react-msaview 6.5.0 → 8.0.0

package/dist/components/header/Header.js

@@ -8,9 +8,11 @@ import FileMenu from './FileMenu.js';
 import GappynessSlider from './GappynessSlider.js';
 import HeaderInfoArea from './HeaderInfoArea.js';
 import HeaderStatusArea from './HeaderStatusArea.js';
+import LoadWarnings from './LoadWarnings.js';
 import MSASettingsMenu from './MSASettingsMenu.js';
 import MultiAlignmentSelector from './MultiAlignmentSelector.js';
 import TreeSettingsMenu from './TreeSettingsMenu.js';
+import UnshareableDataWarning from './UnshareableDataWarning.js';
 import ZoomControls from './ZoomControls.js';
 import ZoomMenu from './ZoomMenu.js';
 const AboutDialog = lazy(() => import('../dialogs/AboutDialog.js'));
@@ -19,6 +21,9 @@ const Header = observer(function ({ model }) {
     useEffect(() => {
         model.setHeaderHeight(height ?? 0);
     }, [model, height]);
+    useEffect(() => () => {
+        model.setHeaderHeight(0);
+    }, [model]);
     return (React.createElement("div", { ref: ref, style: { display: 'flex' } },
         React.createElement(FileMenu, { model: model }),
         React.createElement(ColorSchemeMenu, { model: model }),
@@ -31,6 +36,8 @@ const Header = observer(function ({ model }) {
             React.createElement(MultiAlignmentSelector, { model: model })),
         React.createElement(HeaderInfoArea, { model: model }),
         React.createElement(Spacer, null),
+        React.createElement(LoadWarnings, { model: model }),
+        React.createElement(UnshareableDataWarning, { model: model }),
         React.createElement(HeaderStatusArea, { model: model }),
         React.createElement(Tooltip, { title: "About" },
             React.createElement(IconButton, { "aria-label": "About", onClick: () => {

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;AAE9C,OAAO,UAAU,MAAM,+BAA+B,CAAA;AACtD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,EAAE,UAAU,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,eAAe,MAAM,sBAAuB,CAAA;AACnD,OAAO,QAAQ,MAAM,eAAgB,CAAA;AACrC,OAAO,eAAe,MAAM,sBAAuB,CAAA;AACnD,OAAO,cAAc,MAAM,qBAAsB,CAAA;AACjD,OAAO,gBAAgB,MAAM,uBAAwB,CAAA;AACrD,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAC7C,OAAO,eAAe,MAAM,sBAAuB,CAAA;AACnD,OAAO,sBAAsB,MAAM,6BAA8B,CAAA;AACjE,OAAO,gBAAgB,MAAM,uBAAwB,CAAA;AACrD,OAAO,sBAAsB,MAAM,6BAA8B,CAAA;AACjE,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAC7C,OAAO,QAAQ,MAAM,eAAgB,CAAA;AAIrC,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA4B,CAAC,CAAC,CAAA;AAEpE,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,SAAS,CACP,GAAG,EAAE,CAAC,GAAG,EAAE;QACT,KAAK,CAAC,eAAe,CAAC,CAAC,CAAC,CAAA;IAC1B,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QACvC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QAC1B,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QAC1B,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,6BAAK,KAAK,EAAE,EAAE,WAAW,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;YAC7C,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI,CACpC;QACN,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI;QAChC,oBAAC,MAAM,OAAG;QACV,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QACxC,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,OAAO,IAAC,KAAK,EAAC,OAAO;YACpB,oBAAC,UAAU,kBACE,OAAO,EAClB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;gBAC1D,CAAC;gBAED,oBAAC,IAAI,OAAG,CACG,CACL,CACN,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/HeaderStatusArea.js

@@ -15,8 +15,6 @@ const HeaderStatusArea = observer(({ model }) => {
     return status ? (React.createElement(Typography, { className: classes.margin },
         React.createElement(LoadingEllipses, { message: status.msg, component: "span" }),
         ' ',
-        status.url ? (React.createElement("a", { href: status.url, target: "_blank", rel: "noreferrer" }, "(status)")) : null,
-        ' ',
         status.onCancel ? (React.createElement(Button, { size: "small", onClick: () => status.onCancel?.() }, "Cancel")) : null)) : null;
 });
 export default HeaderStatusArea;

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;AAEzB,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,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,QAAQ,CAAC,CAAC,CAAC,CACjB,oBAAC,MAAM,IAAC,IAAI,EAAC,OAAO,EAAC,OAAO,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,aAE9C,CACV,CAAC,CAAC,CAAC,IAAI,CACG,CACd,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

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

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+declare const LoadWarnings: ({ model }: {
+    model: MsaViewModel;
+}) => React.JSX.Element | null;
+export default LoadWarnings;

package/dist/components/header/LoadWarnings.js

@@ -0,0 +1,35 @@
+import React from 'react';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
+import Warning from '@mui/icons-material/Warning';
+import { Tooltip, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+const useStyles = makeStyles()(theme => ({
+    warning: {
+        display: 'flex',
+        alignItems: 'center',
+        gap: 4,
+        margin: 'auto',
+        marginLeft: 10,
+        whiteSpace: 'nowrap',
+        color: theme.palette.warning.main,
+        cursor: 'pointer',
+    },
+}));
+// A failed optional layer, such as a 404 on the annotations or row metadata
+// that is not JSON, shows here as a dismissible warning. Setting `error` would
+// clear dataInitialized and hide the loaded alignment.
+const LoadWarnings = observer(function ({ model }) {
+    const { warnings } = model;
+    const { classes } = useStyles();
+    if (warnings.length === 0) {
+        return null;
+    }
+    return (React.createElement(Tooltip, { title: `${warnings.join(' ')} (click to dismiss)` },
+        React.createElement(Typography, { component: "div", className: classes.warning, onClick: () => {
+                model.clearWarnings();
+            } },
+            React.createElement(Warning, { fontSize: "small" }),
+            warnings.length > 1 ? `${warnings.length} warnings` : 'Warning')));
+});
+export default LoadWarnings;
+//# sourceMappingURL=LoadWarnings.js.map

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

@@ -0,0 +1 @@
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package/dist/components/header/MultiAlignmentSelector.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MultiAlignmentSelector.js","sourceRoot":"","sources":["../../../src/components/header/MultiAlignmentSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,UAAU,EAChD,KAAK,GAGN;IACC,MAAM,EAAE,gBAAgB,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAClD,8EAA8E;IAC9E,6EAA6E;IAC7E,2EAA2E;IAC3E,sEAAsE;IACtE,MAAM,IAAI,GAAG,IAAI,GAAG,EAAkB,CAAA;IACtC,OAAO,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACjC,oBAAC,SAAS,IACR,MAAM,QACN,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,gBAAgB,EACvB,IAAI,EAAC,OAAO,EACZ,QAAQ,EAAE,KAAK,CAAC,EAAE;YAChB,KAAK,CAAC,mBAAmB,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;QAChD,CAAC,IAEA,cAAc,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;QACpC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;QAC/B,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;QACvB,OAAO,CACL,oBAAC,QAAQ,IAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,IAAI,CAAC,EAAE,EAAE,KAAK,EAAE,KAAK,IAC7D,MAAM,CACE,CACZ,CAAA;IACH,CAAC,CAAC,CACQ,CACb,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AACF,eAAe,sBAAsB,CAAA"}

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

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { SvgIconProps } from '@mui/material/SvgIcon';
+export declare function MouseScroll(props: SvgIconProps): React.JSX.Element;
+export declare function MouseZoomBoth(props: SvgIconProps): React.JSX.Element;
+export declare function MouseZoomHorizontal(props: SvgIconProps): React.JSX.Element;
+export declare function MouseZoomVertical(props: SvgIconProps): React.JSX.Element;

package/dist/components/header/ScrollZoomIcons.js

@@ -0,0 +1,35 @@
+import React from 'react';
+import SvgIcon from '@mui/material/SvgIcon';
+// Mouse glyphs with outward arrows on the axes a wheel zoom scales.
+// @mui/icons-material ships only the plain `Mouse`, and three variants that
+// differ only in their arrows have to share one body to stay apart at 24px.
+// The body's inner subpath runs the opposite sweep, which punches the hole the
+// wheel bar sits in.
+const BODY = 'M12 5a4 4 0 0 0-4 4v6a4 4 0 0 0 8 0V9a4 4 0 0 0-4-4zm0 2a2 2 0 0 1 2 2v6a2 2 0 0 1-4 0V9a2 2 0 0 1 2-2z';
+const WHEEL = 'M11.2 8.6h1.6v3.2h-1.6z';
+const LEFT = 'M.4 12 5 15V9z';
+const RIGHT = 'M23.6 12 19 9v6z';
+const UP = 'M12 .4 15 4H9z';
+const DOWN = 'M12 23.6 9 20h6z';
+function MouseZoom({ arrows, ...rest }) {
+    return (React.createElement(SvgIcon, { ...rest },
+        React.createElement("path", { d: BODY }),
+        React.createElement("path", { d: WHEEL }),
+        arrows.map(d => (React.createElement("path", { key: d, d: d })))));
+}
+// the bare body, for a wheel that scrolls. @mui/icons-material's own `Mouse` is
+// a solid silhouette, which would jump to a different drawing when the menu
+// changes the mode.
+export function MouseScroll(props) {
+    return React.createElement(MouseZoom, { ...props, arrows: [] });
+}
+export function MouseZoomBoth(props) {
+    return React.createElement(MouseZoom, { ...props, arrows: [LEFT, RIGHT, UP, DOWN] });
+}
+export function MouseZoomHorizontal(props) {
+    return React.createElement(MouseZoom, { ...props, arrows: [LEFT, RIGHT] });
+}
+export function MouseZoomVertical(props) {
+    return React.createElement(MouseZoom, { ...props, arrows: [UP, DOWN] });
+}
+//# sourceMappingURL=ScrollZoomIcons.js.map

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

@@ -0,0 +1 @@
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package/dist/components/header/TreeSettingsMenu.js

@@ -2,9 +2,11 @@ import React from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 import AccountTree from '@mui/icons-material/AccountTree';
 import { observer } from 'mobx-react';
+import { maxNeighborJoiningRows } from '../../constants.js';
 import { treeSettingsMenuItems } from './settingsMenuItems.js';
 const TreeSettingsMenu = observer(function ({ model, }) {
     const { rows } = model;
+    const tooManyRows = rows.length > maxNeighborJoiningRows;
     return (React.createElement(CascadingMenuButton, { "data-testid": "tree_settings_menu", tooltip: "Tree settings", closeAfterItemClick: false, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: [
             ...treeSettingsMenuItems(model),
             ...(rows.length >= 2
@@ -14,7 +16,11 @@ const TreeSettingsMenu = observer(function ({ model, }) {
                         type: 'subMenu',
                         subMenu: [
                             {
-                                label: 'Calculate neighbor joining tree (BLOSUM62)',
+                                // the label shows the cap before a click would freeze the tab
+                                label: tooManyRows
+                                    ? `Calculate neighbor joining tree (over ${maxNeighborJoiningRows} rows, use FastTree)`
+                                    : 'Calculate neighbor joining tree (BLOSUM62)',
+                                disabled: tooManyRows,
                                 onClick: () => {
                                     try {
                                         model.calculateNeighborJoiningTreeFromMSA();

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeSettingsMenu.js","sourceRoot":"","sources":["../../../src/components/header/TreeSettingsMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,WAAW,MAAM,iCAAiC,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAA;AAC3D,OAAO,EAAE,qBAAqB,EAAE,MAAM,wBAAwB,CAAA;AAI9D,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,EAC1C,KAAK,GAGN;IACC,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IACtB,MAAM,WAAW,GAAG,IAAI,CAAC,MAAM,GAAG,sBAAsB,CAAA;IACxD,OAAO,CACL,oBAAC,mBAAmB,mBACN,oBAAoB,EAChC,OAAO,EAAC,eAAe,EACvB,mBAAmB,EAAE,KAAK,EAC1B,YAAY,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,eAAe,EAAE,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,SAAS,EAAE;YACT,GAAG,qBAAqB,CAAC,KAAK,CAAC;YAC/B,GAAG,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC;gBAClB,CAAC,CAAC;oBACE;wBACE,KAAK,EAAE,UAAU;wBACjB,IAAI,EAAE,SAAkB;wBACxB,OAAO,EAAE;4BACP;gCACE,8DAA8D;gCAC9D,KAAK,EAAE,WAAW;oCAChB,CAAC,CAAC,yCAAyC,sBAAsB,sBAAsB;oCACvF,CAAC,CAAC,4CAA4C;gCAChD,QAAQ,EAAE,WAAW;gCACrB,OAAO,EAAE,GAAG,EAAE;oCACZ,IAAI,CAAC;wCACH,KAAK,CAAC,mCAAmC,EAAE,CAAA;oCAC7C,CAAC;oCAAC,OAAO,CAAC,EAAE,CAAC;wCACX,OAAO,CAAC,KAAK,CAAC,8BAA8B,EAAE,CAAC,CAAC,CAAA;wCAChD,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;oCACnB,CAAC;gCACH,CAAC;6BACF;yBACF;qBACF;iBACF;gBACH,CAAC,CAAC,EAAE,CAAC;SACR;QAED,oBAAC,WAAW,OAAG,CACK,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

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

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+declare const UnshareableDataWarning: ({ model, }: {
+    model: MsaViewModel;
+}) => React.JSX.Element | null;
+export default UnshareableDataWarning;

package/dist/components/header/UnshareableDataWarning.js

@@ -0,0 +1,40 @@
+import React from 'react';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
+import LinkOff from '@mui/icons-material/LinkOff';
+import { Tooltip, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+const useStyles = makeStyles()(theme => ({
+    warning: {
+        display: 'flex',
+        alignItems: 'center',
+        gap: 4,
+        margin: 'auto',
+        marginLeft: 10,
+        whiteSpace: 'nowrap',
+        color: theme.palette.warning.main,
+        cursor: 'help',
+    },
+}));
+function size(bytes) {
+    return bytes < 1_000_000
+        ? `${Math.round(bytes / 1000)} kB`
+        : `${(bytes / 1_000_000).toFixed(1)} MB`;
+}
+// Lists loaded documents the snapshot, and so a shared URL, omits. See
+// `unshareableData` on the model.
+const UnshareableDataWarning = observer(function ({ model, }) {
+    const { unshareableData } = model;
+    const { classes } = useStyles();
+    if (unshareableData.length === 0) {
+        return null;
+    }
+    const what = unshareableData
+        .map(({ what, bytes }) => `${what} (${size(bytes)})`)
+        .join(' and the ');
+    return (React.createElement(Tooltip, { title: `The ${what} came from this computer and is too large to travel in a URL, so a link to this page opens without it. Serve the file over HTTP and open it by URL to share the view.` },
+        React.createElement(Typography, { component: "div", className: classes.warning },
+            React.createElement(LinkOff, { fontSize: "small" }),
+            "Not in the link")));
+});
+export default UnshareableDataWarning;
+//# sourceMappingURL=UnshareableDataWarning.js.map

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

@@ -0,0 +1 @@
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package/dist/components/header/ZoomControls.js

@@ -1,10 +1,40 @@
 import React from 'react';
-import Mouse from '@mui/icons-material/Mouse';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 import ZoomIn from '@mui/icons-material/ZoomIn';
 import ZoomOut from '@mui/icons-material/ZoomOut';
-import { IconButton, ToggleButton, Tooltip } from '@mui/material';
+import { IconButton, Tooltip } from '@mui/material';
 import { observer } from 'mobx-react';
+import { MouseScroll, MouseZoomBoth, MouseZoomHorizontal, MouseZoomVertical, } from './ScrollZoomIcons.js';
+const scrollMode = {
+    label: 'Scrolls the alignment',
+    Icon: MouseScroll,
+    helpText: 'Ctrl+wheel zooms both axes at the cursor.',
+};
+const wheelModes = [
+    scrollMode,
+    {
+        label: 'Zooms both axes',
+        axis: 'both',
+        Icon: MouseZoomBoth,
+        helpText: 'Hold shift to pan while the wheel zooms.',
+    },
+    {
+        label: 'Zooms columns only',
+        axis: 'horizontal',
+        Icon: MouseZoomHorizontal,
+        helpText: 'Holds the row height, so the labels and letters stay at their size while the alignment compresses.',
+    },
+    {
+        label: 'Zooms rows only',
+        axis: 'vertical',
+        Icon: MouseZoomVertical,
+        helpText: 'Holds the column width, so the alignment stays as wide while the rows grow or shrink.',
+    },
+];
 const ZoomControls = observer(function ZoomControls({ model, }) {
+    const { scrollZoom, scrollZoomAxis } = model;
+    const activeAxis = scrollZoom ? scrollZoomAxis : undefined;
+    const current = wheelModes.find(m => m.axis === activeAxis) ?? scrollMode;
     return (React.createElement(React.Fragment, null,
         React.createElement(Tooltip, { title: "Zoom in" },
             React.createElement(IconButton, { "aria-label": "Zoom in", onClick: () => {
@@ -16,10 +46,23 @@ const ZoomControls = observer(function ZoomControls({ model, }) {
                     model.zoomOut();
                 } },
                 React.createElement(ZoomOut, null))),
-        React.createElement(ToggleButton, { value: "scrollZoom", selected: model.scrollZoom, "aria-label": "Toggle scroll-to-zoom", title: "Toggle scroll-to-zoom (zoom on plain mouse wheel; ctrl+wheel always zooms)", size: "small", sx: { border: 'none' }, onChange: () => {
-                model.setScrollZoom(!model.scrollZoom);
-            } },
-            React.createElement(Mouse, null))));
+        React.createElement(CascadingMenuButton, { "data-testid": "scroll_zoom_menu", tooltip: `Mouse wheel: ${current.label.toLowerCase()} (ctrl+wheel always zooms)`, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: [
+                { type: 'subHeader', label: 'Mouse wheel' },
+                ...wheelModes.map(({ label, axis, Icon, helpText }) => ({
+                    label,
+                    icon: Icon,
+                    helpText,
+                    type: 'radio',
+                    checked: current.label === label,
+                    onClick: () => {
+                        model.setScrollZoom(axis !== undefined);
+                        if (axis !== undefined) {
+                            model.setScrollZoomAxis(axis);
+                        }
+                    },
+                })),
+            ] },
+            React.createElement(current.Icon, 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;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAC/C,OAAO,OAAO,MAAM,6BAA6B,CAAA;AACjD,OAAO,EAAE,UAAU,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EACL,WAAW,EACX,aAAa,EACb,mBAAmB,EACnB,iBAAiB,GAClB,MAAM,sBAAuB,CAAA;AAa9B,MAAM,UAAU,GAAc;IAC5B,KAAK,EAAE,uBAAuB;IAC9B,IAAI,EAAE,WAAW;IACjB,QAAQ,EAAE,2CAA2C;CACtD,CAAA;AAED,MAAM,UAAU,GAAgB;IAC9B,UAAU;IACV;QACE,KAAK,EAAE,iBAAiB;QACxB,IAAI,EAAE,MAAM;QACZ,IAAI,EAAE,aAAa;QACnB,QAAQ,EAAE,0CAA0C;KACrD;IACD;QACE,KAAK,EAAE,oBAAoB;QAC3B,IAAI,EAAE,YAAY;QAClB,IAAI,EAAE,mBAAmB;QACzB,QAAQ,EACN,oGAAoG;KACvG;IACD;QACE,KAAK,EAAE,iBAAiB;QACxB,IAAI,EAAE,UAAU;QAChB,IAAI,EAAE,iBAAiB;QACvB,QAAQ,EACN,uFAAuF;KAC1F;CACF,CAAA;AAED,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,YAAY,CAAC,EAClD,KAAK,GAGN;IACC,MAAM,EAAE,UAAU,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,UAAU,GAAG,UAAU,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,SAAS,CAAA;IAC1D,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,UAAU,CAAC,IAAI,UAAU,CAAA;IACzE,OAAO,CACL;QACE,oBAAC,OAAO,IAAC,KAAK,EAAC,SAAS;YACtB,oBAAC,UAAU,kBACE,SAAS,EACpB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,MAAM,EAAE,CAAA;gBAChB,CAAC;gBAED,oBAAC,MAAM,OAAG,CACC,CACL;QACV,oBAAC,OAAO,IAAC,KAAK,EAAC,UAAU;YACvB,oBAAC,UAAU,kBACE,UAAU,EACrB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,OAAO,EAAE,CAAA;gBACjB,CAAC;gBAED,oBAAC,OAAO,OAAG,CACA,CACL;QACV,oBAAC,mBAAmB,mBACN,kBAAkB,EAC9B,OAAO,EAAE,gBAAgB,OAAO,CAAC,KAAK,CAAC,WAAW,EAAE,4BAA4B,EAChF,YAAY,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,eAAe,EAAE,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,SAAS,EAAE;gBACT,EAAE,IAAI,EAAE,WAAW,EAAE,KAAK,EAAE,aAAa,EAAE;gBAC3C,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,QAAQ,EAAE,EAAE,EAAE,CAAC,CAAC;oBACtD,KAAK;oBACL,IAAI,EAAE,IAAI;oBACV,QAAQ;oBACR,IAAI,EAAE,OAAgB;oBACtB,OAAO,EAAE,OAAO,CAAC,KAAK,KAAK,KAAK;oBAChC,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,aAAa,CAAC,IAAI,KAAK,SAAS,CAAC,CAAA;wBACvC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;4BACvB,KAAK,CAAC,iBAAiB,CAAC,IAAI,CAAC,CAAA;wBAC/B,CAAC;oBACH,CAAC;iBACF,CAAC,CAAC;aACJ;YAED,oBAAC,OAAO,CAAC,IAAI,OAAG,CACI,CACrB,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AACF,eAAe,YAAY,CAAA"}

package/dist/components/header/getAnnotationsMenu.js

@@ -1,22 +1,22 @@
 import { lazy } from 'react';
 import FilterAlt from '@mui/icons-material/FilterAlt';
 import FolderOpen from '@mui/icons-material/FolderOpen';
-import Search from '@mui/icons-material/Search';
+import MenuBook from '@mui/icons-material/MenuBook';
 import Sort from '@mui/icons-material/Sort';
 import Visibility from '@mui/icons-material/Visibility';
 const FeatureFilterDialog = lazy(() => import('../dialogs/FeatureDialog.js'));
-const InterProScanFileDialog = lazy(() => import('../dialogs/InterProScanFileDialog.js'));
-const InterProScanDialog = lazy(() => import('../dialogs/InterProScanDialog.js'));
+const AnnotationFileDialog = lazy(() => import('../dialogs/AnnotationFileDialog.js'));
+const domainsTutorial = 'https://gmod.org/JBrowseMSA/tutorials/protein_family';
 export function getAnnotationsMenu({ model }) {
     const { showDomains, actuallyShowDomains, subFeatureRows, noDomains } = model;
     const noneLoaded = noDomains ? ' (none loaded)' : '';
     return [
         {
-            label: 'Open InterProScan results...',
+            label: 'Open annotation file...',
             icon: FolderOpen,
             onClick: () => {
                 model.queueDialog(handleClose => [
-                    InterProScanFileDialog,
+                    AnnotationFileDialog,
                     {
                         handleClose,
                         model,
@@ -24,17 +24,14 @@ export function getAnnotationsMenu({ model }) {
                 ]);
             },
         },
+        // `react-msaview-cli interpro` reads InterPro's precomputed matches in
+        // seconds, and `interproscan` covers rows InterPro has not seen; this links
+        // the tutorial for both
         {
-            label: 'Query InterProScan...',
-            icon: Search,
+            label: 'How to get a domain file...',
+            icon: MenuBook,
             onClick: () => {
-                model.queueDialog(handleClose => [
-                    InterProScanDialog,
-                    {
-                        handleClose,
-                        model,
-                    },
-                ]);
+                window.open(domainsTutorial, '_blank', 'noopener,noreferrer');
             },
         },
         {

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

@@ -1 +1 @@
-{"version":3,"file":"getAnnotationsMenu.js","sourceRoot":"","sources":["../../../src/components/header/getAnnotationsMenu.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,SAAS,MAAM,+BAA+B,CAAA;AACrD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAC/C,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAIvD,MAAM,mBAAmB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,6BAA8B,CAAC,CAAC,CAAA;AAC9E,MAAM,sBAAsB,GAAG,IAAI,CACjC,GAAG,EAAE,CAAC,MAAM,CAAC,sCAAuC,CAAC,CACtD,CAAA;AACD,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,kCAAmC,CAAC,CAClD,CAAA;AAED,MAAM,UAAU,kBAAkB,CAAC,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,WAAW,EAAE,mBAAmB,EAAE,cAAc,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC7E,MAAM,UAAU,GAAG,SAAS,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,CAAA;IACpD,OAAO;QACL;YACE,KAAK,EAAE,8BAA8B;YACrC,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;oBAC/B,sBAAsB;oBACtB;wBACE,WAAW;wBACX,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;QACD;YACE,KAAK,EAAE,uBAAuB;YAC9B,IAAI,EAAE,MAAM;YACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;oBAC/B,kBAAkB;oBAClB;wBACE,WAAW;wBACX,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;QACD;YACE,KAAK,EAAE,mBAAmB,UAAU,EAAE;YACtC,QAAQ,EAAE,SAAS;YACnB,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,mBAAmB;YAC5B,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;SACF;QACD;YACE,KAAK,EAAE,qBAAqB,UAAU,EAAE;YACxC,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,mBAAmB,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK;YACrD,IAAI,EAAE,IAAI;YACV,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;YAC1C,CAAC;SACF;QACD;YACE,KAAK,EAAE,qBAAqB,UAAU,EAAE;YACxC,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,mBAAmB;oBACnB;wBACE,OAAO;wBACP,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;KACF,CAAA;AACH,CAAC"}
+{"version":3,"file":"getAnnotationsMenu.js","sourceRoot":"","sources":["../../../src/components/header/getAnnotationsMenu.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,SAAS,MAAM,+BAA+B,CAAA;AACrD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,QAAQ,MAAM,8BAA8B,CAAA;AACnD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAIvD,MAAM,mBAAmB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,6BAA8B,CAAC,CAAC,CAAA;AAC9E,MAAM,oBAAoB,GAAG,IAAI,CAC/B,GAAG,EAAE,CAAC,MAAM,CAAC,oCAAqC,CAAC,CACpD,CAAA;AAED,MAAM,eAAe,GAAG,sDAAsD,CAAA;AAE9E,MAAM,UAAU,kBAAkB,CAAC,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,WAAW,EAAE,mBAAmB,EAAE,cAAc,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC7E,MAAM,UAAU,GAAG,SAAS,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,CAAA;IACpD,OAAO;QACL;YACE,KAAK,EAAE,yBAAyB;YAChC,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;oBAC/B,oBAAoB;oBACpB;wBACE,WAAW;wBACX,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;QACD,uEAAuE;QACvE,4EAA4E;QAC5E,wBAAwB;QACxB;YACE,KAAK,EAAE,6BAA6B;YACpC,IAAI,EAAE,QAAQ;YACd,OAAO,EAAE,GAAG,EAAE;gBACZ,MAAM,CAAC,IAAI,CAAC,eAAe,EAAE,QAAQ,EAAE,qBAAqB,CAAC,CAAA;YAC/D,CAAC;SACF;QACD;YACE,KAAK,EAAE,mBAAmB,UAAU,EAAE;YACtC,QAAQ,EAAE,SAAS;YACnB,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,mBAAmB;YAC5B,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;SACF;QACD;YACE,KAAK,EAAE,qBAAqB,UAAU,EAAE;YACxC,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,mBAAmB,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK;YACrD,IAAI,EAAE,IAAI;YACV,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;YAC1C,CAAC;SACF;QACD;YACE,KAAK,EAAE,qBAAqB,UAAU,EAAE;YACxC,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,mBAAmB;oBACnB;wBACE,OAAO;wBACP,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;KACF,CAAA;AACH,CAAC"}

package/dist/components/header/settingsMenuItems.js

@@ -8,9 +8,7 @@ function toggle(label, checked, set) {
         },
     };
 }
-// Every track the alignment can show, with its current state. Without this the
-// "Close" item on a track's own dropdown is a one-way door -- there is nowhere
-// else in the UI to turn a track back on.
+// the only place in the UI to turn a closed track back on
 function tracksSubMenu(model) {
     const shown = new Set(model.turnedOnTracks.map(t => t.model.id));
     return model.tracks.map(({ model: { id, name } }) => toggle(name, shown.has(id), () => {
@@ -26,14 +24,13 @@ export function msaSettingsMenuItems(model) {
             subMenu: tracksSubMenu(model),
         },
         { type: 'divider' },
-        toggle('Show column statistics on hover', showColumnStats, arg => {
+        toggle('Show track values on hover', showColumnStats, arg => {
             model.setShowColumnStats(arg);
         }),
         toggle('Draw letters', drawMsaLetters, arg => {
             model.setDrawMsaLetters(arg);
         }),
-        // the checkbox reads as the inverse of the property it sets: bgColor draws
-        // the tile, and turning it off is what leaves the letter itself colored
+        // inverted: bgColor colors the tile, and off colors the letter
         toggle('Color letters instead of background of tiles', !bgColor, arg => {
             model.setBgColor(!arg);
         }),
@@ -43,7 +40,7 @@ export function msaSettingsMenuItems(model) {
     ];
 }
 export function treeSettingsMenuItems(model) {
-    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawLabels, } = model;
+    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawNodeLabels, drawLabels, showTreeOverview, } = model;
     return [
         toggle('Show branch length', showBranchLen, arg => {
             model.setShowBranchLen(arg);
@@ -54,6 +51,12 @@ export function treeSettingsMenuItems(model) {
         toggle('Draw bubbles on tree branches', drawNodeBubbles, arg => {
             model.setDrawNodeBubbles(arg);
         }),
+        toggle('Draw internal node labels', drawNodeLabels, arg => {
+            model.setDrawNodeLabels(arg);
+        }),
+        toggle('Show tree overview', showTreeOverview, arg => {
+            model.setShowTreeOverview(arg);
+        }),
         toggle('Tree labels align right', labelsAlignRight, arg => {
             model.setLabelsAlignRight(arg);
         }),

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

@@ -1 +1 @@
-{"version":3,"file":"settingsMenuItems.js","sourceRoot":"","sources":["../../../src/components/header/settingsMenuItems.ts"],"names":[],"mappings":"AAGA,SAAS,MAAM,CAAC,KAAa,EAAE,OAAgB,EAAE,GAA2B;IAC1E,OAAO;QACL,KAAK;QACL,IAAI,EAAE,UAAmB;QACzB,OAAO;QACP,OAAO,EAAE,GAAG,EAAE;YACZ,GAAG,CAAC,CAAC,OAAO,CAAC,CAAA;QACf,CAAC;KACF,CAAA;AACH,CAAC;AAED,+EAA+E;AAC/E,+EAA+E;AAC/E,0CAA0C;AAC1C,SAAS,aAAa,CAAC,KAAmB;IACxC,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAA;IAChE,OAAO,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,EAAE,CAClD,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,GAAG,EAAE;QAC/B,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;IACvB,CAAC,CAAC,CACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,KAAmB;IACtD,MAAM,EAAE,cAAc,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,OAAO;QACL;YACE,KAAK,EAAE,QAAQ;YACf,IAAI,EAAE,SAAkB;YACxB,OAAO,EAAE,aAAa,CAAC,KAAK,CAAC;SAC9B;QACD,EAAE,IAAI,EAAE,SAAkB,EAAE;QAC5B,MAAM,CAAC,iCAAiC,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC/D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,cAAc,EAAE,cAAc,EAAE,GAAG,CAAC,EAAE;YAC3C,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAA;QAC9B,CAAC,CAAC;QACF,2EAA2E;QAC3E,wEAAwE;QACxE,MAAM,CAAC,8CAA8C,EAAE,CAAC,OAAO,EAAE,GAAG,CAAC,EAAE;YACrE,KAAK,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,8BAA8B,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YACrD,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,KAAmB;IACvD,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,eAAe,EACf,UAAU,GACX,GAAG,KAAK,CAAA;IACT,OAAO;QACL,MAAM,CAAC,oBAAoB,EAAE,aAAa,EAAE,GAAG,CAAC,EAAE;YAChD,KAAK,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAA;QAC7B,CAAC,CAAC;QACF,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YAClC,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,+BAA+B,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC7D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,yBAAyB,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;YACxD,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC,CAAC;QACF,MAAM,CAAC,aAAa,EAAE,UAAU,EAAE,GAAG,CAAC,EAAE;YACtC,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC1B,CAAC,CAAC;KACH,CAAA;AACH,CAAC"}
+{"version":3,"file":"settingsMenuItems.js","sourceRoot":"","sources":["../../../src/components/header/settingsMenuItems.ts"],"names":[],"mappings":"AAGA,SAAS,MAAM,CAAC,KAAa,EAAE,OAAgB,EAAE,GAA2B;IAC1E,OAAO;QACL,KAAK;QACL,IAAI,EAAE,UAAmB;QACzB,OAAO;QACP,OAAO,EAAE,GAAG,EAAE;YACZ,GAAG,CAAC,CAAC,OAAO,CAAC,CAAA;QACf,CAAC;KACF,CAAA;AACH,CAAC;AAED,0DAA0D;AAC1D,SAAS,aAAa,CAAC,KAAmB;IACxC,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAA;IAChE,OAAO,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,EAAE,CAClD,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,GAAG,EAAE;QAC/B,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;IACvB,CAAC,CAAC,CACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,KAAmB;IACtD,MAAM,EAAE,cAAc,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,OAAO;QACL;YACE,KAAK,EAAE,QAAQ;YACf,IAAI,EAAE,SAAkB;YACxB,OAAO,EAAE,aAAa,CAAC,KAAK,CAAC;SAC9B;QACD,EAAE,IAAI,EAAE,SAAkB,EAAE;QAC5B,MAAM,CAAC,4BAA4B,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC1D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,cAAc,EAAE,cAAc,EAAE,GAAG,CAAC,EAAE;YAC3C,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAA;QAC9B,CAAC,CAAC;QACF,+DAA+D;QAC/D,MAAM,CAAC,8CAA8C,EAAE,CAAC,OAAO,EAAE,GAAG,CAAC,EAAE;YACrE,KAAK,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,8BAA8B,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YACrD,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,KAAmB;IACvD,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,eAAe,EACf,cAAc,EACd,UAAU,EACV,gBAAgB,GACjB,GAAG,KAAK,CAAA;IACT,OAAO;QACL,MAAM,CAAC,oBAAoB,EAAE,aAAa,EAAE,GAAG,CAAC,EAAE;YAChD,KAAK,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAA;QAC7B,CAAC,CAAC;QACF,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YAClC,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,+BAA+B,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC7D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,2BAA2B,EAAE,cAAc,EAAE,GAAG,CAAC,EAAE;YACxD,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAA;QAC9B,CAAC,CAAC;QACF,MAAM,CAAC,oBAAoB,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;YACnD,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC,CAAC;QACF,MAAM,CAAC,yBAAyB,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;YACxD,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC,CAAC;QACF,MAAM,CAAC,aAAa,EAAE,UAAU,EAAE,GAAG,CAAC,EAAE;YACtC,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC1B,CAAC,CAAC;KACH,CAAA;AACH,CAAC"}

package/dist/components/import/ImportForm.js

@@ -12,7 +12,7 @@ const ImportForm = observer(function ({ model }) {
     return (React.createElement(Container, null,
         React.createElement("div", { style: { width: '50%' } },
             error ? React.createElement(ErrorMessage, { error: error }) : null,
-            React.createElement(Typography, null, "Open an MSA file (stockholm or clustal format) and/or a tree file (newick format)."),
+            React.createElement(Typography, null, "Open an MSA file (FASTA, Stockholm, Clustal, A3M or EMF format) and/or a tree file (Newick format)."),
             React.createElement(Typography, { color: "error" }, "Note: you can open up just an MSA or just a tree, both are not required. Some MSA files e.g. stockholm format have an embedded tree also and this is fine, and opening a separate tree file is not required.")),
         React.createElement("div", { style: {
                 display: 'flex',

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

@@ -1 +1 @@
-{"version":3,"file":"ImportForm.js","sourceRoot":"","sources":["../../../src/components/import/ImportForm.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC7D,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC7D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,kBAAkB,MAAM,yBAA0B,CAAA;AACzD,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAA;AAKhC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxD,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,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,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,UAAU,6FAGE;YACb,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,mNAKZ,CACT;QAEN,6BACE,KAAK,EAAE;gBACL,OAAO,EAAE,MAAM;gBACf,cAAc,EAAE,QAAQ;gBACxB,UAAU,EAAE,QAAQ;gBACpB,GAAG,EAAE,EAAE;aACR;YAED;gBACE;oBACE,oBAAC,UAAU,0BAA6B;oBACxC,oBAAC,YAAY,IAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CACxD;gBACN;oBACE,oBAAC,UAAU,2BAA8B;oBACzC,oBAAC,YAAY,IAAC,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,GAAI,CAC1D;gBACN;oBACE,oBAAC,UAAU,gDAAmD;oBAC9D,oBAAC,YAAY,IAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CACxD,CACF;YACN;gBACE,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,CAAC;4BACH,IAAI,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAA;wBACzC,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACnB,CAAC;oBACH,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,QAAQ,EAAE,CAAC,OAAO,IAAI,CAAC,QAAQ,WAGxB,CACL;YAEN;gBACE,oBAAC,UAAU,mBAAsB;gBACjC,oBAAC,kBAAkB,IAAC,KAAK,EAAE,KAAK,GAAI,CAChC,CACF,CACI,CACb,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}
+{"version":3,"file":"ImportForm.js","sourceRoot":"","sources":["../../../src/components/import/ImportForm.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC7D,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC7D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,kBAAkB,MAAM,yBAA0B,CAAA;AACzD,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAA;AAKhC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxD,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,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,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,UAAU,8GAGE;YACb,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,mNAKZ,CACT;QAEN,6BACE,KAAK,EAAE;gBACL,OAAO,EAAE,MAAM;gBACf,cAAc,EAAE,QAAQ;gBACxB,UAAU,EAAE,QAAQ;gBACpB,GAAG,EAAE,EAAE;aACR;YAED;gBACE;oBACE,oBAAC,UAAU,0BAA6B;oBACxC,oBAAC,YAAY,IAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CACxD;gBACN;oBACE,oBAAC,UAAU,2BAA8B;oBACzC,oBAAC,YAAY,IAAC,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,GAAI,CAC1D;gBACN;oBACE,oBAAC,UAAU,gDAAmD;oBAC9D,oBAAC,YAAY,IAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CACxD,CACF;YACN;gBACE,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,CAAC;4BACH,IAAI,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAA;wBACzC,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACnB,CAAC;oBACH,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,QAAQ,EAAE,CAAC,OAAO,IAAI,CAAC,QAAQ,WAGxB,CACL;YAEN;gBACE,oBAAC,UAAU,mBAAsB;gBACjC,oBAAC,kBAAkB,IAAC,KAAK,EAAE,KAAK,GAAI,CAChC,CACF,CACI,CACb,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/import/ImportFormExamples.js

@@ -4,7 +4,7 @@ import { observer } from 'mobx-react';
 import { smallMSA, smallMSAOnly, smallTree } from './data/seq2.js';
 import { load } from './util.js';
 const BASE = 'https://jbrowse.org/genomes/multiple_sequence_alignments';
-const TREES = 'https://jbrowse.org/genomes/newicktrees';
+const TREES = 'https://jbrowse.org/genomes/newick_trees';
 const examples = [
     {
         label: '230k COVID-19 samples (tree only)',
@@ -19,11 +19,7 @@ const examples = [
         inline: { msa: smallMSAOnly },
     },
     {
-        label: 'PFAM SARS-CoV2 multi-stockholm',
-        msa: `${BASE}/pfam-cov2.stock`,
-    },
-    {
-        label: 'PFAM SARS-CoV2 multi-stockholm w/ domains loaded',
+        label: 'PFAM SARS-CoV2 multi-stockholm with domains',
         msa: `${BASE}/pfam-cov2.stock`,
         gff: `${BASE}/pfam-cov2-domains.gff`,
     },

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

@@ -1 +1 @@
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package/dist/components/import/util.js

@@ -8,6 +8,8 @@ export function load(model, msaFile, treeFile, gffFile) {
     }
     if (gffFile) {
         model.setGFFFilehandle(gffFile);
+        // a file opened by hand shows even if the overlay was hidden earlier
+        model.setShowDomains(true);
     }
 }
 //# sourceMappingURL=util.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/components/import/util.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,IAAI,CAClB,KAAmB,EACnB,OAAsB,EACtB,QAAuB,EACvB,OAAsB;IAEtB,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;IACzB,IAAI,OAAO,EAAE,CAAC;QACZ,KAAK,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAA;IACjC,CAAC;IACD,IAAI,QAAQ,EAAE,CAAC;QACb,KAAK,CAAC,iBAAiB,CAAC,QAAQ,CAAC,CAAA;IACnC,CAAC;IACD,IAAI,OAAO,EAAE,CAAC;QACZ,KAAK,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAA;QAC/B,qEAAqE;QACrE,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;IAC5B,CAAC;AACH,CAAC"}

package/dist/components/minimap/Minimap.js

@@ -9,8 +9,7 @@ const Minimap = observer(function ({ model }) {
     const { minimapHeight, msaCanvasWidth, highResScaleFactor } = model;
     const theme = useTheme();
     const { unit, s, w, polygonHeight, polygonPoints } = getMinimapLayout(model);
-    // the whole alignment, sampled down to the bar: it says where the conserved
-    // blocks and the gappy stretches are, which is what a scroll aims at
+    // the whole alignment, sampled down to the bar
     const barWidth = Math.round(msaCanvasWidth * highResScaleFactor);
     const barHeight = Math.round(MINIMAP_BAR_HEIGHT * highResScaleFactor);
     const ref = useCanvasAutorun({

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

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