react-msaview 3.1.11 → 3.2.0

package/dist/components/dialogs/TabPanel.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+export default function TabPanel({ children, value, index, ...other }: {
+    children?: React.ReactNode;
+    index: number;
+    value: number;
+}): React.JSX.Element;

package/dist/components/dialogs/TabPanel.js

@@ -0,0 +1,6 @@
+import React from 'react';
+// this is from MUI example
+export default function TabPanel({ children, value, index, ...other }) {
+    return (React.createElement("div", { role: "tabpanel", hidden: value !== index, ...other }, value === index && React.createElement("div", null, children)));
+}
+//# sourceMappingURL=TabPanel.js.map

package/dist/components/dialogs/TabPanel.js.map

@@ -0,0 +1 @@
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package/dist/components/dialogs/TracklistDialog.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const _default: ({ model, onClose, }: {
     model: MsaViewModel;
     onClose: () => void;

package/dist/components/dialogs/UserProvidedDomainsDialog.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model';
+declare const UserProvidedDomainsDialog: ({ handleClose, model, }: {
+    handleClose: () => void;
+    model: MsaViewModel;
+}) => React.JSX.Element;
+export default UserProvidedDomainsDialog;

package/dist/components/dialogs/UserProvidedDomainsDialog.js

@@ -0,0 +1,58 @@
+import React, { useState } from 'react';
+import { observer } from 'mobx-react';
+import { Button, DialogActions, DialogContent, FormControlLabel, FormControl, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
+import { getSession } from '@jbrowse/core/util';
+import { Dialog } from '@jbrowse/core/ui';
+import { jsonfetch } from '../../fetchUtils';
+const UserProvidedDomainsDialog = observer(function ({ handleClose, model, }) {
+    const [file, setFile] = useState();
+    const [choice, setChoice] = useState('file');
+    const [interProURL, setInterProURL] = useState('');
+    return (React.createElement(Dialog, { maxWidth: "xl", title: "Open protein domains from file", onClose: () => handleClose(), open: true },
+        React.createElement(DialogContent, null,
+            React.createElement("div", null,
+                React.createElement(Typography, null, "Open a JSON file of InterProScan results that you run remotely on EBI servers or locally"),
+                React.createElement("div", { style: { display: 'flex', margin: 30 } },
+                    React.createElement(FormControl, { component: "fieldset" },
+                        React.createElement(RadioGroup, { value: choice, onChange: event => setChoice(event.target.value) },
+                            React.createElement(FormControlLabel, { value: "url", control: React.createElement(Radio, null), label: "URL" }),
+                            React.createElement(FormControlLabel, { value: "file", control: React.createElement(Radio, null), label: "File" }))),
+                    choice === 'url' ? (React.createElement("div", null,
+                        React.createElement(Typography, null, "Open a InterProScan JSON file remote URL"),
+                        React.createElement(TextField, { label: "URL", value: interProURL, onChange: event => setInterProURL(event.target.value) }))) : null,
+                    choice === 'file' ? (React.createElement("div", { style: { paddingTop: 20 } },
+                        React.createElement(Typography, null, "Open a InterProScan JSON file file from your local drive"),
+                        React.createElement(Button, { variant: "outlined", component: "label" },
+                            "Choose File",
+                            React.createElement("input", { type: "file", hidden: true, onChange: ({ target }) => {
+                                    const file = target?.files?.[0];
+                                    if (file) {
+                                        setFile(file);
+                                    }
+                                } })))) : null))),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    ;
+                    (async () => {
+                        try {
+                            const ret = file
+                                ? JSON.parse(await file.text())
+                                : await jsonfetch(interProURL);
+                            model.setInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
+                            model.setShowDomains(true);
+                            getSession(model).notify('Loaded interproscan results', 'success');
+                        }
+                        catch (e) {
+                            console.error(e);
+                            getSession(model).notifyError(`${e}`, e);
+                        }
+                        finally {
+                            model.setStatus();
+                        }
+                    })();
+                    handleClose();
+                } }, "Open results"))));
+});
+export default UserProvidedDomainsDialog;
+//# sourceMappingURL=UserProvidedDomainsDialog.js.map

package/dist/components/dialogs/UserProvidedDomainsDialog.js.map

@@ -0,0 +1 @@
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package/dist/components/header/Header.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const Header: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/header/Header.js

@@ -1,6 +1,7 @@
-import React, { lazy } from 'react';
+import React, { lazy, useEffect } from 'react';
 import { IconButton } from '@mui/material';
 import { observer } from 'mobx-react';
+import useMeasure from '@jbrowse/core/util/useMeasure';
 // icons
 import Help from '@mui/icons-material/Help';
 // locals
@@ -8,14 +9,16 @@ import ZoomControls from './ZoomControls';
 import MultiAlignmentSelector from './MultiAlignmentSelector';
 import HeaderInfoArea from './HeaderInfoArea';
 import HeaderStatusArea from './HeaderStatusArea';
-import HeaderMenu from './HeaderMenu';
 import HeaderMenuExtra from './HeaderMenuExtra';
 const AboutDialog = lazy(() => import('../dialogs/AboutDialog'));
 const Header = observer(function ({ model }) {
-    return (React.createElement("div", { style: { display: 'flex' } },
-        React.createElement(HeaderMenu, { model: model }),
-        React.createElement(ZoomControls, { model: model }),
+    const [ref, { height }] = useMeasure();
+    useEffect(() => {
+        model.setHeaderHeight(height || 0);
+    }, [model, height]);
+    return (React.createElement("div", { ref: ref, style: { display: 'flex' } },
         React.createElement(HeaderMenuExtra, { model: model }),
+        React.createElement(ZoomControls, { model: model }),
         React.createElement(MultiAlignmentSelector, { model: model }),
         React.createElement(HeaderInfoArea, { model: model }),
         React.createElement(Spacer, null),

package/dist/components/header/Header.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/components/header/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAC9C,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,UAAU,MAAM,+BAA+B,CAAA;AAKtD,QAAQ;AACR,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAE3C,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;AAC7D,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAE/C,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,wBAAwB,CAAC,CAAC,CAAA;AAEhE,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAClE,MAAM,CAAC,GAAG,EAAE,EAAE,MAAM,EAAE,CAAC,GAAG,UAAU,EAAE,CAAA;IACtC,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,eAAe,CAAC,MAAM,IAAI,CAAC,CAAC,CAAA;IACpC,CAAC,EAAE,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IACnB,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QACvC,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QACxC,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI;QAChC,oBAAC,MAAM,OAAG;QACV,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC;YAEvE,oBAAC,IAAI,OAAG,CACG,CACT,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,MAAM;IACb,OAAO,6BAAK,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,GAAI,CAAA;AACpC,CAAC;AAED,eAAe,MAAM,CAAA"}

package/dist/components/header/HeaderInfoArea.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const HeaderInfoArea: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element | null;

package/dist/components/header/HeaderMenu.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const HeaderMenu: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/header/HeaderMenuExtra.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const HeaderMenuExtra: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/header/HeaderMenuExtra.js

@@ -2,27 +2,46 @@ import React, { lazy } from 'react';
 import { observer } from 'mobx-react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 // icons
-import MoreVert from '@mui/icons-material/MoreVert';
+import MoreVert from '@mui/icons-material/Menu';
 import Sort from '@mui/icons-material/Sort';
 import Visibility from '@mui/icons-material/Visibility';
 import FilterAlt from '@mui/icons-material/FilterAlt';
 import Search from '@mui/icons-material/Search';
 import PhotoCamera from '@mui/icons-material/PhotoCamera';
-import RestartAlt from '@mui/icons-material/RestartAlt';
+import Settings from '@mui/icons-material/Settings';
+import Assignment from '@mui/icons-material/Assignment';
+import List from '@mui/icons-material/List';
+import FolderOpen from '@mui/icons-material/FolderOpen';
 // lazies
+const SettingsDialog = lazy(() => import('../dialogs/SettingsDialog'));
+const MetadataDialog = lazy(() => import('../dialogs/MetadataDialog'));
+const TracklistDialog = lazy(() => import('../dialogs/TracklistDialog'));
 const ExportSVGDialog = lazy(() => import('../dialogs/ExportSVGDialog'));
 const FeatureFilterDialog = lazy(() => import('../dialogs/FeatureDialog'));
+const UserProvidedDomainsDialog = lazy(() => import('../dialogs/UserProvidedDomainsDialog'));
 const InterProScanDialog = lazy(() => import('../dialogs/InterProScanDialog'));
-const HeaderMenuExtra = observer(function ({ model }) {
-    const { featureMode, subFeatureRows, noAnnotations, interProScanJobIds } = model;
+const HeaderMenuExtra = observer(({ model }) => {
+    const { showDomains, actuallyShowDomains, subFeatureRows, noDomains } = model;
     return (React.createElement(CascadingMenuButton, { menuItems: [
             {
-                label: 'Reset zoom to default',
-                icon: RestartAlt,
-                onClick: () => {
-                    model.setColWidth(16);
-                    model.setRowHeight(20);
-                },
+                label: 'Return to import form',
+                icon: FolderOpen,
+                onClick: () => model.reset(),
+            },
+            {
+                label: 'Settings',
+                onClick: () => model.queueDialog(onClose => [SettingsDialog, { model, onClose }]),
+                icon: Settings,
+            },
+            {
+                label: 'Metadata',
+                onClick: () => model.queueDialog(onClose => [MetadataDialog, { model, onClose }]),
+                icon: Assignment,
+            },
+            {
+                label: 'Extra tracks',
+                onClick: () => model.queueDialog(onClose => [TracklistDialog, { model, onClose }]),
+                icon: List,
             },
             {
                 label: 'Export SVG',
@@ -34,22 +53,41 @@ const HeaderMenuExtra = observer(function ({ model }) {
                 type: 'subMenu',
                 subMenu: [
                     {
-                        label: 'Show domains' + (noAnnotations ? ' (no domains loaded)' : ''),
+                        label: 'Open domains...',
+                        icon: FolderOpen,
+                        onClick: () => model.queueDialog(handleClose => [
+                            UserProvidedDomainsDialog,
+                            { handleClose, model },
+                        ]),
+                    },
+                    {
+                        label: 'Query InterProScan for domains...',
+                        icon: Search,
+                        onClick: () => model.queueDialog(handleClose => [
+                            InterProScanDialog,
+                            { handleClose, model },
+                        ]),
+                    },
+                    {
+                        label: `Show domains${noDomains ? ' (no domains loaded)' : ''}`,
+                        disabled: noDomains,
                         icon: Visibility,
-                        checked: featureMode,
+                        checked: actuallyShowDomains ? showDomains : false,
                         type: 'checkbox',
-                        onClick: () => model.setFeatureMode(!featureMode),
+                        onClick: () => model.setShowDomains(!showDomains),
                     },
                     {
-                        label: 'Use sub-row layout',
-                        checked: subFeatureRows,
+                        label: `Use sub-row layout${noDomains ? ' (no domains loaded)' : ''}`,
+                        disabled: noDomains,
+                        checked: actuallyShowDomains ? subFeatureRows : false,
                         icon: Sort,
                         type: 'checkbox',
                         onClick: () => model.setSubFeatureRows(!subFeatureRows),
                     },
                     {
-                        label: 'Filter domains',
+                        label: `Filter domains${noDomains ? ' (no domains loaded)' : ''}`,
                         icon: FilterAlt,
+                        disabled: noDomains,
                         onClick: () => {
                             model.queueDialog(onClose => [
                                 FeatureFilterDialog,
@@ -57,31 +95,6 @@ const HeaderMenuExtra = observer(function ({ model }) {
                             ]);
                         },
                     },
-                    {
-                        label: 'Query InterProScan for domains...',
-                        icon: Search,
-                        onClick: () => model.queueDialog(onClose => [
-                            InterProScanDialog,
-                            { onClose, model },
-                        ]),
-                    },
-                    {
-                        label: 'Load previous InterProScan results...',
-                        icon: Search,
-                        type: 'subMenu',
-                        subMenu: interProScanJobIds.length
-                            ? interProScanJobIds.map(({ jobId, date }) => ({
-                                label: new Date(date).toLocaleString('en-US') + ' - ' + jobId,
-                                onClick: () => model.loadInterProScanResults(jobId),
-                            }))
-                            : [
-                                {
-                                    label: 'No previous searches',
-                                    disabled: true,
-                                    onClick: () => { },
-                                },
-                            ],
-                    },
                 ],
             },
             ...(model.extraViewMenuItems?.() || []),

package/dist/components/header/HeaderMenuExtra.js.map

@@ -1 +1 @@
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package/dist/components/header/HeaderStatusArea.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const HeaderStatusArea: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element | null;

package/dist/components/header/HeaderStatusArea.js

@@ -2,6 +2,7 @@ import React from 'react';
 import { Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
+import { LoadingEllipses } from '@jbrowse/core/ui';
 const useStyles = makeStyles()({
     margin: {
         margin: 'auto',
@@ -12,7 +13,7 @@ const HeaderStatusArea = observer(({ model }) => {
     const { status } = model;
     const { classes } = useStyles();
     return status ? (React.createElement(Typography, { className: classes.margin },
-        status.msg,
+        React.createElement(LoadingEllipses, { message: status.msg, component: "span" }),
         ' ',
         status.url ? (React.createElement("a", { href: status.url, target: "_blank", rel: "noreferrer" }, "(status)")) : null)) : null;
 });

package/dist/components/header/HeaderStatusArea.js.map

@@ -1 +1 @@
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+{"version":3,"file":"HeaderStatusArea.js","sourceRoot":"","sources":["../../../src/components/header/HeaderStatusArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAKlD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,gBAAgB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACvE,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,MAAM;QACnC,oBAAC,eAAe,IAAC,OAAO,EAAE,MAAM,CAAC,GAAG,EAAE,SAAS,EAAC,MAAM,GAAG;QAAC,GAAG;QAC5D,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CACZ,2BAAG,IAAI,EAAE,MAAM,CAAC,GAAG,EAAE,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,YAAY,eAEjD,CACL,CAAC,CAAC,CAAC,IAAI,CACG,CACd,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/components/header/MultiAlignmentSelector.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const MultiAlignmentSelector: ({ model, }: {
     model: MsaViewModel;
 }) => React.JSX.Element | null;

package/dist/components/header/ZoomControls.js

@@ -1,15 +1,45 @@
 import React from 'react';
 import { IconButton } from '@mui/material';
 import { observer } from 'mobx-react';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 // icons
 import ZoomIn from '@mui/icons-material/ZoomIn';
 import ZoomOut from '@mui/icons-material/ZoomOut';
+import MoreVert from '@mui/icons-material/MoreVert';
+import RestartAlt from '@mui/icons-material/RestartAlt';
 const ZoomControls = observer(function ZoomControls({ model, }) {
     return (React.createElement(React.Fragment, null,
         React.createElement(IconButton, { onClick: () => model.zoomIn() },
             React.createElement(ZoomIn, null)),
         React.createElement(IconButton, { onClick: () => model.zoomOut() },
-            React.createElement(ZoomOut, null))));
+            React.createElement(ZoomOut, null)),
+        React.createElement(CascadingMenuButton, { menuItems: [
+                {
+                    label: 'Zoom in horizontal',
+                    onClick: () => model.zoomInHorizontal(),
+                },
+                {
+                    label: 'Zoom in vertical',
+                    onClick: () => model.zoomInVertical(),
+                },
+                {
+                    label: 'Zoom out horizontal',
+                    onClick: () => model.zoomOutHorizontal(),
+                },
+                {
+                    label: 'Zoom out vertical',
+                    onClick: () => model.zoomOutVertical(),
+                },
+                {
+                    label: 'Reset zoom to default',
+                    icon: RestartAlt,
+                    onClick: () => {
+                        model.setColWidth(16);
+                        model.setRowHeight(20);
+                    },
+                },
+            ] },
+            React.createElement(MoreVert, null))));
 });
 export default ZoomControls;
 //# sourceMappingURL=ZoomControls.js.map

package/dist/components/header/ZoomControls.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ZoomControls.js","sourceRoot":"","sources":["../../../src/components/header/ZoomControls.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AAKtE,QAAQ;AACR,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAC/C,OAAO,OAAO,MAAM,6BAA6B,CAAA;AACjD,OAAO,QAAQ,MAAM,8BAA8B,CAAA;AACnD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAEvD,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,YAAY,CAAC,EAClD,KAAK,GAGN;IACC,OAAO,CACL;QACE,oBAAC,UAAU,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,MAAM,EAAE;YACvC,oBAAC,MAAM,OAAG,CACC;QACb,oBAAC,UAAU,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,OAAO,EAAE;YACxC,oBAAC,OAAO,OAAG,CACA;QACb,oBAAC,mBAAmB,IAClB,SAAS,EAAE;gBACT;oBACE,KAAK,EAAE,oBAAoB;oBAC3B,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,gBAAgB,EAAE;iBACxC;gBACD;oBACE,KAAK,EAAE,kBAAkB;oBACzB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,cAAc,EAAE;iBACtC;gBACD;oBACE,KAAK,EAAE,qBAAqB;oBAC5B,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,iBAAiB,EAAE;iBACzC;gBAED;oBACE,KAAK,EAAE,mBAAmB;oBAC1B,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,eAAe,EAAE;iBACvC;gBACD;oBACE,KAAK,EAAE,uBAAuB;oBAC9B,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;wBACrB,KAAK,CAAC,YAAY,CAAC,EAAE,CAAC,CAAA;oBACxB,CAAC;iBACF;aACF;YAED,oBAAC,QAAQ,OAAG,CACQ,CACrB,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AACF,eAAe,YAAY,CAAA"}

package/dist/components/import/ImportForm.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const _default: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/import/ImportForm.js

@@ -4,7 +4,7 @@ import { Button, Container, Grid, Typography } from '@mui/material';
 import { FileSelector } from '@jbrowse/core/ui';
 import { load } from './util';
 import ImportFormExamples from './ImportFormExamples';
-export default observer(({ model }) => {
+export default observer(function ({ model }) {
     const [msaFile, setMsaFile] = useState();
     const [treeFile, setTreeFile] = useState();
     const { error } = model;

package/dist/components/import/ImportForm.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ImportForm.js","sourceRoot":"","sources":["../../../src/components/import/ImportForm.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AACnE,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAK/C,OAAO,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAC7B,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AAErD,eAAe,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAClE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxD,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAEvB,OAAO,CACL,oBAAC,SAAS;QACR,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE;YACzB,KAAK,CAAC,CAAC,CAAC,CACP,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE;gBACzB,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO;;oBAAS,GAAG,KAAK,EAAE,CAAc,CACtD,CACP,CAAC,CAAC,CAAC,IAAI;YACR,oBAAC,UAAU,6FAGE;YACb,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,mNAKZ,CACT;QAEN,oBAAC,IAAI,IAAC,SAAS,QAAC,OAAO,EAAE,EAAE,EAAE,cAAc,EAAC,QAAQ,EAAC,UAAU,EAAC,QAAQ;YACtE,oBAAC,IAAI,IAAC,IAAI;gBACR,oBAAC,UAAU,0BAA6B;gBACxC,oBAAC,YAAY,IAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI;gBAC5D,oBAAC,UAAU,2BAA8B;gBACzC,oBAAC,YAAY,IAAC,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,GAAI,CACzD;YAEP,oBAAC,IAAI,IAAC,IAAI;gBACR,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,CAAC,EAC7C,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,QAAQ,EAAE,CAAC,OAAO,IAAI,CAAC,QAAQ,WAGxB,CACJ;YAEP,oBAAC,IAAI,IAAC,IAAI;gBACR,oBAAC,UAAU,mBAAsB;gBACjC,oBAAC,kBAAkB,IAAC,KAAK,EAAE,KAAK,GAAI,CAC/B,CACF,CACG,CACb,CAAA;AACH,CAAC,CAAC,CAAA"}

package/dist/components/import/ImportFormExamples.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const ImportFormExamples: ({ model, }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/import/ImportFormExamples.js

@@ -3,17 +3,19 @@ import { Typography, Link } from '@mui/material';
 import { observer } from 'mobx-react';
 import { smallTree, smallMSA, smallMSAOnly } from './data/seq2';
 import { load } from './util';
-const ListItem = ({ onClick, model, children, }) => (React.createElement("li", null,
-    React.createElement(Link, { onClick: event => {
-            model.setError(undefined);
-            event.preventDefault();
-            onClick();
-        }, href: "#" },
-        React.createElement(Typography, { display: "inline" }, children))));
+function ListItem({ onClick, model, children, }) {
+    return (React.createElement("li", null,
+        React.createElement(Link, { onClick: event => {
+                model.setError(undefined);
+                event.preventDefault();
+                onClick();
+            }, href: "#" },
+            React.createElement(Typography, { display: "inline" }, children))));
+}
 const ImportFormExamples = observer(function ({ model, }) {
     return (React.createElement("ul", null,
         React.createElement(ListItem, { model: model, onClick: () => load(model, undefined, {
-                uri: 'https://jbrowse.org/genomes/newick_trees/sarscov2phylo.pub.ft.nh',
+                uri: 'https://jbrowse.org/genomes/newicktrees/sarscov2phylo.pub.ft.nh',
                 locationType: 'UriLocation',
             }) }, "230k COVID-19 samples (tree only)"),
         React.createElement(ListItem, { model: model, onClick: () => {

package/dist/components/import/ImportFormExamples.js.map

@@ -1 +1 @@
-{"version":3,"file":"ImportFormExamples.js","sourceRoot":"","sources":["../../../src/components/import/ImportFormExamples.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,aAAa,CAAA;AAC/D,OAAO,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE7B,MAAM,QAAQ,GAAG,CAAC,EAChB,OAAO,EACP,KAAK,EACL,QAAQ,GAKT,EAAE,EAAE,CAAC,CACJ;IACE,oBAAC,IAAI,IACH,OAAO,EAAE,KAAK,CAAC,EAAE;YACf,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;YACzB,KAAK,CAAC,cAAc,EAAE,CAAA;YACtB,OAAO,EAAE,CAAA;QACX,CAAC,EACD,IAAI,EAAC,GAAG;QAER,oBAAC,UAAU,IAAC,OAAO,EAAC,QAAQ,IAAE,QAAQ,CAAc,CAC/C,CACJ,CACN,CAAA;AAED,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,KAAK,GAGN;IACC,OAAO,CACL;QACE,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE,SAAS,EAAE;gBACrB,GAAG,EAAE,kEAAkE;gBACvE,YAAY,EAAE,aAAa;aAC5B,CAAC,wCAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,OAAO,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,IAAI,EAAE,SAAS,EAAE,CAAC,CAAA;YACnD,CAAC,6BAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,OAAO,CAAC,EAAE,GAAG,EAAE,YAAY,EAAE,CAAC,CAAA;YACtC,CAAC,qBAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,0EAA0E;gBAC/E,YAAY,EAAE,aAAa;aAC5B,CAAC,qCAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,uEAAuE;gBAC5E,YAAY,EAAE,aAAa;aAC5B,CAAC,4BAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,2EAA2E;gBAChF,YAAY,EAAE,aAAa;aAC5B,CAAC,uDAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,0EAA0E;gBAC/E,YAAY,EAAE,aAAa;aAC5B,CAAC,qEAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CACF,KAAK,EACL;gBACE,GAAG,EAAE,mGAAmG;gBACxG,YAAY,EAAE,aAAa;aAC5B,EACD;gBACE,GAAG,EAAE,mGAAmG;gBACxG,YAAY,EAAE,aAAa;aAC5B,CACF,wCAIM;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,sCAAsC;gBAC3C,YAAY,EAAE,aAAa;aAC5B,CAAC,8BAIK,CACR,CACN,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}
+{"version":3,"file":"ImportFormExamples.js","sourceRoot":"","sources":["../../../src/components/import/ImportFormExamples.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,aAAa,CAAA;AAC/D,OAAO,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE7B,SAAS,QAAQ,CAAC,EAChB,OAAO,EACP,KAAK,EACL,QAAQ,GAKT;IACC,OAAO,CACL;QACE,oBAAC,IAAI,IACH,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;gBACzB,KAAK,CAAC,cAAc,EAAE,CAAA;gBACtB,OAAO,EAAE,CAAA;YACX,CAAC,EACD,IAAI,EAAC,GAAG;YAER,oBAAC,UAAU,IAAC,OAAO,EAAC,QAAQ,IAAE,QAAQ,CAAc,CAC/C,CACJ,CACN,CAAA;AACH,CAAC;AAED,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,KAAK,GAGN;IACC,OAAO,CACL;QACE,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE,SAAS,EAAE;gBACrB,GAAG,EAAE,iEAAiE;gBACtE,YAAY,EAAE,aAAa;aAC5B,CAAC,wCAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,OAAO,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,IAAI,EAAE,SAAS,EAAE,CAAC,CAAA;YACnD,CAAC,6BAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,OAAO,CAAC,EAAE,GAAG,EAAE,YAAY,EAAE,CAAC,CAAA;YACtC,CAAC,qBAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,0EAA0E;gBAC/E,YAAY,EAAE,aAAa;aAC5B,CAAC,qCAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,uEAAuE;gBAC5E,YAAY,EAAE,aAAa;aAC5B,CAAC,4BAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,2EAA2E;gBAChF,YAAY,EAAE,aAAa;aAC5B,CAAC,uDAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,0EAA0E;gBAC/E,YAAY,EAAE,aAAa;aAC5B,CAAC,qEAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CACF,KAAK,EACL;gBACE,GAAG,EAAE,mGAAmG;gBACxG,YAAY,EAAE,aAAa;aAC5B,EACD;gBACE,GAAG,EAAE,mGAAmG;gBACxG,YAAY,EAAE,aAAa;aAC5B,CACF,wCAIM;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,sCAAsC;gBAC3C,YAAY,EAAE,aAAa;aAC5B,CAAC,8BAIK,CACR,CACN,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}

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

@@ -1,3 +1,3 @@
-import { FileLocation } from '@jbrowse/core/util';
-import { MsaViewModel } from '../../model';
+import type { FileLocation } from '@jbrowse/core/util';
+import type { MsaViewModel } from '../../model';
 export declare function load(model: MsaViewModel, msaFile?: FileLocation, treeFile?: FileLocation): Promise<void>;

package/dist/components/minimap/Minimap.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const Minimap: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/minimap/Minimap.js

@@ -4,13 +4,14 @@ const Minimap = observer(function ({ model }) {
     const [mouseDown, setMouseDown] = useState();
     const scheduled = useRef(false);
     const [hovered, setHovered] = useState(false);
-    const { scrollX, msaAreaWidth: W, minimapHeight: H, colWidth, numColumns, } = model;
-    const unit = W / numColumns / colWidth;
+    const { scrollX, msaAreaWidth, minimapHeight, colWidth, numColumns } = model;
+    const unit = msaAreaWidth / numColumns / colWidth;
     const left = -scrollX;
-    const right = left + W;
+    const right = left + msaAreaWidth;
     const s = left * unit;
     const e = right * unit;
     const fill = 'rgba(66, 119, 127, 0.3)';
+    const w = Math.max(e - s, 20);
     useEffect(() => {
         function fn(event) {
             if (mouseDown !== undefined) {
@@ -35,12 +36,12 @@ const Minimap = observer(function ({ model }) {
             };
         }
     }, [model, unit, mouseDown]);
-    const BAR_HEIGHT = 12;
-    const H2 = H - 12;
-    return (React.createElement("div", { style: { position: 'relative', height: H, width: '100%' } },
+    const barHeight = 12;
+    const polygonHeight = minimapHeight - barHeight;
+    return (React.createElement("div", { style: { position: 'relative', height: minimapHeight, width: '100%' } },
         React.createElement("div", { style: {
                 boxSizing: 'border-box',
-                height: BAR_HEIGHT,
+                height: barHeight,
                 border: '1px solid #555',
             } }),
         React.createElement("div", { style: {
@@ -49,10 +50,8 @@ const Minimap = observer(function ({ model }) {
                 left: Math.max(0, s),
                 background: hovered ? 'rgba(66,119,127,0.6)' : fill,
                 cursor: 'pointer',
-                border: '1px solid #555',
-                boxSizing: 'border-box',
-                height: BAR_HEIGHT,
-                width: e - s,
+                height: barHeight,
+                width: w,
                 zIndex: 100,
             }, onMouseOver: () => setHovered(true), onMouseOut: () => setHovered(false), onMouseDown: event => {
                 setMouseDown({
@@ -60,12 +59,12 @@ const Minimap = observer(function ({ model }) {
                     scrollX: model.scrollX,
                 });
             } }),
-        React.createElement("svg", { height: H2, style: { width: '100%' } },
+        React.createElement("svg", { height: polygonHeight, style: { width: '100%' } },
             React.createElement("polygon", { fill: fill, points: [
-                    [e, 0],
+                    [s + w, 0],
                     [s, 0],
-                    [0, H2],
-                    [W, H2],
+                    [0, polygonHeight],
+                    [msaAreaWidth, polygonHeight],
                 ].toString() }))));
 });
 export default Minimap;

package/dist/components/minimap/Minimap.js.map

@@ -1 +1 @@
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