react-msaview 9.0.0 → 9.1.1

package/dist/components/dialogs/metadataRecord.js

@@ -0,0 +1,38 @@
+import React from 'react';
+import { referenceFieldLabels } from './metadataLabels.js';
+const referenceTags = ['RM', 'RT', 'RA', 'RL', 'RC'];
+function pubmed(id) {
+    return /^\d+$/.test(id) ? (React.createElement("a", { href: `https://pubmed.ncbi.nlm.nih.gov/${id}/`, target: "_blank", rel: "noreferrer" }, id)) : (id);
+}
+function groupReferences(general) {
+    const numbers = general.RN;
+    if (!Array.isArray(numbers) || numbers.length === 0) {
+        return general;
+    }
+    const present = referenceTags.filter(tag => general[tag] != null);
+    const aligned = present.every(tag => {
+        const values = general[tag];
+        return Array.isArray(values) && values.length === numbers.length;
+    });
+    if (!aligned) {
+        return general;
+    }
+    const rest = Object.fromEntries(Object.entries(general).filter(([tag]) => tag !== 'RN' && !referenceTags.includes(tag)));
+    const references = Object.fromEntries(numbers.map((number, i) => [
+        number,
+        Object.fromEntries(present.map(tag => {
+            const value = general[tag][i];
+            return [
+                referenceFieldLabels[tag],
+                tag === 'RM' ? pubmed(value) : value,
+            ];
+        })),
+    ]));
+    return { ...rest, References: references };
+}
+export function groupGeneral(general) {
+    return general && typeof general === 'object'
+        ? groupReferences(general)
+        : {};
+}
+//# sourceMappingURL=metadataRecord.js.map

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

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

@@ -1,6 +1,10 @@
 import React from 'react';
 import type { MsaViewModel } from '../../model.ts';
-declare const Header: ({ model }: {
+export interface ToolbarSlots {
+    toolbarStart?: React.ReactNode;
+    toolbarEnd?: React.ReactNode;
+}
+declare const Header: ({ model, toolbarStart, toolbarEnd, }: {
     model: MsaViewModel;
-}) => React.JSX.Element;
+} & ToolbarSlots) => React.JSX.Element;
 export default Header;

package/dist/components/header/Header.js

@@ -1,24 +1,19 @@
-import React, { lazy, useEffect } from 'react';
+import React, { useEffect } from 'react';
 import useMeasure from '@jbrowse/core/util/useMeasure';
-import Help from '@mui/icons-material/Help';
-import { IconButton, Tooltip } from '@mui/material';
+import Tune from '@mui/icons-material/Tune';
+import { AppBar, Button, IconButton, Toolbar, Tooltip } from '@mui/material';
 import { observer } from 'mobx-react';
 import StatusMessage from '../StatusMessage.js';
-import ColorSchemeMenu from './ColorSchemeMenu.js';
-import FileMenu from './FileMenu.js';
-import GappynessSlider from './GappynessSlider.js';
-import GoToBox from './GoToBox.js';
 import HeaderInfoArea from './HeaderInfoArea.js';
+import HiddenColumnsChip from './HiddenColumnsChip.js';
 import LoadWarnings from './LoadWarnings.js';
-import MSASettingsMenu from './MSASettingsMenu.js';
+import MenuBar from './MenuBar.js';
 import MultiAlignmentSelector from './MultiAlignmentSelector.js';
+import ScrollZoomCheckbox from './ScrollZoomCheckbox.js';
 import SelectionMenu from './SelectionMenu.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'));
-const Header = observer(function ({ model }) {
+const Header = observer(function ({ model, toolbarStart, toolbarEnd, }) {
     const [ref, { height }] = useMeasure();
     useEffect(() => {
         model.setHeaderHeight(height ?? 0);
@@ -26,28 +21,29 @@ const Header = observer(function ({ model }) {
     useEffect(() => () => {
         model.setHeaderHeight(0);
     }, [model]);
-    return (React.createElement("div", { ref: ref, style: { display: 'flex', flexWrap: 'wrap' } },
-        React.createElement(FileMenu, { model: model }),
-        React.createElement(ColorSchemeMenu, { model: model }),
-        React.createElement(TreeSettingsMenu, { model: model }),
-        React.createElement(MSASettingsMenu, { model: model }),
-        React.createElement(ZoomControls, { model: model }),
-        React.createElement(ZoomMenu, { model: model }),
-        React.createElement(GappynessSlider, { model: model }),
-        React.createElement(GoToBox, { model: model }),
-        React.createElement("div", { style: { paddingLeft: 20, margin: 'auto' } },
-            React.createElement(MultiAlignmentSelector, { model: model })),
-        React.createElement("div", { style: { flex: '1 1 0', minWidth: 0, display: 'flex' } },
-            React.createElement(SelectionMenu, { model: model }),
-            React.createElement(HeaderInfoArea, { model: model })),
-        React.createElement(LoadWarnings, { model: model }),
-        React.createElement(UnshareableDataWarning, { model: model }),
-        React.createElement(StatusMessage, { model: model, variant: "header" }),
-        React.createElement(Tooltip, { title: "About" },
-            React.createElement(IconButton, { "aria-label": "About", onClick: () => {
-                    model.queueDialog(onClose => [AboutDialog, { onClose }]);
-                } },
-                React.createElement(Help, null)))));
+    return (React.createElement(AppBar, { ref: ref, position: "static", color: "default", elevation: 0, sx: { borderBottom: 1, borderColor: 'divider' } },
+        React.createElement(Toolbar, { variant: "dense", disableGutters: true, sx: { minHeight: 40, flexWrap: 'wrap', px: 0.5 } },
+            toolbarStart,
+            React.createElement(MenuBar, { model: model }),
+            model.embeddedMode ? (React.createElement(Tooltip, { title: "Settings" },
+                React.createElement(IconButton, { "data-testid": "settings_button", "aria-label": "Settings", color: model.settingsOpen ? 'primary' : 'inherit', onClick: () => {
+                        model.setSettingsOpen(!model.settingsOpen);
+                    } },
+                    React.createElement(Tune, null)))) : (React.createElement(Button, { "data-testid": "settings_button", size: "small", startIcon: React.createElement(Tune, null), color: model.settingsOpen ? 'primary' : 'inherit', variant: model.settingsOpen ? 'outlined' : 'text', onClick: () => {
+                    model.setSettingsOpen(!model.settingsOpen);
+                }, sx: { mx: 0.5, flexShrink: 0 } }, "Settings")),
+            React.createElement(ZoomControls, { model: model }),
+            React.createElement(ScrollZoomCheckbox, { model: model }),
+            React.createElement(HiddenColumnsChip, { model: model }),
+            React.createElement("div", { style: { paddingLeft: 20, margin: 'auto' } },
+                React.createElement(MultiAlignmentSelector, { model: model })),
+            React.createElement("div", { style: { flex: '1 1 0', minWidth: 0, display: 'flex' } },
+                React.createElement(SelectionMenu, { model: model }),
+                React.createElement(HeaderInfoArea, { model: model })),
+            React.createElement(LoadWarnings, { model: model }),
+            React.createElement(UnshareableDataWarning, { model: model }),
+            React.createElement(StatusMessage, { model: model, variant: "header" }),
+            toolbarEnd)));
 });
 export default Header;
 //# sourceMappingURL=Header.js.map

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

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

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

package/dist/components/header/HiddenColumnsChip.js

@@ -0,0 +1,15 @@
+import React, { lazy } from 'react';
+import { Chip, Tooltip } from '@mui/material';
+import { observer } from 'mobx-react';
+const GapThresholdDialog = lazy(() => import('../dialogs/GapThresholdDialog.js'));
+const HiddenColumnsChip = observer(function ({ model, }) {
+    const n = model.blanks.length;
+    return n > 0 ? (React.createElement(Tooltip, { title: `Hiding columns with ≥${model.allowedGappyness}% gaps. Click to change the threshold, × to show every column` },
+        React.createElement(Chip, { "data-testid": "hidden_columns_chip", size: "small", variant: "outlined", label: `${n.toLocaleString('en-US')} gappy column${n === 1 ? '' : 's'} hidden`, style: { margin: 'auto 8px', flexShrink: 0 }, onClick: () => {
+                model.queueDialog(onClose => [GapThresholdDialog, { model, onClose }]);
+            }, onDelete: () => {
+                model.setHideGaps(false);
+            } }))) : null;
+});
+export default HiddenColumnsChip;
+//# sourceMappingURL=HiddenColumnsChip.js.map

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

@@ -0,0 +1 @@
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package/dist/components/header/{FileMenu.d.ts → MenuBar.d.ts}

@@ -1,6 +1,6 @@
 import React from 'react';
 import type { MsaViewModel } from '../../model.ts';
-declare const FileMenu: ({ model }: {
+declare const MenuBar: ({ model }: {
     model: MsaViewModel;
-}) => React.JSX.Element;
-export default FileMenu;
+}) => React.JSX.Element[];
+export default MenuBar;

package/dist/components/header/MenuBar.js

@@ -0,0 +1,33 @@
+import React from 'react';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import Build from '@mui/icons-material/Build';
+import Help from '@mui/icons-material/Help';
+import InsertDriveFile from '@mui/icons-material/InsertDriveFile';
+import Visibility from '@mui/icons-material/Visibility';
+import { Tooltip } from '@mui/material';
+import { observer } from 'mobx-react';
+import { fileMenuItems, helpMenuItems, toolsMenuItems, viewMenuItems, } from './menuBarItems.js';
+// CascadingMenuButton renders an IconButton on every core a host may ship, so
+// these styles give it the look of a small text Button
+const menuButtonSx = {
+    borderRadius: 1,
+    typography: 'button',
+    color: 'text.primary',
+    px: 1,
+    py: 0.5,
+};
+const menus = [
+    ['File', fileMenuItems, React.createElement(InsertDriveFile, { key: "file" })],
+    ['View', viewMenuItems, React.createElement(Visibility, { key: "view" })],
+    ['Tools', toolsMenuItems, React.createElement(Build, { key: "tools" })],
+    ['Help', helpMenuItems, React.createElement(Help, { key: "help" })],
+];
+const MenuBar = observer(function ({ model }) {
+    const { embeddedMode } = model;
+    return menus.map(([name, items, icon]) => {
+        const button = (React.createElement(CascadingMenuButton, { key: name, "data-testid": `${name.toLowerCase()}_menu`, "aria-label": name, menuItems: items(model), sx: menuButtonSx }, embeddedMode ? icon : name));
+        return embeddedMode ? (React.createElement(Tooltip, { key: name, title: name }, button)) : (button);
+    });
+});
+export default MenuBar;
+//# sourceMappingURL=MenuBar.js.map

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

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

@@ -0,0 +1,7 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+export declare const scrollZoomLabel = "Zoom on scroll";
+declare const ScrollZoomCheckbox: ({ model, }: {
+    model: MsaViewModel;
+}) => React.JSX.Element;
+export default ScrollZoomCheckbox;

package/dist/components/header/ScrollZoomCheckbox.js

@@ -0,0 +1,19 @@
+import React from 'react';
+import { Checkbox, FormControlLabel, Tooltip } from '@mui/material';
+import { observer } from 'mobx-react';
+// the label and the control jbrowse-components' ScrollZoomToggle uses, kept
+// local because a host's older core lacks that export
+export const scrollZoomLabel = 'Zoom on scroll';
+const scrollZoomHelp = 'The mouse wheel zooms the alignment instead of scrolling it; shift+scroll still scrolls. ctrl+scroll (⌘+scroll on a Mac) zooms either way.';
+const ScrollZoomCheckbox = observer(function ({ model, }) {
+    return (React.createElement(Tooltip, { title: scrollZoomHelp, describeChild: true },
+        React.createElement(FormControlLabel, { "data-testid": "scroll-zoom-toggle", style: {
+                marginLeft: 4,
+                marginRight: model.embeddedMode ? 0 : 8,
+                whiteSpace: 'nowrap',
+            }, control: React.createElement(Checkbox, { size: "small", checked: model.scrollZoom, onChange: () => {
+                    model.setScrollZoom(!model.scrollZoom);
+                }, style: { padding: 6 } }), label: model.embeddedMode ? '' : scrollZoomLabel, slotProps: { typography: { variant: 'body2' } } })));
+});
+export default ScrollZoomCheckbox;
+//# sourceMappingURL=ScrollZoomCheckbox.js.map

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

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

@@ -1,40 +1,11 @@
 import React from 'react';
-import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import FitScreen from '@mui/icons-material/FitScreen';
+import RestartAlt from '@mui/icons-material/RestartAlt';
 import ZoomIn from '@mui/icons-material/ZoomIn';
 import ZoomOut from '@mui/icons-material/ZoomOut';
 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: () => {
@@ -46,23 +17,16 @@ const ZoomControls = observer(function ZoomControls({ model, }) {
                     model.zoomOut();
                 } },
                 React.createElement(ZoomOut, 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))));
+        React.createElement(Tooltip, { title: "Fit the whole alignment in the window" },
+            React.createElement(IconButton, { "aria-label": "Fit to window", onClick: () => {
+                    model.fit();
+                } },
+                React.createElement(FitScreen, null))),
+        React.createElement(Tooltip, { title: "Reset zoom to the default cell size (0)" },
+            React.createElement(IconButton, { "aria-label": "Reset zoom", onClick: () => {
+                    model.resetZoom();
+                } },
+                React.createElement(RestartAlt, null)))));
 });
 export default ZoomControls;
 //# sourceMappingURL=ZoomControls.js.map

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

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

@@ -0,0 +1,4 @@
+import type { MsaViewModel } from '../../model.ts';
+import type { MenuItem } from '@jbrowse/core/ui/Menu';
+export declare const catalogedSchemeNames: string[];
+export declare function colorSchemeMenuItems(model: MsaViewModel): MenuItem[];

package/dist/components/header/colorSchemeMenuItems.js

@@ -0,0 +1,106 @@
+const schemes = [
+    { name: 'maeditor', label: 'MAEditor', alphabet: 'protein', featured: true },
+    {
+        name: 'clustalx_protein',
+        label: 'Clustal X',
+        alphabet: 'protein',
+        featured: true,
+    },
+    {
+        name: 'clustalx_protein_dynamic',
+        label: 'Clustal X, by column conservation',
+        alphabet: 'protein',
+        featured: true,
+    },
+    {
+        name: 'blosum62_dynamic',
+        label: 'BLOSUM62 similarity',
+        alphabet: 'protein',
+        featured: true,
+    },
+    {
+        name: 'jalview_hydrophobicity',
+        label: 'Hydrophobicity',
+        alphabet: 'protein',
+        featured: true,
+    },
+    {
+        name: 'nucleotide',
+        label: 'Nucleotide',
+        alphabet: 'nucleotide',
+        featured: true,
+    },
+    {
+        name: 'rainbow_dna',
+        label: 'Rainbow',
+        alphabet: 'nucleotide',
+        featured: true,
+    },
+    {
+        name: 'percent_identity_dynamic',
+        label: 'Percent identity',
+        alphabet: 'any',
+        featured: true,
+    },
+    { name: 'none', label: 'None', alphabet: 'any', featured: true },
+    { name: 'clustal', label: 'Clustal', alphabet: 'protein' },
+    { name: 'lesk', label: 'Lesk', alphabet: 'protein' },
+    { name: 'flower', label: 'Flower', alphabet: 'protein' },
+    { name: 'cinema', label: 'Cinema', alphabet: 'protein' },
+    { name: 'jalview_zappo', label: 'Zappo', alphabet: 'protein' },
+    { name: 'jalview_taylor', label: 'Taylor', alphabet: 'protein' },
+    { name: 'jalview_buried', label: 'Buried index', alphabet: 'protein' },
+    { name: 'jalview_prophelix', label: 'Helix propensity', alphabet: 'protein' },
+    {
+        name: 'jalview_propstrand',
+        label: 'Strand propensity',
+        alphabet: 'protein',
+    },
+    { name: 'jalview_propturn', label: 'Turn propensity', alphabet: 'protein' },
+    { name: 'clustalx_dna', label: 'Clustal X (DNA)', alphabet: 'nucleotide' },
+    { name: 'jbrowse_dna', label: 'JBrowse (DNA)', alphabet: 'nucleotide' },
+];
+export const catalogedSchemeNames = schemes.map(s => s.name);
+// While a `customColorScheme` map is set, a checked Custom entry stands for it
+// and no named scheme is checked. Picking a named scheme clears the map. The
+// active scheme always shows at the top level.
+export function colorSchemeMenuItems(model) {
+    const { colorSchemeName, customColorScheme, sequenceType } = model;
+    const alphabet = sequenceType === 'amino' ? 'protein' : 'nucleotide';
+    function radio(entry) {
+        return {
+            label: entry.label,
+            type: 'radio',
+            checked: !customColorScheme && colorSchemeName === entry.name,
+            onClick: () => {
+                model.setColorSchemeName(entry.name);
+                // a scheme picked while the domains fill the cells would color
+                // nothing, so the pick hands the cells back to the residues
+                if (model.cellFill === 'domain') {
+                    model.setCellFill('residue');
+                }
+            },
+        };
+    }
+    const top = (e) => (e.featured && (e.alphabet === 'any' || e.alphabet === alphabet)) ||
+        (!customColorScheme && e.name === colorSchemeName);
+    return [
+        ...(customColorScheme
+            ? [
+                {
+                    label: 'Custom',
+                    type: 'radio',
+                    checked: true,
+                    onClick: () => { },
+                },
+            ]
+            : []),
+        ...schemes.filter(top).map(radio),
+        {
+            label: 'More schemes',
+            type: 'subMenu',
+            subMenu: schemes.filter(e => !top(e)).map(radio),
+        },
+    ];
+}
+//# sourceMappingURL=colorSchemeMenuItems.js.map

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

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

@@ -1,31 +1,4 @@
 import type { MsaViewModel } from '../../model.ts';
-export declare function getAnnotationsMenu({ model }: {
-    model: MsaViewModel;
-}): ({
-    label: string;
-    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-        muiName: string;
-    };
-    onClick: () => void;
-    checked?: undefined;
-    type?: undefined;
-    disabled?: undefined;
-} | {
-    label: string;
-    disabled: boolean;
-    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-        muiName: string;
-    };
-    checked: boolean;
-    type: 'checkbox';
-    onClick: () => void;
-} | {
-    checked?: undefined;
-    type?: undefined;
-    label: string;
-    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-        muiName: string;
-    };
-    disabled: boolean;
-    onClick: () => void;
-})[];
+import type { MenuItem } from '@jbrowse/core/ui/Menu';
+export declare function openAnnotationFileItem(model: MsaViewModel): MenuItem;
+export declare function annotationsSubMenu(model: MsaViewModel): MenuItem[];