react-msaview 3.1.12 → 3.2.1

package/dist/components/dialogs/ExportSVGDialog.js

@@ -7,32 +7,44 @@ export default function ExportSVGDialog({ model, onClose, }) {
     const [exportType, setExportType] = useState('viewport');
     const [error, setError] = useState();
     const theme = useTheme();
-    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Export SVG" },
+    return (React.createElement(Dialog, { onClose: () => {
+            onClose();
+        }, open: true, title: "Export SVG" },
         React.createElement(DialogContent, null,
             error ? React.createElement(ErrorMessage, { error: error }) : null,
             React.createElement(Typography, null, "Settings:"),
-            React.createElement(Checkbox2, { label: "Include minimap?", disabled: exportType === 'entire', checked: includeMinimap, onChange: () => setIncludeMinimap(!includeMinimap) }),
+            React.createElement(Checkbox2, { label: "Include minimap?", disabled: exportType === 'entire', checked: includeMinimap, onChange: () => {
+                    setIncludeMinimap(!includeMinimap);
+                } }),
             React.createElement("div", null,
                 React.createElement(FormControl, null,
                     React.createElement(FormLabel, null, "Export type"),
-                    React.createElement(RadioGroup, { value: exportType, onChange: event => setExportType(event.target.value) },
+                    React.createElement(RadioGroup, { value: exportType, onChange: event => {
+                            setExportType(event.target.value);
+                        } },
                         React.createElement(FormControlLabel, { value: "entire", control: React.createElement(Radio, null), label: "Entire MSA" }),
                         React.createElement(FormControlLabel, { value: "viewport", control: React.createElement(Radio, null), label: "Current viewport only" }))))),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "primary", onClick: async () => {
-                    try {
-                        await model.exportSVG({
-                            theme,
-                            includeMinimap: exportType === 'entire' ? false : includeMinimap,
-                            exportType,
-                        });
-                    }
-                    catch (e) {
-                        console.error(e);
-                        setError(e);
-                    }
-                    onClose();
+            React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    ;
+                    (async () => {
+                        try {
+                            await model.exportSVG({
+                                theme,
+                                includeMinimap: exportType === 'entire' ? false : includeMinimap,
+                                exportType,
+                            });
+                        }
+                        catch (e) {
+                            console.error(e);
+                            setError(e);
+                        }
+                        onClose();
+                    })();
                 } }, "Submit"),
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => onClose() }, "Cancel"))));
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    onClose();
+                } }, "Cancel"))));
 }
 //# sourceMappingURL=ExportSVGDialog.js.map

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;AACvC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AACvD,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,gBAAgB,EAChB,WAAW,EACX,SAAS,EACT,UAAU,EACV,KAAK,EACL,UAAU,EACV,QAAQ,GACT,MAAM,eAAe,CAAA;AAGtB,OAAO,SAAS,MAAM,cAAc,CAAA;AAEpC,MAAM,CAAC,OAAO,UAAU,eAAe,CAAC,EACtC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC1D,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAA;IACxD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,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;YACF;gBACE,oBAAC,WAAW;oBACV,oBAAC,SAAS,sBAAwB;oBAClC,oBAAC,UAAU,IACT,KAAK,EAAE,UAAU,EACjB,QAAQ,EAAE,KAAK,CAAC,EAAE;4BAChB,aAAa,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;wBACnC,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,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,KAAK,CAAC,SAAS,CAAC;gCACpB,KAAK;gCACL,cAAc,EACZ,UAAU,KAAK,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,cAAc;gCAClD,UAAU;6BACX,CAAC,CAAA;wBACJ,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACb,CAAC;wBACD,OAAO,EAAE,CAAA;oBACX,CAAC,CAAC,EAAE,CAAA;gBACN,CAAC,aAGM;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"}

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const FeatureTypeDialog: ({ onClose, model, }: {
     onClose: () => void;
     model: MsaViewModel;

package/dist/components/dialogs/FeatureDialog.js

@@ -18,8 +18,8 @@ const Toggles = observer(function ({ model }) {
             } }, "Toggle all off")));
 });
 const Table = observer(function ({ model }) {
-    const { tidyTypes, featureFilters } = model;
-    const values = [...tidyTypes.values()];
+    const { tidyInterProAnnotationTypes, featureFilters } = model;
+    const values = [...tidyInterProAnnotationTypes.values()];
     const palette = getPalette(values.length - 1);
     return (React.createElement(React.Fragment, null,
         React.createElement(Toggles, { model: model }),
@@ -32,7 +32,9 @@ const Table = observer(function ({ model }) {
                     React.createElement("td", null, "description"))),
             React.createElement("tbody", null, values.map(({ accession, name, description }, idx) => (React.createElement("tr", { key: accession },
                 React.createElement("td", null,
-                    React.createElement("input", { type: "checkbox", checked: featureFilters.get(accession) ?? false, onChange: () => model.setFilter(accession, !model.featureFilters.get(accession)) })),
+                    React.createElement("input", { type: "checkbox", checked: featureFilters.get(accession) ?? false, onChange: () => {
+                            model.setFilter(accession, !model.featureFilters.get(accession));
+                        } })),
                 React.createElement("td", null, accession),
                 React.createElement("td", null, name),
                 React.createElement("td", null, description),
@@ -44,7 +46,9 @@ const Table = observer(function ({ model }) {
                         } })))))))));
 });
 const FeatureTypeDialog = observer(function ({ onClose, model, }) {
-    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Feature filters", maxWidth: "xl" },
+    return (React.createElement(Dialog, { onClose: () => {
+            onClose();
+        }, open: true, title: "Feature filters", maxWidth: "xl" },
         React.createElement(DialogContent, null,
             React.createElement(Table, { model: model }))));
 });

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

@@ -1 +1 @@
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+{"version":3,"file":"FeatureDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/FeatureDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAIrD,OAAO,EAAE,UAAU,EAAE,MAAM,sBAAsB,CAAA;AAEjD,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,OAAO,CACL;QACE,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,MAAM,GAAG,IAAI,cAAc,CAAC,IAAI,EAAE,EAAE,CAAC;oBACxC,KAAK,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;gBAC5B,CAAC;YACH,CAAC,oBAGM;QAET,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,MAAM,GAAG,IAAI,cAAc,CAAC,IAAI,EAAE,EAAE,CAAC;oBACxC,KAAK,CAAC,SAAS,CAAC,GAAG,EAAE,KAAK,CAAC,CAAA;gBAC7B,CAAC;YACH,CAAC,qBAGM,CACL,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACjE,MAAM,EAAE,2BAA2B,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAC7D,MAAM,MAAM,GAAG,CAAC,GAAG,2BAA2B,CAAC,MAAM,EAAE,CAAC,CAAA;IACxD,MAAM,OAAO,GAAG,UAAU,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IAC7C,OAAO,CACL;QACE,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB;YACE;gBACE;oBACE,+BAAM;oBACN,4CAAkB;oBAClB,uCAAa;oBACb,8CAAoB,CACjB,CACC;YACR,mCACG,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,WAAW,EAAE,EAAE,GAAG,EAAE,EAAE,CAAC,CACrD,4BAAI,GAAG,EAAE,SAAS;gBAChB;oBACE,+BACE,IAAI,EAAC,UAAU,EACf,OAAO,EAAE,cAAc,CAAC,GAAG,CAAC,SAAS,CAAC,IAAI,KAAK,EAC/C,QAAQ,EAAE,GAAG,EAAE;4BACb,KAAK,CAAC,SAAS,CACb,SAAS,EACT,CAAC,KAAK,CAAC,cAAc,CAAC,GAAG,CAAC,SAAS,CAAC,CACrC,CAAA;wBACH,CAAC,GACD,CACC;gBACL,gCAAK,SAAS,CAAM;gBACpB,gCAAK,IAAI,CAAM;gBACf,gCAAK,WAAW,CAAM;gBACtB;oBACE,6BACE,KAAK,EAAE;4BACL,KAAK,EAAE,EAAE;4BACT,MAAM,EAAE,EAAE;4BACV,UAAU,EAAE,OAAO,CAAC,GAAG,CAAC,IAAI,OAAO;yBACpC,GACD,CACC,CACF,CACN,CAAC,CACI,CACF,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,OAAO,EACP,KAAK,GAIN;IACC,OAAO,CACL,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;YACZ,OAAO,EAAE,CAAA;QACX,CAAC,EACD,IAAI,QACJ,KAAK,EAAC,iBAAiB,EACvB,QAAQ,EAAC,IAAI;QAEb,oBAAC,aAAa;YACZ,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,GAAI,CACT,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const InterProScanDialog: ({ handleClose, model, }: {
     handleClose: () => void;
     model: MsaViewModel;

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

@@ -3,6 +3,7 @@ import { observer } from 'mobx-react';
 import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
 import { getSession } from '@jbrowse/core/util';
 import { launchInterProScan } from '../../launchInterProScan';
+import { Dialog } from '@jbrowse/core/ui';
 const InterProScanDialog = observer(function ({ handleClose, model, }) {
     const [vals, setVals] = useState([
         {
@@ -132,29 +133,41 @@ const InterProScanDialog = observer(function ({ handleClose, model, }) {
     ]);
     const programs = vals.filter(e => e.checked).map(e => e.name);
     const [show, setShow] = useState(false);
-    return (React.createElement(React.Fragment, null,
+    return (React.createElement(Dialog, { maxWidth: "xl", title: "Query InterProScan API for domains", onClose: () => {
+            handleClose();
+        }, open: true },
         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) },
+            React.createElement(Typography, null, "This will run InterProScan via the InterProScan API on all rows of the current MSA"),
+            React.createElement(Button, { onClick: () => {
+                    setShow(!show);
+                } },
                 show ? 'Hide' : 'Show',
                 " advanced options"),
             show ? (React.createElement("div", null,
                 React.createElement(Typography, null, "Select algorithms for InterProScan to run"),
                 React.createElement("div", null,
-                    React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => setVals(vals.map(v => ({ ...v, checked: false }))) }, "Select none"),
-                    React.createElement(Button, { variant: "contained", color: "primary", onClick: () => setVals(vals.map(v => ({ ...v, checked: true }))) }, "Select all")),
+                    React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            setVals(vals.map(v => ({ ...v, checked: false })));
+                        } }, "Select none"),
+                    React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
+                            setVals(vals.map(v => ({ ...v, checked: true })));
+                        } }, "Select all")),
                 React.createElement("table", null,
                     React.createElement("tbody", null, vals
                         .sort((a, b) => a.category.localeCompare(b.category))
                         .map(({ name, checked, category }) => (React.createElement("tr", { key: name },
                         React.createElement("td", null,
-                            React.createElement("input", { type: "checkbox", key: name, checked: checked, onChange: () => setVals(vals.map(e => e.name === name
-                                    ? { ...e, checked: !e.checked }
-                                    : e)) })),
+                            React.createElement("input", { type: "checkbox", key: name, checked: checked, onChange: () => {
+                                    setVals(vals.map(e => e.name === name
+                                        ? { ...e, checked: !e.checked }
+                                        : e));
+                                } })),
                         React.createElement("td", null, name),
                         React.createElement("td", null, category)))))))) : null),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
             React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
                     // eslint-disable-next-line @typescript-eslint/no-floating-promises
                     ;
@@ -172,7 +185,9 @@ const InterProScanDialog = observer(function ({ handleClose, model, }) {
                                     .filter(f => !!f[1])
                                     .map(row => `>${row[0]}\n${row[1]}`)
                                     .join('\n'),
-                                onProgress: arg => model.setStatus(arg),
+                                onProgress: arg => {
+                                    model.setStatus(arg);
+                                },
                                 model,
                             });
                         }
@@ -188,4 +203,4 @@ const InterProScanDialog = observer(function ({ handleClose, model, }) {
                 } }, "Send sequences to InterProScan"))));
 });
 export default InterProScanDialog;
-//# sourceMappingURL=InterProScanPanel.js.map
+//# sourceMappingURL=InterProScanDialog.js.map

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

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const MetadataDialog: ({ model, onClose, }: {
     model: MsaViewModel;
     onClose: () => void;

package/dist/components/dialogs/MetadataDialog.js

@@ -6,7 +6,9 @@ import { Attributes, BaseCard, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatu
 import SequenceTextArea from '../SequenceTextArea';
 const MetadataDialog = observer(function ({ model, onClose, }) {
     const { header } = model;
-    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Metadata", maxWidth: "xl" },
+    return (React.createElement(Dialog, { onClose: () => {
+            onClose();
+        }, open: true, title: "Metadata", maxWidth: "xl" },
         React.createElement(DialogContent, null,
             React.createElement(Attributes, { attributes: header }),
             React.createElement(BaseCard, { title: "sequence" },

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

@@ -1 +1 @@
-{"version":3,"file":"MetadataDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/MetadataDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,UAAU,EACV,QAAQ,GACT,MAAM,mDAAmD,CAAA;AAI1D,OAAO,gBAAgB,MAAM,qBAAqB,CAAA;AAElD,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IAExB,OAAO,CACL,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,EAAE,IAAI,QAAC,KAAK,EAAC,UAAU,EAAC,QAAQ,EAAC,IAAI;QACnE,oBAAC,aAAa;YACZ,oBAAC,UAAU,IAAC,UAAU,EAAE,MAAM,GAAI;YAClC,oBAAC,QAAQ,IAAC,KAAK,EAAC,UAAU;gBACxB,oBAAC,gBAAgB,IAAC,GAAG,EAAE,KAAK,CAAC,IAAI,GAAI,CAC5B,CACG,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}
+{"version":3,"file":"MetadataDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/MetadataDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,UAAU,EACV,QAAQ,GACT,MAAM,mDAAmD,CAAA;AAI1D,OAAO,gBAAgB,MAAM,qBAAqB,CAAA;AAElD,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IAExB,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;YACZ,oBAAC,UAAU,IAAC,UAAU,EAAE,MAAM,GAAI;YAClC,oBAAC,QAAQ,IAAC,KAAK,EAAC,UAAU;gBACxB,oBAAC,gBAAgB,IAAC,GAAG,EAAE,KAAK,CAAC,IAAI,GAAI,CAC5B,CACG,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const SettingsDialog: ({ model, onClose, }: {
     model: MsaViewModel;
     onClose: () => void;

package/dist/components/dialogs/SettingsDialog.js

@@ -12,6 +12,9 @@ const useStyles = makeStyles()(theme => ({
     flex: {
         display: 'flex',
     },
+    minw: {
+        width: '80em',
+    },
 }));
 const SettingsContent = observer(function ({ model }) {
     return (React.createElement(React.Fragment, null,
@@ -23,46 +26,90 @@ const TreeSettings = observer(function TreeSettings({ model, }) {
     const { drawTree, drawLabels, drawNodeBubbles, labelsAlignRight, noTree, showBranchLen, treeWidthMatchesArea, treeWidth, } = model;
     return (React.createElement("div", null,
         React.createElement("h1", null, "Tree options"),
-        React.createElement(Checkbox2, { checked: showBranchLen, onChange: () => model.setShowBranchLen(!showBranchLen), label: "Show branch length?" }),
-        React.createElement(Checkbox2, { checked: drawNodeBubbles, onChange: () => model.setDrawNodeBubbles(!drawNodeBubbles), label: "Draw clickable bubbles on tree branches?" }),
-        React.createElement(Checkbox2, { checked: drawTree, onChange: () => model.setDrawTree(!drawTree), label: "Show tree?" }),
-        React.createElement(Checkbox2, { checked: labelsAlignRight, onChange: () => model.setLabelsAlignRight(!labelsAlignRight), label: "Tree labels align right?" }),
-        React.createElement(Checkbox2, { checked: drawLabels, onChange: () => model.setDrawLabels(!drawLabels), label: "Draw labels" }),
+        React.createElement(Checkbox2, { checked: showBranchLen, onChange: () => {
+                model.setShowBranchLen(!showBranchLen);
+            }, label: "Show branch length?" }),
+        React.createElement(Checkbox2, { checked: drawNodeBubbles, onChange: () => {
+                model.setDrawNodeBubbles(!drawNodeBubbles);
+            }, label: "Draw clickable bubbles on tree branches?" }),
+        React.createElement(Checkbox2, { checked: drawTree, onChange: () => {
+                model.setDrawTree(!drawTree);
+            }, label: "Show tree?" }),
+        React.createElement(Checkbox2, { checked: labelsAlignRight, onChange: () => {
+                model.setLabelsAlignRight(!labelsAlignRight);
+            }, label: "Tree labels align right?" }),
+        React.createElement(Checkbox2, { checked: drawLabels, onChange: () => {
+                model.setDrawLabels(!drawLabels);
+            }, label: "Draw labels" }),
         noTree ? null : (React.createElement("div", null,
-            React.createElement(Checkbox2, { checked: treeWidthMatchesArea, onChange: () => model.setTreeWidthMatchesArea(!treeWidthMatchesArea), label: "Make tree width fit to tree area?" }),
+            React.createElement(Checkbox2, { checked: treeWidthMatchesArea, onChange: () => {
+                    model.setTreeWidthMatchesArea(!treeWidthMatchesArea);
+                }, label: "Make tree width fit to tree area?" }),
             treeWidthMatchesArea ? null : (React.createElement("div", { className: classes.flex },
                 React.createElement(Typography, null,
                     "Tree width (",
                     treeWidth,
                     "px)"),
-                React.createElement(Slider, { className: classes.field, min: 50, max: 600, value: treeWidth, onChange: (_, val) => model.setTreeWidth(val) })))))));
+                React.createElement(Slider, { className: classes.field, min: 50, max: 600, value: treeWidth, onChange: (_, val) => {
+                        model.setTreeWidth(val);
+                    } })))))));
 });
 const MSASettings = observer(function MSASettings({ model, }) {
     const { classes } = useStyles();
-    const { bgColor, colWidth, colorSchemeName, rowHeight } = model;
+    const { bgColor, contrastLettering, colWidth, allowedGappyness, drawMsaLetters, colorSchemeName, hideGaps, rowHeight, } = model;
     return (React.createElement("div", null,
         React.createElement("h1", null, "MSA options"),
-        React.createElement(Checkbox2, { checked: bgColor, onChange: () => model.setBgColor(!bgColor), label: "Color background tiles of MSA?" }),
+        React.createElement(Checkbox2, { checked: drawMsaLetters, onChange: () => {
+                model.setDrawMsaLetters(!drawMsaLetters);
+            }, label: "Draw letters" }),
+        React.createElement(Checkbox2, { checked: bgColor, onChange: () => {
+                model.setBgColor(!bgColor);
+            }, label: "Color background tiles of MSA?" }),
+        React.createElement(Checkbox2, { checked: contrastLettering, onChange: () => {
+                model.setContrastLettering(!contrastLettering);
+            }, label: "Use contrast lettering" }),
+        React.createElement(Checkbox2, { checked: hideGaps, onChange: () => {
+                model.setHideGaps(!hideGaps);
+            }, label: `Hide columns that are ${allowedGappyness}% gaps` }),
+        hideGaps ? (React.createElement("div", { className: classes.flex },
+            React.createElement(Typography, null,
+                "Allowed gappyness (",
+                100 - allowedGappyness,
+                "%)"),
+            React.createElement(Slider, { className: classes.field, min: 1, max: 100, value: allowedGappyness, onChange: (_, val) => {
+                    model.setAllowedGappyness(val);
+                } }))) : null,
         React.createElement("div", { className: classes.flex },
             React.createElement(Typography, null,
                 "Column width (",
                 colWidth,
                 "px)"),
-            React.createElement(Slider, { className: classes.field, min: 1, max: 50, value: colWidth, onChange: (_, val) => model.setColWidth(val) })),
+            React.createElement(Slider, { className: classes.field, min: 1, max: 50, value: colWidth, onChange: (_, val) => {
+                    model.setColWidth(val);
+                } })),
         React.createElement("div", { className: classes.flex },
             React.createElement(Typography, null,
                 "Row height (",
                 rowHeight,
                 "px)"),
-            React.createElement(Slider, { className: classes.field, min: 1, max: 50, value: rowHeight, onChange: (_, val) => model.setRowHeight(val) })),
-        React.createElement(TextField, { select: true, label: "Color scheme", value: colorSchemeName, onChange: event => model.setColorSchemeName(event.target.value) }, Object.keys(colorSchemes).map(option => (React.createElement(MenuItem, { key: option, value: option }, option))))));
+            React.createElement(Slider, { className: classes.field, min: 1, max: 50, value: rowHeight, onChange: (_, val) => {
+                    model.setRowHeight(val);
+                } })),
+        React.createElement(TextField, { select: true, label: "Color scheme", value: colorSchemeName, onChange: event => {
+                model.setColorSchemeName(event.target.value);
+            } }, Object.keys(colorSchemes).map(option => (React.createElement(MenuItem, { key: option, value: option }, option))))));
 });
 const SettingsDialog = observer(function ({ model, onClose, }) {
-    return (React.createElement(Dialog, { open: true, onClose: () => onClose(), title: "Settings", maxWidth: "xl" },
-        React.createElement(DialogContent, { style: { width: '80em' } },
+    const { classes } = useStyles();
+    return (React.createElement(Dialog, { open: true, onClose: () => {
+            onClose();
+        }, title: "Settings", maxWidth: "xl" },
+        React.createElement(DialogContent, { className: classes.minw },
             React.createElement(SettingsContent, { model: model }),
             React.createElement(DialogActions, null,
-                React.createElement(Button, { onClick: () => onClose(), variant: "contained", color: "primary" }, "Submit")))));
+                React.createElement(Button, { onClick: () => {
+                        onClose();
+                    }, variant: "contained", color: "primary" }, "Submit")))));
 });
 export default SettingsDialog;
 //# sourceMappingURL=SettingsDialog.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"SettingsDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/SettingsDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,QAAQ,EACR,MAAM,EACN,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AAGtB,OAAO,YAAY,MAAM,oBAAoB,CAAA;AAC7C,OAAO,SAAS,MAAM,cAAc,CAAA;AAEpC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM;KAChB;IACD,IAAI,EAAE;QACJ,KAAK,EAAE,MAAM;KACd;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC3E,OAAO,CACL;QACE,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,GAAI,CAC5B,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,YAAY,CAAC,EAClD,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EACJ,QAAQ,EACR,UAAU,EACV,eAAe,EACf,gBAAgB,EAChB,MAAM,EACN,aAAa,EACb,oBAAoB,EACpB,SAAS,GACV,GAAG,KAAK,CAAA;IAET,OAAO,CACL;QACE,+CAAqB;QACrB,oBAAC,SAAS,IACR,OAAO,EAAE,aAAa,EACtB,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC,CAAA;YACxC,CAAC,EACD,KAAK,EAAC,qBAAqB,GAC3B;QAEF,oBAAC,SAAS,IACR,OAAO,EAAE,eAAe,EACxB,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,kBAAkB,CAAC,CAAC,eAAe,CAAC,CAAA;YAC5C,CAAC,EACD,KAAK,EAAC,0CAA0C,GAChD;QACF,oBAAC,SAAS,IACR,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;YAC9B,CAAC,EACD,KAAK,EAAC,YAAY,GAClB;QAEF,oBAAC,SAAS,IACR,OAAO,EAAE,gBAAgB,EACzB,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,mBAAmB,CAAC,CAAC,gBAAgB,CAAC,CAAA;YAC9C,CAAC,EACD,KAAK,EAAC,0BAA0B,GAChC;QAEF,oBAAC,SAAS,IACR,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,aAAa,CAAC,CAAC,UAAU,CAAC,CAAA;YAClC,CAAC,EACD,KAAK,EAAC,aAAa,GACnB;QACD,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACf;YACE,oBAAC,SAAS,IACR,OAAO,EAAE,oBAAoB,EAC7B,QAAQ,EAAE,GAAG,EAAE;oBACb,KAAK,CAAC,uBAAuB,CAAC,CAAC,oBAAoB,CAAC,CAAA;gBACtD,CAAC,EACD,KAAK,EAAC,mCAAmC,GACzC;YACD,oBAAoB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAC7B,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;gBAC1B,oBAAC,UAAU;;oBAAc,SAAS;0BAAiB;gBACnD,oBAAC,MAAM,IACL,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,GAAG,EAAE,EAAE,EACP,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,SAAS,EAChB,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;wBACnB,KAAK,CAAC,YAAY,CAAC,GAAa,CAAC,CAAA;oBACnC,CAAC,GACD,CACE,CACP,CACG,CACP,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,WAAW,CAAC,EAChD,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EACJ,OAAO,EACP,iBAAiB,EACjB,QAAQ,EACR,gBAAgB,EAChB,cAAc,EACd,eAAe,EACf,QAAQ,EACR,SAAS,GACV,GAAG,KAAK,CAAA;IAET,OAAO,CACL;QACE,8CAAoB;QACpB,oBAAC,SAAS,IACR,OAAO,EAAE,cAAc,EACvB,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;YAC1C,CAAC,EACD,KAAK,EAAC,cAAc,GACpB;QACF,oBAAC,SAAS,IACR,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,UAAU,CAAC,CAAC,OAAO,CAAC,CAAA;YAC5B,CAAC,EACD,KAAK,EAAC,gCAAgC,GACtC;QACF,oBAAC,SAAS,IACR,OAAO,EAAE,iBAAiB,EAC1B,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,oBAAoB,CAAC,CAAC,iBAAiB,CAAC,CAAA;YAChD,CAAC,EACD,KAAK,EAAC,wBAAwB,GAC9B;QACF,oBAAC,SAAS,IACR,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;YAC9B,CAAC,EACD,KAAK,EAAE,yBAAyB,gBAAgB,QAAQ,GACxD;QACD,QAAQ,CAAC,CAAC,CAAC,CACV,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,UAAU;;gBAAqB,GAAG,GAAG,gBAAgB;qBAAgB;YACtE,oBAAC,MAAM,IACL,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,gBAAgB,EACvB,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;oBACnB,KAAK,CAAC,mBAAmB,CAAC,GAAa,CAAC,CAAA;gBAC1C,CAAC,GACD,CACE,CACP,CAAC,CAAC,CAAC,IAAI;QACR,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,UAAU;;gBAAgB,QAAQ;sBAAiB;YACpD,oBAAC,MAAM,IACL,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,EAAE,EACP,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;oBACnB,KAAK,CAAC,WAAW,CAAC,GAAa,CAAC,CAAA;gBAClC,CAAC,GACD,CACE;QACN,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,UAAU;;gBAAc,SAAS;sBAAiB;YACnD,oBAAC,MAAM,IACL,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,EAAE,EACP,KAAK,EAAE,SAAS,EAChB,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;oBACnB,KAAK,CAAC,YAAY,CAAC,GAAa,CAAC,CAAA;gBACnC,CAAC,GACD,CACE;QAEN,oBAAC,SAAS,IACR,MAAM,QACN,KAAK,EAAC,cAAc,EACpB,KAAK,EAAE,eAAe,EACtB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,KAAK,CAAC,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YAC9C,CAAC,IAEA,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CACvC,oBAAC,QAAQ,IAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,IACjC,MAAM,CACE,CACZ,CAAC,CACQ,CACR,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,oBAAC,MAAM,IACL,IAAI,QACJ,OAAO,EAAE,GAAG,EAAE;YACZ,OAAO,EAAE,CAAA;QACX,CAAC,EACD,KAAK,EAAC,UAAU,EAChB,QAAQ,EAAC,IAAI;QAEb,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;YACjC,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAA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package/dist/components/dialogs/TracklistDialog.d.ts

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

package/dist/components/dialogs/TracklistDialog.js

@@ -2,9 +2,11 @@ import React from 'react';
 import { Dialog } from '@jbrowse/core/ui';
 import { DialogContent, FormControlLabel, FormGroup, Checkbox, DialogActions, Button, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
-export default observer(function ({ model, onClose, }) {
+const TracklistDialog = observer(function ({ model, onClose, }) {
     const { tracks } = model;
-    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Add track" },
+    return (React.createElement(Dialog, { onClose: () => {
+            onClose();
+        }, open: true, title: "Add track" },
         React.createElement(DialogContent, null,
             React.createElement(Typography, null, "Open relevant per-alignment tracks e.g. protein domains"),
             React.createElement(FormGroup, null, tracks.map(track => {
@@ -13,6 +15,9 @@ export default observer(function ({ model, onClose, }) {
                         } }), label: track.model.name }));
             })),
             React.createElement(DialogActions, null,
-                React.createElement(Button, { onClick: () => onClose(), variant: "contained", color: "primary" }, "Close")))));
+                React.createElement(Button, { onClick: () => {
+                        onClose();
+                    }, variant: "contained", color: "primary" }, "Close")))));
 });
+export default TracklistDialog;
 //# sourceMappingURL=TracklistDialog.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"TracklistDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/TracklistDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,aAAa,EACb,gBAAgB,EAChB,SAAS,EACT,QAAQ,EACR,aAAa,EACb,MAAM,EACN,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IAExB,OAAO,CACL,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;YACZ,OAAO,EAAE,CAAA;QACX,CAAC,EACD,IAAI,QACJ,KAAK,EAAC,WAAW;QAEjB,oBAAC,aAAa;YACZ,oBAAC,UAAU,kEAEE;YAEb,oBAAC,SAAS,QACP,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE;gBAClB,OAAO,CACL,oBAAC,gBAAgB,IACf,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,EACnB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,CAAC,KAAK,CAAC,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,EACnD,QAAQ,EAAE,GAAG,EAAE;4BACb,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;wBACnC,CAAC,GACD,EAEJ,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,GACvB,CACH,CAAA;YACH,CAAC,CAAC,CACQ;YACZ,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;wBACZ,OAAO,EAAE,CAAA;oBACX,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,YAGR,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

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

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

package/dist/components/dialogs/UserProvidedDomainsDialog.js

@@ -0,0 +1,64 @@
+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 { Dialog } from '@jbrowse/core/ui';
+import { jsonfetch } from '../../fetchUtils';
+const UserProvidedDomainsDialog = 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: () => {
+            handleClose();
+        }, open: true },
+        React.createElement(DialogContent, null,
+            React.createElement("div", null,
+                React.createElement(Typography, null, "Open a JSON file of InterProScan results that you run remotely on EBI servers or locally"),
+                React.createElement("div", { style: { display: 'flex', margin: 30 } },
+                    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.setInterProAnnotations(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 UserProvidedDomainsDialog;
+//# sourceMappingURL=UserProvidedDomainsDialog.js.map

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

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const Header: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/header/Header.js

@@ -1,6 +1,7 @@
-import React, { lazy } from 'react';
+import React, { lazy, useEffect } from 'react';
 import { IconButton } from '@mui/material';
 import { observer } from 'mobx-react';
+import useMeasure from '@jbrowse/core/util/useMeasure';
 // icons
 import Help from '@mui/icons-material/Help';
 // locals
@@ -11,14 +12,20 @@ import HeaderStatusArea from './HeaderStatusArea';
 import HeaderMenuExtra from './HeaderMenuExtra';
 const AboutDialog = lazy(() => import('../dialogs/AboutDialog'));
 const Header = observer(function ({ model }) {
-    return (React.createElement("div", { style: { display: 'flex' } },
-        React.createElement(ZoomControls, { model: model }),
+    const [ref, { height }] = useMeasure();
+    useEffect(() => {
+        model.setHeaderHeight(height || 0);
+    }, [model, height]);
+    return (React.createElement("div", { ref: ref, style: { display: 'flex' } },
         React.createElement(HeaderMenuExtra, { model: model }),
+        React.createElement(ZoomControls, { model: model }),
         React.createElement(MultiAlignmentSelector, { model: model }),
         React.createElement(HeaderInfoArea, { model: model }),
         React.createElement(Spacer, null),
         React.createElement(HeaderStatusArea, { model: model }),
-        React.createElement(IconButton, { onClick: () => model.queueDialog(onClose => [AboutDialog, { onClose }]) },
+        React.createElement(IconButton, { onClick: () => {
+                model.queueDialog(onClose => [AboutDialog, { onClose }]);
+            } },
             React.createElement(Help, null))));
 });
 function Spacer() {

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

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const HeaderInfoArea: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element | null;