react-msaview 3.1.11 → 3.1.12

package/dist/components/SequenceTextArea.js

@@ -19,7 +19,10 @@ export default function SequenceTextArea({ str }) {
     const { classes } = useStyles();
     const [copied, setCopied] = useState(false);
     const [showGaps, setShowGaps] = useState(false);
+    const [showEmpty, setShowEmpty] = useState(false);
     const disp = str
+        .map(([s1, s2]) => [s1, showGaps ? s2 : s2.replaceAll('-', '')])
+        .filter(f => (showEmpty ? true : !!f[1]))
         .map(([s1, s2]) => `>${s1}\n${showGaps ? s2 : s2.replaceAll('-', '')}`)
         .join('\n');
     return (React.createElement(React.Fragment, null,
@@ -29,6 +32,7 @@ export default function SequenceTextArea({ str }) {
                 setTimeout(() => setCopied(false), 500);
             } }, copied ? 'Copied!' : 'Copy to clipboard'),
         React.createElement(Checkbox2, { label: "Show gaps", checked: showGaps, onChange: () => setShowGaps(!showGaps) }),
+        React.createElement(Checkbox2, { label: "Show empty", checked: showEmpty, onChange: () => setShowEmpty(!showEmpty) }),
         React.createElement(TextField, { variant: "outlined", multiline: true, className: classes.dialogContent, minRows: 5, maxRows: 10, fullWidth: true, value: disp, InputProps: {
                 readOnly: true,
                 classes: {

package/dist/components/SequenceTextArea.js.map

@@ -1 +1 @@
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package/dist/components/dialogs/DomainDialog.d.ts

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

package/dist/components/dialogs/DomainDialog.js

@@ -0,0 +1,19 @@
+import React, { useState } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { Tab, Tabs } from '@mui/material';
+// locals
+import InterProScanPanel from './InterProScanPanel';
+import UserProvidedResultPanel from './UserProvidedResultPanel';
+import TabPanel from './TabPanel';
+export default function LaunchDomainViewDialog({ handleClose, model, }) {
+    const [choice, setChoice] = useState(0);
+    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch protein view", onClose: () => handleClose(), open: true },
+        React.createElement(Tabs, { value: choice, onChange: (_, val) => setChoice(val) },
+            React.createElement(Tab, { value: 0, label: "Automatic lookup" }),
+            React.createElement(Tab, { value: 1, label: "Manual" })),
+        React.createElement(TabPanel, { value: choice, index: 0 },
+            React.createElement(InterProScanPanel, { model: model, handleClose: handleClose })),
+        React.createElement(TabPanel, { value: choice, index: 1 },
+            React.createElement(UserProvidedResultPanel, { model: model, handleClose: handleClose }))));
+}
+//# sourceMappingURL=DomainDialog.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"DomainDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/DomainDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAEzC,SAAS;AACT,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAC/D,OAAO,QAAQ,MAAM,YAAY,CAAA;AAGjC,MAAM,CAAC,OAAO,UAAU,sBAAsB,CAAC,EAC7C,WAAW,EACX,KAAK,GAIN;IACC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IACvC,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,qBAAqB,EAC3B,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,IAAI;QAEJ,oBAAC,IAAI,IAAC,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC;YACvD,oBAAC,GAAG,IAAC,KAAK,EAAE,CAAC,EAAE,KAAK,EAAC,kBAAkB,GAAG;YAC1C,oBAAC,GAAG,IAAC,KAAK,EAAE,CAAC,EAAE,KAAK,EAAC,QAAQ,GAAG,CAC3B;QACP,oBAAC,QAAQ,IAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,CAAC;YAC/B,oBAAC,iBAAiB,IAAC,KAAK,EAAE,KAAK,EAAE,WAAW,EAAE,WAAW,GAAI,CACpD;QACX,oBAAC,QAAQ,IAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,CAAC;YAC/B,oBAAC,uBAAuB,IAAC,KAAK,EAAE,KAAK,EAAE,WAAW,EAAE,WAAW,GAAI,CAC1D,CACJ,CACV,CAAA;AACH,CAAC"}

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

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

package/dist/components/dialogs/{InterProScanDialog.js → InterProScanPanel.js}

@@ -1,8 +1,9 @@
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
-import { Dialog } from '@jbrowse/core/ui';
 import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
-const FeatureTypeDialog = observer(function ({ onClose, model, }) {
+import { getSession } from '@jbrowse/core/util';
+import { launchInterProScan } from '../../launchInterProScan';
+const InterProScanDialog = observer(function ({ handleClose, model, }) {
     const [vals, setVals] = useState([
         {
             name: 'NCBIfam',
@@ -131,7 +132,7 @@ const FeatureTypeDialog = observer(function ({ onClose, model, }) {
     ]);
     const programs = vals.filter(e => e.checked).map(e => e.name);
     const [show, setShow] = useState(false);
-    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Feature types", maxWidth: "xl" },
+    return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, null,
             React.createElement(Typography, null, "This will run InterProScan on all rows of the current MSA"),
             React.createElement(Button, { onClick: () => setShow(!show) },
@@ -153,11 +154,38 @@ const FeatureTypeDialog = observer(function ({ onClose, model, }) {
                         React.createElement("td", null, name),
                         React.createElement("td", null, category)))))))) : null),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => onClose() }, "Cancel"),
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
             React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                    model.queryInterProScan(programs).catch(e => model.setError(e));
-                    onClose();
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    ;
+                    (async () => {
+                        try {
+                            const { rows } = model;
+                            if (rows.length > 140) {
+                                throw new Error('Too many sequences, please run InterProScan offline');
+                            }
+                            await launchInterProScan({
+                                algorithm: 'interproscan',
+                                programs: programs,
+                                seq: rows
+                                    .map(row => [row[0], row[1].replaceAll('-', '')])
+                                    .filter(f => !!f[1])
+                                    .map(row => `>${row[0]}\n${row[1]}`)
+                                    .join('\n'),
+                                onProgress: arg => model.setStatus(arg),
+                                model,
+                            });
+                        }
+                        catch (e) {
+                            console.error(e);
+                            getSession(model).notifyError(`${e}`, e);
+                        }
+                        finally {
+                            model.setStatus();
+                        }
+                    })();
+                    handleClose();
                 } }, "Send sequences to InterProScan"))));
 });
-export default FeatureTypeDialog;
-//# sourceMappingURL=InterProScanDialog.js.map
+export default InterProScanDialog;
+//# sourceMappingURL=InterProScanPanel.js.map

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

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

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

package/dist/components/dialogs/TabPanel.js

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

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

@@ -0,0 +1 @@
+{"version":3,"file":"TabPanel.js","sourceRoot":"","sources":["../../../src/components/dialogs/TabPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,2BAA2B;AAC3B,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAC/B,QAAQ,EACR,KAAK,EACL,KAAK,EACL,GAAG,KAAK,EAKT;IACC,OAAO,CACL,6BAAK,IAAI,EAAC,UAAU,EAAC,MAAM,EAAE,KAAK,KAAK,KAAK,KAAM,KAAK,IACpD,KAAK,KAAK,KAAK,IAAI,iCAAM,QAAQ,CAAO,CACrC,CACP,CAAA;AACH,CAAC"}

package/dist/components/dialogs/{InterProScanDialog.d.ts → UserProvidedResultPanel.d.ts}

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

package/dist/components/dialogs/UserProvidedResultPanel.js

@@ -0,0 +1,56 @@
+import React, { useState } from 'react';
+import { observer } from 'mobx-react';
+import { Button, DialogActions, DialogContent, FormControlLabel, FormControl, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
+import { getSession } from '@jbrowse/core/util';
+import { jsonfetch } from '../../fetchUtils';
+const FeatureTypeDialog = observer(function ({ handleClose, model, }) {
+    const [file, setFile] = useState();
+    const [choice, setChoice] = useState('file');
+    const [interProURL, setInterProURL] = useState('');
+    return (React.createElement(React.Fragment, null,
+        React.createElement(DialogContent, null,
+            React.createElement("div", { style: { display: 'flex', margin: 30 } },
+                React.createElement(Typography, null, "Open a JSON file of InterProScan results that you run remotely on EBI servers or locally"),
+                React.createElement(FormControl, { component: "fieldset" },
+                    React.createElement(RadioGroup, { value: choice, onChange: event => setChoice(event.target.value) },
+                        React.createElement(FormControlLabel, { value: "url", control: React.createElement(Radio, null), label: "URL" }),
+                        React.createElement(FormControlLabel, { value: "file", control: React.createElement(Radio, null), label: "File" }))),
+                choice === 'url' ? (React.createElement("div", null,
+                    React.createElement(Typography, null, "Open a InterProScan JSON file remote URL"),
+                    React.createElement(TextField, { label: "URL", value: interProURL, onChange: event => setInterProURL(event.target.value) }))) : null,
+                choice === 'file' ? (React.createElement("div", { style: { paddingTop: 20 } },
+                    React.createElement(Typography, null, "Open a InterProScan JSON file file from your local drive"),
+                    React.createElement(Button, { variant: "outlined", component: "label" },
+                        "Choose File",
+                        React.createElement("input", { type: "file", hidden: true, onChange: ({ target }) => {
+                                const file = target?.files?.[0];
+                                if (file) {
+                                    setFile(file);
+                                }
+                            } })))) : null)),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    ;
+                    (async () => {
+                        try {
+                            const ret = file
+                                ? JSON.parse(await file.text())
+                                : await jsonfetch(interProURL);
+                            model.setLoadedInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
+                            model.setShowDomains(true);
+                            getSession(model).notify('Loaded interproscan results', 'success');
+                        }
+                        catch (e) {
+                            console.error(e);
+                            getSession(model).notifyError(`${e}`, e);
+                        }
+                        finally {
+                            model.setStatus();
+                        }
+                    })();
+                    handleClose();
+                } }, "Open results"))));
+});
+export default FeatureTypeDialog;
+//# sourceMappingURL=UserProvidedResultPanel.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"UserProvidedResultPanel.js","sourceRoot":"","sources":["../../../src/components/dialogs/UserProvidedResultPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,gBAAgB,EAChB,WAAW,EACX,KAAK,EACL,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAI/C,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAA;AAG5C,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,WAAW,EACX,KAAK,GAIN;IACC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,EAAQ,CAAA;IACxC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAA;IAC5C,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAElD,OAAO,CACL;QACE,oBAAC,aAAa;YACZ,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE;gBACzC,oBAAC,UAAU,mGAGE;gBAEb,oBAAC,WAAW,IAAC,SAAS,EAAC,UAAU;oBAC/B,oBAAC,UAAU,IACT,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC;wBAEhD,oBAAC,gBAAgB,IAAC,KAAK,EAAC,KAAK,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,KAAK,GAAG;wBAChE,oBAAC,gBAAgB,IAAC,KAAK,EAAC,MAAM,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,MAAM,GAAG,CACvD,CACD;gBACb,MAAM,KAAK,KAAK,CAAC,CAAC,CAAC,CAClB;oBACE,oBAAC,UAAU,mDAAsD;oBACjE,oBAAC,SAAS,IACR,KAAK,EAAC,KAAK,EACX,KAAK,EAAE,WAAW,EAClB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,cAAc,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GACrD,CACE,CACP,CAAC,CAAC,CAAC,IAAI;gBACP,MAAM,KAAK,MAAM,CAAC,CAAC,CAAC,CACnB,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE;oBAC5B,oBAAC,UAAU,mEAEE;oBACb,oBAAC,MAAM,IAAC,OAAO,EAAC,UAAU,EAAC,SAAS,EAAC,OAAO;;wBAE1C,+BACE,IAAI,EAAC,MAAM,EACX,MAAM,QACN,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE;gCACvB,MAAM,IAAI,GAAG,MAAM,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;gCAC/B,IAAI,IAAI,EAAE,CAAC;oCACT,OAAO,CAAC,IAAI,CAAC,CAAA;gCACf,CAAC;4BACH,CAAC,GACD,CACK,CACL,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACQ;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;oBACZ,mEAAmE;oBACnE,CAAC;oBAAA,CAAC,KAAK,IAAI,EAAE;wBACX,IAAI,CAAC;4BACH,MAAM,GAAG,GAAyB,IAAI;gCACpC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,IAAI,CAAC,IAAI,EAAE,CAAC;gCAC/B,CAAC,CAAC,MAAM,SAAS,CAAC,WAAW,CAAC,CAAA;4BAEhC,KAAK,CAAC,4BAA4B,CAChC,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAC5D,CAAA;4BACD,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;4BAC1B,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CACtB,6BAA6B,EAC7B,SAAS,CACV,CAAA;wBACH,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;wBAC1C,CAAC;gCAAS,CAAC;4BACT,KAAK,CAAC,SAAS,EAAE,CAAA;wBACnB,CAAC;oBACH,CAAC,CAAC,EAAE,CAAA;oBACJ,WAAW,EAAE,CAAA;gBACf,CAAC,mBAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

package/dist/components/header/Header.js

@@ -8,12 +8,10 @@ import ZoomControls from './ZoomControls';
 import MultiAlignmentSelector from './MultiAlignmentSelector';
 import HeaderInfoArea from './HeaderInfoArea';
 import HeaderStatusArea from './HeaderStatusArea';
-import HeaderMenu from './HeaderMenu';
 import HeaderMenuExtra from './HeaderMenuExtra';
 const AboutDialog = lazy(() => import('../dialogs/AboutDialog'));
 const Header = observer(function ({ model }) {
     return (React.createElement("div", { style: { display: 'flex' } },
-        React.createElement(HeaderMenu, { model: model }),
         React.createElement(ZoomControls, { model: model }),
         React.createElement(HeaderMenuExtra, { model: model }),
         React.createElement(MultiAlignmentSelector, { model: model }),

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

@@ -1 +1 @@
-{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/components/header/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AACnC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,QAAQ;AACR,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAE3C,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;AAC7D,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAE/C,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,wBAAwB,CAAC,CAAC,CAAA;AAEhE,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAClE,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI;QAC5B,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QACxC,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI;QAChC,oBAAC,MAAM,OAAG;QACV,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC;YAEvE,oBAAC,IAAI,OAAG,CACG,CACT,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,MAAM;IACb,OAAO,6BAAK,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,GAAI,CAAA;AACpC,CAAC;AAED,eAAe,MAAM,CAAA"}
+{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/components/header/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AACnC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,QAAQ;AACR,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAE3C,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;AAC7D,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAE/C,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,wBAAwB,CAAC,CAAC,CAAA;AAEhE,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAClE,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QACxC,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI;QAChC,oBAAC,MAAM,OAAG;QACV,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC;YAEvE,oBAAC,IAAI,OAAG,CACG,CACT,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,MAAM;IACb,OAAO,6BAAK,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,GAAI,CAAA;AACpC,CAAC;AAED,eAAe,MAAM,CAAA"}

package/dist/components/header/HeaderMenuExtra.js

@@ -1,6 +1,7 @@
 import React, { lazy } from 'react';
 import { observer } from 'mobx-react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+// locals
 // icons
 import MoreVert from '@mui/icons-material/MoreVert';
 import Sort from '@mui/icons-material/Sort';
@@ -9,13 +10,40 @@ import FilterAlt from '@mui/icons-material/FilterAlt';
 import Search from '@mui/icons-material/Search';
 import PhotoCamera from '@mui/icons-material/PhotoCamera';
 import RestartAlt from '@mui/icons-material/RestartAlt';
+import FolderOpen from '@mui/icons-material/FolderOpen';
+import Settings from '@mui/icons-material/Settings';
+import Assignment from '@mui/icons-material/Assignment';
+import List from '@mui/icons-material/List';
 // lazies
+const SettingsDialog = lazy(() => import('../dialogs/SettingsDialog'));
+const MetadataDialog = lazy(() => import('../dialogs/MetadataDialog'));
+const TracklistDialog = lazy(() => import('../dialogs/TracklistDialog'));
 const ExportSVGDialog = lazy(() => import('../dialogs/ExportSVGDialog'));
 const FeatureFilterDialog = lazy(() => import('../dialogs/FeatureDialog'));
-const InterProScanDialog = lazy(() => import('../dialogs/InterProScanDialog'));
+const DomainDialog = lazy(() => import('../dialogs/DomainDialog'));
 const HeaderMenuExtra = observer(function ({ model }) {
-    const { featureMode, subFeatureRows, noAnnotations, interProScanJobIds } = model;
+    const { showDomains, subFeatureRows, noAnnotations } = model;
     return (React.createElement(CascadingMenuButton, { menuItems: [
+            {
+                label: 'Return to import form',
+                icon: FolderOpen,
+                onClick: () => model.reset(),
+            },
+            {
+                label: 'Settings',
+                onClick: () => model.queueDialog(onClose => [SettingsDialog, { model, onClose }]),
+                icon: Settings,
+            },
+            {
+                label: 'Metadata',
+                onClick: () => model.queueDialog(onClose => [MetadataDialog, { model, onClose }]),
+                icon: Assignment,
+            },
+            {
+                label: 'Extra tracks',
+                onClick: () => model.queueDialog(onClose => [TracklistDialog, { model, onClose }]),
+                icon: List,
+            },
             {
                 label: 'Reset zoom to default',
                 icon: RestartAlt,
@@ -36,9 +64,9 @@ const HeaderMenuExtra = observer(function ({ model }) {
                     {
                         label: 'Show domains' + (noAnnotations ? ' (no domains loaded)' : ''),
                         icon: Visibility,
-                        checked: featureMode,
+                        checked: showDomains,
                         type: 'checkbox',
-                        onClick: () => model.setFeatureMode(!featureMode),
+                        onClick: () => model.setShowDomains(!showDomains),
                     },
                     {
                         label: 'Use sub-row layout',
@@ -58,30 +86,13 @@ const HeaderMenuExtra = observer(function ({ model }) {
                         },
                     },
                     {
-                        label: 'Query InterProScan for domains...',
+                        label: 'View domains',
                         icon: Search,
-                        onClick: () => model.queueDialog(onClose => [
-                            InterProScanDialog,
-                            { onClose, model },
+                        onClick: () => model.queueDialog(handleClose => [
+                            DomainDialog,
+                            { handleClose, model },
                         ]),
                     },
-                    {
-                        label: 'Load previous InterProScan results...',
-                        icon: Search,
-                        type: 'subMenu',
-                        subMenu: interProScanJobIds.length
-                            ? interProScanJobIds.map(({ jobId, date }) => ({
-                                label: new Date(date).toLocaleString('en-US') + ' - ' + jobId,
-                                onClick: () => model.loadInterProScanResults(jobId),
-                            }))
-                            : [
-                                {
-                                    label: 'No previous searches',
-                                    disabled: true,
-                                    onClick: () => { },
-                                },
-                            ],
-                    },
                 ],
             },
             ...(model.extraViewMenuItems?.() || []),

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

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

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

package/dist/components/header/HeaderStatusArea.js

@@ -2,17 +2,18 @@ import React from 'react';
 import { Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
+import { LoadingEllipses } from '@jbrowse/core/ui';
 const useStyles = makeStyles()({
     margin: {
         margin: 'auto',
         marginLeft: 10,
     },
 });
-const HeaderStatusArea = observer(({ model }) => {
+const HeaderStatusArea = observer(function ({ model, }) {
     const { status } = model;
     const { classes } = useStyles();
     return status ? (React.createElement(Typography, { className: classes.margin },
-        status.msg,
+        React.createElement(LoadingEllipses, { message: status.msg, component: "span" }),
         ' ',
         status.url ? (React.createElement("a", { href: status.url, target: "_blank", rel: "noreferrer" }, "(status)")) : null)) : null;
 });

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

@@ -1 +1 @@
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+{"version":3,"file":"HeaderStatusArea.js","sourceRoot":"","sources":["../../../src/components/header/HeaderStatusArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAKlD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,EAC1C,KAAK,GAGN;IACC,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,MAAM;QACnC,oBAAC,eAAe,IAAC,OAAO,EAAE,MAAM,CAAC,GAAG,EAAE,SAAS,EAAC,MAAM,GAAG;QAAC,GAAG;QAC5D,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CACZ,2BAAG,IAAI,EAAE,MAAM,CAAC,GAAG,EAAE,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,YAAY,eAEjD,CACL,CAAC,CAAC,CAAC,IAAI,CACG,CACd,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/components/msa/MSACanvasBlock.js

@@ -19,7 +19,7 @@ const MSABlock = observer(function ({ model, offsetX, offsetY, }) {
         return autorun(() => {
             ctx.resetTransform();
             ctx.clearRect(0, 0, blockSize, blockSize);
-            if (model.featureMode) {
+            if (model.showDomains) {
                 renderBoxFeatureCanvasBlock({
                     ctx,
                     offsetX,

package/dist/components/msa/renderBoxFeatureCanvasBlock.js

@@ -1,6 +1,6 @@
 export function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeYOverride, }) {
-    const { hierarchy, blockSize, rowHeight, highResScaleFactor, featureMode } = model;
-    if (featureMode) {
+    const { hierarchy, blockSize, rowHeight, highResScaleFactor, showDomains } = model;
+    if (showDomains) {
         const k = highResScaleFactorOverride || highResScaleFactor;
         const by = blockSizeYOverride || blockSize;
         ctx.resetTransform();

package/dist/components/msa/renderMSABlock.js

@@ -1,6 +1,6 @@
 import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes';
 export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
-    const { hierarchy, colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, featureMode, } = model;
+    const { hierarchy, colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, showDomains, } = model;
     const k = highResScaleFactorOverride || highResScaleFactor;
     const bx = blockSizeXOverride || blockSize;
     const by = blockSizeYOverride || blockSize;
@@ -15,7 +15,7 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
     const xStart = Math.max(0, Math.floor(offsetX / colWidth));
     const xEnd = Math.max(0, Math.ceil((offsetX + bx) / colWidth));
     const visibleLeaves = leaves.slice(yStart, yEnd);
-    if (!featureMode) {
+    if (!showDomains) {
         drawTiles({
             model,
             ctx,
@@ -61,7 +61,7 @@ function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, })
     }
 }
 function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart, xEnd, }) {
-    const { bgColor, featureMode, colorScheme, columns, colWidth, rowHeight } = model;
+    const { bgColor, showDomains, colorScheme, columns, colWidth, rowHeight } = model;
     if (rowHeight >= 5 && colWidth > rowHeight / 2) {
         for (const node of visibleLeaves) {
             const { data: { name }, } = node;
@@ -73,7 +73,7 @@ function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart,
                 const contrast = contrastScheme[letter.toUpperCase()] || 'black';
                 const x = i * colWidth + offsetX - (offsetX % colWidth);
                 // note: -rowHeight/4 matches +rowHeight/4 in tree
-                ctx.fillStyle = featureMode
+                ctx.fillStyle = showDomains
                     ? 'black'
                     : bgColor
                         ? contrast

package/dist/fetchUtils.d.ts

@@ -1,5 +1,5 @@
 export declare function myfetch(url: string, args?: RequestInit): Promise<Response>;
 export declare function textfetch(url: string, args?: RequestInit): Promise<string>;
-export declare function jsonfetch(url: string, args?: RequestInit): Promise<any>;
+export declare function jsonfetch<T>(url: string, args?: RequestInit): Promise<T>;
 export declare function arraybufferfetch(url: string): Promise<ArrayBuffer>;
 export declare function timeout(time: number): Promise<unknown>;

package/dist/fetchUtils.js.map

@@ -1 +1 @@
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+{"version":3,"file":"fetchUtils.js","sourceRoot":"","sources":["../src/fetchUtils.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,GAAW,EAAE,IAAkB;IAC3D,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAEvC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;QACjB,MAAM,IAAI,KAAK,CACb,QAAQ,QAAQ,CAAC,MAAM,aAAa,GAAG,IAAI,MAAM,QAAQ,CAAC,IAAI,EAAE,EAAE,CACnE,CAAA;IACH,CAAC;IAED,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,GAAW,EAAE,IAAkB;IAC7D,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACzC,OAAO,QAAQ,CAAC,IAAI,EAAE,CAAA;AACxB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAI,GAAW,EAAE,IAAkB;IAChE,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACzC,OAAO,QAAQ,CAAC,IAAI,EAAO,CAAA;AAC7B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,GAAW;IAChD,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,CAAA;IAC9B,OAAO,GAAG,CAAC,WAAW,EAAE,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,IAAY;IAClC,OAAO,IAAI,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CAAA;AAClD,CAAC"}

package/dist/launchInterProScan.d.ts

@@ -1,3 +1,4 @@
+import { MsaViewModel } from './model';
 export interface InterProScanResults {
     matches: {
         signature: {
@@ -20,7 +21,7 @@ export interface InterProScanResponse {
     results: InterProScanResults[];
 }
 export declare function loadInterProScanResults(jobId: string): Promise<InterProScanResponse>;
-export declare function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, }: {
+export declare function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, }: {
     algorithm: string;
     seq: string;
     programs: string[];
@@ -28,5 +29,10 @@ export declare function launchInterProScan({ algorithm, seq, programs, onJobId,
         msg: string;
         url?: string;
     }) => void;
-    onJobId: (arg: string) => void;
-}): Promise<InterProScanResponse>;
+    onJobId?: (arg: string) => void;
+    model: MsaViewModel;
+}): Promise<void>;
+export declare function loadInterProScanResultsWithStatus({ jobId, model, }: {
+    jobId: string;
+    model: MsaViewModel;
+}): Promise<void>;