@jbrowse/core 3.7.0 → 4.0.1

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js

@@ -1,72 +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 });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const Help_1 = __importDefault(require("@mui/icons-material/Help"));
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const ui_1 = require("../../ui");
-const util_1 = require("../../util");
-const SequenceFeatureDetails = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequenceFeatureDetails'))));
-const HelpDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./dialogs/HelpDialog'))));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    formControl: {
-        margin: 0,
-    },
-    container: {
-        marginTop: theme.spacing(4),
-        marginBottom: theme.spacing(4),
-    },
-}));
-const SequenceFeaturePanel = (0, mobx_react_1.observer)(function ({ model, feature, }) {
-    const { classes } = useStyles();
-    const [shown, setShown] = (0, react_1.useState)(false);
-    return ((0, jsx_runtime_1.jsxs)("div", { className: classes.container, children: [(0, jsx_runtime_1.jsx)(material_1.FormControl, { className: classes.formControl, children: (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                        setShown(!shown);
-                    }, children: shown ? 'Hide feature sequence' : 'Show feature sequence' }) }), (0, jsx_runtime_1.jsx)(material_1.IconButton, { onClick: () => {
-                    (0, util_1.getSession)(model).queueDialog(handleClose => [
-                        HelpDialog,
-                        {
-                            handleClose,
-                        },
-                    ]);
-                }, children: (0, jsx_runtime_1.jsx)(Help_1.default, {}) }), shown ? ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: (0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, {}), children: (0, jsx_runtime_1.jsx)(SequenceFeatureDetails, { model: model, feature: feature }, feature.uniqueId) })) : null] }));
-});
-exports.default = SequenceFeaturePanel;

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts

@@ -1,8 +0,0 @@
-import type { SequenceFeatureDetailsModel } from './model';
-import type { SimpleFeatureSerialized } from '../../util';
-declare const SequenceName: ({ mode, model, feature, }: {
-    model: SequenceFeatureDetailsModel;
-    mode: string;
-    feature: SimpleFeatureSerialized;
-}) => import("react/jsx-runtime").JSX.Element;
-export default SequenceName;

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js

@@ -1,28 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const mobx_react_1 = require("mobx-react");
-const util_1 = require("../../util");
-function getStrand(strand) {
-    if (strand === -1) {
-        return '(-)';
-    }
-    else if (strand === 1) {
-        return '(+)';
-    }
-    else {
-        return '';
-    }
-}
-const SequenceName = (0, mobx_react_1.observer)(function ({ mode, model, feature, }) {
-    return ((0, jsx_runtime_1.jsx)("div", { style: { background: 'white' }, children: `>${[
-            [feature.name || feature.id, mode].filter(f => !!f).join('-'),
-            `${feature.refName}:${(0, util_1.toLocale)(feature.start + 1)}-${(0, util_1.toLocale)(feature.end)}${getStrand(feature.strand)}`,
-            mode.endsWith('updownstream')
-                ? `+/- ${(0, util_1.toLocale)(model.upDownBp)} up/downstream bp`
-                : '',
-        ]
-            .filter(f => !!f)
-            .join(' ')}\n` }));
-});
-exports.default = SequenceName;

package/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts

@@ -1,3 +0,0 @@
-import type { SequencePanelProps } from './types';
-declare const SequencePanel: import("react").ForwardRefExoticComponent<SequencePanelProps & import("react").RefAttributes<HTMLDivElement>>;
-export default SequencePanel;

package/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js

@@ -1,34 +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 react_1 = require("react");
-const mobx_react_1 = require("mobx-react");
-const SequenceContents_1 = __importDefault(require("./SequenceContents"));
-const SequenceName_1 = __importDefault(require("./SequenceName"));
-function WordWrap({ children }) {
-    return ((0, jsx_runtime_1.jsx)("pre", { style: {
-            fontFamily: 'monospace',
-            color: 'black',
-            fontSize: 11,
-        }, children: children }));
-}
-function NoWordWrap({ children }) {
-    return ((0, jsx_runtime_1.jsx)("div", { style: {
-            fontFamily: 'monospace',
-            color: 'black',
-            fontSize: 11,
-            maxWidth: 600,
-            whiteSpace: 'wrap',
-            wordBreak: 'break-all',
-        }, children: children }));
-}
-const SequencePanel = (0, mobx_react_1.observer)((0, react_1.forwardRef)(function S(props, ref) {
-    const { sequence, model, feature } = props;
-    const { showCoordinates, mode } = model;
-    const Container = showCoordinates ? WordWrap : NoWordWrap;
-    return ((0, jsx_runtime_1.jsx)("div", { "data-testid": "sequence_panel", ref: ref, style: { maxHeight: 300, overflow: 'auto' }, children: (0, jsx_runtime_1.jsxs)(Container, { children: [(0, jsx_runtime_1.jsx)(SequenceName_1.default, { model: model, mode: mode, feature: feature }), (0, jsx_runtime_1.jsx)(SequenceContents_1.default, { model: model, mode: mode, feature: feature, sequence: sequence })] }) }));
-}));
-exports.default = SequencePanel;

package/BaseFeatureWidget/SequenceFeatureDetails/consts.js

@@ -1,9 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.genomeColor = exports.updownstreamColor = exports.cdsColor = exports.proteinColor = exports.utrColor = exports.intronColor = void 0;
-exports.intronColor = undefined;
-exports.utrColor = 'rgb(200,240,240)';
-exports.proteinColor = 'rgb(220,160,220)';
-exports.cdsColor = 'rgb(220,220,180)';
-exports.updownstreamColor = 'rgba(250,200,200)';
-exports.genomeColor = 'rgb(200,280,200)';

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js

@@ -1,17 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = HelpDialog;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const ui_1 = require("@jbrowse/core/ui");
-const Settings_1 = __importDefault(require("@mui/icons-material/Settings"));
-const material_1 = require("@mui/material");
-function HelpDialog({ handleClose, }) {
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => {
-            handleClose();
-        }, title: "Feature sequence panel help", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "The \"Feature sequence\" panel shows the underlying genomic sequence for a given feature, fetched from the reference genome." }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "For gene features, this panel does special calculations to e.g. stitch together the coding sequence, the options are:" }), (0, jsx_runtime_1.jsxs)("ul", { children: [(0, jsx_runtime_1.jsx)("li", { children: "CDS - shows the stitched together CDS sequences" }), (0, jsx_runtime_1.jsx)("li", { children: "Protein - the translated coding sequence, with the \"standard\" genetic code" }), (0, jsx_runtime_1.jsx)("li", { children: "cDNA - shows the 'copy DNA' of transcript, formed from exon sequences" }), (0, jsx_runtime_1.jsx)("li", { children: "Genomic w/ introns +/- Nbp up+down stream - the sequence underlying the entire gene including including introns, with UTR and CDS highlighted" })] }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "For other feature types, the options are:" }), (0, jsx_runtime_1.jsx)("ul", { children: (0, jsx_runtime_1.jsx)("li", { children: "Genomic +/- Nbp up+down stream - the reference genome sequence underlying the feature, with the up and downstream sequence" }) }), (0, jsx_runtime_1.jsxs)(material_1.Typography, { children: ["Note 1: you can use the \"gear icon\" ", (0, jsx_runtime_1.jsx)(Settings_1.default, {}), " to edit the number of bp displayed up/downstream and in the intron region"] }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Note 2: The 'Copy HTML' function retains the colors from the sequence panel but cannot be pasted into some programs like notepad that only expect plain text." })] }), (0, jsx_runtime_1.jsx)(material_1.DialogActions, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
-                        handleClose();
-                    }, autoFocus: true, variant: "contained", children: "Close" }) })] }));
-}

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts

@@ -1,8 +0,0 @@
-import { type SimpleFeatureSerialized } from '../../../util';
-import type { BaseFeatureWidgetModel } from '../../stateModelFactory';
-declare const SequenceDialog: ({ handleClose, model, feature, }: {
-    handleClose: () => void;
-    feature: SimpleFeatureSerialized;
-    model: BaseFeatureWidgetModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default SequenceDialog;

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js

@@ -1,50 +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 react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const SequenceFeatureMenu_1 = __importDefault(require("./SequenceFeatureMenu"));
-const SequenceTypeSelector_1 = __importDefault(require("./SequenceTypeSelector"));
-const util_1 = require("../../../util");
-const useFeatureSequence_1 = require("../../../util/useFeatureSequence");
-const SequencePanel_1 = __importDefault(require("../SequencePanel"));
-const useStyles = (0, mui_1.makeStyles)()({
-    dialogContent: {
-        width: '80em',
-    },
-    formControl: {
-        margin: 0,
-        marginLeft: 4,
-    },
-});
-const SequenceDialog = (0, mobx_react_1.observer)(function ({ handleClose, model, feature, }) {
-    var _a, _b;
-    const { sequenceFeatureDetails } = model;
-    const { upDownBp } = sequenceFeatureDetails;
-    const { classes } = useStyles();
-    const seqPanelRef = (0, react_1.useRef)(null);
-    const [forceLoad, setForceLoad] = (0, react_1.useState)(false);
-    const session = (0, util_1.getSession)(model);
-    const assemblyName = (_b = (_a = model.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) === null || _b === void 0 ? void 0 : _b[0];
-    const { sequence, error } = (0, useFeatureSequence_1.useFeatureSequence)({
-        assemblyName,
-        session,
-        feature: new util_1.SimpleFeature(feature),
-        upDownBp,
-        forceLoad,
-    });
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { maxWidth: "xl", open: true, title: "Sequence view", onClose: () => {
-            handleClose();
-        }, children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { className: classes.dialogContent, children: [(0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(SequenceTypeSelector_1.default, { model: sequenceFeatureDetails }), (0, jsx_runtime_1.jsx)(SequenceFeatureMenu_1.default, { ref: seqPanelRef, model: sequenceFeatureDetails })] }), (0, jsx_runtime_1.jsxs)("div", { children: [feature.type === 'gene' ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Note: inspect subfeature sequences for protein/CDS computations" })) : null, error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : !sequence ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, {})) : 'error' in sequence ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: sequence.error }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "inherit", onClick: () => {
-                                            setForceLoad(true);
-                                        }, children: "Force load" })] })) : ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: (0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, {}), children: (0, jsx_runtime_1.jsx)(SequencePanel_1.default, { ref: seqPanelRef, feature: feature, sequence: sequence, model: sequenceFeatureDetails }) }))] })] }), (0, jsx_runtime_1.jsx)(material_1.DialogActions, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
-                        handleClose();
-                    }, variant: "contained", children: "Close" }) })] }));
-});
-exports.default = SequenceDialog;

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts

@@ -1,8 +0,0 @@
-import type { MenuItem } from '../../../ui';
-import type { SequenceFeatureDetailsModel } from '../model';
-interface Props {
-    model: SequenceFeatureDetailsModel;
-    extraItems?: MenuItem[];
-}
-declare const SequenceFeatureMenu: import("react").ForwardRefExoticComponent<Props & import("react").RefAttributes<HTMLDivElement>>;
-export default SequenceFeatureMenu;

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js

@@ -1,141 +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 });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const MoreVert_1 = __importDefault(require("@mui/icons-material/MoreVert"));
-const Settings_1 = __importDefault(require("@mui/icons-material/Settings"));
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-const file_saver_1 = require("file-saver");
-const mobx_react_1 = require("mobx-react");
-const CascadingMenuButton_1 = __importDefault(require("../../../ui/CascadingMenuButton"));
-const SequenceFeatureSettingsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SettingsDialog'))));
-const SequenceFeatureMenu = (0, mobx_react_1.observer)((0, react_1.forwardRef)(function SequenceFeatureMenu2({ model, extraItems = [] }, ref) {
-    if (typeof ref === 'function') {
-        throw new Error('needs a non function ref');
-    }
-    const [showSettings, setShowSettings] = (0, react_1.useState)(false);
-    const { showCoordinatesSetting, showGenomicCoordsOption } = model;
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(CascadingMenuButton_1.default, { menuItems: [
-                    {
-                        label: 'Copy plaintext',
-                        onClick: () => {
-                            const r = ref === null || ref === void 0 ? void 0 : ref.current;
-                            if (r) {
-                                (0, copy_to_clipboard_1.default)(r.textContent || '', { format: 'text/plain' });
-                            }
-                        },
-                    },
-                    {
-                        label: 'Copy HTML',
-                        onClick: () => {
-                            const r = ref === null || ref === void 0 ? void 0 : ref.current;
-                            if (r) {
-                                (0, copy_to_clipboard_1.default)(r.outerHTML, { format: 'text/html' });
-                            }
-                        },
-                    },
-                    {
-                        label: 'Download plaintext',
-                        onClick: () => {
-                            const r = ref === null || ref === void 0 ? void 0 : ref.current;
-                            if (r) {
-                                (0, file_saver_1.saveAs)(new Blob([r.textContent || ''], {
-                                    type: 'text/plain;charset=utf-8',
-                                }), 'sequence.txt');
-                            }
-                        },
-                    },
-                    {
-                        label: 'Download HTML',
-                        onClick: () => {
-                            const r = ref === null || ref === void 0 ? void 0 : ref.current;
-                            if (r) {
-                                (0, file_saver_1.saveAs)(new Blob([r.outerHTML || ''], {
-                                    type: 'text/html;charset=utf-8',
-                                }), 'sequence.html');
-                            }
-                        },
-                    },
-                    ...extraItems,
-                    {
-                        label: 'Show coordinates?',
-                        type: 'subMenu',
-                        subMenu: [
-                            {
-                                label: 'No coordinates',
-                                type: 'radio',
-                                checked: showCoordinatesSetting === 'none',
-                                onClick: () => {
-                                    model.setShowCoordinates('none');
-                                },
-                            },
-                            {
-                                label: 'Coordinates relative to feature start',
-                                type: 'radio',
-                                checked: showCoordinatesSetting === 'relative',
-                                onClick: () => {
-                                    model.setShowCoordinates('relative');
-                                },
-                            },
-                            ...(showGenomicCoordsOption
-                                ? [
-                                    {
-                                        label: 'Coordinates relative to genome (only available for continuous genome based sequence types)',
-                                        type: 'radio',
-                                        checked: showCoordinatesSetting === 'genomic',
-                                        onClick: () => {
-                                            model.setShowCoordinates('genomic');
-                                        },
-                                    },
-                                ]
-                                : []),
-                        ],
-                    },
-                    {
-                        label: 'Settings',
-                        icon: Settings_1.default,
-                        onClick: () => {
-                            setShowSettings(true);
-                        },
-                    },
-                ], children: (0, jsx_runtime_1.jsx)(MoreVert_1.default, {}) }), showSettings ? ((0, jsx_runtime_1.jsx)(SequenceFeatureSettingsDialog, { model: model, handleClose: () => {
-                    setShowSettings(false);
-                } })) : null] }));
-}));
-exports.default = SequenceFeatureMenu;

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts

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

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js

@@ -1,66 +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)()({
-    formControl: {
-        margin: 0,
-        marginLeft: 4,
-    },
-});
-const SequenceTypeSelector = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes } = useStyles();
-    const { intronBp, upDownBp, mode, hasCDS, hasExonOrCDS } = model;
-    return ((0, jsx_runtime_1.jsx)(material_1.FormControl, { className: classes.formControl, children: (0, jsx_runtime_1.jsx)(material_1.Select, { size: "small", value: mode, onChange: event => {
-                model.setMode(event.target.value);
-            }, children: Object.entries({
-                ...(hasCDS
-                    ? {
-                        cds: 'CDS',
-                    }
-                    : {}),
-                ...(hasCDS
-                    ? {
-                        protein: 'Protein',
-                    }
-                    : {}),
-                ...(hasExonOrCDS
-                    ? {
-                        cdna: 'cDNA',
-                    }
-                    : {}),
-                ...(hasExonOrCDS
-                    ? {
-                        gene: 'Genomic w/ full introns',
-                    }
-                    : {}),
-                ...(hasExonOrCDS
-                    ? {
-                        gene_updownstream: `Genomic w/ full introns +/- ${upDownBp}bp up+down stream`,
-                    }
-                    : {}),
-                ...(hasExonOrCDS
-                    ? {
-                        gene_collapsed_intron: `Genomic w/ ${intronBp}bp intron`,
-                    }
-                    : {}),
-                ...(hasExonOrCDS
-                    ? {
-                        gene_updownstream_collapsed_intron: `Genomic w/ ${intronBp}bp intron +/- ${upDownBp}bp up+down stream `,
-                    }
-                    : {}),
-                ...(!hasExonOrCDS
-                    ? {
-                        genomic: 'Genomic',
-                    }
-                    : {}),
-                ...(!hasExonOrCDS
-                    ? {
-                        genomic_sequence_updownstream: `Genomic +/- ${upDownBp}bp up+down stream`,
-                    }
-                    : {}),
-            }).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: key, children: val }, key))) }) }));
-});
-exports.default = SequenceTypeSelector;

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts

@@ -1,6 +0,0 @@
-import type { SequenceFeatureDetailsModel } from '../model';
-declare const SequenceFeatureSettingsDialog: ({ handleClose, model, }: {
-    handleClose: () => void;
-    model: SequenceFeatureDetailsModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default SequenceFeatureSettingsDialog;

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js

@@ -1,50 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-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 => ({
-    formElt: {
-        margin: theme.spacing(3),
-        width: 400,
-    },
-    dialogContent: {
-        width: '80em',
-    },
-    root: {
-        padding: 4,
-    },
-}));
-function TextField2(props) {
-    return ((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.TextField, { ...props }) }));
-}
-function FormControl2({ children }) {
-    return ((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.FormControl, { children: children }) }));
-}
-const SequenceFeatureSettingsDialog = (0, mobx_react_1.observer)(function ({ handleClose, model, }) {
-    const { classes } = useStyles();
-    const { upperCaseCDS } = model;
-    const [intronBp, setIntronBp] = (0, react_1.useState)(`${model.intronBp}`);
-    const [upDownBp, setUpDownBp] = (0, react_1.useState)(`${model.upDownBp}`);
-    const intronBpValid = !Number.isNaN(+intronBp);
-    const upDownBpValid = !Number.isNaN(+upDownBp);
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => {
-            handleClose();
-        }, title: "Feature sequence settings", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { className: classes.dialogContent, children: [(0, jsx_runtime_1.jsx)(TextField2, { label: "Number of intronic bases around splice site to display", className: classes.formElt, value: intronBp, helperText: !intronBpValid ? 'Not a number' : '', error: !intronBpValid, onChange: event => {
-                            setIntronBp(event.target.value);
-                        } }), (0, jsx_runtime_1.jsx)(TextField2, { label: "Number of bases up/down stream of feature to display", className: classes.formElt, value: upDownBp, helperText: !upDownBpValid ? 'Not a number' : '', error: !upDownBpValid, onChange: event => {
-                            setUpDownBp(event.target.value);
-                        } }), (0, jsx_runtime_1.jsxs)(FormControl2, { children: [(0, jsx_runtime_1.jsx)(material_1.FormLabel, { children: "Sequence capitalization" }), (0, jsx_runtime_1.jsxs)(material_1.RadioGroup, { value: upperCaseCDS ? 'cds' : 'unchanged', onChange: e => {
-                                    model.setUpperCaseCDS(e.target.value === 'cds');
-                                }, children: [(0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: "cds", control: (0, jsx_runtime_1.jsx)(material_1.Radio, { className: classes.root, size: "small" }), label: "Capitalize CDS and lower case everything else" }), (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: "unchanged", control: (0, jsx_runtime_1.jsx)(material_1.Radio, { className: classes.root, size: "small" }), label: "Capitalization from reference genome sequence" })] })] })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
-                            model.setIntronBp(+intronBp);
-                            model.setUpDownBp(+upDownBp);
-                            handleClose();
-                        }, disabled: !intronBpValid || !upDownBpValid, color: "primary", variant: "contained", children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
-                            handleClose();
-                        }, color: "secondary", autoFocus: true, variant: "contained", children: "Cancel" })] })] }));
-});
-exports.default = SequenceFeatureSettingsDialog;

package/BaseFeatureWidget/SequenceFeatureDetails/index.d.ts

@@ -1 +0,0 @@
-export { default } from './SequenceFeaturePanel';

package/BaseFeatureWidget/SequenceFeatureDetails/index.js

@@ -1,8 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = void 0;
-var SequenceFeaturePanel_1 = require("./SequenceFeaturePanel");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(SequenceFeaturePanel_1).default; } });

package/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts

@@ -1,31 +0,0 @@
-import type { SimpleFeatureSerialized } from '../../util';
-import type { Instance } from 'mobx-state-tree';
-type ShowCoordinatesMode = 'none' | 'relative' | 'genomic';
-type SequenceDisplayMode = '' | 'gene' | 'gene_collapsed_intron' | 'gene_updownstream' | 'cdna' | 'cds' | 'genomic' | 'genomic_sequence_updownstream' | 'protein';
-export declare function SequenceFeatureDetailsF(): import("mobx-state-tree").IModelType<{}, {
-    showCoordinatesSetting: string;
-    intronBp: number;
-    upDownBp: number;
-    upperCaseCDS: boolean;
-    charactersPerRow: number;
-    feature: SimpleFeatureSerialized | undefined;
-    mode: SequenceDisplayMode;
-} & {
-    setFeature(f: SimpleFeatureSerialized): void;
-    setUpDownBp(f: number): void;
-    setIntronBp(f: number): void;
-    setUpperCaseCDS(f: boolean): void;
-    setShowCoordinates(f: ShowCoordinatesMode): void;
-    setMode(mode: SequenceDisplayMode): void;
-} & {
-    readonly showCoordinates: boolean;
-    readonly showGenomicCoordsOption: boolean;
-    readonly hasCDS: boolean | undefined;
-    readonly hasExon: boolean | undefined;
-    readonly hasExonOrCDS: boolean | undefined;
-} & {
-    afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export type SequenceFeatureDetailsStateModel = ReturnType<typeof SequenceFeatureDetailsF>;
-export type SequenceFeatureDetailsModel = Instance<SequenceFeatureDetailsStateModel>;
-export {};