npm - jbrowse-plugin-msaview - Versions diffs - 2.0.3 → 2.0.4 - Mend

jbrowse-plugin-msaview 2.0.3 → 2.0.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (57) hide show

package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAO/C,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAIlC,SAAS,gBAAgB,CAAC,QAAkB,EAAE,CAAS;IACrD,OAAO,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;AAC7C,CAAC;AAED,MAAM,oBAAoB,GAAG,QAAQ,CAAC,SAAS,qBAAqB,CAAC,EACnE,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACpD,MAAM,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,~~CAA8B~~,CAAA;~~IAC5E~~,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,~~CAAC~~,CAAC,CAAA;~~IAC5D~~,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,0CACG,CAAC,EAAE,mBAAmB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;QACrC,MAAM,OAAO,GAAG,gBAAgB,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAA;QACrD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAA;QACnD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAA;YAC9D,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,EAClC,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GACtB,CACH,CAAA;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC,CAAC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}
1	+ {"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAO/C,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAIlC,SAAS,gBAAgB,CAAC,QAAkB,EAAE,CAAS;IACrD,OAAO,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;AAC7C,CAAC;AAED,MAAM,oBAAoB,GAAG,QAAQ,CAAC,SAAS,qBAAqB,CAAC,EACnE,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACpD,MAAM,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAEjC,CAAA;IACb,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,CAAE,CAAC,CAAA;IAC7D,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,0CACG,CAAC,EAAE,mBAAmB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;QACrC,MAAM,OAAO,GAAG,gBAAgB,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAA;QACrD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAA;QACnD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAA;YAC9D,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,EAClC,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GACtB,CACH,CAAA;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC,CAAC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}

package/dist/AddHighlightModel/util.js CHANGED Viewed

@@ -5,7 +5,7 @@ export const useStyles = makeStyles()({
         background: 'rgba(255,255,0,0.2)',
         border: '1px solid rgba(50,50,0,0.2)',
         position: 'absolute',
-        zIndex: 1000,
+        zIndex: 99,
         textAlign: 'center',
         pointerEvents: 'none',
         overflow: 'hidden',

package/dist/AddHighlightModel/util.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/AddHighlightModel/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,CAAC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IACpC,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,qBAAqB;QACjC,MAAM,EAAE,6BAA6B;QACrC,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,~~IAAI~~;~~QACZ~~,SAAS,EAAE,QAAQ;QACnB,aAAa,EAAE,MAAM;QACrB,QAAQ,EAAE,QAAQ;KACnB;CACF,CAAC,CAAA"}
1	+ {"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/AddHighlightModel/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,CAAC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IACpC,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,qBAAqB;QACjC,MAAM,EAAE,6BAA6B;QACrC,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,EAAE;QACV,SAAS,EAAE,QAAQ;QACnB,aAAa,EAAE,MAAM;QACrB,QAAQ,EAAE,QAAQ;KACnB;CACF,CAAC,CAAA"}

package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js CHANGED Viewed

@@ -2,14 +2,19 @@ import React, { useState } from 'react';
 import { Dialog } from '@jbrowse/core/ui';
 import { Box, Tab, Tabs } from '@mui/material';
 // locals
-import { CustomTabPanel, a11yProps } from './TabUtils';
+import CustomTabPanel from './TabUtils';
 import NewNcbiBlastQueryPanel from './NewNCBIBlastQuery';
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel';
+import { a11yProps } from './tabUtil';
 export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
     const [value, setValue] = useState(0);
-    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch MSA view", onClose: () => handleClose(), open: true },
+    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch MSA view", onClose: () => {
+            handleClose();
+        }, open: true },
         React.createElement(Box, { sx: { borderBottom: 1, borderColor: 'divider' } },
-            React.createElement(Tabs, { value: value, onChange: (_, val) => setValue(val) },
+            React.createElement(Tabs, { value: value, onChange: (_, val) => {
+                    setValue(val);
+                } },
                 React.createElement(Tab, { label: "NCBI BLAST query", ...a11yProps(0) }),
                 React.createElement(Tab, { label: "UCSC 100-way dataset", ...a11yProps(1) }))),
         React.createElement(CustomTabPanel, { value: value, index: 0 },

package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"LaunchMsaViewDialog.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/LaunchMsaViewDialog.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,GAAG,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAG9C,SAAS;AAET,OAAO,~~EAAE,~~cAAc,~~EAAE,SAAS,EAAE,~~MAAM,YAAY,CAAA;~~AACtD~~,OAAO,sBAAsB,MAAM,qBAAqB,CAAA;AACxD,OAAO,YAAY,MAAM,sCAAsC,CAAA;~~AAE~~/D,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,EAC9C,WAAW,EACX,OAAO,EACP,KAAK,GAKN;IACC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IAErC,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,iBAAiB,EACvB,OAAO,EAAE,GAAG,EAAE,~~CAAC,~~WAAW,EAAE,~~EAC5B~~,IAAI;QAEJ,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,WAAW,EAAE,SAAS,EAAE;YAClD,oBAAC,IAAI,~~IAAC~~,KAAK,EAAE,KAAK,~~EAAE~~,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,~~CAAC,~~QAAQ,CAAC,GAAG,CAAC;~~gBACrD~~,oBAAC,GAAG,IAAC,KAAK,EAAC,kBAAkB,KAAK,SAAS,CAAC,CAAC,CAAC,GAAI;gBAClD,oBAAC,GAAG,IAAC,KAAK,EAAC,sBAAsB,KAAK,SAAS,CAAC,CAAC,CAAC,GAAI,CACjD,CACH;QACN,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC;YACpC,oBAAC,sBAAsB,IACrB,WAAW,EAAE,WAAW,EACxB,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,GACZ,CACa;QACjB,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC;YACpC,oBAAC,YAAY,IACX,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,GACxB,CACa,CACV,CACV,CAAA;AACH,CAAC"}
1	+ {"version":3,"file":"LaunchMsaViewDialog.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/LaunchMsaViewDialog.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,GAAG,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAG9C,SAAS;AAET,OAAO,cAAc,MAAM,YAAY,CAAA;AACvC,OAAO,sBAAsB,MAAM,qBAAqB,CAAA;AACxD,OAAO,YAAY,MAAM,sCAAsC,CAAA;AAC/D,OAAO,EAAE,SAAS,EAAE,MAAM,WAAW,CAAA;AAErC,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,EAC9C,WAAW,EACX,OAAO,EACP,KAAK,GAKN;IACC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IAErC,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,iBAAiB,EACvB,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC,EACD,IAAI;QAEJ,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,WAAW,EAAE,SAAS,EAAE;YAClD,oBAAC,IAAI,IACH,KAAK,EAAE,KAAK,EACZ,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;oBACnB,QAAQ,CAAC,GAAG,CAAC,CAAA;gBACf,CAAC;gBAED,oBAAC,GAAG,IAAC,KAAK,EAAC,kBAAkB,KAAK,SAAS,CAAC,CAAC,CAAC,GAAI;gBAClD,oBAAC,GAAG,IAAC,KAAK,EAAC,sBAAsB,KAAK,SAAS,CAAC,CAAC,CAAC,GAAI,CACjD,CACH;QACN,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC;YACpC,oBAAC,sBAAsB,IACrB,WAAW,EAAE,WAAW,EACxB,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,GACZ,CACa;QACjB,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC;YACpC,oBAAC,YAAY,IACX,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,GACxB,CACa,CACV,CACV,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js CHANGED Viewed

@@ -40,9 +40,15 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({ handleClose, feature,
     const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'];
     return (React.createElement(DialogContent, { className: classes.dialogContent },
         error ? React.createElement(ErrorMessage, { error: error }) : null,
-        React.createElement(TextField2, { value: blastDatabase, onChange: event => setBlastDatabase(event.target.value), label: "BLAST blastDatabase", select: true }, blastDatabaseOptions.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
-        React.createElement(TextField2, { value: msaAlgorithm, onChange: event => setMsaAlgorithm(event.target.value), label: "MSA Algorithm", select: true }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
-        React.createElement(TextField2, { value: userSelection, onChange: event => setUserSelection(event.target.value), label: "Choose isoform to BLAST", select: true }, options.map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() },
+        React.createElement(TextField2, { value: blastDatabase, onChange: event => {
+                setBlastDatabase(event.target.value);
+            }, label: "BLAST blastDatabase", select: true }, blastDatabaseOptions.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
+        React.createElement(TextField2, { value: msaAlgorithm, onChange: event => {
+                setMsaAlgorithm(event.target.value);
+            }, label: "MSA Algorithm", select: true }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
+        React.createElement(TextField2, { value: userSelection, onChange: event => {
+                setUserSelection(event.target.value);
+            }, label: "Choose isoform to BLAST", select: true }, options.map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() },
             getGeneDisplayName(feature),
             " - ",
             getTranscriptDisplayName(val))))),
@@ -70,7 +76,9 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({ handleClose, feature,
                     });
                     handleClose();
                 }, disabled: !proteinSequence }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => handleClose() }, "Cancel"))));
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
+                    handleClose();
+                } }, "Cancel"))));
 });
 export default NcbiBlastPanel;
 //# sourceMappingURL=NcbiBlastPanel.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js CHANGED Viewed

@@ -7,7 +7,7 @@ export function calculateProteinSequence({ cds, sequence, codonTable, }) {
     let protein = '';
     for (let i = 0; i < str.length; i += 3) {
         // use & symbol for undefined codon, or partial slice
-        protein += codonTable[str.slice(i, i + 3)] || '&';
+        protein += codonTable[str.slice(i, i + 3)] ?? '&';
     }
     return protein;
 }

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.js CHANGED Viewed

@@ -2,42 +2,44 @@ import { useEffect, useState } from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { getConf } from '@jbrowse/core/configuration';
 const BPLIMIT = 500_000;
+async function fetchSeq({ start, end, refName, session, assemblyName, }) {
+    const { assemblyManager, rpcManager } = session;
+    const assembly = await assemblyManager.waitForAssembly(assemblyName);
+    if (!assembly) {
+        throw new Error('assembly not found');
+    }
+    const sessionId = 'getSequence';
+    const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
+        adapterConfig: getConf(assembly, ['sequence', 'adapter']),
+        sessionId,
+        regions: [
+            {
+                start,
+                end,
+                refName: assembly.getCanonicalRefName(refName),
+                assemblyName,
+            },
+        ],
+    }));
+    return feats[0]?.get('seq') ?? '';
+}
 export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = true, }) {
     const [sequence, setSequence] = useState();
     const [error, setError] = useState();
+    const assemblyName = view?.assemblyNames?.[0];
     useEffect(() => {
         if (view) {
-            const { assemblyManager, rpcManager } = getSession(view);
-            const [assemblyName] = view?.assemblyNames || [];
-            async function fetchSeq(start, end, refName) {
-                const assembly = await assemblyManager.waitForAssembly(assemblyName);
-                if (!assembly) {
-                    throw new Error('assembly not found');
-                }
-                const sessionId = 'getSequence';
-                const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
-                    adapterConfig: getConf(assembly, ['sequence', 'adapter']),
-                    sessionId,
-                    regions: [
-                        {
-                            start,
-                            end,
-                            refName: assembly.getCanonicalRefName(refName),
-                            assemblyName,
-                        },
-                    ],
-                });
-                const [feat] = feats;
-                return feat?.get('seq') || '';
-            }
             // eslint-disable-next-line @typescript-eslint/no-floating-promises
             ;
             (async () => {
                 try {
                     setError(undefined);
                     setSequence(undefined);
-                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                    const session = getSession(view);
                     const { start, end, refName } = feature.toJSON();
+                    if (!assemblyName) {
+                        throw new Error('No assembly found');
+                    }
                     if (!forceLoad && end - start > BPLIMIT) {
                         setSequence({
                             error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
@@ -46,10 +48,29 @@ export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = tr
                     else {
                         const b = start - upDownBp;
                         const e = end + upDownBp;
-                        const seq = await fetchSeq(start, end, refName);
-                        const up = await fetchSeq(Math.max(0, b), start, refName);
-                        const down = await fetchSeq(end, e, refName);
-                        setSequence({ seq, upstream: up, downstream: down });
+                        setSequence({
+                            seq: await fetchSeq({
+                                start,
+                                end,
+                                refName,
+                                assemblyName,
+                                session,
+                            }),
+                            upstream: await fetchSeq({
+                                start: Math.max(0, b),
+                                end: start,
+                                refName,
+                                assemblyName,
+                                session,
+                            }),
+                            downstream: await fetchSeq({
+                                start: end,
+                                end: e,
+                                refName,
+                                assemblyName,
+                                session,
+                            }),
+                        });
                     }
                 }
                 catch (e) {
@@ -58,7 +79,7 @@ export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = tr
                 }
             })();
         }
-    }, [feature, view, upDownBp, forceLoad]);
+    }, [feature, view, upDownBp, assemblyName, forceLoad]);
     return { sequence, error };
 }
 //# sourceMappingURL=useFeatureSequence.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js CHANGED Viewed

@@ -51,7 +51,9 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
                 React.createElement("a", { href: "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/alignments/" }, "knownCanonical.multiz100way.protAA.fa.gz")),
             error ? React.createElement(ErrorMessage, { error: error }) : null,
             geneNameList && !ret ? (React.createElement("div", { style: { color: 'red' } }, "No MSA data for this gene found")) : null,
-            React.createElement(TextField, { value: userSelection, onChange: event => setUserSelection(event.target.value), label: "Choose isoform to view MSA for", select: true },
+            React.createElement(TextField, { value: userSelection, onChange: event => {
+                    setUserSelection(event.target.value);
+                }, label: "Choose isoform to view MSA for", select: true },
                 options
                     .filter(val => set.has(getId(val)))
                     .map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() },
@@ -84,7 +86,9 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
                         }
                     })();
                 } }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => handleClose() }, "Cancel"))));
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
+                    handleClose();
+                } }, "Cancel"))));
 });
 export default PreLoadedMSA;
 //# sourceMappingURL=PreLoadedMSADataPanel.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/TabUtils.d.ts CHANGED Viewed

@@ -4,9 +4,5 @@ interface TabPanelProps {
     index: number;
     value: number;
 }
-export declare function CustomTabPanel(props: TabPanelProps): React.JSX.Element;
-export declare function a11yProps(index: number): {
-    id: string;
-    'aria-controls': string;
-};
+export default function CustomTabPanel(props: TabPanelProps): React.JSX.Element;
 export {};

package/dist/LaunchMsaView/components/TabUtils.js CHANGED Viewed

@@ -1,13 +1,7 @@
 import React from 'react';
 import { Box } from '@mui/material';
-export function CustomTabPanel(props) {
+export default function CustomTabPanel(props) {
     const { children, value, index, ...other } = props;
     return (React.createElement("div", { role: "tabpanel", hidden: value !== index, id: `gtabpanel-${index}`, "aria-labelledby": `gtab-${index}`, ...other }, value === index && React.createElement(Box, { sx: { p: 3 } }, children)));
 }
-export function a11yProps(index) {
-    return {
-        id: `gtab-${index}`,
-        'aria-controls': `gtabpanel-${index}`,
-    };
-}
 //# sourceMappingURL=TabUtils.js.map

package/dist/LaunchMsaView/components/TabUtils.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"TabUtils.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TabUtils.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,GAAG,EAAE,MAAM,eAAe,CAAA;AAQnC,MAAM,UAAU,cAAc,CAAC,KAAoB;~~IACjD~~,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,KAAK,EAAE,GAAG,KAAK,CAAA;IAElD,OAAO,CACL,6BACE,IAAI,EAAC,UAAU,EACf,MAAM,EAAE,KAAK,KAAK,KAAK,EACvB,EAAE,EAAE,aAAa,KAAK,EAAE,qBACP,QAAQ,KAAK,EAAE,KAC5B,KAAK,IAER,KAAK,KAAK,KAAK,IAAI,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,IAAG,QAAQ,CAAO,CACnD,CACP,CAAA;AACH,CAAC~~;AACD,MAAM,UAAU,SAAS,CAAC,KAAa;IACrC,OAAO;QACL,EAAE,EAAE,QAAQ,KAAK,EAAE;QACnB,eAAe,EAAE,aAAa,KAAK,EAAE;KACtC,CAAA;AACH,CAAC~~"}
1	+ {"version":3,"file":"TabUtils.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TabUtils.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,GAAG,EAAE,MAAM,eAAe,CAAA;AAQnC,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,KAAoB;IACzD,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,KAAK,EAAE,GAAG,KAAK,CAAA;IAElD,OAAO,CACL,6BACE,IAAI,EAAC,UAAU,EACf,MAAM,EAAE,KAAK,KAAK,KAAK,EACvB,EAAE,EAAE,aAAa,KAAK,EAAE,qBACP,QAAQ,KAAK,EAAE,KAC5B,KAAK,IAER,KAAK,KAAK,KAAK,IAAI,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,IAAG,QAAQ,CAAO,CACnD,CACP,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/tabUtil.d.ts ADDED Viewed

@@ -0,0 +1,4 @@
+export declare function a11yProps(index: number): {
+    id: string;
+    'aria-controls': string;
+};

package/dist/LaunchMsaView/components/tabUtil.js ADDED Viewed

@@ -0,0 +1,7 @@
+export function a11yProps(index) {
+    return {
+        id: `gtab-${index}`,
+        'aria-controls': `gtabpanel-${index}`,
+    };
+}
+//# sourceMappingURL=tabUtil.js.map

package/dist/LaunchMsaView/components/tabUtil.js.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"tabUtil.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/tabUtil.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,SAAS,CAAC,KAAa;IACrC,OAAO;QACL,EAAE,EAAE,QAAQ,KAAK,EAAE;QACnB,eAAe,EAAE,aAAa,KAAK,EAAE;KACtC,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/index.js CHANGED Viewed

@@ -7,7 +7,7 @@ function isDisplay(elt) {
     return elt.name === 'LinearBasicDisplay';
 }
 function extendStateModel(stateModel) {
-    return stateModel.views(self => {
+    return stateModel.views((self) => {
         const superContextMenuItems = self.contextMenuItems;
         return {
             contextMenuItems() {
@@ -21,8 +21,7 @@ function extendStateModel(stateModel) {
                                 label: 'Launch MSA view',
                                 icon: AddIcon,
                                 onClick: () => {
-                                    const session = getSession(track);
-                                    session.queueDialog(handleClose => [
+                                    getSession(track).queueDialog(handleClose => [
                                         LaunchMsaViewDialog,
                                         {
                                             model: track,

package/dist/LaunchMsaView/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/util.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 import { Feature } from '@jbrowse/core/util';
 export declare function getTranscriptFeatures(feature: Feature): Feature[];
-export declare function getId(val?: Feature): any;
+export declare function getId(val?: Feature): string;
 export declare function getTranscriptDisplayName(val?: Feature): string;
 export declare function getGeneDisplayName(val?: Feature): string;

package/dist/LaunchMsaView/util.js CHANGED Viewed

@@ -8,7 +8,7 @@ export function getTranscriptFeatures(feature) {
             subfeatures.filter(f => f.get('subfeatures')?.some(f => f.get('type') === 'CDS'));
 }
 export function getId(val) {
-    return val === undefined ? '' : val.get('name') || val.get('id');
+    return val?.get('name') || val?.get('id') || '';
 }
 export function getTranscriptDisplayName(val) {
     return val === undefined

package/dist/LaunchMsaView/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/MsaViewPanel/components/LoadingBLAST.js CHANGED Viewed

@@ -29,7 +29,7 @@ const LoadingBLAST = observer(function LoadingBLAST2({ model, }) {
     const { classes } = useStyles();
     return (React.createElement("div", { className: classes.margin },
         React.createElement(LoadingEllipses, { message: "Running NCBI BLAST", variant: "h5" }),
-        error ? (React.createElement(RIDError, { rid: rid, error: error })) : rid ? (React.createElement(RIDProgress, { rid: rid, progress: progress })) : null,
+        error ? (React.createElement(RIDError, { rid: rid, error: error })) : (rid ? (React.createElement(RIDProgress, { rid: rid, progress: progress })) : null),
         React.createElement(Typography, null, processing || 'Initializing BLAST query')));
 });
 export default LoadingBLAST;

package/dist/MsaViewPanel/components/LoadingBLAST.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/MsaViewPanel/doLaunchBlast.js CHANGED Viewed

@@ -8,19 +8,32 @@ export async function doLaunchBlast({ self, }) {
         query,
         blastDatabase,
         blastProgram,
-        onProgress: arg => self.setProgress(arg),
-        onRid: rid => self.setRid(rid),
+        onProgress: arg => {
+            self.setProgress(arg);
+        },
+        onRid: rid => {
+            self.setRid(rid);
+        },
     });
     const sequence = [
         `>QUERY\n${query}`,
         ...hits
-            .map(h => [makeId(h.description[0]), strip(h.hsps[0].hseq)])
+            .map(h => [
+            makeId(h.description[0] ?? {
+                accession: 'unknown',
+                id: 'unknown',
+                sciname: 'unknown',
+            }),
+            strip(h.hsps[0]?.hseq ?? ''),
+        ])
             .map(([id, seq]) => `>${id}\n${seq}`),
     ].join('\n');
     const data = await launchMSA({
         algorithm: msaAlgorithm,
         sequence,
-        onProgress: arg => self.setProgress(arg),
+        onProgress: arg => {
+            self.setProgress(arg);
+        },
     });
     return data;
 }

package/dist/MsaViewPanel/doLaunchBlast.js.map CHANGED Viewed

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