react-msaview 9.0.0 → 9.1.1

package/dist/components/Track.js.map

@@ -1 +1 @@
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package/dist/components/controls.d.ts

@@ -0,0 +1,11 @@
+export interface Control {
+    label: string;
+    action: string;
+}
+export interface KeyControl extends Control {
+    keys: string[];
+    shiftKey?: boolean;
+}
+export declare const keyboardControls: KeyControl[];
+export declare const mouseControls: Control[];
+export declare const alignmentAriaLabel: string;

package/dist/components/controls.js

@@ -0,0 +1,49 @@
+const arrows = ['ArrowLeft', 'ArrowRight', 'ArrowUp', 'ArrowDown'];
+export const keyboardControls = [
+    { label: 'Arrow keys', action: 'Scroll one cell', keys: arrows },
+    {
+        label: 'Shift + arrow keys',
+        action: 'Scroll one page',
+        keys: arrows,
+        shiftKey: true,
+    },
+    { label: '+ and -', action: 'Zoom in and out', keys: ['+', '=', '-'] },
+    { label: '0', action: 'Reset to the default cell size', keys: ['0'] },
+    {
+        label: 'Home and End',
+        action: 'Jump to the first and last column',
+        keys: ['Home', 'End'],
+    },
+    { label: 'Escape', action: 'Clear the selection', keys: ['Escape'] },
+];
+const selectCells = {
+    label: 'Shift + drag',
+    action: 'Select a block of cells',
+};
+export const mouseControls = [
+    { label: 'Drag', action: 'Pan the alignment' },
+    {
+        label: 'Wheel',
+        action: 'Scroll, or zoom with Zoom on scroll checked',
+    },
+    { label: 'Ctrl + wheel', action: 'Zoom at the cursor' },
+    selectCells,
+    {
+        label: 'Drag along a track',
+        action: 'Select a range of columns across every row',
+    },
+    {
+        label: 'Click a tree node',
+        action: 'Collapse, rotate, reroot or show only that clade',
+    },
+    {
+        label: 'Click the tree overview',
+        action: 'Show only the clade under the pointer',
+    },
+    { label: 'Drag a divider', action: 'Resize the tree area or a track' },
+];
+export const alignmentAriaLabel = [
+    'Alignment',
+    ...[...keyboardControls, selectCells].map(c => `${c.label}: ${c.action}`),
+].join('. ');
+//# sourceMappingURL=controls.js.map

package/dist/components/controls.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"controls.js","sourceRoot":"","sources":["../../src/components/controls.ts"],"names":[],"mappings":"AAUA,MAAM,MAAM,GAAG,CAAC,WAAW,EAAE,YAAY,EAAE,SAAS,EAAE,WAAW,CAAC,CAAA;AAElE,MAAM,CAAC,MAAM,gBAAgB,GAAiB;IAC5C,EAAE,KAAK,EAAE,YAAY,EAAE,MAAM,EAAE,iBAAiB,EAAE,IAAI,EAAE,MAAM,EAAE;IAChE;QACE,KAAK,EAAE,oBAAoB;QAC3B,MAAM,EAAE,iBAAiB;QACzB,IAAI,EAAE,MAAM;QACZ,QAAQ,EAAE,IAAI;KACf;IACD,EAAE,KAAK,EAAE,SAAS,EAAE,MAAM,EAAE,iBAAiB,EAAE,IAAI,EAAE,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE;IACtE,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,gCAAgC,EAAE,IAAI,EAAE,CAAC,GAAG,CAAC,EAAE;IACrE;QACE,KAAK,EAAE,cAAc;QACrB,MAAM,EAAE,mCAAmC;QAC3C,IAAI,EAAE,CAAC,MAAM,EAAE,KAAK,CAAC;KACtB;IACD,EAAE,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,qBAAqB,EAAE,IAAI,EAAE,CAAC,QAAQ,CAAC,EAAE;CACrE,CAAA;AAED,MAAM,WAAW,GAAY;IAC3B,KAAK,EAAE,cAAc;IACrB,MAAM,EAAE,yBAAyB;CAClC,CAAA;AAED,MAAM,CAAC,MAAM,aAAa,GAAc;IACtC,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,mBAAmB,EAAE;IAC9C;QACE,KAAK,EAAE,OAAO;QACd,MAAM,EAAE,6CAA6C;KACtD;IACD,EAAE,KAAK,EAAE,cAAc,EAAE,MAAM,EAAE,oBAAoB,EAAE;IACvD,WAAW;IACX;QACE,KAAK,EAAE,oBAAoB;QAC3B,MAAM,EAAE,4CAA4C;KACrD;IACD;QACE,KAAK,EAAE,mBAAmB;QAC1B,MAAM,EAAE,kDAAkD;KAC3D;IACD;QACE,KAAK,EAAE,yBAAyB;QAChC,MAAM,EAAE,uCAAuC;KAChD;IACD,EAAE,KAAK,EAAE,gBAAgB,EAAE,MAAM,EAAE,iCAAiC,EAAE;CACvE,CAAA;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG;IAChC,WAAW;IACX,GAAG,CAAC,GAAG,gBAAgB,EAAE,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,MAAM,EAAE,CAAC;CAC1E,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA"}

package/dist/components/dialogs/AnnotationFileDialog.js

@@ -1,19 +1,9 @@
 import React, { useState } from 'react';
 import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
-import { Button, DialogActions, DialogContent, FormControl, FormControlLabel, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
+import { Button, DialogActions, DialogContent, FormControl, FormControlLabel, Link, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
-import { annotationsToGFF, interProScanResponseToAnnotations, } from 'msa-parsers';
-// GFF3 as the CLI writes it, or the JSON an InterProScan run returns. Both
-// arrive as text and the model keeps GFF, so the JSON is converted on the way
-// in rather than given a second path through the model
-function toGFF(text) {
-    const trimmed = text.trimStart();
-    if (!trimmed.startsWith('{')) {
-        return text;
-    }
-    const response = JSON.parse(trimmed);
-    return annotationsToGFF(interProScanResponseToAnnotations(response));
-}
+import { annotationTextToGFF } from 'msa-parsers';
+const domainsTutorial = 'https://gmod.org/JBrowseMSA/tutorials/protein_family';
 async function fetchText(url) {
     const response = await fetch(url);
     if (!response.ok) {
@@ -36,7 +26,10 @@ const AnnotationFileDialog = observer(function ({ handleClose, model, }) {
         }, open: true },
         React.createElement(DialogContent, null,
             error ? React.createElement(ErrorMessage, { error: error }) : null,
-            React.createElement(Typography, null, "Open a GFF3 file of annotations, such as the one `react-msaview-cli interpro` writes, or the JSON an InterProScan run returns."),
+            React.createElement(Typography, null,
+                "Open a GFF3 file of annotations, such as the one `react-msaview-cli interpro` writes, or the JSON an InterProScan run returns.",
+                ' ',
+                React.createElement(Link, { href: domainsTutorial, target: "_blank", rel: "noopener noreferrer" }, "How to make one")),
             React.createElement("div", { style: { display: 'flex', margin: 30 } },
                 React.createElement(FormControl, { component: "fieldset" },
                     React.createElement(RadioGroup, { value: choice, onChange: event => {
@@ -71,11 +64,12 @@ const AnnotationFileDialog = observer(function ({ handleClose, model, }) {
                                 ? file.text()
                                 : fetchText(url));
                             // through the model's own GFF text, so the annotations travel
-                            // in the snapshot and the shared URL like every other layer.
-                            // Setting them straight onto the volatile left a view whose
-                            // link opened without them
-                            model.setGFF(toGFF(text));
+                            // in the snapshot and the shared URL like every other layer. A
+                            // filehandle left set would make the snapshot drop that text
+                            model.setGFFFilehandle(undefined);
+                            model.setGFF(annotationTextToGFF(text));
                             model.setShowDomains(true);
+                            model.setCellFill('domain');
                             handleClose();
                         }
                         catch (e) {

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

@@ -1 +1 @@
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package/dist/components/dialogs/ExportSVGDialog.js

@@ -2,6 +2,7 @@ import React, { useState } from 'react';
 import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
 import { Alert, Button, CircularProgress, DialogActions, DialogContent, FormControl, FormControlLabel, FormLabel, Radio, RadioGroup, Typography, useTheme, } from '@mui/material';
 import { observer } from 'mobx-react';
+import { exportPageSize, getLayout } from '../../exportLayout.js';
 import Checkbox2 from '../Checkbox2.js';
 // Run after the browser has painted. A requestAnimationFrame callback still
 // runs *before* the frame it was queued for, so one alone hands the main thread
@@ -19,12 +20,9 @@ const ExportSVGDialog = observer(function ({ model, onClose, }) {
     const [error, setError] = useState();
     const [exporting, setExporting] = useState(false);
     const theme = useTheme();
-    const { totalWidth, totalHeight, effectiveTreeAreaWidth, rowPanelsWidth, turnedOnTracks, totalTrackAreaHeight, numColumns, leaves, showMsaLetters, treeOverviewHeight, } = model;
+    const { turnedOnTracks, numColumns, leaves, showMsaLetters } = model;
     const hasTracks = turnedOnTracks.length > 0;
-    const entireWidth = totalWidth + effectiveTreeAreaWidth + rowPanelsWidth;
-    const entireHeight = totalHeight +
-        (includeTracks ? totalTrackAreaHeight : 0) +
-        treeOverviewHeight;
+    const entire = exportPageSize(model, getLayout(model, { theme, exportType: 'entire', includeTracks }));
     // the background is one raster image whatever its size, so what the figure
     // actually costs is its residue letters: each is an svg element of its own.
     // Past roughly this many the export runs to tens of seconds and can exhaust
@@ -56,9 +54,9 @@ const ExportSVGDialog = observer(function ({ model, onClose, }) {
                         React.createElement(FormControlLabel, { value: "viewport", control: React.createElement(Radio, null), label: "Current viewport only" })))),
             isLargeExport ? (React.createElement(Alert, { severity: "warning", style: { marginTop: 8 } },
                 "The entire MSA is ",
-                Math.round(entireWidth),
+                Math.round(entire.width),
                 "x",
-                Math.round(entireHeight),
+                Math.round(entire.height),
                 " pixels and draws",
                 ' ',
                 Math.round(glyphs / 1000),

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

@@ -1 +1 @@
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+{"version":3,"file":"ExportSVGDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/ExportSVGDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AACvD,OAAO,EACL,KAAK,EACL,MAAM,EACN,gBAAgB,EAChB,aAAa,EACb,aAAa,EACb,WAAW,EACX,gBAAgB,EAChB,SAAS,EACT,KAAK,EACL,UAAU,EACV,UAAU,EACV,QAAQ,GACT,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAA;AACjE,OAAO,SAAS,MAAM,iBAAkB,CAAA;AAIxC,4EAA4E;AAC5E,gFAAgF;AAChF,+EAA+E;AAC/E,gBAAgB;AAChB,SAAS,UAAU,CAAC,EAAc;IAChC,qBAAqB,CAAC,GAAG,EAAE;QACzB,qBAAqB,CAAC,EAAE,CAAC,CAAA;IAC3B,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC1D,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IACxD,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAC1C,UAAU,CACX,CAAA;IACD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACjD,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IACpE,MAAM,SAAS,GAAG,cAAc,CAAC,MAAM,GAAG,CAAC,CAAA;IAC3C,MAAM,MAAM,GAAG,cAAc,CAC3B,KAAK,EACL,SAAS,CAAC,KAAK,EAAE,EAAE,KAAK,EAAE,UAAU,EAAE,QAAQ,EAAE,aAAa,EAAE,CAAC,CACjE,CAAA;IACD,2EAA2E;IAC3E,4EAA4E;IAC5E,4EAA4E;IAC5E,4BAA4B;IAC5B,MAAM,MAAM,GACV,cAAc,IAAI,UAAU,KAAK,QAAQ,CAAC,CAAC,CAAC,UAAU,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5E,MAAM,aAAa,GAAG,MAAM,GAAG,OAAO,CAAA;IACtC,OAAO,CACL,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;YACZ,OAAO,EAAE,CAAA;QACX,CAAC,EACD,IAAI,QACJ,KAAK,EAAC,YAAY;QAElB,oBAAC,aAAa;YACX,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,UAAU,oBAAuB;YAClC,oBAAC,SAAS,IACR,KAAK,EAAC,kBAAkB,EACxB,QAAQ,EAAE,UAAU,KAAK,QAAQ,EACjC,OAAO,EAAE,cAAc,EACvB,QAAQ,EAAE,GAAG,EAAE;oBACb,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;gBACpC,CAAC,GACD;YACD,SAAS,CAAC,CAAC,CAAC,CACX,oBAAC,SAAS,IACR,KAAK,EAAC,iBAAiB,EACvB,OAAO,EAAE,aAAa,EACtB,QAAQ,EAAE,GAAG,EAAE;oBACb,gBAAgB,CAAC,CAAC,aAAa,CAAC,CAAA;gBAClC,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;YACR;gBACE,oBAAC,WAAW;oBACV,oBAAC,SAAS,sBAAwB;oBAClC,oBAAC,UAAU,IACT,KAAK,EAAE,UAAU,EACjB,QAAQ,EAAE,KAAK,CAAC,EAAE;4BAChB,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,MAAM,CAAA;4BAC9B,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;gCAC/C,aAAa,CAAC,KAAK,CAAC,CAAA;4BACtB,CAAC;wBACH,CAAC;wBAED,oBAAC,gBAAgB,IACf,KAAK,EAAC,QAAQ,EACd,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,YAAY,GAClB;wBACF,oBAAC,gBAAgB,IACf,KAAK,EAAC,UAAU,EAChB,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,uBAAuB,GAC7B,CACS,CACD,CACV;YACL,aAAa,CAAC,CAAC,CAAC,CACf,oBAAC,KAAK,IAAC,QAAQ,EAAC,SAAS,EAAC,KAAK,EAAE,EAAE,SAAS,EAAE,CAAC,EAAE;;gBAC5B,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC;;gBAC1C,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC;;gBAAmB,GAAG;gBAC/C,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,IAAI,CAAC;4LAGpB,CACT,CAAC,CAAC,CAAC,IAAI,CACM;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS;gBACf,oEAAoE;gBACpE,qEAAqE;gBACrE,wCAAwC;gBACxC,QAAQ,EAAE,SAAS,EACnB,SAAS,EACP,SAAS,CAAC,CAAC,CAAC,oBAAC,gBAAgB,IAAC,IAAI,EAAE,EAAE,EAAE,KAAK,EAAC,SAAS,GAAG,CAAC,CAAC,CAAC,IAAI,EAEnE,OAAO,EAAE,GAAG,EAAE;oBACZ,YAAY,CAAC,IAAI,CAAC,CAAA;oBAClB,UAAU,CAAC,GAAG,EAAE;wBACd,KAAK,KAAK;6BACP,SAAS,CAAC;4BACT,KAAK;4BACL,cAAc;4BACd,aAAa,EAAE,SAAS,IAAI,aAAa;4BACzC,UAAU;yBACX,CAAC;6BACD,IAAI,CAAC,GAAG,EAAE;4BACT,OAAO,EAAE,CAAA;wBACX,CAAC,CAAC;6BACD,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;4BACpB,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACb,CAAC,CAAC;6BACD,OAAO,CAAC,GAAG,EAAE;4BACZ,YAAY,CAAC,KAAK,CAAC,CAAA;wBACrB,CAAC,CAAC,CAAA;oBACN,CAAC,CAAC,CAAA;gBACJ,CAAC,IAEA,SAAS,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,QAAQ,CAC7B;YACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,OAAO,EAAE,CAAA;gBACX,CAAC,aAGM,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/dialogs/FeatureDialog.js

@@ -49,8 +49,8 @@ const FeatureTable = observer(function ({ model }) {
                     React.createElement(TableCell, null, "description"))),
             React.createElement(TableBody, null, types.map(({ accession, name, description }) => (React.createElement(TableRow, { key: accession },
                 React.createElement(TableCell, { padding: "checkbox" },
-                    React.createElement(Checkbox, { checked: !model.turnedOffFeatures.get(accession), onChange: () => {
-                            model.setFilter(accession, !!model.turnedOffFeatures.get(accession));
+                    React.createElement(Checkbox, { checked: !model.featureOff(accession), onChange: () => {
+                            model.setFilter(accession, model.featureOff(accession));
                         } })),
                 React.createElement(TableCell, null,
                     React.createElement("div", { style: {

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

@@ -1 +1 @@
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package/dist/components/{header/TreeSettingsMenu.d.ts → dialogs/GapThresholdDialog.d.ts}

@@ -1,6 +1,7 @@
 import React from 'react';
 import type { MsaViewModel } from '../../model.ts';
-declare const TreeSettingsMenu: ({ model, }: {
+declare const GapThresholdDialog: ({ model, onClose, }: {
     model: MsaViewModel;
+    onClose: () => void;
 }) => React.JSX.Element;
-export default TreeSettingsMenu;
+export default GapThresholdDialog;

package/dist/components/dialogs/GapThresholdDialog.js

@@ -0,0 +1,15 @@
+import React from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import GappynessSlider from './GappynessSlider.js';
+const GapThresholdDialog = observer(function ({ model, onClose, }) {
+    return (React.createElement(Dialog, { open: true, onClose: onClose, title: "Hide gappy columns" },
+        React.createElement(DialogContent, null,
+            React.createElement(Typography, { variant: "body2", sx: { mb: 2 } }, "The viewer hides each column where at least this share of the rows has a gap."),
+            React.createElement(GappynessSlider, { model: model })),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", onClick: onClose }, "Close"))));
+});
+export default GapThresholdDialog;
+//# sourceMappingURL=GapThresholdDialog.js.map

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

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

@@ -2,5 +2,5 @@ import React from 'react';
 import type { MsaViewModel } from '../../model.ts';
 declare const GappynessSlider: ({ model, }: {
     model: MsaViewModel;
-}) => React.JSX.Element | null;
+}) => React.JSX.Element;
 export default GappynessSlider;

package/dist/components/{header → dialogs}/GappynessSlider.js

@@ -2,15 +2,11 @@ import React, { useState } from 'react';
 import { Slider, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 const GappynessSlider = observer(function GappynessSlider({ model, }) {
-    const { hideGaps, allowedGappyness } = model;
     const [dragValue, setDragValue] = useState();
-    const value = dragValue ?? allowedGappyness;
-    if (!hideGaps) {
-        return null;
-    }
+    const value = dragValue ?? model.allowedGappyness;
     return (React.createElement("div", { style: { display: 'flex', alignItems: 'center', gap: 8 } },
         React.createElement(Typography, { style: { whiteSpace: 'nowrap' } },
-            "Hide columns w/ \u2265",
+            "\u2265",
             value,
             "% gaps"),
         React.createElement(Slider
@@ -25,10 +21,7 @@ const GappynessSlider = observer(function GappynessSlider({ model, }) {
         // The thumb follows local state while dragging and the model takes the
         // value on release, since each write recomputes the gap columns over
         // the whole alignment.
-        //
-        // The thumb centers on the track's ends, so the margin keeps its
-        // overhang off the label and the row search beside it.
-        , { "data-testid": "gappyness_slider", style: { width: 100, marginInline: 10 }, min: 1, max: 100, value: value, onChange: (_, val) => {
+        , { "data-testid": "gappyness_slider", style: { width: 200, marginInline: 10 }, min: 1, max: 100, value: value, onChange: (_, val) => {
                 setDragValue(val);
             }, onChangeCommitted: (_, val) => {
                 model.setAllowedGappyness(val);

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

@@ -0,0 +1 @@
+{"version":3,"file":"GappynessSlider.js","sourceRoot":"","sources":["../../../src/components/dialogs/GappynessSlider.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,eAAe,GAAG,QAAQ,CAAC,SAAS,eAAe,CAAC,EACxD,KAAK,GAGN;IACC,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,EAAU,CAAA;IACpD,MAAM,KAAK,GAAG,SAAS,IAAI,KAAK,CAAC,gBAAgB,CAAA;IACjD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAC,EAAE;QAI3D,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,UAAU,EAAE,QAAQ,EAAE;;YACpC,KAAK;qBACC;QACb,oBAAC,MAAM;QACL,qEAAqE;QACrE,6DAA6D;QAC7D,wEAAwE;QACxE,yCAAyC;QACzC,EAAE;QACF,sEAAsE;QACtE,0DAA0D;QAC1D,EAAE;QACF,uEAAuE;QACvE,qEAAqE;QACrE,uBAAuB;2BACX,kBAAkB,EAC9B,KAAK,EAAE,EAAE,KAAK,EAAE,GAAG,EAAE,YAAY,EAAE,EAAE,EAAE,EACvC,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,KAAK,EACZ,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;gBACnB,YAAY,CAAC,GAAG,CAAC,CAAA;YACnB,CAAC,EACD,iBAAiB,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;gBAC5B,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;gBAC9B,YAAY,CAAC,SAAS,CAAC,CAAA;YACzB,CAAC,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/{header → dialogs}/GoToBox.d.ts

@@ -332,7 +332,9 @@ export declare function labelledInput(params: AutocompleteRenderInputParams): {
         'aria-label': string;
     };
 };
-declare const GoToBox: ({ model }: {
+export declare function canGoTo(model: MsaViewModel): boolean;
+declare const GoToBox: ({ model, onFound, }: {
     model: MsaViewModel;
-}) => React.JSX.Element | null;
+    onFound?: () => void;
+}) => React.JSX.Element;
 export default GoToBox;

package/dist/components/dialogs/GoToBox.js

@@ -0,0 +1,48 @@
+import React, { useState } from 'react';
+import { Autocomplete, TextField } from '@mui/material';
+import { observer } from 'mobx-react';
+import { findableRowNames, goTo, rowNameSuggestions } from './goTo.js';
+const label = 'Go to row or column';
+// MUI 9 hands renderInput `slotProps`; MUI 7, which every released JBrowse host
+// serves, hands it `inputProps` and no `slotProps` at all
+export function labelledInput(params) {
+    const { slotProps, inputProps } = params;
+    return slotProps
+        ? {
+            slotProps: {
+                ...slotProps,
+                htmlInput: { ...slotProps.htmlInput, 'aria-label': label },
+            },
+        }
+        : { inputProps: { ...inputProps, 'aria-label': label } };
+}
+// the menu that opens the dialog hands focus back to its button as it closes,
+// after an autoFocus input would have taken it
+function focusNextFrame(el) {
+    if (el) {
+        requestAnimationFrame(() => {
+            el.focus();
+        });
+    }
+}
+export function canGoTo(model) {
+    return findableRowNames(model).length > 1 || model.numColumns > 0;
+}
+const GoToBox = observer(function ({ model, onFound, }) {
+    const [missed, setMissed] = useState(false);
+    return (React.createElement(Autocomplete, { freeSolo: true, options: findableRowNames(model), filterOptions: (options, { inputValue }) => rowNameSuggestions(options, inputValue), value: null, blurOnSelect: true, onInputChange: () => {
+            setMissed(false);
+        }, onChange: (_, text) => {
+            if (text) {
+                const found = goTo(model, text);
+                setMissed(!found);
+                if (found) {
+                    onFound?.();
+                }
+            }
+        }, renderInput: params => (React.createElement(TextField, { ...params, inputRef: focusNextFrame, error: missed, placeholder: "Row name or column number", helperText: missed
+                ? 'No row or column matches'
+                : 'Or name:N for residue N of that row', ...labelledInput(params) })) }));
+});
+export default GoToBox;
+//# sourceMappingURL=GoToBox.js.map

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

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

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+export default function GoToDialog({ model, onClose, }: {
+    model: MsaViewModel;
+    onClose: () => void;
+}): React.JSX.Element;

package/dist/components/dialogs/GoToDialog.js

@@ -0,0 +1,10 @@
+import React from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { DialogContent } from '@mui/material';
+import GoToBox from './GoToBox.js';
+export default function GoToDialog({ model, onClose, }) {
+    return (React.createElement(Dialog, { open: true, onClose: onClose, title: "Go to row or column", maxWidth: "xs", fullWidth: true },
+        React.createElement(DialogContent, null,
+            React.createElement(GoToBox, { model: model, onFound: onClose }))));
+}
+//# sourceMappingURL=GoToDialog.js.map

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

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

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+export default function HelpDialog({ model, onClose, }: {
+    model: MsaViewModel;
+    onClose: () => void;
+}): React.JSX.Element;

package/dist/components/dialogs/HelpDialog.js

@@ -0,0 +1,30 @@
+import React, { lazy } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, Table, TableBody, TableCell, TableRow, Typography, } from '@mui/material';
+import { version } from '../../version.js';
+import { keyboardControls, mouseControls } from '../controls.js';
+const AboutDialog = lazy(() => import('./AboutDialog.js'));
+function ControlTable({ title, rows }) {
+    return (React.createElement(React.Fragment, null,
+        React.createElement(Typography, { variant: "subtitle2", sx: { mt: 1 } }, title),
+        React.createElement(Table, { size: "small", "aria-label": title },
+            React.createElement(TableBody, null, rows.map(({ label, action }) => (React.createElement(TableRow, { key: label },
+                React.createElement(TableCell, { sx: { whiteSpace: 'nowrap', fontWeight: 500 } }, label),
+                React.createElement(TableCell, null, action))))))));
+}
+export default function HelpDialog({ model, onClose, }) {
+    return (React.createElement(Dialog, { open: true, title: "Mouse & keyboard", onClose: onClose },
+        React.createElement(DialogContent, null,
+            React.createElement(ControlTable, { title: "Mouse", rows: mouseControls }),
+            React.createElement(ControlTable, { title: "Keyboard (click the alignment first)", rows: keyboardControls })),
+        React.createElement(DialogActions, null,
+            React.createElement(Typography, { variant: "caption", sx: { mr: 'auto', pl: 1 } },
+                "MSAView ",
+                version),
+            React.createElement(Button, { onClick: () => {
+                    model.queueDialog(done => [AboutDialog, { onClose: done }]);
+                    onClose();
+                } }, "About & credits"),
+            React.createElement(Button, { variant: "contained", onClick: onClose }, "Close"))));
+}
+//# sourceMappingURL=HelpDialog.js.map

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

@@ -0,0 +1 @@
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package/dist/components/dialogs/MetadataDialog.js

@@ -2,15 +2,23 @@ import React from 'react';
 import { Dialog } from '@jbrowse/core/ui';
 import { DialogContent, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
-import MetadataTable, { isEmpty } from '../MetadataTable.js';
+import MetadataTable, { isEmpty, isRecord } from '../MetadataTable.js';
 import SequenceTextArea from '../SequenceTextArea.js';
+import { gfLabels, monospaceKeys, sectionLabels } from './metadataLabels.js';
+import { groupGeneral } from './metadataRecord.js';
 const MetadataDialog = observer(function ({ model, onClose, }) {
-    const { header } = model;
+    const entries = Object.entries(model.header).filter(([, value]) => value != null && !isEmpty(value));
+    const fields = Object.fromEntries(entries.filter(([, value]) => !isRecord(value)));
+    const sections = entries.filter(([, value]) => isRecord(value));
     return (React.createElement(Dialog, { onClose: () => {
             onClose();
         }, open: true, title: "Metadata", maxWidth: "xl" },
         React.createElement(DialogContent, null,
-            Object.values(header).every(isEmpty) ? (React.createElement(Typography, null, "This alignment has no metadata.")) : (React.createElement(MetadataTable, { record: header })),
+            entries.length === 0 ? (React.createElement(Typography, null, "This alignment has no metadata.")) : (React.createElement(React.Fragment, null,
+                Object.keys(fields).length > 0 ? (React.createElement(MetadataTable, { record: fields })) : null,
+                sections.map(([section, value]) => (React.createElement("div", { key: section },
+                    React.createElement(Typography, { variant: "h6" }, sectionLabels[section] ?? section),
+                    section === 'General' ? (React.createElement(MetadataTable, { record: groupGeneral(value), labels: gfLabels, monospaceKeys: monospaceKeys })) : (React.createElement(MetadataTable, { record: value }))))))),
             React.createElement(Typography, { variant: "h6" }, "Sequences"),
             React.createElement(SequenceTextArea, { str: model.rows }))));
 });

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

@@ -1 +1 @@
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+{"version":3,"file":"MetadataDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/MetadataDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,aAAa,EAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAsB,CAAA;AACvE,OAAO,gBAAgB,MAAM,wBAAyB,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,aAAa,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAA;AAC5E,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAsB,CAAA;AAInD,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,MAAM,CACjD,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,KAAK,IAAI,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAChD,CAAA;IACD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAC/B,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAChD,CAAA;IACD,MAAM,QAAQ,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAA;IAC/D,OAAO,CACL,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;YACZ,OAAO,EAAE,CAAA;QACX,CAAC,EACD,IAAI,QACJ,KAAK,EAAC,UAAU,EAChB,QAAQ,EAAC,IAAI;QAEb,oBAAC,aAAa;YACX,OAAO,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CACtB,oBAAC,UAAU,0CAA6C,CACzD,CAAC,CAAC,CAAC,CACF;gBACG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAChC,oBAAC,aAAa,IAAC,MAAM,EAAE,MAAM,GAAI,CAClC,CAAC,CAAC,CAAC,IAAI;gBACP,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAClC,6BAAK,GAAG,EAAE,OAAO;oBACf,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI,IACrB,aAAa,CAAC,OAAO,CAAC,IAAI,OAAO,CACvB;oBACZ,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,CACvB,oBAAC,aAAa,IACZ,MAAM,EAAE,YAAY,CAAC,KAAK,CAAC,EAC3B,MAAM,EAAE,QAAQ,EAChB,aAAa,EAAE,aAAa,GAC5B,CACH,CAAC,CAAC,CAAC,CACF,oBAAC,aAAa,IAAC,MAAM,EAAE,KAAgC,GAAI,CAC5D,CACG,CACP,CAAC,CACD,CACJ;YACD,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI,gBAAuB;YAC/C,oBAAC,gBAAgB,IAAC,GAAG,EAAE,KAAK,CAAC,IAAI,GAAI,CACvB,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

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

@@ -0,0 +1,5 @@
+import type { MsaViewModel } from '../../model.ts';
+export declare function findableRowNames(model: MsaViewModel): string[];
+export declare function rowNameSuggestions(names: string[], input: string, limit?: number): string[];
+/** centers the view on the entry's target and lights it; false if none */
+export declare function goTo(model: MsaViewModel, text: string): boolean;

package/dist/components/{header → dialogs}/goTo.js

@@ -17,7 +17,7 @@ export function rowNameSuggestions(names, input, limit = 50) {
  * column the ruler numbers N, or residue N of a row written `name:N`. A name
  * is tried whole first, so a row called `chr1:100` stays reachable.
  */
-export function resolveGoTo(model, text) {
+function resolveGoTo(model, text) {
     const query = text.trim();
     const row = model.rowNamesSet.get(query);
     if (row !== undefined) {

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

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

@@ -0,0 +1,4 @@
+export declare const sectionLabels: Record<string, string>;
+export declare const gfLabels: Record<string, string>;
+export declare const referenceFieldLabels: Record<string, string>;
+export declare const monospaceKeys: Set<string>;

package/dist/components/dialogs/metadataLabels.js

@@ -0,0 +1,52 @@
+export const sectionLabels = {
+    General: 'Alignment',
+    Accessions: 'Row accessions',
+    Dbxref: 'Row cross-references',
+};
+export const gfLabels = {
+    ID: 'Identifier',
+    AC: 'Accession',
+    DE: 'Description',
+    AU: 'Authors',
+    SE: 'Source of seed',
+    SS: 'Source of structure',
+    BM: 'Build method',
+    SM: 'Search method',
+    GA: 'Gathering threshold',
+    TC: 'Trusted cutoff',
+    NC: 'Noise cutoff',
+    TP: 'Family type',
+    CL: 'Clan',
+    MB: 'Clan members',
+    PI: 'Previous identifiers',
+    DR: 'Database references',
+    CC: 'Comment',
+    WK: 'Wikipedia',
+    NE: 'Pfam family nested in this one',
+    NL: 'Nesting location',
+    NH: 'Tree (Newick)',
+    SQ: 'Number of sequences',
+    RC: 'Reference comment',
+    RN: 'Reference number',
+    RM: 'PubMed ID',
+    RT: 'Reference title',
+    RA: 'Reference authors',
+    RL: 'Reference journal',
+    CB: 'Curation: build',
+    DC: 'Database comment',
+    DW: 'Database web link',
+    OS: 'Organism',
+    OC: 'Organism classification',
+    AM: 'Alignment method',
+    FT: 'Feature',
+    SO: 'Sequence Ontology term',
+};
+export const referenceFieldLabels = {
+    RT: 'Title',
+    RA: 'Authors',
+    RL: 'Journal',
+    RM: 'PubMed',
+    RC: 'Comment',
+};
+export const monospaceKeys = new Set(['NH']);
+//# sourceMappingURL=metadataLabels.js.map

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

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

@@ -0,0 +1 @@
+export declare function groupGeneral(general: unknown): Record<string, unknown>;