react-msaview 5.10.0 → 6.1.0

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

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

@@ -5,133 +5,56 @@ import { Button, DialogActions, DialogContent, Typography } from '@mui/material'
 import { observer } from 'mobx-react';
 import { getUngappedSequence } from 'msa-parsers';
 import { launchInterProScan } from '../../launchInterProScan.js';
+const FAMILIES = 'Families, domains, sites & repeats';
+const FEATURES = 'Other sequence features';
+const STRUCTURAL = 'Structural domains';
+const OTHER = 'Other category';
+// The analyses the EBI iprscan5 endpoint accepts, all on by default. Static, so
+// it lives out here rather than being rebuilt on every render of the dialog.
+const interProScanPrograms = [
+    {
+        name: 'NCBIfam',
+        category: FAMILIES,
+        description: 'NCBI RefSeq FAMs including TIGRFAMs',
+    },
+    {
+        name: 'SFLD',
+        category: FAMILIES,
+        description: 'Structure function linkage database',
+    },
+    {
+        name: 'Phobius',
+        category: FEATURES,
+        description: 'A combined transmembrane topology and signal peptide predictor',
+    },
+    { name: 'SignalP', category: FEATURES },
+    { name: 'SignalP_EUK', category: OTHER },
+    { name: 'SignalP_GRAM_POSITIVE', category: OTHER },
+    { name: 'SignalP_GRAM_NEGATIVE', category: OTHER },
+    { name: 'SuperFamily', category: STRUCTURAL },
+    { name: 'Panther', category: FAMILIES },
+    { name: 'Gene3d', category: STRUCTURAL },
+    { name: 'HAMAP', category: FAMILIES },
+    { name: 'PrositeProfiles', category: FAMILIES },
+    { name: 'PrositePatterns', category: FAMILIES },
+    { name: 'Coils', category: FEATURES },
+    { name: 'SMART', category: FAMILIES },
+    {
+        name: 'CDD',
+        category: FAMILIES,
+        description: 'Conserved Domains Database',
+    },
+    { name: 'PRINTS', category: FAMILIES },
+    { name: 'PfamA', category: FAMILIES },
+    { name: 'MobiDBLite', category: FEATURES },
+    { name: 'PIRSF', category: OTHER },
+    { name: 'TMHMM', category: FEATURES },
+    { name: 'AntiFam', category: OTHER },
+    { name: 'FunFam', category: OTHER },
+    { name: 'PIRSR', category: FAMILIES },
+].map(program => ({ ...program, checked: true }));
 const InterProScanDialog = observer(function ({ handleClose, model, }) {
-    const [vals, setVals] = useState([
-        {
-            name: 'NCBIfam',
-            description: 'NCBI RefSeq FAMs including TIGRFAMs',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'SFLD',
-            description: 'Structure function linkage database',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'Phobius',
-            checked: true,
-            description: 'A combined transmembrane topology and signal peptide predictor',
-            category: 'Other sequence features',
-        },
-        {
-            name: 'SignalP',
-            checked: true,
-            category: 'Other sequence features',
-        },
-        {
-            name: 'SignalP_EUK',
-            category: 'Other category',
-            checked: true,
-        },
-        {
-            name: 'SignalP_GRAM_POSITIVE',
-            category: 'Other category',
-            checked: true,
-        },
-        {
-            name: 'SignalP_GRAM_NEGATIVE',
-            checked: true,
-            category: 'Other category',
-        },
-        {
-            name: 'SuperFamily',
-            category: 'Structural domains',
-            checked: true,
-        },
-        {
-            name: 'Panther',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'Gene3d',
-            category: 'Structural domains',
-            checked: true,
-        },
-        {
-            name: 'HAMAP',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'PrositeProfiles',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'PrositePatterns',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'Coils',
-            category: 'Other sequence features',
-            checked: true,
-        },
-        {
-            name: 'SMART',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'CDD',
-            description: 'Conserved Domains Database',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'PRINTS',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'PfamA',
-            category: 'Families, domains, sites & repeats',
-            checked: true,
-        },
-        {
-            name: 'MobiDBLite',
-            checked: true,
-            category: 'Other sequence features',
-        },
-        {
-            name: 'PIRSF',
-            checked: true,
-            category: 'Other category',
-        },
-        {
-            name: 'TMHMM',
-            checked: true,
-            category: 'Other sequence features',
-        },
-        {
-            name: 'AntiFam',
-            checked: true,
-            category: 'Other category',
-        },
-        {
-            name: 'FunFam',
-            checked: true,
-            category: 'Other category',
-        },
-        {
-            name: 'PIRSR',
-            checked: true,
-            category: 'Families, domains, sites & repeats',
-        },
-    ]);
+    const [vals, setVals] = useState(interProScanPrograms);
     const programs = vals.filter(e => e.checked).map(e => e.name);
     const [show, setShow] = useState(false);
     return (React.createElement(Dialog, { maxWidth: "xl", title: "Query InterProScan API for domains", onClose: () => {
@@ -156,14 +79,14 @@ const InterProScanDialog = observer(function ({ handleClose, model, }) {
                 React.createElement("table", null,
                     React.createElement("tbody", null, vals
                         .toSorted((a, b) => a.category.localeCompare(b.category))
-                        .map(({ name, checked, category }) => (React.createElement("tr", { key: name },
+                        .map(({ name, checked, category, description }) => (React.createElement("tr", { key: name },
                         React.createElement("td", null,
-                            React.createElement("input", { type: "checkbox", key: name, checked: checked, onChange: () => {
+                            React.createElement("input", { type: "checkbox", checked: checked, onChange: () => {
                                     setVals(vals.map(e => e.name === name
                                         ? { ...e, checked: !e.checked }
                                         : e));
                                 } })),
-                        React.createElement("td", null, name),
+                        React.createElement("td", { title: description }, name),
                         React.createElement("td", null, category)))))))) : null),
         React.createElement(DialogActions, null,
             React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {

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

@@ -1 +1 @@
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package/dist/components/dialogs/{UserProvidedDomainsDialog.d.ts → InterProScanFileDialog.d.ts}

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

package/dist/components/dialogs/{UserProvidedDomainsDialog.js → InterProScanFileDialog.js}

@@ -3,12 +3,13 @@ import { Dialog } from '@jbrowse/core/ui';
 import { getSession } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, FormControl, FormControlLabel, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
+import { interProScanResponseToAnnotations } from 'msa-parsers';
 import { jsonfetch } from '../../fetchUtils.js';
-const UserProvidedDomainsDialog = observer(function ({ handleClose, model, }) {
+const InterProScanFileDialog = observer(function ({ handleClose, model, }) {
     const [file, setFile] = useState();
     const [choice, setChoice] = useState('file');
     const [interProURL, setInterProURL] = useState('');
-    return (React.createElement(Dialog, { maxWidth: "xl", title: "Open protein domains from file", onClose: () => {
+    return (React.createElement(Dialog, { maxWidth: "xl", title: "Open InterProScan results", onClose: () => {
             handleClose();
         }, open: true },
         React.createElement(DialogContent, null,
@@ -45,12 +46,7 @@ const UserProvidedDomainsDialog = observer(function ({ handleClose, model, }) {
                             const ret = file
                                 ? JSON.parse(await file.text())
                                 : await jsonfetch(interProURL);
-                            // key each result by its xref id; a result without one has no
-                            // row to attach to, and keying it `undefined` would draw a
-                            // phantom row's worth of domains
-                            model.setDomains(Object.fromEntries(ret.results
-                                .map(r => [r.xref[0]?.id, r])
-                                .filter(e => e[0] !== undefined)));
+                            model.setAnnotations(interProScanResponseToAnnotations(ret));
                             getSession(model).notify('Loaded interproscan results', 'success');
                         }
                         catch (e) {
@@ -64,5 +60,5 @@ const UserProvidedDomainsDialog = observer(function ({ handleClose, model, }) {
                     handleClose();
                 } }, "Open results"))));
 });
-export default UserProvidedDomainsDialog;
-//# sourceMappingURL=UserProvidedDomainsDialog.js.map
+export default InterProScanFileDialog;
+//# sourceMappingURL=InterProScanFileDialog.js.map

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

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

@@ -1,9 +1,7 @@
 import React from 'react';
+import type { BasicTrack } from '../../types.ts';
 declare const TrackInfoDialog: ({ model, onClose, }: {
-    model: {
-        name: string;
-        data: string;
-    };
+    model: BasicTrack['model'];
     onClose: () => void;
 }) => React.JSX.Element;
 export default TrackInfoDialog;

package/dist/components/dialogs/TrackInfoDialog.js

@@ -1,9 +1,9 @@
-import React, { useState } from 'react';
+import React from 'react';
 import { Dialog } from '@jbrowse/core/ui';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
-import { Button, DialogActions, DialogContent } from '@mui/material';
+import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
-import copy from '../../vendor/copyToClipboard.js';
+import CopyButton from '../CopyButton.js';
 const useStyles = makeStyles()(theme => ({
     textArea: {
         padding: theme.spacing(2),
@@ -13,18 +13,12 @@ const useStyles = makeStyles()(theme => ({
     },
 }));
 const TrackInfoDialog = observer(function ({ model, onClose, }) {
-    const [label, setLabel] = useState('Copy to clipboard');
+    const { name, data } = model;
     const { classes } = useStyles();
-    return (React.createElement(Dialog, { open: true, onClose: onClose, fullWidth: true, maxWidth: "lg", title: `Track info - ${model.name}` },
-        React.createElement(DialogContent, null,
-            React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                    copy(model.data);
-                    setLabel('Copied!');
-                    setTimeout(() => {
-                        setLabel('Copy to clipboard');
-                    }, 300);
-                } }, label),
-            React.createElement("pre", { className: classes.textArea }, model.data)),
+    return (React.createElement(Dialog, { open: true, onClose: onClose, fullWidth: true, maxWidth: "lg", title: `Track info - ${name}` },
+        React.createElement(DialogContent, null, data === undefined ? (React.createElement(Typography, null, "This track has no text data.")) : (React.createElement(React.Fragment, null,
+            React.createElement(CopyButton, { text: data }),
+            React.createElement("pre", { className: classes.textArea }, data)))),
         React.createElement(DialogActions, null,
             React.createElement(Button, { variant: "contained", onClick: onClose, color: "secondary" }, "Close"))));
 });

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

@@ -1 +1 @@
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+{"version":3,"file":"TrackInfoDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/TrackInfoDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAChF,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,UAAU,MAAM,kBAAmB,CAAA;AAI1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,QAAQ,EAAE;QACR,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACzB,QAAQ,EAAE,MAAM;QAChB,UAAU,EAAE,MAAM;QAClB,SAAS,EAAE,YAAY;KACxB;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IAC5B,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,oBAAC,MAAM,IACL,IAAI,QACJ,OAAO,EAAE,OAAO,EAChB,SAAS,QACT,QAAQ,EAAC,IAAI,EACb,KAAK,EAAE,gBAAgB,IAAI,EAAE;QAE7B,oBAAC,aAAa,QAGX,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,CACpB,oBAAC,UAAU,uCAA0C,CACtD,CAAC,CAAC,CAAC,CACF;YACE,oBAAC,UAAU,IAAC,IAAI,EAAE,IAAI,GAAI;YAC1B,6BAAK,SAAS,EAAE,OAAO,CAAC,QAAQ,IAAG,IAAI,CAAO,CAC7C,CACJ,CACa;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IAAC,OAAO,EAAC,WAAW,EAAC,OAAO,EAAE,OAAO,EAAE,KAAK,EAAC,WAAW,YAEtD,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/header/FileMenu.js

@@ -5,7 +5,7 @@ import FolderOpen from '@mui/icons-material/FolderOpen';
 import Menu from '@mui/icons-material/Menu';
 import PhotoCamera from '@mui/icons-material/PhotoCamera';
 import { observer } from 'mobx-react';
-import { getDomainMenu } from './getDomainsMenu.js';
+import { getAnnotationsMenu } from './getAnnotationsMenu.js';
 const MetadataDialog = lazy(() => import('../dialogs/MetadataDialog.js'));
 const ExportSVGDialog = lazy(() => import('../dialogs/ExportSVGDialog.js'));
 const FileMenu = observer(({ model }) => {
@@ -31,9 +31,9 @@ const FileMenu = observer(({ model }) => {
                 },
             },
             {
-                label: 'Domain settings',
+                label: 'Annotations',
                 type: 'subMenu',
-                subMenu: getDomainMenu({
+                subMenu: getAnnotationsMenu({
                     model,
                 }),
             },

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

@@ -1 +1 @@
-{"version":3,"file":"FileMenu.js","sourceRoot":"","sources":["../../../src/components/header/FileMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,WAAW,MAAM,iCAAiC,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAA;AAInD,MAAM,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA+B,CAAC,CAAC,CAAA;AAC1E,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,+BAAgC,CAAC,CAAC,CAAA;AAE5E,MAAM,QAAQ,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IAC/D,OAAO,CACL,oBAAC,mBAAmB,mBACN,WAAW,EACvB,OAAO,EAAC,MAAM,EACd,SAAS,EAAE;YACT;gBACE,KAAK,EAAE,uBAAuB;gBAC9B,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,KAAK,EAAE,CAAA;gBACf,CAAC;aACF;YACD;gBACE,KAAK,EAAE,UAAU;gBACjB,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,cAAc;wBACd;4BACE,KAAK;4BACL,OAAO;yBACR;qBACF,CAAC,CAAA;gBACJ,CAAC;aACF;YACD;gBACE,KAAK,EAAE,iBAAiB;gBACxB,IAAI,EAAE,SAAS;gBACf,OAAO,EAAE,aAAa,CAAC;oBACrB,KAAK;iBACN,CAAC;aACH;YACD;gBACE,KAAK,EAAE,YAAY;gBACnB,IAAI,EAAE,WAAW;gBACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,eAAe;wBACf;4BACE,OAAO;4BACP,KAAK;yBACN;qBACF,CAAC,CAAA;gBACJ,CAAC;aACF;SACF,EACD,YAAY,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,eAAe,EAAE,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE;QAExD,oBAAC,IAAI,OAAG,CACY,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}
+{"version":3,"file":"FileMenu.js","sourceRoot":"","sources":["../../../src/components/header/FileMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,WAAW,MAAM,iCAAiC,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAA;AAI5D,MAAM,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA+B,CAAC,CAAC,CAAA;AAC1E,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,+BAAgC,CAAC,CAAC,CAAA;AAE5E,MAAM,QAAQ,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IAC/D,OAAO,CACL,oBAAC,mBAAmB,mBACN,WAAW,EACvB,OAAO,EAAC,MAAM,EACd,SAAS,EAAE;YACT;gBACE,KAAK,EAAE,uBAAuB;gBAC9B,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,KAAK,EAAE,CAAA;gBACf,CAAC;aACF;YACD;gBACE,KAAK,EAAE,UAAU;gBACjB,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,cAAc;wBACd;4BACE,KAAK;4BACL,OAAO;yBACR;qBACF,CAAC,CAAA;gBACJ,CAAC;aACF;YACD;gBACE,KAAK,EAAE,aAAa;gBACpB,IAAI,EAAE,SAAS;gBACf,OAAO,EAAE,kBAAkB,CAAC;oBAC1B,KAAK;iBACN,CAAC;aACH;YACD;gBACE,KAAK,EAAE,YAAY;gBACnB,IAAI,EAAE,WAAW;gBACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,eAAe;wBACf;4BACE,OAAO;4BACP,KAAK;yBACN;qBACF,CAAC,CAAA;gBACJ,CAAC;aACF;SACF,EACD,YAAY,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,eAAe,EAAE,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE;QAExD,oBAAC,IAAI,OAAG,CACY,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/header/GappynessSlider.js

@@ -8,7 +8,7 @@ const GappynessSlider = observer(function GappynessSlider({ model, }) {
     }
     return (React.createElement("div", { style: { display: 'flex', alignItems: 'center', gap: 8 } },
         React.createElement(Typography, { style: { whiteSpace: 'nowrap' } },
-            "Hide columns w/ >",
+            "Hide columns w/ \u2265",
             allowedGappyness,
             "% gaps"),
         React.createElement(Slider

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

@@ -1 +1 @@
-{"version":3,"file":"GappynessSlider.js","sourceRoot":"","sources":["../../../src/components/header/GappynessSlider.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,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,EAAE,QAAQ,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IAC5C,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,IAAI,CAAA;IACb,CAAC;IACD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAC,EAAE;QAC3D,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,UAAU,EAAE,QAAQ,EAAE;;YACpB,gBAAgB;qBAC1B;QACb,oBAAC,MAAM;QACL,wEAAwE;QACxE,wEAAwE;QACxE,yEAAyE;QACzE,wEAAwE;QACxE,oEAAoE;QACpE,yEAAyE;QACzE,sEAAsE;QACtE,kDAAkD;QAClD,EAAE;QACF,wEAAwE;QACxE,8DAA8D;QAC9D,oEAAoE;2BACxD,kBAAkB,EAC9B,KAAK,EAAE,EAAE,KAAK,EAAE,GAAG,EAAE,EACrB,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,gBAAgB,EACvB,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;gBACnB,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;YAChC,CAAC,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}
+{"version":3,"file":"GappynessSlider.js","sourceRoot":"","sources":["../../../src/components/header/GappynessSlider.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,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,EAAE,QAAQ,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IAC5C,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,IAAI,CAAA;IACb,CAAC;IACD,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;;YACpB,gBAAgB;qBAC1B;QACb,oBAAC,MAAM;QACL,wEAAwE;QACxE,wEAAwE;QACxE,yEAAyE;QACzE,wEAAwE;QACxE,oEAAoE;QACpE,yEAAyE;QACzE,sEAAsE;QACtE,kDAAkD;QAClD,EAAE;QACF,wEAAwE;QACxE,8DAA8D;QAC9D,oEAAoE;2BACxD,kBAAkB,EAC9B,KAAK,EAAE,EAAE,KAAK,EAAE,GAAG,EAAE,EACrB,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,gBAAgB,EACvB,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;gBACnB,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;YAChC,CAAC,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/header/{getDomainsMenu.d.ts → getAnnotationsMenu.d.ts}

@@ -1,5 +1,5 @@
 import type { MsaViewModel } from '../../model.ts';
-export declare function getDomainMenu({ model }: {
+export declare function getAnnotationsMenu({ model }: {
     model: MsaViewModel;
 }): ({
     label: string;

package/dist/components/header/{getDomainsMenu.js → getAnnotationsMenu.js}

@@ -5,17 +5,18 @@ import Search from '@mui/icons-material/Search';
 import Sort from '@mui/icons-material/Sort';
 import Visibility from '@mui/icons-material/Visibility';
 const FeatureFilterDialog = lazy(() => import('../dialogs/FeatureDialog.js'));
-const UserProvidedDomainsDialog = lazy(() => import('../dialogs/UserProvidedDomainsDialog.js'));
+const InterProScanFileDialog = lazy(() => import('../dialogs/InterProScanFileDialog.js'));
 const InterProScanDialog = lazy(() => import('../dialogs/InterProScanDialog.js'));
-export function getDomainMenu({ model }) {
+export function getAnnotationsMenu({ model }) {
     const { showDomains, actuallyShowDomains, subFeatureRows, noDomains } = model;
+    const noneLoaded = noDomains ? ' (none loaded)' : '';
     return [
         {
-            label: 'Open domains...',
+            label: 'Open InterProScan results...',
             icon: FolderOpen,
             onClick: () => {
                 model.queueDialog(handleClose => [
-                    UserProvidedDomainsDialog,
+                    InterProScanFileDialog,
                     {
                         handleClose,
                         model,
@@ -24,7 +25,7 @@ export function getDomainMenu({ model }) {
             },
         },
         {
-            label: 'Query InterProScan for domains...',
+            label: 'Query InterProScan...',
             icon: Search,
             onClick: () => {
                 model.queueDialog(handleClose => [
@@ -37,7 +38,7 @@ export function getDomainMenu({ model }) {
             },
         },
         {
-            label: `Show domains${noDomains ? ' (no domains loaded)' : ''}`,
+            label: `Show annotations${noneLoaded}`,
             disabled: noDomains,
             icon: Visibility,
             checked: actuallyShowDomains,
@@ -47,7 +48,7 @@ export function getDomainMenu({ model }) {
             },
         },
         {
-            label: `Use sub-row layout${noDomains ? ' (no domains loaded)' : ''}`,
+            label: `Use sub-row layout${noneLoaded}`,
             disabled: noDomains,
             checked: actuallyShowDomains ? subFeatureRows : false,
             icon: Sort,
@@ -57,7 +58,7 @@ export function getDomainMenu({ model }) {
             },
         },
         {
-            label: `Filter domains${noDomains ? ' (no domains loaded)' : ''}`,
+            label: `Filter annotations${noneLoaded}`,
             icon: FilterAlt,
             disabled: noDomains,
             onClick: () => {
@@ -72,4 +73,4 @@ export function getDomainMenu({ model }) {
         },
     ];
 }
-//# sourceMappingURL=getDomainsMenu.js.map
+//# sourceMappingURL=getAnnotationsMenu.js.map

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

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

@@ -8,9 +8,24 @@ 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.
+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), () => {
+        model.toggleTrack(id);
+    }));
+}
 export function msaSettingsMenuItems(model) {
     const { drawMsaLetters, hideGaps, bgColor, showColumnStats } = model;
     return [
+        {
+            label: 'Tracks',
+            type: 'subMenu',
+            subMenu: tracksSubMenu(model),
+        },
+        { type: 'divider' },
         toggle('Show column statistics on hover', showColumnStats, arg => {
             model.setShowColumnStats(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,MAAM,UAAU,oBAAoB,CAAC,KAAmB;IACtD,MAAM,EAAE,cAAc,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,OAAO;QACL,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,yCAAyC,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YACvE,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,+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,yCAAyC,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YACvE,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"}

package/dist/components/import/ImportForm.js

@@ -28,7 +28,7 @@ const ImportForm = observer(function ({ model }) {
                     React.createElement(Typography, null, "Tree file or URL"),
                     React.createElement(FileSelector, { location: treeFile, setLocation: setTreeFile })),
                 React.createElement("div", null,
-                    React.createElement(Typography, null, "InterProScan GFF file or URL (optional)"),
+                    React.createElement(Typography, null, "Annotation GFF file or URL (optional)"),
                     React.createElement(FileSelector, { location: gffFile, setLocation: setGffFile }))),
             React.createElement("div", null,
                 React.createElement(Button, { onClick: () => {

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

@@ -1 +1 @@
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