@jbrowse/plugin-linear-genome-view 2.1.7 → 2.2.0

package/esm/LinearBasicDisplay/model.js

@@ -7,121 +7,177 @@ import VisibilityIcon from '@mui/icons-material/Visibility';
 // locals
 import { BaseLinearDisplay } from '../BaseLinearDisplay';
 const SetMaxHeightDlg = lazy(() => import('./components/SetMaxHeight'));
-const stateModelFactory = (configSchema) => types
-    .compose('LinearBasicDisplay', BaseLinearDisplay, types.model({
-    type: types.literal('LinearBasicDisplay'),
-    trackShowLabels: types.maybe(types.boolean),
-    trackShowDescriptions: types.maybe(types.boolean),
-    trackDisplayMode: types.maybe(types.string),
-    trackMaxHeight: types.maybe(types.number),
-    configuration: ConfigurationReference(configSchema),
-}))
-    .views(self => ({
-    get rendererTypeName() {
-        return getConf(self, ['renderer', 'type']);
-    },
-    get showLabels() {
-        var _a;
-        return (_a = self.trackShowLabels) !== null && _a !== void 0 ? _a : getConf(self, ['renderer', 'showLabels']);
-    },
-    get showDescriptions() {
-        var _a;
-        return ((_a = self.trackShowDescriptions) !== null && _a !== void 0 ? _a : getConf(self, ['renderer', 'showDescriptions']));
-    },
-    get maxHeight() {
-        var _a;
-        return (_a = self.trackMaxHeight) !== null && _a !== void 0 ? _a : getConf(self, ['renderer', 'maxHeight']);
-    },
-    get displayMode() {
-        var _a;
-        return ((_a = self.trackDisplayMode) !== null && _a !== void 0 ? _a : getConf(self, ['renderer', 'displayMode']));
-    },
-}))
-    .views(self => ({
-    get rendererConfig() {
-        const configBlob = getConf(self, ['renderer']) || {};
-        const config = configBlob;
-        return self.rendererType.configSchema.create({
-            ...config,
-            showLabels: self.showLabels,
-            showDescriptions: self.showDescriptions,
-            displayMode: self.displayMode,
-            maxHeight: self.maxHeight,
-        }, getEnv(self));
-    },
-}))
-    .actions(self => ({
-    toggleShowLabels() {
-        self.trackShowLabels = !self.showLabels;
-    },
-    toggleShowDescriptions() {
-        self.trackShowDescriptions = !self.showDescriptions;
-    },
-    setDisplayMode(val) {
-        self.trackDisplayMode = val;
-    },
-    setMaxHeight(val) {
-        self.trackMaxHeight = val;
-    },
-}))
-    .views(self => {
-    const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
-    return {
-        renderProps() {
-            const config = self.rendererConfig;
-            const superProps = superRenderProps();
-            const superPropsOmit = superProps;
-            return {
-                ...superPropsOmit,
-                config,
-            };
+/**
+ * #stateModel LinearBasicDisplay
+ * used by `FeatureTrack`, has simple settings like "show/hide feature labels", etc.
+ */
+function stateModelFactory(configSchema) {
+    return types
+        .compose('LinearBasicDisplay', BaseLinearDisplay, types.model({
+        /**
+         * #property
+         */
+        type: types.literal('LinearBasicDisplay'),
+        /**
+         * #property
+         */
+        trackShowLabels: types.maybe(types.boolean),
+        /**
+         * #property
+         */
+        trackShowDescriptions: types.maybe(types.boolean),
+        /**
+         * #property
+         */
+        trackDisplayMode: types.maybe(types.string),
+        /**
+         * #property
+         */
+        trackMaxHeight: types.maybe(types.number),
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(configSchema),
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get rendererTypeName() {
+            return getConf(self, ['renderer', 'type']);
         },
-        trackMenuItems() {
-            return [
-                ...superTrackMenuItems(),
-                {
-                    label: 'Show labels',
-                    icon: VisibilityIcon,
-                    type: 'checkbox',
-                    checked: self.showLabels,
-                    onClick: () => {
-                        self.toggleShowLabels();
+        /**
+         * #getter
+         */
+        get showLabels() {
+            var _a;
+            return (_a = self.trackShowLabels) !== null && _a !== void 0 ? _a : getConf(self, ['renderer', 'showLabels']);
+        },
+        /**
+         * #getter
+         */
+        get showDescriptions() {
+            var _a;
+            return ((_a = self.trackShowDescriptions) !== null && _a !== void 0 ? _a : getConf(self, ['renderer', 'showDescriptions']));
+        },
+        /**
+         * #getter
+         */
+        get maxHeight() {
+            var _a;
+            return (_a = self.trackMaxHeight) !== null && _a !== void 0 ? _a : getConf(self, ['renderer', 'maxHeight']);
+        },
+        /**
+         * #getter
+         */
+        get displayMode() {
+            var _a;
+            return ((_a = self.trackDisplayMode) !== null && _a !== void 0 ? _a : getConf(self, ['renderer', 'displayMode']));
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get rendererConfig() {
+            const configBlob = getConf(self, ['renderer']) || {};
+            const config = configBlob;
+            return self.rendererType.configSchema.create({
+                ...config,
+                showLabels: self.showLabels,
+                showDescriptions: self.showDescriptions,
+                displayMode: self.displayMode,
+                maxHeight: self.maxHeight,
+            }, getEnv(self));
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        toggleShowLabels() {
+            self.trackShowLabels = !self.showLabels;
+        },
+        /**
+         * #action
+         */
+        toggleShowDescriptions() {
+            self.trackShowDescriptions = !self.showDescriptions;
+        },
+        /**
+         * #action
+         */
+        setDisplayMode(val) {
+            self.trackDisplayMode = val;
+        },
+        /**
+         * #action
+         */
+        setMaxHeight(val) {
+            self.trackMaxHeight = val;
+        },
+    }))
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
+        return {
+            /**
+             * #method
+             */
+            renderProps() {
+                const config = self.rendererConfig;
+                const superProps = superRenderProps();
+                const superPropsOmit = superProps;
+                return {
+                    ...superPropsOmit,
+                    config,
+                };
+            },
+            /**
+             * #method
+             */
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Show labels',
+                        icon: VisibilityIcon,
+                        type: 'checkbox',
+                        checked: self.showLabels,
+                        onClick: () => self.toggleShowLabels(),
                     },
-                },
-                {
-                    label: 'Show descriptions',
-                    icon: VisibilityIcon,
-                    type: 'checkbox',
-                    checked: self.showDescriptions,
-                    onClick: () => self.toggleShowDescriptions(),
-                },
-                {
-                    label: 'Display mode',
-                    icon: VisibilityIcon,
-                    subMenu: [
-                        'compact',
-                        'reducedRepresentation',
-                        'normal',
-                        'collapse',
-                    ].map(val => ({
-                        label: val,
+                    {
+                        label: 'Show descriptions',
+                        icon: VisibilityIcon,
+                        type: 'checkbox',
+                        checked: self.showDescriptions,
+                        onClick: () => self.toggleShowDescriptions(),
+                    },
+                    {
+                        label: 'Display mode',
+                        icon: VisibilityIcon,
+                        subMenu: [
+                            'compact',
+                            'reducedRepresentation',
+                            'normal',
+                            'collapse',
+                        ].map(val => ({
+                            label: val,
+                            onClick: () => self.setDisplayMode(val),
+                        })),
+                    },
+                    {
+                        label: 'Set max height',
                         onClick: () => {
-                            self.setDisplayMode(val);
+                            getSession(self).queueDialog(handleClose => [
+                                SetMaxHeightDlg,
+                                { model: self, handleClose },
+                            ]);
                         },
-                    })),
-                },
-                {
-                    label: 'Set max height',
-                    onClick: () => {
-                        getSession(self).queueDialog(handleClose => [
-                            SetMaxHeightDlg,
-                            { model: self, handleClose },
-                        ]);
                     },
-                },
-            ];
-        },
-    };
-});
+                ];
+            },
+        };
+    });
+}
 export default stateModelFactory;
 //# sourceMappingURL=model.js.map

package/esm/LinearBasicDisplay/model.js.map

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package/esm/LinearGenomeView/components/ImportForm.js

@@ -1,14 +1,13 @@
-import React, { useState, lazy } from 'react';
+import React, { useState, useEffect, lazy } from 'react';
 import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
 import { getSession } from '@jbrowse/core/util';
-import { Button, CircularProgress, Container, Grid } from '@mui/material';
+import { Button, CircularProgress, FormControl, Container, Grid, } from '@mui/material';
 import { ErrorMessage, AssemblySelector } from '@jbrowse/core/ui';
 import CloseIcon from '@mui/icons-material/Close';
 // locals
 import RefNameAutocomplete from './RefNameAutocomplete';
 import { fetchResults, splitLast } from './util';
-import { WIDGET_HEIGHT } from '..';
 const SearchResultsDialog = lazy(() => import('./SearchResultsDialog'));
 const useStyles = makeStyles()(theme => ({
     importFormContainer: {
@@ -37,8 +36,13 @@ const ImportForm = observer(({ model }) => {
         : 'No configured assemblies';
     const regions = (assembly === null || assembly === void 0 ? void 0 : assembly.regions) || [];
     const err = assemblyError || importError;
-    const [myVal, setValue] = useState('');
-    const value = myVal || ((_a = regions[0]) === null || _a === void 0 ? void 0 : _a.refName);
+    const [value, setValue] = useState('');
+    const r0 = (_a = regions[0]) === null || _a === void 0 ? void 0 : _a.refName;
+    // useEffect resets to an "initial state" of displaying first region from assembly
+    // after assembly change
+    useEffect(() => {
+        setValue(r0);
+    }, [r0]);
     function navToOption(option) {
         const location = option.getLocation();
         const trackId = option.getTrackId();
@@ -92,7 +96,6 @@ const ImportForm = observer(({ model }) => {
             session.notify(`${e}`, 'warning');
         }
     }
-    const height = WIDGET_HEIGHT + 5;
     // implementation notes:
     // having this wrapped in a form allows intuitive use of enter key to submit
     return (React.createElement("div", { className: classes.container },
@@ -107,31 +110,34 @@ const ImportForm = observer(({ model }) => {
                 } },
                 React.createElement(Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
                     React.createElement(Grid, { item: true },
-                        React.createElement(AssemblySelector, { onChange: val => {
-                                setImportError('');
-                                setSelectedAsm(val);
-                                setValue('');
-                            }, session: session, selected: selectedAsm, InputProps: { style: { height } } })),
-                    React.createElement(Grid, { item: true }, selectedAsm ? (err ? (React.createElement(CloseIcon, { style: { color: 'red' } })) : value ? (React.createElement(RefNameAutocomplete, { fetchResults: queryString => fetchResults({
-                            queryString,
-                            assembly,
-                            textSearchManager,
-                            rankSearchResults,
-                            searchScope,
-                        }), model: model, assemblyName: assemblyError ? undefined : selectedAsm, value: value, 
-                        // note: minWidth 270 accomodates full width of helperText
-                        minWidth: 270, onChange: str => setValue(str), onSelect: val => setOption(val), TextFieldProps: {
-                            variant: 'outlined',
-                            helperText: 'Enter sequence name, feature name, or location',
-                            style: { minWidth: '175px' },
-                            InputProps: { style: { height } },
-                        } })) : (React.createElement(CircularProgress, { role: "progressbar", size: 20, disableShrink: true }))) : null),
+                        React.createElement(FormControl, null,
+                            React.createElement(AssemblySelector, { onChange: val => {
+                                    setImportError('');
+                                    setSelectedAsm(val);
+                                    setValue('');
+                                }, session: session, selected: selectedAsm }))),
+                    React.createElement(Grid, { item: true }, selectedAsm ? (err ? (React.createElement(CloseIcon, { style: { color: 'red' } })) : value ? (React.createElement(FormControl, null,
+                        React.createElement(RefNameAutocomplete, { fetchResults: queryString => fetchResults({
+                                queryString,
+                                assembly,
+                                textSearchManager,
+                                rankSearchResults,
+                                searchScope,
+                            }), model: model, assemblyName: assemblyError ? undefined : selectedAsm, value: value, 
+                            // note: minWidth 270 accomodates full width of helperText
+                            minWidth: 270, onChange: str => setValue(str), onSelect: val => setOption(val), TextFieldProps: {
+                                variant: 'outlined',
+                                helperText: 'Enter sequence name, feature name, or location',
+                                style: { minWidth: '175px' },
+                            } }))) : (React.createElement(CircularProgress, { role: "progressbar", size: 20, disableShrink: true }))) : null),
                     React.createElement(Grid, { item: true },
-                        React.createElement(Button, { type: "submit", disabled: !value, className: classes.button, variant: "contained", color: "primary" }, "Open"),
-                        React.createElement(Button, { disabled: !value, className: classes.button, onClick: () => {
-                                model.setError(undefined);
-                                model.showAllRegionsInAssembly(selectedAsm);
-                            }, variant: "contained", color: "secondary" }, "Show all regions in assembly"))))),
+                        React.createElement(FormControl, null,
+                            React.createElement(Button, { type: "submit", disabled: !value, className: classes.button, variant: "contained", color: "primary" }, "Open")),
+                        React.createElement(FormControl, null,
+                            React.createElement(Button, { disabled: !value, className: classes.button, onClick: () => {
+                                    model.setError(undefined);
+                                    model.showAllRegionsInAssembly(selectedAsm);
+                                }, variant: "contained", color: "secondary" }, "Show all regions in assembly")))))),
         isSearchDialogDisplayed ? (React.createElement(SearchResultsDialog, { model: model, optAssemblyName: selectedAsm, handleClose: () => model.setSearchResults(undefined, undefined) })) : null));
 });
 export default ImportForm;

package/esm/LinearGenomeView/components/ImportForm.js.map

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package/esm/LinearGenomeView/components/LinearGenomeView.js

@@ -3,7 +3,7 @@ import { Button, Paper, Typography } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import { ErrorBoundary } from 'react-error-boundary';
 import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
-import { ErrorMessage } from '@jbrowse/core/ui';
+import { LoadingEllipses, ErrorMessage } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 import TrackContainer from './TrackContainer';
 import TracksContainer from './TracksContainer';
@@ -16,32 +16,12 @@ const useStyles = makeStyles()(theme => ({
         paddingTop: theme.spacing(1),
         paddingBottom: theme.spacing(1),
     },
-    dots: {
-        '&::after': {
-            display: 'inline-block',
-            animation: '$ellipsis 1.5s infinite',
-            content: '"."',
-            width: '1em',
-            textAlign: 'left',
-        },
-    },
-    '@keyframes ellipsis': {
-        '0%': {
-            content: '"."',
-        },
-        '33%': {
-            content: '".."',
-        },
-        '66%': {
-            content: '"..."',
-        },
-    },
 }));
 const LinearGenomeView = observer(({ model }) => {
     const { tracks, error, initialized, hasDisplayedRegions } = model;
     const { classes } = useStyles();
     if (!initialized && !error) {
-        return (React.createElement(Typography, { className: classes.dots, variant: "h5" }, "Loading"));
+        return React.createElement(LoadingEllipses, { variant: "h5" });
     }
     if (!hasDisplayedRegions || error) {
         return React.createElement(ImportForm, { model: model });

package/esm/LinearGenomeView/components/LinearGenomeView.js.map

@@ -1 +1 @@
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+{"version":3,"file":"LinearGenomeView.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/LinearGenomeView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AACzD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAA;AACpD,OAAO,EAAE,aAAa,IAAI,iBAAiB,EAAE,MAAM,wBAAwB,CAAA;AAC3E,OAAO,EAAE,eAAe,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAChE,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AAIvD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,SAAS,EAAE,QAAQ;QACnB,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAC5B,aAAa,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAChC;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,gBAAgB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAAkB,EAAE,EAAE;IAC9D,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,mBAAmB,EAAE,GAAG,KAAK,CAAA;IACjE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAE/B,IAAI,CAAC,WAAW,IAAI,CAAC,KAAK,EAAE;QAC1B,OAAO,oBAAC,eAAe,IAAC,OAAO,EAAC,IAAI,GAAG,CAAA;KACxC;IACD,IAAI,CAAC,mBAAmB,IAAI,KAAK,EAAE;QACjC,OAAO,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAAA;KACpC;IAED,MAAM,qBAAqB,GAAG,KAAK,CAAC,qBAAqB,EAAE,CAAA;IAC3D,MAAM,eAAe,GAAG,KAAK,CAAC,eAAe,EAAE,CAAA;IAE/C,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QACjC,KAAK,CAAC,kBAAkB,CAAC,CAAC,CAAC,CAC1B,oBAAC,iBAAiB,IAChB,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,wBAAwB,CAAC,KAAK,CAAC,GACxD,CACH,CAAC,CAAC,CAAC,IAAI;QACP,KAAK,CAAC,uBAAuB,CAAC,CAAC,CAAC,CAC/B,oBAAC,mBAAmB,IAClB,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,gBAAgB,CAAC,SAAS,EAAE,SAAS,CAAC,GAC/D,CACH,CAAC,CAAC,CAAC,IAAI;QACR,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,oBAAC,qBAAqB,IAAC,KAAK,EAAE,KAAK,GAAI;QACvC,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,IAC1B,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAChB,oBAAC,KAAK,IAAC,OAAO,EAAC,UAAU,EAAC,SAAS,EAAE,OAAO,CAAC,IAAI,IAC9C,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC,CAAC,CAC3B;YACE,oBAAC,UAAU,4BAA+B;YAC1C,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,KAAK,CAAC,qBAAqB,EACpC,KAAK,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,EACvB,SAAS,EAAE,oBAAC,iBAAiB,OAAG,0BAGzB,CACR,CACJ,CAAC,CAAC,CAAC,CACF,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,GAAQ,CACvC,CACK,CACT,CAAC,CAAC,CAAC,CACF,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAClB,oBAAC,aAAa,IACZ,GAAG,EAAE,KAAK,CAAC,EAAE,EACb,iBAAiB,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;YAEhE,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CAChC,CACjB,CAAC,CACH,CACe,CACd,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/esm/LinearGenomeView/components/LinearGenomeViewSvg.js

@@ -110,6 +110,7 @@ function SVGTracks({ displayResults, model, offset, }) {
 // render LGV to SVG
 export async function renderToSvg(model, opts) {
     await when(() => model.initialized);
+    const { Wrapper = ({ children }) => React.createElement(React.Fragment, null, children) } = opts;
     const { width, tracks, showCytobands } = model;
     const shift = 50;
     const offset = headerHeight +
@@ -124,10 +125,11 @@ export async function renderToSvg(model, opts) {
         return { track, result };
     }));
     // the xlink namespace is used for rendering <image> tag
-    return renderToStaticMarkup(React.createElement("svg", { width: width, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, width + shift * 2, height].toString() },
-        React.createElement("rect", { width: width + shift * 2, height: height, fill: "white" }),
-        React.createElement("g", { stroke: "none", transform: `translate(${shift} ${fontSize})` },
-            React.createElement(SVGHeader, { model: model }),
-            React.createElement(SVGTracks, { model: model, displayResults: displayResults, offset: offset }))));
+    return renderToStaticMarkup(React.createElement(Wrapper, null,
+        React.createElement("svg", { width: width, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, width + shift * 2, height].toString() },
+            React.createElement("rect", { width: width + shift * 2, height: height, fill: "white" }),
+            React.createElement("g", { stroke: "none", transform: `translate(${shift} ${fontSize})` },
+                React.createElement(SVGHeader, { model: model }),
+                React.createElement(SVGTracks, { model: model, displayResults: displayResults, offset: offset })))));
 }
 //# sourceMappingURL=LinearGenomeViewSvg.js.map

package/esm/LinearGenomeView/components/LinearGenomeViewSvg.js.map

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