jbrowse-plugin-msaview 2.3.3 → 2.3.8

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js

@@ -20,6 +20,9 @@ const useStyles = makeStyles()({
         margin: 30,
         maxWidth: 600,
     },
+    infoText: {
+        marginTop: 20,
+    },
 });
 const NCBIBlastManualPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
     const { classes } = useStyles();
@@ -36,7 +39,7 @@ const NCBIBlastManualPanel = observer(function ({ handleClose, feature, model, c
             proteinSequence ? (React.createElement("div", { className: classes.ncbiLink },
                 "Link to NCBI BLAST: ",
                 React.createElement(ExternalLink, { href: link }, link2))) : null,
-            React.createElement(Typography, { style: { marginTop: 20 } }, "Click the link above and run your BLAST query, and once you have results, click \"Multiple Alignment\" at the top of the results page to be redirected to COBALT, NCBI's multiple sequence aligner. Once COBALT completes, you can download an MSA (.aln file) and optionally a Newick tree (.nh) and paste the results into JBrowse")),
+            React.createElement(Typography, { className: classes.infoText }, "Click the link above and run your BLAST query, and once you have results, click \"Multiple Alignment\" at the top of the results page to be redirected to COBALT, NCBI's multiple sequence aligner. Once COBALT completes, you can download an MSA (.aln file) and optionally a Newick tree (.nh) and paste the results into JBrowse")),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
                     handleClose();

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map

@@ -1 +1 @@
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+{"version":3,"file":"NCBIBlastManualPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,iBAAiB,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAA;AAChE,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAChF,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,YAAY,MAAM,kCAAkC,CAAA;AAC3D,OAAO,EAAE,oBAAoB,EAAE,MAAM,YAAY,CAAA;AACjD,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAKlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;IACD,QAAQ,EAAE;QACR,SAAS,EAAE,WAAW;QACtB,MAAM,EAAE,EAAE;QACV,QAAQ,EAAE,GAAG;KACd;IACD,QAAQ,EAAE;QACR,SAAS,EAAE,EAAE;KACd;CACF,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,WAAW,EACX,OAAO,EACP,KAAK,EACL,QAAQ,EACR,OAAO,GAOR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EACJ,OAAO,EACP,UAAU,EACV,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,GACN,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAE7C,MAAM,EAAE,GAAG,oBAAoB,CAAC,eAAe,CAAC,CAAA;IAChD,MAAM,IAAI,GAAG,GAAG,OAAO,6DAA6D,EAAE,EAAE,CAAA;IACxF,MAAM,KAAK,GAAG,GAAG,OAAO,6DAA6D,QAAQ,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAA;IAEvG,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,QAAQ;YACR,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAE9C,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,EAChB,OAAO,EAAE,OAAO,EAChB,UAAU,EAAE,UAAU,EACtB,kBAAkB,EAAE,kBAAkB,EACtC,kBAAkB,EAAE,aAAa,EACjC,eAAe,EAAE,eAAe,GAChC;YAED,eAAe,CAAC,CAAC,CAAC,CACjB,6BAAK,SAAS,EAAE,OAAO,CAAC,QAAQ;;gBACV,oBAAC,YAAY,IAAC,IAAI,EAAE,IAAI,IAAG,KAAK,CAAgB,CAChE,CACP,CAAC,CAAC,CAAC,IAAI;YAER,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,QAAQ,2UAM1B,CACC;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,YAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js

@@ -2,12 +2,18 @@ import React, { useState } from 'react';
 import { useLocalStorage } from '@jbrowse/core/util';
 import SettingsIcon from '@mui/icons-material/Settings';
 import { IconButton } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
 import NCBIBlastAutomaticPanel from './NCBIBlastAutomaticPanel';
 import NCBIBlastManualPanel from './NCBIBlastManualPanel';
 import NCBIBlastMethodSelector from './NCBIBlastMethodSelector';
 import NCBIBlastRIDPanel from './NCBIBlastRIDPanel';
 import NCBISettingsDialog from './NCBISettingsDialog';
 import { BASE_BLAST_URL } from './consts';
+const useStyles = makeStyles()({
+    settingsButton: {
+        float: 'right',
+    },
+});
 const panelMap = {
     automatic: NCBIBlastAutomaticPanel,
     rid: NCBIBlastRIDPanel,
@@ -17,9 +23,10 @@ export default function NCBIBlastPanel({ handleClose, model, feature, }) {
     const [lookupMethod, setLookupMethod] = useState('automatic');
     const [baseUrl, setBaseUrl] = useLocalStorage('msa-blastRootUrl', BASE_BLAST_URL);
     const [settingsOpen, setSettingsOpen] = useState(false);
+    const { classes } = useStyles();
     const Panel = panelMap[lookupMethod];
     return (React.createElement(React.Fragment, null,
-        React.createElement(IconButton, { style: { float: 'right' }, size: "small", onClick: () => {
+        React.createElement(IconButton, { className: classes.settingsButton, size: "small", onClick: () => {
                 setSettingsOpen(true);
             } },
             React.createElement(SettingsIcon, null)),

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js.map

@@ -1 +1 @@
-{"version":3,"file":"NCBIBlastPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACpD,OAAO,YAAY,MAAM,8BAA8B,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAC/D,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAC/D,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,UAAU,CAAA;AAIzC,MAAM,QAAQ,GAAG;IACf,SAAS,EAAE,uBAAuB;IAClC,GAAG,EAAE,iBAAiB;IACtB,MAAM,EAAE,oBAAoB;CACpB,CAAA;AAEV,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EACrC,WAAW,EACX,KAAK,EACL,OAAO,GAKR;IACC,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,WAAW,CAAC,CAAA;IAC7D,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,eAAe,CAC3C,kBAAkB,EAClB,cAAc,CACf,CAAA;IACD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEvD,MAAM,KAAK,GAAG,QAAQ,CAAC,YAAqC,CAAC,CAAA;IAE7D,OAAO,CACL;QACE,oBAAC,UAAU,IACT,KAAK,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,EACzB,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,eAAe,CAAC,IAAI,CAAC,CAAA;YACvB,CAAC;YAED,oBAAC,YAAY,OAAG,CACL;QAEb,oBAAC,KAAK,IACJ,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,EACxB,OAAO,EAAE,OAAO;YAEhB,oBAAC,uBAAuB,IACtB,YAAY,EAAE,YAAY,EAC1B,eAAe,EAAE,eAAe,GAChC,CACI;QAEP,YAAY,CAAC,CAAC,CAAC,CACd,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,MAAM,CAAC,EAAE;gBACpB,IAAI,MAAM,EAAE,CAAC;oBACX,UAAU,CAAC,MAAM,CAAC,CAAA;gBACpB,CAAC;gBACD,eAAe,CAAC,KAAK,CAAC,CAAA;YACxB,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC"}
+{"version":3,"file":"NCBIBlastPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACpD,OAAO,YAAY,MAAM,8BAA8B,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAC/D,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAC/D,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,UAAU,CAAA;AAIzC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,cAAc,EAAE;QACd,KAAK,EAAE,OAAO;KACf;CACF,CAAC,CAAA;AAEF,MAAM,QAAQ,GAAG;IACf,SAAS,EAAE,uBAAuB;IAClC,GAAG,EAAE,iBAAiB;IACtB,MAAM,EAAE,oBAAoB;CACpB,CAAA;AAEV,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EACrC,WAAW,EACX,KAAK,EACL,OAAO,GAKR;IACC,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,WAAW,CAAC,CAAA;IAC7D,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,eAAe,CAC3C,kBAAkB,EAClB,cAAc,CACf,CAAA;IACD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACvD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAE/B,MAAM,KAAK,GAAG,QAAQ,CAAC,YAAqC,CAAC,CAAA;IAE7D,OAAO,CACL;QACE,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,cAAc,EACjC,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,eAAe,CAAC,IAAI,CAAC,CAAA;YACvB,CAAC;YAED,oBAAC,YAAY,OAAG,CACL;QAEb,oBAAC,KAAK,IACJ,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,EACxB,OAAO,EAAE,OAAO;YAEhB,oBAAC,uBAAuB,IACtB,YAAY,EAAE,YAAY,EAC1B,eAAe,EAAE,eAAe,GAChC,CACI;QAEP,YAAY,CAAC,CAAC,CAAC,CACd,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,MAAM,CAAC,EAAE;gBACpB,IAAI,MAAM,EAAE,CAAC;oBACX,UAAU,CAAC,MAAM,CAAC,CAAA;gBACpB,CAAC;gBACD,eAAe,CAAC,KAAK,CAAC,CAAA;YACxB,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js

@@ -15,6 +15,15 @@ const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
     },
+    marginBottom: {
+        marginBottom: 16,
+    },
+    ridField: {
+        width: 150,
+    },
+    infoText: {
+        marginTop: 20,
+    },
 });
 const NCBIBlastRIDPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
     const { classes } = useStyles();
@@ -24,23 +33,22 @@ const NCBIBlastRIDPanel = observer(function ({ handleClose, feature, model, chil
     const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] = useState('clustalo');
     const { options, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, } = useTranscriptSelection({ feature, view });
     const e = proteinSequenceError ?? launchViewError;
-    const style = { width: 150 };
     const trimmedRid = rid.trim();
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             children,
             e ? React.createElement(ErrorMessage, { error: e }) : null,
-            React.createElement(Typography, { variant: "body2", style: { marginBottom: 16 } }, "Enter the RID (Request ID) from a previously submitted NCBI BLAST query. You can find the RID in the BLAST results page URL or at the top of the results page. RIDs are typically valid for 24-36 hours after submission."),
-            React.createElement(TextField2, { variant: "outlined", label: "BLAST RID", placeholder: "e.g., ABC12345", fullWidth: true, style: { marginBottom: 16 }, value: rid, onChange: event => {
+            React.createElement(Typography, { variant: "body2", className: classes.marginBottom }, "Enter the RID (Request ID) from a previously submitted NCBI BLAST query. You can find the RID in the BLAST results page URL or at the top of the results page. RIDs are typically valid for 24-36 hours after submission."),
+            React.createElement(TextField2, { variant: "outlined", label: "BLAST RID", placeholder: "e.g., ABC12345", fullWidth: true, className: classes.marginBottom, value: rid, onChange: event => {
                     setRid(event.target.value);
                 } }),
-            trimmedRid ? (React.createElement(Typography, { variant: "body2", style: { marginBottom: 16 } },
+            trimmedRid ? (React.createElement(Typography, { variant: "body2", className: classes.marginBottom },
                 React.createElement(ExternalLink, { href: `${baseUrl}?CMD=Get&RID=${trimmedRid}` }, "View BLAST results on NCBI"))) : null,
-            React.createElement(TextField2, { variant: "outlined", label: "MSA Algorithm", style: style, select: true, value: selectedMsaAlgorithm, onChange: event => {
+            React.createElement(TextField2, { variant: "outlined", label: "MSA Algorithm", className: classes.ridField, select: true, value: selectedMsaAlgorithm, onChange: event => {
                     setSelectedMsaAlgorithm(event.target.value);
                 } }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
             React.createElement(TranscriptSelector, { feature: feature, options: options, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
-            React.createElement(Typography, { style: { marginTop: 20 } }, "This will fetch the BLAST results for the provided RID and run them through a multiple sequence alignment. The protein sequence from the selected transcript will be added as the query sequence in the MSA.")),
+            React.createElement(Typography, { className: classes.infoText }, "This will fetch the BLAST results for the provided RID and run them through a multiple sequence alignment. The protein sequence from the selected transcript will be added as the query sequence in the MSA.")),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
                     try {
@@ -62,12 +70,12 @@ const NCBIBlastRIDPanel = observer(function ({ handleClose, feature, model, chil
                                 rid: trimmedRid,
                             },
                         });
+                        handleClose();
                     }
                     catch (e) {
                         console.error(e);
                         setLaunchViewError(e);
                     }
-                    handleClose();
                 }, disabled: !proteinSequence || !trimmedRid }, "Submit"),
             React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
                     handleClose();

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js.map

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js

@@ -1,15 +1,22 @@
 import React, { useState } from 'react';
 import { Button, Dialog, DialogActions, DialogContent, DialogTitle, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
 import { BASE_BLAST_URL } from './consts';
 import TextField2 from '../../../components/TextField2';
+const useStyles = makeStyles()({
+    urlField: {
+        minWidth: 300,
+    },
+});
 export default function NCBISettingsDialog({ handleClose, baseUrl, }) {
+    const { classes } = useStyles();
     const [tempBaseUrl, setTempBaseUrl] = useState(baseUrl);
     return (React.createElement(Dialog, { open: true, maxWidth: "lg", onClose: () => {
             handleClose();
         } },
         React.createElement(DialogTitle, null, "BLAST Settings"),
         React.createElement(DialogContent, null,
-            React.createElement(TextField2, { autoFocus: true, margin: "dense", label: "BLAST Base URL", fullWidth: true, variant: "outlined", value: tempBaseUrl, style: { minWidth: '300px' }, onChange: e => {
+            React.createElement(TextField2, { autoFocus: true, margin: "dense", label: "BLAST Base URL", fullWidth: true, variant: "outlined", value: tempBaseUrl, className: classes.urlField, onChange: e => {
                     setTempBaseUrl(e.target.value);
                 } }),
             React.createElement(Button, { variant: "contained", onClick: () => {

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js.map

@@ -1 +1 @@
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+{"version":3,"file":"NCBISettingsDialog.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EACL,MAAM,EACN,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,GACZ,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,cAAc,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAEvD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,QAAQ,EAAE;QACR,QAAQ,EAAE,GAAG;KACd;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,WAAW,EACX,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;IACvD,OAAO,CACL,oBAAC,MAAM,IACL,IAAI,QACJ,QAAQ,EAAC,IAAI,EACb,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC;QAED,oBAAC,WAAW,yBAA6B;QACzC,oBAAC,aAAa;YACZ,oBAAC,UAAU,IACT,SAAS,QACT,MAAM,EAAC,OAAO,EACd,KAAK,EAAC,gBAAgB,EACtB,SAAS,QACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,WAAW,EAClB,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,QAAQ,EAAE,CAAC,CAAC,EAAE;oBACZ,cAAc,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAChC,CAAC,GACD;YACF,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,cAAc,CAAC,cAAc,CAAC,CAAA;gBAChC,CAAC,YAGM,CACK;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,CAAC,WAAW,CAAC,CAAA;gBAC1B,CAAC,WAGM,CACK,CACT,CACV,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.d.ts

@@ -0,0 +1,7 @@
+export declare function useCachedBlastResults(geneIds: string[]): {
+    results: any[];
+    error: any;
+    isLoading: boolean;
+    handleDelete: (id: string) => Promise<void>;
+    handleClearAll: () => Promise<void>;
+};

package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js

@@ -0,0 +1,32 @@
+import useSWR from 'swr';
+import { clearAllCachedResults, deleteCachedResult, getAllCachedResults, } from '../../../utils/blastCache';
+const swrConfig = {
+    revalidateOnFocus: false,
+    revalidateOnReconnect: false,
+    revalidateIfStale: false,
+    refreshWhenHidden: false,
+    refreshWhenOffline: false,
+    shouldRetryOnError: false,
+};
+export function useCachedBlastResults(geneIds) {
+    const { data: results, error, mutate, } = useSWR(`cached-blast-${geneIds.join(',')}`, async () => {
+        const cached = await getAllCachedResults();
+        return cached.filter(r => r.geneId && geneIds.includes(r.geneId));
+    }, swrConfig);
+    const handleDelete = async (id) => {
+        await deleteCachedResult(id);
+        await mutate(results => results?.filter(result => result.id !== id) ?? [], false);
+    };
+    const handleClearAll = async () => {
+        await clearAllCachedResults();
+        await mutate([], false);
+    };
+    return {
+        results: results ?? [],
+        error,
+        isLoading: !results && !error,
+        handleDelete,
+        handleClearAll,
+    };
+}
+//# sourceMappingURL=useCachedBlastResults.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"useCachedBlastResults.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,KAAK,CAAA;AAExB,OAAO,EACL,qBAAqB,EACrB,kBAAkB,EAClB,mBAAmB,GACpB,MAAM,2BAA2B,CAAA;AAElC,MAAM,SAAS,GAAG;IAChB,iBAAiB,EAAE,KAAK;IACxB,qBAAqB,EAAE,KAAK;IAC5B,iBAAiB,EAAE,KAAK;IACxB,iBAAiB,EAAE,KAAK;IACxB,kBAAkB,EAAE,KAAK;IACzB,kBAAkB,EAAE,KAAK;CAC1B,CAAA;AAED,MAAM,UAAU,qBAAqB,CAAC,OAAiB;IACrD,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,KAAK,EACL,MAAM,GACP,GAAG,MAAM,CACR,gBAAgB,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EACnC,KAAK,IAAI,EAAE;QACT,MAAM,MAAM,GAAG,MAAM,mBAAmB,EAAE,CAAA;QAC1C,OAAO,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,IAAI,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;IACnE,CAAC,EACD,SAAS,CACV,CAAA;IAED,MAAM,YAAY,GAAG,KAAK,EAAE,EAAU,EAAE,EAAE;QACxC,MAAM,kBAAkB,CAAC,EAAE,CAAC,CAAA;QAC5B,MAAM,MAAM,CACV,OAAO,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,CAAC,IAAI,EAAE,EAC5D,KAAK,CACN,CAAA;IACH,CAAC,CAAA;IAED,MAAM,cAAc,GAAG,KAAK,IAAI,EAAE;QAChC,MAAM,qBAAqB,EAAE,CAAA;QAC7B,MAAM,MAAM,CAAC,EAAE,EAAE,KAAK,CAAC,CAAA;IACzB,CAAC,CAAA;IAED,OAAO;QACL,OAAO,EAAE,OAAO,IAAI,EAAE;QACtB,KAAK;QACL,SAAS,EAAE,CAAC,OAAO,IAAI,CAAC,KAAK;QAC7B,YAAY;QACZ,cAAc;KACf,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -17,6 +17,9 @@ const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
     },
+    selectedContainer: {
+        marginTop: 50,
+    },
 });
 const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
     const session = getSession(model);
@@ -55,7 +58,7 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
             React.createElement(TextField2, { select: true, label: "Select MSA dataset", value: selectedDatasetId, onChange: event => {
                     setSelectedDatasetId(event.target.value);
                 } }, datasets?.map(d => (React.createElement(MenuItem, { key: d.datasetId, value: d.datasetId }, d.name)))),
-            selectedDataset ? (React.createElement("div", { style: { marginTop: 50 } },
+            selectedDataset ? (React.createElement("div", { className: classes.selectedContainer },
                 !msaListLoading && msaDataLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading MSA for (${selectedId})` })) : null,
                 msaListLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading available MSAs for (${selectedDataset.name})` })) : null,
                 msaList ? (React.createElement("div", null,
@@ -86,7 +89,9 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
                         setViewError(e);
                     }
                 } }, "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

@@ -1 +1 @@
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+{"version":3,"file":"PreLoadedMSADataPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAC/E,OAAO,EAAE,iBAAiB,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC1E,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9E,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,MAAM,MAAM,KAAK,CAAA;AACxB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAC/C,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAClE,OAAO,EAAE,QAAQ,EAAE,MAAM,UAAU,CAAA;AACnC,OAAO,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAA;AACvD,OAAO,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAA;AAMnE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,iBAAiB,EAAE;QACjB,SAAS,EAAE,EAAE;KACd;CACF,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EACtC,KAAK,EACL,OAAO,EACP,WAAW,GAKZ;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IAC9B,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,EAAW,CAAA;IAErD,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;IAC3B,MAAM,QAAQ,GAAG,cAAc,CAAC,OAAO,EAAE,CAAC,KAAK,EAAE,UAAU,CAAC,CAE/C,CAAA;IACb,MAAM,CAAC,iBAAiB,EAAE,oBAAoB,CAAC,GAAG,QAAQ,CACxD,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,SAAS,CACzB,CAAA;IACD,MAAM,eAAe,GAAG,QAAQ,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,KAAK,iBAAiB,CAAC,CAAA;IAC9E,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,SAAS,EAAE,cAAc,EACzB,KAAK,EAAE,iBAAiB,GACzB,GAAG,MAAM,CACR,iBAAiB,CAAC,CAAC,CAAC,GAAG,iBAAiB,WAAW,CAAC,CAAC,CAAC,eAAe,EACrE,GAAG,EAAE,CACH,eAAe;QACb,CAAC,CAAC,YAAY,CAAC;YACX,MAAM,EAAE,eAAe,CAAC,OAAO;YAC/B,aAAa;SACd,CAAC;QACJ,CAAC,CAAC,SAAS,EACf,QAAQ,CACT,CAAA;IAED,MAAM,EACJ,OAAO,EAAE,WAAW,EACpB,UAAU,EACV,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,EAAE,oBAAoB,GAC5B,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAC,CAAA;IAEhE,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,SAAS,EAAE,cAAc,EACzB,KAAK,EAAE,iBAAiB,GACzB,GAAG,MAAM,CACR,UAAU,IAAI,iBAAiB;QAC7B,CAAC,CAAC,GAAG,iBAAiB,IAAI,UAAU,IAAI,OAAO,EAAE,MAAM,MAAM;QAC7D,CAAC,CAAC,UAAU,EACd,GAAG,EAAE,CACH,UAAU,IAAI,eAAe,IAAI,OAAO;QACtC,CAAC,CAAC,QAAQ,CAAC;YACP,KAAK,EAAE,UAAU;YACjB,MAAM,EAAE,eAAe,CAAC,OAAO;YAC/B,aAAa;SACd,CAAC;QACJ,CAAC,CAAC,SAAS,EACf,QAAQ,CACT,CAAA;IAED,MAAM,CAAC,GACL,iBAAiB,IAAI,iBAAiB,IAAI,oBAAoB,IAAI,SAAS,CAAA;IAC7E,IAAI,CAAC,EAAE,CAAC;QACN,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IAClB,CAAC;IACD,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YAEtC,oBAAC,UAAU,IACT,MAAM,QACN,KAAK,EAAC,oBAAoB,EAC1B,KAAK,EAAE,iBAAiB,EACxB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,oBAAoB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC1C,CAAC,IAEA,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAClB,oBAAC,QAAQ,IAAC,GAAG,EAAE,CAAC,CAAC,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,SAAS,IAC3C,CAAC,CAAC,IAAI,CACE,CACZ,CAAC,CACS;YAEZ,eAAe,CAAC,CAAC,CAAC,CACjB,6BAAK,SAAS,EAAE,OAAO,CAAC,iBAAiB;gBACtC,CAAC,cAAc,IAAI,cAAc,CAAC,CAAC,CAAC,CACnC,oBAAC,eAAe,IACd,OAAO,EAAC,IAAI,EACZ,OAAO,EAAE,oBAAoB,UAAU,GAAG,GAC1C,CACH,CAAC,CAAC,CAAC,IAAI;gBACP,cAAc,CAAC,CAAC,CAAC,CAChB,oBAAC,eAAe,IACd,OAAO,EAAC,IAAI,EACZ,OAAO,EAAE,+BAA+B,eAAe,CAAC,IAAI,GAAG,GAC/D,CACH,CAAC,CAAC,CAAC,IAAI;gBAEP,OAAO,CAAC,CAAC,CAAC,CACT;oBACE,oBAAC,aAAa,IAAC,IAAI,EAAE,eAAe,CAAC,WAAW,GAAI;oBACpD,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,EAChB,OAAO,EAAE,WAAW,EACpB,UAAU,EAAE,UAAU,EACtB,kBAAkB,EAAE,kBAAkB,EACtC,kBAAkB,EAAE,aAAa,EACjC,eAAe,EAAE,eAAe,EAChC,QAAQ,EAAE,OAAO,GACjB,CACE,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAC,CAAC,CAAC,IAAI,CACM;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,QAAQ,EAAE,CAAC,kBAAkB,IAAI,CAAC,OAAO,EAAE,MAAM,EACjD,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,CAAC;wBACH,IAAI,CAAC,kBAAkB,IAAI,CAAC,OAAO,EAAE,CAAC;4BACpC,OAAM;wBACR,CAAC;wBACD,MAAM,YAAY,GAAG,GAAG,UAAU,IAAI,aAAa,CAAC,CAAC,CAAC,EAAE,CAAA;wBACxD,uBAAuB,CAAC;4BACtB,OAAO;4BACP,YAAY,EAAE,kBAAkB,CAAC,kBAAkB,CAAC;4BACpD,IAAI;4BACJ,YAAY;4BACZ,OAAO,EAAE,kBAAkB;4BAC3B,IAAI,EAAE;gCACJ,GAAG,EAAE,OAAO;qCACT,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;qCACjD,IAAI,CAAC,IAAI,CAAC;6BACd;yBACF,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,YAAY,CAAC,CAAC,CAAC,CAAA;oBACjB,CAAC;gBACH,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

package/dist/LaunchMsaView/components/TabPanel.js

@@ -1,6 +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)));
+    return (React.createElement("div", { role: "tabpanel", hidden: value !== index, ...other }, value === index ? React.createElement("div", null, children) : null));
 }
 //# sourceMappingURL=TabPanel.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"TabPanel.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/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"}
+{"version":3,"file":"TabPanel.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/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,CAAC,CAAC,CAAC,iCAAM,QAAQ,CAAO,CAAC,CAAC,CAAC,IAAI,CAC3C,CACP,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/TranscriptSelector.js

@@ -10,6 +10,10 @@ const useStyles = makeStyles()({
     minWidth: {
         minWidth: 300,
     },
+    centered: {
+        alignContent: 'center',
+        marginLeft: 20,
+    },
 });
 export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, onTranscriptChange, proteinSequence, validIds, }) {
     const { classes } = useStyles();
@@ -32,12 +36,12 @@ export default function TranscriptSelector({ feature, options, selectedId, selec
                     mod ? ` (possible fragment)` : '',
                     validIds ? (inSet ? ' (has data)' : ' (no data)') : ''));
             })),
-            React.createElement("div", { style: { alignContent: 'center', marginLeft: 20 } },
+            React.createElement("div", { className: classes.centered },
                 React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
                         setShowSequence(!showSequence);
                     } }, showSequence ? 'Hide sequence' : 'Show sequence'))),
-        showSequence && (React.createElement(ReadOnlyTextField2, { value: proteinSequence
+        showSequence ? (React.createElement(ReadOnlyTextField2, { value: proteinSequence
                 ? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
-                : 'Loading...' }))));
+                : 'Loading...' })) : null));
 }
 //# sourceMappingURL=TranscriptSelector.js.map

package/dist/LaunchMsaView/components/TranscriptSelector.js.map

@@ -1 +1 @@
-{"version":3,"file":"TranscriptSelector.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TranscriptSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAC3D,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,kBAAkB,MAAM,qCAAqC,CAAA;AACpE,OAAO,EACL,gBAAgB,EAChB,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,mBAAmB,GACpB,MAAM,SAAS,CAAA;AAIhB,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM;KAChB;IACD,QAAQ,EAAE;QACR,QAAQ,EAAE,GAAG;KACd;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,OAAO,EACP,OAAO,EACP,UAAU,EACV,kBAAkB,EAClB,kBAAkB,EAClB,eAAe,EACf,QAAQ,GAST;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEvD,OAAO,CACL;QACE,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,qBAAqB,kBAAkB,CAAC,OAAO,CAAC,EAAE,EACzD,MAAM,QACN,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,KAAK,EAAE,UAAU,EACjB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC,IAEA,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACjB,MAAM,KAAK,GAAG,QAAQ;oBACpB,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,gBAAgB,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC;oBAChD,CAAC,CAAC,IAAI,CAAA;gBACR,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,mBAAmB,CAAC,GAAG,CAAC,CAAA;gBAC7C,OAAO,CACL,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,EAAE,QAAQ,EAAE,CAAC,KAAK;oBACzD,wBAAwB,CAAC,GAAG,CAAC;;oBAAI,GAAG;;oBAAM,GAAG;oBAC7C,GAAG,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE;oBACjC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,EAAE,CAC9C,CACZ,CAAA;YACH,CAAC,CAAC,CACQ;YACZ,6BAAK,KAAK,EAAE,EAAE,YAAY,EAAE,QAAQ,EAAE,UAAU,EAAE,EAAE,EAAE;gBACpD,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;wBACZ,eAAe,CAAC,CAAC,YAAY,CAAC,CAAA;oBAChC,CAAC,IAEA,YAAY,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,eAAe,CAC1C,CACL,CACF;QAEL,YAAY,IAAI,CACf,oBAAC,kBAAkB,IACjB,KAAK,EACH,eAAe;gBACb,CAAC,CAAC,IAAI,wBAAwB,CAAC,kBAAkB,CAAC,KAAK,eAAe,EAAE;gBACxE,CAAC,CAAC,YAAY,GAElB,CACH,CACA,CACJ,CAAA;AACH,CAAC"}
+{"version":3,"file":"TranscriptSelector.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TranscriptSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAC3D,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,kBAAkB,MAAM,qCAAqC,CAAA;AACpE,OAAO,EACL,gBAAgB,EAChB,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,mBAAmB,GACpB,MAAM,SAAS,CAAA;AAIhB,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM;KAChB;IACD,QAAQ,EAAE;QACR,QAAQ,EAAE,GAAG;KACd;IACD,QAAQ,EAAE;QACR,YAAY,EAAE,QAAQ;QACtB,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,OAAO,EACP,OAAO,EACP,UAAU,EACV,kBAAkB,EAClB,kBAAkB,EAClB,eAAe,EACf,QAAQ,GAST;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEvD,OAAO,CACL;QACE,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,qBAAqB,kBAAkB,CAAC,OAAO,CAAC,EAAE,EACzD,MAAM,QACN,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,KAAK,EAAE,UAAU,EACjB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC,IAEA,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACjB,MAAM,KAAK,GAAG,QAAQ;oBACpB,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,gBAAgB,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC;oBAChD,CAAC,CAAC,IAAI,CAAA;gBACR,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,mBAAmB,CAAC,GAAG,CAAC,CAAA;gBAC7C,OAAO,CACL,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,EAAE,QAAQ,EAAE,CAAC,KAAK;oBACzD,wBAAwB,CAAC,GAAG,CAAC;;oBAAI,GAAG;;oBAAM,GAAG;oBAC7C,GAAG,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE;oBACjC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,EAAE,CAC9C,CACZ,CAAA;YACH,CAAC,CAAC,CACQ;YACZ,6BAAK,SAAS,EAAE,OAAO,CAAC,QAAQ;gBAC9B,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;wBACZ,eAAe,CAAC,CAAC,YAAY,CAAC,CAAA;oBAChC,CAAC,IAEA,YAAY,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,eAAe,CAC1C,CACL,CACF;QAEL,YAAY,CAAC,CAAC,CAAC,CACd,oBAAC,kBAAkB,IACjB,KAAK,EACH,eAAe;gBACb,CAAC,CAAC,IAAI,wBAAwB,CAAC,kBAAkB,CAAC,KAAK,eAAe,EAAE;gBACxE,CAAC,CAAC,YAAY,GAElB,CACH,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/useTranscriptSelection.js

@@ -1,31 +1,32 @@
-import { useEffect, useMemo, useState } from 'react';
+import { useMemo, useState } from 'react';
 import { featureMatchesId, getId, getSortedTranscriptFeatures } from '../util';
 import { useFeatureSequence } from './useFeatureSequence';
 function featureInValidIds(feature, validIds) {
     return validIds.some(id => featureMatchesId(feature, id));
 }
+function findValidSelection(currentId, options, validIds) {
+    if (!validIds || validIds.length === 0) {
+        return undefined;
+    }
+    const currentFeature = options.find(opt => getId(opt) === currentId);
+    if (!currentFeature || featureInValidIds(currentFeature, validIds)) {
+        return undefined;
+    }
+    const validOption = options.find(opt => featureInValidIds(opt, validIds));
+    return validOption ? getId(validOption) : undefined;
+}
 export function useTranscriptSelection({ feature, view, validIds, }) {
     const options = useMemo(() => getSortedTranscriptFeatures(feature), [feature]);
     const [selectedId, setSelectedId] = useState(() => getId(options[0]));
-    const selectedTranscript = options.find(val => getId(val) === selectedId);
+    const validatedSelectedId = findValidSelection(selectedId, options, validIds) || selectedId;
+    const selectedTranscript = options.find(val => getId(val) === validatedSelectedId);
     const { proteinSequence, error } = useFeatureSequence({
         view,
         feature: selectedTranscript,
     });
-    useEffect(() => {
-        if (validIds && validIds.length > 0) {
-            const currentFeature = options.find(opt => getId(opt) === selectedId);
-            if (currentFeature && !featureInValidIds(currentFeature, validIds)) {
-                const validOption = options.find(opt => featureInValidIds(opt, validIds));
-                if (validOption) {
-                    setSelectedId(getId(validOption));
-                }
-            }
-        }
-    }, [validIds, options, selectedId]);
     return {
         options,
-        selectedId,
+        selectedId: validatedSelectedId,
         setSelectedId,
         selectedTranscript,
         proteinSequence,

package/dist/LaunchMsaView/components/useTranscriptSelection.js.map

@@ -1 +1 @@
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+{"version":3,"file":"useTranscriptSelection.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/useTranscriptSelection.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEzC,OAAO,EAAE,gBAAgB,EAAE,KAAK,EAAE,2BAA2B,EAAE,MAAM,SAAS,CAAA;AAC9E,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAA;AAIzD,SAAS,iBAAiB,CAAC,OAAgB,EAAE,QAAkB;IAC7D,OAAO,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,gBAAgB,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;AAC3D,CAAC;AAED,SAAS,kBAAkB,CACzB,SAAiB,EACjB,OAAkB,EAClB,QAA8B;IAE9B,IAAI,CAAC,QAAQ,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvC,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,SAAS,CAAC,CAAA;IACpE,IAAI,CAAC,cAAc,IAAI,iBAAiB,CAAC,cAAc,EAAE,QAAQ,CAAC,EAAE,CAAC;QACnE,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,iBAAiB,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC,CAAA;IACzE,OAAO,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AACrD,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,EACrC,OAAO,EACP,IAAI,EACJ,QAAQ,GAKT;IACC,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,2BAA2B,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;IAC9E,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrE,MAAM,mBAAmB,GACvB,kBAAkB,CAAC,UAAU,EAAE,OAAO,EAAE,QAAQ,CAAC,IAAI,UAAU,CAAA;IACjE,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CACrC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,mBAAmB,CAC1C,CAAA;IACD,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,kBAAkB,CAAC;QACpD,IAAI;QACJ,OAAO,EAAE,kBAAkB;KAC5B,CAAC,CAAA;IAEF,OAAO;QACL,OAAO;QACP,UAAU,EAAE,mBAAmB;QAC/B,aAAa;QACb,kBAAkB;QAClB,eAAe;QACf,KAAK;QACL,QAAQ;KACT,CAAA;AACH,CAAC"}

package/dist/MsaViewPanel/afterCreateAutoruns.js

@@ -2,7 +2,7 @@ import { getSession } from '@jbrowse/core/util';
 import { doLaunchBlast } from './doLaunchBlast';
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
 import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
-import { gappedToUngappedPosition } from './structureConnection';
+import { gappedToUngappedPosition, isProteinView } from './structureConnection';
 import { getUniprotIdFromAlphaFoldUrl } from './util';
 export function loadStoredData(self) {
     const { dataStoreId, rows } = self;
@@ -150,7 +150,7 @@ export function highlightConnectedStructures(self) {
         return;
     }
     for (const conn of connectedProteinViews) {
-        const structure = conn.proteinView?.structures?.[conn.structureIdx];
+        const structure = conn.proteinView.structures[conn.structureIdx];
         if (!structure) {
             continue;
         }
@@ -177,25 +177,27 @@ export function highlightConnectedStructures(self) {
     }
 }
 export function autoConnectStructures(self) {
-    const { views } = getSession(self);
+    const views = getSession(self).views;
     const { connectedViewId, uniprotId, rows, connectedStructures } = self;
     if (!uniprotId || rows.length === 0) {
         return;
     }
     for (const view of views) {
-        const v = view;
-        if (v.type !== 'ProteinView' || !v.structures) {
+        if (!isProteinView(view)) {
             continue;
         }
-        for (let structureIdx = 0; structureIdx < v.structures.length; structureIdx++) {
-            const structure = v.structures[structureIdx];
+        for (let structureIdx = 0; structureIdx < view.structures.length; structureIdx++) {
+            const structure = view.structures[structureIdx];
+            if (!structure) {
+                continue;
+            }
             if (structure.connectedViewId !== connectedViewId) {
                 continue;
             }
             if (structure.uniprotId !== uniprotId) {
                 continue;
             }
-            const alreadyConnected = connectedStructures.some(c => c.proteinViewId === v.id && c.structureIdx === structureIdx);
+            const alreadyConnected = connectedStructures.some(c => c.proteinViewId === view.id && c.structureIdx === structureIdx);
             if (alreadyConnected) {
                 continue;
             }
@@ -203,7 +205,7 @@ export function autoConnectStructures(self) {
                 continue;
             }
             try {
-                self.connectToStructure(v.id, structureIdx);
+                self.connectToStructure(view.id, structureIdx);
             }
             catch (e) {
                 console.error('Failed to auto-connect to ProteinView:', e);
@@ -212,18 +214,17 @@ export function autoConnectStructures(self) {
     }
 }
 export function observeProteinHighlights(self) {
-    const { views } = getSession(self);
+    const views = getSession(self).views;
     const { connectedViewId, transcriptToMsaMap, querySeqName } = self;
     if (!connectedViewId || !transcriptToMsaMap) {
         return;
     }
-    const columns = [];
+    const columns = new Set();
     for (const view of views) {
-        const v = view;
-        if (v.type !== 'ProteinView' || !v.structures) {
+        if (!isProteinView(view)) {
             continue;
         }
-        for (const structure of v.structures) {
+        for (const structure of view.structures) {
             if (structure.connectedViewId !== connectedViewId) {
                 continue;
             }
@@ -237,15 +238,13 @@ export function observeProteinHighlights(self) {
                     const proteinPos = g2p[coord];
                     if (proteinPos !== undefined) {
                         const col = self.seqPosToGlobalCol(querySeqName, proteinPos);
-                        if (!columns.includes(col)) {
-                            columns.push(col);
-                        }
+                        columns.add(col);
                     }
                 }
             }
         }
     }
-    const visibleColumns = columns
+    const visibleColumns = Array.from(columns)
         .map(col => self.globalColToVisibleCol(col))
         .filter((col) => col !== undefined);
     self.setHighlightedColumns(visibleColumns.length > 0 ? visibleColumns : undefined);

package/dist/MsaViewPanel/afterCreateAutoruns.js.map

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