/icons-material/MoreHoriz"));
+// locals
+const util_2 = require("../util");
+const ui_1 = require("@jbrowse/core/ui");
+const useStyles = (0, mui_1.makeStyles)()({
+    compactCheckbox: {
+        padding: 0,
+    },
+    checkboxLabel: {
+        marginRight: 0,
+        '&:hover': {
+            backgroundColor: '#eee',
+        },
+    },
+});
+function TrackLabel({ data }) {
+    var _a, _b;
+    const { classes } = useStyles();
+    const { checked, conf, model, drawerPosition, id, name, onChange, selected } = data;
+    const [info, setInfo] = (0, react_1.useState)();
+    const description = (conf && (0, configuration_1.readConfObject)(conf, ['description'])) || '';
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(material_1.Tooltip, { title: description + (selected ? ' (in selection)' : ''), placement: drawerPosition === 'left' ? 'right' : 'left' },
+            react_1.default.createElement(material_1.FormControlLabel, { className: classes.checkboxLabel, control: react_1.default.createElement(material_1.Checkbox, { className: classes.compactCheckbox, checked: checked, onChange: () => onChange(id), disabled: (0, util_2.isUnsupported)(name), inputProps: {
+                        // @ts-ignore
+                        'data-testid': `htsTrackEntry-${id}`,
+                    } }), label: react_1.default.createElement("div", { style: { background: selected ? '#cccc' : undefined } },
+                    react_1.default.createElement(ui_1.SanitizedHTML, { html: name })) })),
+        react_1.default.createElement(material_1.IconButton, { onClick: e => setInfo({ target: e.currentTarget, id, conf }), style: { padding: 0 }, color: "secondary", "data-testid": `htsTrackEntryMenu-${id}` },
+            react_1.default.createElement(MoreHoriz_1.default, null)),
+        info ? (react_1.default.createElement(Menu_1.default, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: [
+                ...(((_b = (_a = (0, util_1.getSession)(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, info.conf)) || []),
+                {
+                    label: 'Add to selection',
+                    onClick: () => model.addToSelection([info.conf]),
+                },
+                ...(selected
+                    ? [
+                        {
+                            label: 'Remove from selection',
+                            onClick: () => model.removeFromSelection([info.conf]),
+                        },
+                    ]
+                    : []),
+            ], onMenuItemClick: (_event, callback) => {
+                callback();
+                setInfo(undefined);
+            }, open: Boolean(info), onClose: () => setInfo(undefined) })) : null));
+}
+exports.default = TrackLabel;
+//# sourceMappingURL=TrackLabel.js.map

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js.map

@@ -0,0 +1 @@
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package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackListNode.d.ts

@@ -0,0 +1,10 @@
+/// <reference types="react" />
+import { NodeData } from '../util';
+export default function Node({ data, isOpen, style, setOpen, }: {
+    data: NodeData;
+    isOpen: boolean;
+    style?: {
+        height: number;
+    };
+    setOpen: (arg: boolean) => void;
+}): JSX.Element;

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackListNode.js

@@ -0,0 +1,54 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mui_1 = require("tss-react/mui");
+// locals
+const TrackCategory_1 = __importDefault(require("./TrackCategory"));
+const TrackLabel_1 = __importDefault(require("./TrackLabel"));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    // this accordionBase element's small padding is used to give a margin to
+    // accordionColor it a "margin" because the virtualized elements can't really
+    // use margin in a conventional way (it doesn't affect layout)
+    accordionBase: {
+        display: 'flex',
+    },
+    accordionCard: {
+        padding: 3,
+        cursor: 'pointer',
+        display: 'flex',
+    },
+    nestingLevelMarker: {
+        position: 'absolute',
+        borderLeft: '1.5px solid #555',
+    },
+    // accordionColor set's display:flex so that the child accordionText use
+    // vertically centered text
+    accordionColor: {
+        background: theme.palette.tertiary.main,
+        color: theme.palette.tertiary.contrastText,
+        width: '100%',
+        display: 'flex',
+        paddingLeft: 5,
+    },
+}));
+// An individual node in the track selector. Note: manually sets cursor:
+// pointer improves usability for what can be clicked
+function Node({ data, isOpen, style, setOpen, }) {
+    const { isLeaf, nestingLevel } = data;
+    const { classes } = useStyles();
+    const width = 10;
+    const marginLeft = nestingLevel * width + (isLeaf ? width : 0);
+    return (react_1.default.createElement("div", { style: style, className: !isLeaf ? classes.accordionBase : undefined },
+        new Array(nestingLevel).fill(0).map((_, idx) => (react_1.default.createElement("div", { key: `mark-${idx}`, style: { left: idx * width + 4, height: style === null || style === void 0 ? void 0 : style.height }, className: classes.nestingLevelMarker }))),
+        react_1.default.createElement("div", { className: !isLeaf ? classes.accordionCard : undefined, style: {
+                marginLeft,
+                whiteSpace: 'nowrap',
+                width: '100%',
+            } },
+            react_1.default.createElement("div", { className: !isLeaf ? classes.accordionColor : undefined }, !isLeaf ? (react_1.default.createElement(TrackCategory_1.default, { isOpen: isOpen, data: data, setOpen: setOpen })) : (react_1.default.createElement(TrackLabel_1.default, { data: data }))))));
+}
+exports.default = Node;
+//# sourceMappingURL=TrackListNode.js.map

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackListNode.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"TrackListNode.js","sourceRoot":"","sources":["../../../../src/HierarchicalTrackSelectorWidget/components/tree/TrackListNode.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,uCAA0C;AAE1C,SAAS;AACT,oEAAsC;AACtC,8DAAqC;AAGrC,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,yEAAyE;IACzE,6EAA6E;IAC7E,8DAA8D;IAC9D,aAAa,EAAE;QACb,OAAO,EAAE,MAAM;KAChB;IAED,aAAa,EAAE;QACb,OAAO,EAAE,CAAC;QACV,MAAM,EAAE,SAAS;QACjB,OAAO,EAAE,MAAM;KAChB;IAED,kBAAkB,EAAE;QAClB,QAAQ,EAAE,UAAU;QACpB,UAAU,EAAE,kBAAkB;KAC/B;IACD,wEAAwE;IACxE,2BAA2B;IAC3B,cAAc,EAAE;QACd,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC,IAAI;QACvC,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC,YAAY;QAC1C,KAAK,EAAE,MAAM;QACb,OAAO,EAAE,MAAM;QACf,WAAW,EAAE,CAAC;KACf;CACF,CAAC,CAAC,CAAA;AAEH,wEAAwE;AACxE,qDAAqD;AACrD,SAAwB,IAAI,CAAC,EAC3B,IAAI,EACJ,MAAM,EACN,KAAK,EACL,OAAO,GAMR;IACC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,IAAI,CAAA;IAErC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,MAAM,UAAU,GAAG,YAAY,GAAG,KAAK,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAE9D,OAAO,CACL,uCAAK,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,SAAS;QACtE,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CAC/C,uCACE,GAAG,EAAE,QAAQ,GAAG,EAAE,EAClB,KAAK,EAAE,EAAE,IAAI,EAAE,GAAG,GAAG,KAAK,GAAG,CAAC,EAAE,MAAM,EAAE,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,MAAM,EAAE,EACvD,SAAS,EAAE,OAAO,CAAC,kBAAkB,GACrC,CACH,CAAC;QACF,uCACE,SAAS,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,SAAS,EACtD,KAAK,EAAE;gBACL,UAAU;gBACV,UAAU,EAAE,QAAQ;gBACpB,KAAK,EAAE,MAAM;aACd;YAED,uCAAK,SAAS,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC,CAAC,SAAS,IACzD,CAAC,MAAM,CAAC,CAAC,CAAC,CACT,8BAAC,uBAAQ,IAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,OAAO,EAAE,OAAO,GAAI,CAC3D,CAAC,CAAC,CAAC,CACF,8BAAC,oBAAU,IAAC,IAAI,EAAE,IAAI,GAAI,CAC3B,CACG,CACF,CACF,CACP,CAAA;AACH,CAAC;AA5CD,uBA4CC"}

package/dist/HierarchicalTrackSelectorWidget/components/util.d.ts

@@ -1,3 +1,19 @@
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { TreeNode } from '../model';
+import { HierarchicalTrackSelectorModel, TreeNode } from '../model';
+export interface NodeData {
+    nestingLevel: number;
+    checked: boolean;
+    conf: AnyConfigurationModel;
+    drawerPosition: unknown;
+    id: string;
+    isLeaf: boolean;
+    name: string;
+    onChange: Function;
+    toggleCollapse: (arg: string) => void;
+    tree: TreeNode;
+    selected: boolean;
+    model: HierarchicalTrackSelectorModel;
+}
 export declare function getAllChildren(subtree?: TreeNode): AnyConfigurationModel[];
+export declare function treeToMap(tree: TreeNode, map?: Map<string, TreeNode>): Map<string, TreeNode>;
+export declare function isUnsupported(name?: string): boolean;

package/dist/HierarchicalTrackSelectorWidget/components/util.js

@@ -1,9 +1,24 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getAllChildren = void 0;
+exports.isUnsupported = exports.treeToMap = exports.getAllChildren = void 0;
 function getAllChildren(subtree) {
     // @ts-ignore
     return ((subtree === null || subtree === void 0 ? void 0 : subtree.children.map(t => t.children.length ? getAllChildren(t) : t.conf)) || []).flat(Infinity);
 }
 exports.getAllChildren = getAllChildren;
+function treeToMap(tree, map = new Map()) {
+    if (tree.id && tree.children.length) {
+        map.set(tree.id, tree);
+    }
+    for (let i = 0; i < tree.children.length; i++) {
+        const node = tree.children[i];
+        treeToMap(node, map);
+    }
+    return map;
+}
+exports.treeToMap = treeToMap;
+function isUnsupported(name = '') {
+    return name.endsWith('(Unsupported)') || name.endsWith('(Unknown)');
+}
+exports.isUnsupported = isUnsupported;
 //# sourceMappingURL=util.js.map

package/dist/HierarchicalTrackSelectorWidget/components/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/HierarchicalTrackSelectorWidget/components/util.ts"],"names":[],"mappings":";;;AAGA,SAAgB,cAAc,CAAC,OAAkB;IAC/C,aAAa;IACb,OAAO,CACL,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CACxB,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,IAA8B,CAC1E,KAAI,EAAE,CACR,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;AAClB,CAAC;AAPD,wCAOC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/HierarchicalTrackSelectorWidget/components/util.ts"],"names":[],"mappings":";;;AAkBA,SAAgB,cAAc,CAAC,OAAkB;IAC/C,aAAa;IACb,OAAO,CACL,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CACxB,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,IAA8B,CAC1E,KAAI,EAAE,CACR,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;AAClB,CAAC;AAPD,wCAOC;AAED,SAAgB,SAAS,CAAC,IAAc,EAAE,MAAM,IAAI,GAAG,EAAoB;IACzE,IAAI,IAAI,CAAC,EAAE,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE;QACnC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;KACvB;IACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QAC7B,SAAS,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;KACrB;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AATD,8BASC;AAED,SAAgB,aAAa,CAAC,IAAI,GAAG,EAAE;IACrC,OAAO,IAAI,CAAC,QAAQ,CAAC,eAAe,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAA;AACrE,CAAC;AAFD,sCAEC"}

package/dist/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,6 +1,8 @@
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { AbstractSessionModel } from '@jbrowse/core/util';
 import PluginManager from '@jbrowse/core/PluginManager';
+export declare function matches(query: string, conf: AnyConfigurationModel, session: AbstractSessionModel): any;
 export type TreeNode = {
     name: string;
     id: string;
@@ -16,7 +18,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
     collapsed: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
-    filterText: import("mobx-state-tree").IType<string | undefined, string, string>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
     selection: ({
@@ -24,7 +25,9 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+    filterText: string;
 } & {
+    setSelection(elt: AnyConfigurationModel[]): void;
     addToSelection(elt: AnyConfigurationModel[]): void;
     removeFromSelection(elt: AnyConfigurationModel[]): void;
     clearSelection(): void;

package/dist/HierarchicalTrackSelectorWidget/model.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.generateHierarchy = void 0;
+exports.generateHierarchy = exports.matches = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
@@ -9,12 +9,13 @@ const mst_1 = require("@jbrowse/core/util/types/mst");
 function hasAnyOverlap(a1 = [], a2 = []) {
     return !!a1.find(value => a2.includes(value));
 }
-function passesFilter(filter, config, session) {
-    const categories = (0, configuration_1.readConfObject)(config, 'category');
-    const filterLower = filter.toLowerCase();
-    return ((0, tracks_1.getTrackName)(config, session).toLowerCase().includes(filterLower) ||
-        !!(categories === null || categories === void 0 ? void 0 : categories.filter(c => c.toLowerCase().includes(filterLower)).length));
+function matches(query, conf, session) {
+    const categories = (0, configuration_1.readConfObject)(conf, 'category');
+    const queryLower = query.toLowerCase();
+    return ((0, tracks_1.getTrackName)(conf, session).toLowerCase().includes(queryLower) ||
+        !!(categories === null || categories === void 0 ? void 0 : categories.filter(c => c.toLowerCase().includes(queryLower)).length));
 }
+exports.matches = matches;
 function filterTracks(tracks, self, assemblyName) {
     const { assemblyManager } = (0, util_1.getSession)(self);
     const { pluginManager } = (0, util_1.getEnv)(self);
@@ -37,7 +38,7 @@ function generateHierarchy(model, trackConfigurations, collapsed, extra) {
     const { filterText, view } = model;
     const session = (0, util_1.getSession)(model);
     trackConfigurations
-        .filter(conf => passesFilter(filterText, conf, session))
+        .filter(conf => matches(filterText, conf, session))
         .forEach(conf => {
         // copy the categories since this array can be mutated downstream
         const categories = [...((0, configuration_1.readConfObject)(conf, 'category') || [])];
@@ -86,13 +87,16 @@ function stateTreeFactory(pluginManager) {
         id: mst_1.ElementId,
         type: mobx_state_tree_1.types.literal('HierarchicalTrackSelectorWidget'),
         collapsed: mobx_state_tree_1.types.map(mobx_state_tree_1.types.boolean),
-        filterText: '',
         view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
     })
         .volatile(() => ({
         selection: [],
+        filterText: '',
     }))
         .actions(self => ({
+        setSelection(elt) {
+            self.selection = elt;
+        },
         addToSelection(elt) {
             self.selection = (0, util_1.dedupe)([...self.selection, ...elt], e => e.trackId);
         },

package/dist/HierarchicalTrackSelectorWidget/model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/HierarchicalTrackSelectorWidget/model.ts"],"names":[],"mappings":";;;AAAA,qDAA8D;AAC9D,+DAIoC;AACpC,6CAK2B;AAC3B,sDAAwD;AACxD,sDAAwD;AAGxD,SAAS,aAAa,CAAI,KAAU,EAAE,EAAE,KAAU,EAAE;IAClD,OAAO,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAA;AAC/C,CAAC;AAED,SAAgB,OAAO,CACrB,KAAa,EACb,IAA2B,EAC3B,OAA6B;IAE7B,MAAM,UAAU,GAAG,IAAA,8BAAc,EAAC,IAAI,EAAE,UAAU,CAAyB,CAAA;IAC3E,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,EAAE,CAAA;IACtC,OAAO,CACL,IAAA,qBAAY,EAAC,IAAI,EAAE,OAAO,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,UAAU,CAAC;QAC9D,CAAC,CAAC,CAAA,UAAU,aAAV,UAAU,uBAAV,UAAU,CAAE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,MAAM,CAAA,CACvE,CAAA;AACH,CAAC;AAXD,0BAWC;AAWD,SAAS,YAAY,CACnB,MAA+B,EAC/B,IAAgC,EAChC,YAAoB;IAEpB,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;IAC5C,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,aAAM,EAAC,IAAI,CAAC,CAAA;IACtC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAElD,IAAI,CAAC,QAAQ,EAAE;QACb,OAAO,EAAE,CAAA;KACV;IACD,MAAM,EAAE,UAAU,EAAE,GAAG,QAAQ,CAAA;IAC/B,OAAO,MAAM;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,aAAa,CAAC,UAAU,EAAE,IAAA,8BAAc,EAAC,CAAC,EAAE,eAAe,CAAC,CAAC,CAAC;SAC1E,MAAM,CAAC,CAAC,CAAC,EAAE;QACV,MAAM,EAAE,YAAY,EAAE,GAAG,aAAa,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClE,MAAM,cAAc,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAmB,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACxE,MAAM,aAAa,GAAG,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAmB,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACrE,OAAO,aAAa,CAAC,cAAc,EAAE,aAAa,CAAC,CAAA;IACrD,CAAC,CAAC,CAAA;AACN,CAAC;AAED,SAAgB,iBAAiB,CAC/B,KAAqC,EACrC,mBAA4C,EAC5C,SAAwD,EACxD,KAAc;IAEd,MAAM,SAAS,GAAG,EAAE,QAAQ,EAAE,EAAgB,EAAc,CAAA;IAC5D,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IAClC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IAEjC,mBAAmB;SAChB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,OAAO,CAAC,UAAU,EAAE,IAAI,EAAE,OAAO,CAAC,CAAC;SAClD,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,iEAAiE;QACjE,MAAM,UAAU,GAAG,CAAC,GAAG,CAAC,IAAA,8BAAc,EAAC,IAAI,EAAE,UAAU,CAAC,IAAI,EAAE,CAAC,CAAC,CAAA;QAEhE,uEAAuE;QACvE,kEAAkE;QAClE,0BAA0B;QAC1B,IAAI,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE;YACzC,UAAU,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;SACtC;QAED,IAAI,SAAS,GAAG,SAAS,CAAA;QAEzB,wDAAwD;QACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC1C,MAAM,QAAQ,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YAC9B,MAAM,GAAG,GAAG,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAA;YAC7D,MAAM,EAAE,GAAG,KAAK,GAAG,GAAG,GAAG,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YAC7D,IAAI,CAAC,GAAG,EAAE;gBACR,MAAM,CAAC,GAAG;oBACR,QAAQ,EAAE,EAAE;oBACZ,IAAI,EAAE,QAAQ;oBACd,EAAE;oBACF,eAAe,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC;iBACpC,CAAA;gBACD,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBAC1B,SAAS,GAAG,CAAC,CAAA;aACd;iBAAM;gBACL,SAAS,GAAG,GAAG,CAAA;aAChB;SACF;QACD,MAAM,MAAM,GAAG,IAAI,CAAC,MAAoD,CAAA;QAExE,uEAAuE;QACvE,SAAS,CAAC,QAAQ,CAAC,MAAM,CACvB,SAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,EACxD,CAAC,EACD;YACE,EAAE,EAAE,IAAI,CAAC,OAAO;YAChB,IAAI,EAAE,IAAA,qBAAY,EAAC,IAAI,EAAE,OAAO,CAAC;YACjC,IAAI;YACJ,OAAO,EAAE,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,KAAK,IAAI,CAAC;YACrD,QAAQ,EAAE,EAAE;SACb,CACF,CAAA;IACH,CAAC,CAAC,CAAA;IAEJ,OAAO,SAAS,CAAC,QAAQ,CAAA;AAC3B,CAAC;AA5DD,8CA4DC;AAED,SAAwB,gBAAgB,CAAC,aAA4B;IACnE,OAAO,uBAAK;SACT,KAAK,CAAC,iCAAiC,EAAE;QACxC,EAAE,EAAE,eAAS;QACb,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,iCAAiC,CAAC;QACtD,SAAS,EAAE,uBAAK,CAAC,GAAG,CAAC,uBAAK,CAAC,OAAO,CAAC;QACnC,IAAI,EAAE,uBAAK,CAAC,aAAa,CACvB,aAAa,CAAC,gBAAgB,CAAC,MAAM,EAAE,YAAY,CAAC,CACrD;KACF,CAAC;SACD,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,SAAS,EAAE,EAA6B;QACxC,UAAU,EAAE,EAAE;KACf,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,YAAY,CAAC,GAA4B;YACvC,IAAI,CAAC,SAAS,GAAG,GAAG,CAAA;QACtB,CAAC;QACD,cAAc,CAAC,GAA4B;YACzC,IAAI,CAAC,SAAS,GAAG,IAAA,aAAM,EAAC,CAAC,GAAG,IAAI,CAAC,SAAS,EAAE,GAAG,GAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;QACtE,CAAC;QACD,mBAAmB,CAAC,GAA4B;YAC9C,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;QAC/D,CAAC;QACD,cAAc;YACZ,IAAI,CAAC,SAAS,GAAG,EAAE,CAAA;QACrB,CAAC;QACD,OAAO,CAAC,IAAa;YACnB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD,cAAc,CAAC,QAAgB;YAC7B,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC7D,CAAC;QACD,eAAe;YACb,IAAI,CAAC,UAAU,GAAG,EAAE,CAAA;QACtB,CAAC;QACD,aAAa,CAAC,OAAe;YAC3B,IAAI,CAAC,UAAU,GAAG,OAAO,CAAA;QAC3B,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd,kBAAkB,CAAC,YAAoB;YACrC,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAC5C,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;YAClD,MAAM,SAAS,GAAG,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,aAAa,CAAC,QAAQ,CAAA;YAClD,MAAM,QAAQ,GAAG,aAAa,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAC1D,IAAI,CAAC,SAAS,EAAE;gBACd,OAAO,SAAS,CAAA;aACjB;YACD,KAAK,MAAM,OAAO,IAAI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package/esm/AddTrackWidget/components/DefaultAddTrackWorkflow.js

@@ -16,15 +16,12 @@ const useStyles = makeStyles()(theme => ({
         backgroundColor: theme.palette.background.default,
     },
     button: {
-        marginTop: theme.spacing(1),
         marginRight: theme.spacing(1),
     },
     actionsContainer: {
+        marginTop: theme.spacing(10),
         marginBottom: theme.spacing(2),
     },
-    stepContent: {
-        margin: theme.spacing(1),
-    },
     alertContainer: {
         padding: `${theme.spacing(2)}px 0px ${theme.spacing(2)}px 0px`,
     },

package/esm/AddTrackWidget/components/DefaultAddTrackWorkflow.js.map

@@ -1 +1 @@
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package/esm/AddTrackWidget/components/TrackSourceSelect.js

@@ -6,9 +6,7 @@ import { getRoot } from 'mobx-state-tree';
 import { observer } from 'mobx-react';
 const useStyles = makeStyles()(theme => ({
     paper: {
-        display: 'flex',
-        flexDirection: 'column',
-        padding: theme.spacing(1),
+        padding: theme.spacing(2),
     },
     spacer: {
         height: theme.spacing(8),
@@ -16,7 +14,6 @@ const useStyles = makeStyles()(theme => ({
 }));
 function TrackSourceSelect({ model }) {
     const { classes } = useStyles();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const rootModel = getRoot(model);
     return (React.createElement(Paper, { className: classes.paper },
         React.createElement(FileSelector, { name: "Main file", description: "", location: model.trackData, setLocation: model.setTrackData, setName: model.setTrackName, rootModel: rootModel }),

package/esm/AddTrackWidget/components/TrackSourceSelect.js.map

@@ -1 +1 @@
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