npm - jbrowse-plugin-msaview - Versions diffs - 2.3.5 → 2.4.0 - Mend

jbrowse-plugin-msaview 2.3.5 → 2.4.0

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 (148) hide show

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js CHANGED Viewed

@@ -7,7 +7,7 @@ import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import CachedBlastResults from './CachedBlastResults';
 import { blastLaunchView } from './blastLaunchView';
-import { msaAlgorithms } from './consts';
+import { blastDatabaseOptions, blastPrograms, msaAlgorithms } from './consts';
 import { useCachedBlastResults } from './useCachedBlastResults';
 import TextField2 from '../../../components/TextField2';
 import { getGeneDisplayName, getGeneIdentifiers, getTranscriptDisplayName, } from '../../util';
@@ -34,8 +34,6 @@ const useStyles = makeStyles()({
         marginTop: 20,
     },
 });
-const blastDatabaseOptions = ['nr', 'nr_cluster_seq'];
-const blastPrograms = ['blastp', 'quick-blastp'];
 const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
     const { classes } = useStyles();
     const view = getContainingView(model);
@@ -52,8 +50,7 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
             children,
             e ? React.createElement(ErrorMessage, { error: e }) : null,
             React.createElement(TextField2, { variant: "outlined", label: "BLAST database", className: classes.selectField, select: true, value: selectedBlastDatabase, onChange: event => {
-                    const newDb = event.target
-                        .value;
+                    const newDb = event.target.value;
                     setSelectedBlastDatabase(newDb);
                     if (newDb === 'nr_cluster_seq') {
                         setSelectedBlastProgram('blastp');
@@ -94,14 +91,16 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
                                 proteinSequence,
                             },
                         });
+                        handleClose();
                     }
                     catch (e) {
                         console.error(e);
                         setLaunchViewError(e);
                     }
-                    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 NCBIBlastAutomaticPanel;
 //# sourceMappingURL=NCBIBlastAutomaticPanel.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"NCBIBlastAutomaticPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,cAAc,MAAM,gCAAgC,CAAA;AAC3D,OAAO,EACL,SAAS,EACT,gBAAgB,EAChB,gBAAgB,EAChB,MAAM,EACN,aAAa,EACb,aAAa,EACb,QAAQ,EACR,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAA;AACnD,OAAO,EAAE,oBAAoB,EAAE,aAAa,EAAE,aAAa,EAAE,MAAM,UAAU,CAAA;AAC7E,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EACL,kBAAkB,EAClB,kBAAkB,EAClB,wBAAwB,GACzB,MAAM,YAAY,CAAA;AACnB,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAMlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,WAAW,EAAE;QACX,KAAK,EAAE,GAAG;KACX;IACD,sBAAsB,EAAE;QACtB,OAAO,EAAE,MAAM;KAChB;IACD,iBAAiB,EAAE;QACjB,UAAU,EAAE,CAAC;QACb,YAAY,EAAE,QAAQ;KACvB;IACD,sBAAsB,EAAE;QACtB,SAAS,EAAE,EAAE;KACd;IACD,QAAQ,EAAE;QACR,SAAS,EAAE,EAAE;KACd;CACF,CAAC,CAAA;AAEF,MAAM,uBAAuB,GAAG,QAAQ,CAAC,UAAU,EACjD,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,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,QAAQ,EAAW,CAAA;IACjE,MAAM,CAAC,qBAAqB,EAAE,wBAAwB,CAAC,GACrD,QAAQ,CAAgB,IAAI,CAAC,CAAA;IAC/B,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GACnD,QAAQ,CAAe,UAAU,CAAC,CAAA;IACpC,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GACnD,QAAQ,CAAe,cAAc,CAAC,CAAA;IAExC,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,kBAAkB,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;IACrE,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,kBAAkB,EAAE,GACzD,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAEhC,MAAM,EACJ,OAAO,EACP,UAAU,EACV,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,EAAE,oBAAoB,GAC5B,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAC7C,MAAM,CAAC,GAAG,oBAAoB,IAAI,eAAe,IAAI,kBAAkB,CAAA;IACvE,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,QAAQ;YACR,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YACtC,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,gBAAgB,EACtB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,MAAM,QACN,KAAK,EAAE,qBAAqB,EAC5B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,MAAM,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,KAAsB,CAAA;oBACjD,wBAAwB,CAAC,KAAK,CAAC,CAAA;oBAC/B,IAAI,KAAK,KAAK,gBAAgB,EAAE,CAAC;wBAC/B,uBAAuB,CAAC,QAAQ,CAAC,CAAA;oBACnC,CAAC;gBACH,CAAC,IAEA,oBAAoB,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAC/B,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;YAEb,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,eAAe,EACrB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,MAAM,QACN,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,uBAAuB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAqB,CAAC,CAAA;gBAC7D,CAAC,IAEA,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACxB,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;YAEb,6BAAK,SAAS,EAAE,OAAO,CAAC,sBAAsB;gBAC5C,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,eAAe,EACrB,QAAQ,EAAE,qBAAqB,KAAK,gBAAgB,EACpD,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,MAAM,QACN,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,uBAAuB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAqB,CAAC,CAAA;oBAC7D,CAAC,IAEA,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACxB,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;gBACZ,qBAAqB,KAAK,gBAAgB,CAAC,CAAC,CAAC,CAC5C,oBAAC,UAAU,IACT,OAAO,EAAC,WAAW,EACnB,SAAS,EAAE,OAAO,CAAC,iBAAiB,4CAGzB,CACd,CAAC,CAAC,CAAC,IAAI,CACJ;YAEN,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;YAEF,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,QAAQ,kiBAS1B;YAEZ,aAAa,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAC1B,oBAAC,SAAS,IAAC,SAAS,EAAE,OAAO,CAAC,sBAAsB;gBAClD,oBAAC,gBAAgB,IAAC,UAAU,EAAE,oBAAC,cAAc,OAAG;oBAC9C,oBAAC,UAAU,iCAAoC,CAC9B;gBACnB,oBAAC,gBAAgB;oBACf,oBAAC,kBAAkB,IACjB,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,WAAW,EACxB,OAAO,EAAE,OAAO,GAChB,CACe,CACT,CACb,CAAC,CAAC,CAAC,IAAI,CACM;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,CAAC;wBACH,IAAI,CAAC,kBAAkB,EAAE,CAAC;4BACxB,OAAM;wBACR,CAAC;wBACD,kBAAkB,CAAC,SAAS,CAAC,CAAA;wBAC7B,eAAe,CAAC;4BACd,OAAO,EAAE,kBAAkB;4BAC3B,IAAI;4BACJ,YAAY,EAAE,WAAW,kBAAkB,CAAC,OAAO,CAAC,MAAM,wBAAwB,CAAC,kBAAkB,CAAC,EAAE;4BACxG,WAAW,EAAE;gCACX,OAAO;gCACP,YAAY,EAAE,oBAAoB;gCAClC,aAAa,EAAE,qBAAqB;gCACpC,YAAY,EAAE,oBAAoB;gCAClC,kBAAkB;gCAClB,eAAe;6BAChB;yBACF,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,kBAAkB,CAAC,CAAC,CAAC,CAAA;oBACvB,CAAC;gBACH,CAAC,EACD,QAAQ,EAAE,CAAC,eAAe,aAGnB;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;A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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js CHANGED Viewed

@@ -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();
@@ -36,13 +39,10 @@ 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();
-                } }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
                 } }, "Close"))));
 });
 export default NCBIBlastManualPanel;

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

	@@ -1 +1 @@
1	- {"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;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,~~KAAK~~,EAAE,~~EAAE~~,~~SAAS~~,~~EAAE~~,~~EAAE~~,~~EAAE,2UAMvB,~~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"}
1	+ {"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,YAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}

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

@@ -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 CHANGED Viewed

	@@ -1 +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"}
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;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 CHANGED Viewed

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"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/blastLaunchView.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import type { JBrowsePluginMsaViewModel } from '../../../MsaViewPanel/model';
+import type { BlastParams } from '../../../MsaViewPanel/model';
 import type { CachedBlastResult } from '../../../utils/blastCache';
 import type { Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
@@ -6,10 +6,10 @@ export declare function blastLaunchView({ newViewTitle, view, feature, blastPara
     newViewTitle: string;
     view: LinearGenomeViewModel;
     feature: Feature;
-    blastParams: Record<string, unknown>;
-}): JBrowsePluginMsaViewModel;
+    blastParams: BlastParams;
+}): void;
 export declare function blastLaunchViewFromCache({ newViewTitle, view, cached, }: {
     newViewTitle: string;
     view: LinearGenomeViewModel;
     cached: CachedBlastResult;
-}): JBrowsePluginMsaViewModel;
+}): void;

package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js CHANGED Viewed

@@ -1,6 +1,6 @@
 import { getSession } from '@jbrowse/core/util';
 export function blastLaunchView({ newViewTitle, view, feature, blastParams, }) {
-    return getSession(view).addView('MsaView', {
+    getSession(view).addView('MsaView', {
         type: 'MsaView',
         displayName: newViewTitle,
         connectedViewId: view.id,
@@ -12,7 +12,7 @@ export function blastLaunchView({ newViewTitle, view, feature, blastParams, }) {
     });
 }
 export function blastLaunchViewFromCache({ newViewTitle, view, cached, }) {
-    return getSession(view).addView('MsaView', {
+    getSession(view).addView('MsaView', {
         type: 'MsaView',
         displayName: newViewTitle,
         connectedViewId: view.id,

package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"blastLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAO/C,MAAM,UAAU,eAAe,CAAC,EAC9B,YAAY,EACZ,IAAI,EACJ,OAAO,EACP,WAAW,GAMZ;IACC,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QAClC,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;QAClC,eAAe,EAAE,IAAI;QACrB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,WAAW;KACZ,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,YAAY,EACZ,IAAI,EACJ,MAAM,GAKP;IACC,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QAClC,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,eAAe,EAAE,IAAI;QACrB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,IAAI,EAAE;YACJ,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,IAAI,EAAE,MAAM,CAAC,IAAI;YACjB,YAAY,EAAE,MAAM,CAAC,YAAY;SAClC;KACF,CAAC,CAAA;AACJ,CAAC"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.d.ts CHANGED Viewed

@@ -1,3 +1,7 @@
 export declare const BASE_BLAST_URL = "https://blast.ncbi.nlm.nih.gov/Blast.cgi";
 export declare const msaAlgorithms: readonly ["clustalo", "muscle", "kalign", "mafft"];
 export type MsaAlgorithm = (typeof msaAlgorithms)[number];
+export declare const blastDatabaseOptions: readonly ["nr", "nr_cluster_seq"];
+export type BlastDatabase = (typeof blastDatabaseOptions)[number];
+export declare const blastPrograms: readonly ["blastp", "quick-blastp"];
+export type BlastProgram = (typeof blastPrograms)[number];

package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js CHANGED Viewed

@@ -1,3 +1,5 @@
 export const BASE_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi';
 export const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'];
+export const blastDatabaseOptions = ['nr', 'nr_cluster_seq'];
+export const blastPrograms = ['blastp', 'quick-blastp'];
 //# sourceMappingURL=consts.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"consts.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/consts.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,cAAc,GAAG,0CAA0C,CAAA;~~AACxE~~,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,UAAU,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,CAAU,CAAA"}
1	+ {"version":3,"file":"consts.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/consts.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,cAAc,GAAG,0CAA0C,CAAA;AAExE,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,UAAU,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,CAAU,CAAA;AAG/E,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC,IAAI,EAAE,gBAAgB,CAAU,CAAA;AAGrE,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,QAAQ,EAAE,cAAc,CAAU,CAAA"}

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

@@ -4,6 +4,9 @@ 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 () => {

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

	@@ -1 +1 @@
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;~~CACzB~~,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"}
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 CHANGED Viewed

@@ -1,5 +1,4 @@
 import React, { useState } from 'react';
-import { readConfObject } from '@jbrowse/core/configuration';
 import { ErrorMessage, LoadingEllipses, SanitizedHTML } from '@jbrowse/core/ui';
 import { getContainingView, getEnv, getSession } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material';
@@ -13,10 +12,14 @@ import { useTranscriptSelection } from '../useTranscriptSelection';
 import { swrFlags } from './consts';
 import { fetchMSA, fetchMSAList } from './fetchMSAData';
 import { preCalculatedLaunchView } from './preCalculatedLaunchView';
+import { readMsaDatasets } from './types';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
     },
+    selectedContainer: {
+        marginTop: 50,
+    },
 });
 const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
     const session = getSession(model);
@@ -25,37 +28,26 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
     const { pluginManager } = getEnv(model);
     const { assemblyNames } = view;
     const [viewError, setViewError] = useState();
-    const { jbrowse } = session;
-    const datasets = readConfObject(jbrowse, ['msa', 'datasets']);
+    const datasets = readMsaDatasets(session.jbrowse);
     const [selectedDatasetId, setSelectedDatasetId] = useState(datasets?.[0]?.datasetId);
     const selectedDataset = datasets?.find(d => d.datasetId === selectedDatasetId);
-    const { data: msaList, isLoading: msaListLoading, error: msaListFetchError, } = useSWR(selectedDatasetId ? `${selectedDatasetId}-msa-list` : 'none-msa-list', () => selectedDataset
-        ? fetchMSAList({
-            config: selectedDataset.adapter,
-            pluginManager,
-        })
-        : undefined, swrFlags);
+    const { data: msaList, isLoading: msaListLoading, error: msaListFetchError, } = useSWR(selectedDataset ? `${selectedDataset.datasetId}-msa-list` : null, () => fetchMSAList({ config: selectedDataset.adapter, pluginManager }), swrFlags);
     const { options: transcripts, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, } = useTranscriptSelection({ feature, view, validIds: msaList });
-    const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useSWR(selectedId && selectedDatasetId
-        ? `${selectedDatasetId}-${selectedId}-${msaList?.length}-msa`
-        : 'none-msa', () => selectedId && selectedDataset && msaList
-        ? fetchMSA({
-            msaId: selectedId,
-            config: selectedDataset.adapter,
-            pluginManager,
-        })
-        : undefined, swrFlags);
+    const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useSWR(selectedId && selectedDataset && msaList
+        ? `${selectedDataset.datasetId}-${selectedId}-${msaList.length}-msa`
+        : null, () => fetchMSA({
+        msaId: selectedId,
+        config: selectedDataset.adapter,
+        pluginManager,
+    }), swrFlags);
     const e = msaListFetchError ?? msaDataFetchError ?? proteinSequenceError ?? viewError;
-    if (e) {
-        console.error(e);
-    }
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             e ? React.createElement(ErrorMessage, { error: e }) : null,
             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 +78,9 @@ 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 CHANGED Viewed

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

@@ -5,3 +5,4 @@ export interface Dataset {
     description?: string;
     adapter: AnyConfigurationModel;
 }
+export declare function readMsaDatasets(jbrowse: AnyConfigurationModel): Dataset[] | undefined;

package/dist/LaunchMsaView/components/PreLoadedMSA/types.js CHANGED Viewed

@@ -1,2 +1,5 @@
-export {};
+import { readConfObject } from '@jbrowse/core/configuration';
+export function readMsaDatasets(jbrowse) {
+    return readConfObject(jbrowse, ['msa', 'datasets']);
+}
 //# sourceMappingURL=types.js.map

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

	@@ -1 +1 @@
1	- {"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/types.ts"],"names":[],"mappings":""}
1	+ {"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/types.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAW5D,MAAM,UAAU,eAAe,CAAC,OAA8B;IAC5D,OAAO,cAAc,CAAC,OAAO,EAAE,CAAC,KAAK,EAAE,UAAU,CAAC,CAA0B,CAAA;AAC9E,CAAC"}

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

@@ -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 CHANGED Viewed

	@@ -1 +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"}
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,CAAC,CAAC,CAAC,iCAAM,QAAQ,CAAO,CAAC,CAAC,CAAC,IAAI,CAC3C,CACP,CAAA;AACH,CAAC"}

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

@@ -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 CHANGED Viewed

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

@@ -5,7 +5,4 @@ export interface Feat {
 }
 export interface SeqState {
     seq: string;
-    upstream?: string;
-    downstream?: string;
-    error?: unknown;
 }

package/dist/LaunchMsaView/components/useFeatureSequence.d.ts CHANGED Viewed

@@ -1,13 +1,13 @@
 import type { Feature } from '@jbrowse/core/util';
-export declare function useFeatureSequence({ view, feature, upDownBp, forceLoad, }: {
+export declare function useFeatureSequence({ view, feature, }: {
     view: {
         assemblyNames?: string[];
     } | undefined;
     feature?: Feature;
-    upDownBp?: number;
-    forceLoad?: boolean;
 }): {
     proteinSequence: string;
-    sequence: import("./types").SeqState | undefined;
+    sequence: {
+        seq: string;
+    } | undefined;
     error: any;
 };

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

@@ -1,13 +1,11 @@
 import { getProteinSequenceFromFeature } from './calculateProteinSequence';
 import { useSWRFeatureSequence } from './useSWRFeatureSequence';
-export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = true, }) {
+export function useFeatureSequence({ view, feature, }) {
     const { sequence, error } = useSWRFeatureSequence({
         view,
         feature,
-        upDownBp,
-        forceLoad,
     });
-    const proteinSequence = sequence && !('error' in sequence) && feature
+    const proteinSequence = sequence && feature
         ? getProteinSequenceFromFeature({
             seq: sequence.seq,
             feature,

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

	@@ -1 +1 @@
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