jbrowse-plugin-msaview 2.1.0 → 2.2.0

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

@@ -0,0 +1,89 @@
+import React, { useEffect, useState } from 'react';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import { getContainingView, } from '@jbrowse/core/util';
+import { Button, DialogActions, DialogContent, MenuItem, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { blastLaunchView } from './blastLaunchView';
+import TextField2 from '../../../TextField2';
+import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
+import TranscriptSelector from '../TranscriptSelector';
+import { useFeatureSequence } from '../useFeatureSequence';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+});
+const blastDatabaseOptions = ['nr', 'nr_cluster_seq'];
+const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'];
+const blastPrograms = ['blastp', 'quick-blastp'];
+const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
+    const { classes } = useStyles();
+    const view = getContainingView(model);
+    const [launchViewError, setLaunchViewError] = useState();
+    const [selectedBlastDatabase, setSelectedBlastDatabase] = useState('nr');
+    const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] = useState('clustalo');
+    const options = getTranscriptFeatures(feature);
+    const [selectedTranscriptId, setSelectedTranscriptId] = useState(getId(options[0]));
+    const [selectedBlastProgram, setSelectedBlastProgram] = useState('blastp');
+    const selectedTranscript = options.find(val => getId(val) === selectedTranscriptId);
+    const { error, proteinSequence } = useFeatureSequence({
+        view,
+        feature: selectedTranscript,
+    });
+    useEffect(() => {
+        if (selectedBlastDatabase === 'nr_cluster_seq') {
+            setSelectedBlastProgram('blastp');
+        }
+    }, [selectedBlastDatabase]);
+    const e = error ?? launchViewError;
+    return (React.createElement(React.Fragment, null,
+        React.createElement(DialogContent, { className: classes.dialogContent },
+            children,
+            e ? React.createElement(ErrorMessage, { error: e }) : null,
+            React.createElement(TextField2, { variant: "outlined", label: "BLAST database", style: { width: 150 }, select: true, value: selectedBlastDatabase, onChange: event => {
+                    setSelectedBlastDatabase(event.target.value);
+                } }, blastDatabaseOptions.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
+            React.createElement(TextField2, { variant: "outlined", label: "MSA Algorithm", style: { width: 150 }, select: true, value: selectedMsaAlgorithm, onChange: event => {
+                    setSelectedMsaAlgorithm(event.target.value);
+                } }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
+            React.createElement("div", { style: { display: 'flex' } },
+                React.createElement(TextField2, { variant: "outlined", label: "BLAST program", disabled: selectedBlastDatabase === 'nr_cluster_seq', style: { width: 150 }, select: true, value: selectedBlastProgram, onChange: event => {
+                        setSelectedBlastProgram(event.target.value);
+                    } }, blastPrograms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
+                selectedBlastDatabase === 'nr_cluster_seq' ? (React.createElement(Typography, { variant: "subtitle2", style: { marginLeft: 4, alignContent: 'center' } }, "Can only use blastp on nr_cluster_seq")) : null),
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscriptId: selectedTranscriptId, onTranscriptChange: setSelectedTranscriptId, proteinSequence: proteinSequence }),
+            React.createElement(Typography, { style: { marginTop: 20 } }, "This panel will automatically submit a query to NCBI. Using blastp can take 10+ minutes to run, quick-blastp is generally a lot faster but is not available for the clustered database. After completion, all the hits will be run through a multiple sequence alignment. Note: we are not able to currently run NCBI COBALT automatically on the BLAST results, even though that is the method NCBI uses on their website. If you need a COBALT alignment, please use the manual approach of submitting BLAST yourself and downloading the resulting files")),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
+                    try {
+                        setLaunchViewError(undefined);
+                        blastLaunchView({
+                            feature: selectedTranscript,
+                            view,
+                            newViewTitle: `BLAST - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+                            blastParams: {
+                                baseUrl,
+                                blastProgram: selectedBlastProgram,
+                                blastDatabase: selectedBlastDatabase,
+                                msaAlgorithm: selectedMsaAlgorithm,
+                                selectedTranscript,
+                                proteinSequence,
+                            },
+                        });
+                    }
+                    catch (e) {
+                        console.error(e);
+                        setLaunchViewError(e);
+                    }
+                    handleClose();
+                }, disabled: !proteinSequence }, "Submit"),
+            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

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.d.ts

@@ -0,0 +1,10 @@
+import React from 'react';
+import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
+declare const NCBIBlastManualPanel: ({ handleClose, feature, model, children, baseUrl, }: {
+    children: React.ReactNode;
+    model: AbstractTrackModel;
+    feature: Feature;
+    baseUrl: string;
+    handleClose: () => void;
+}) => React.JSX.Element;
+export default NCBIBlastManualPanel;

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

@@ -0,0 +1,55 @@
+import React, { useState } from 'react';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import { getContainingView, shorten2 } from '@jbrowse/core/util';
+import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import ExternalLink from '../../../ExternalLink';
+import { getId, getTranscriptFeatures } from '../../util';
+import TranscriptSelector from '../TranscriptSelector';
+import { useFeatureSequence } from '../useFeatureSequence';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+    ncbiLink: {
+        wordBreak: 'break-all',
+        margin: 30,
+        maxWidth: 600,
+    },
+});
+const NCBIBlastManualPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
+    const { classes } = useStyles();
+    const view = getContainingView(model);
+    const options = getTranscriptFeatures(feature);
+    const [userSelection, setUserSelection] = useState(getId(options[0]));
+    const selectedTranscript = options.find(val => getId(val) === userSelection);
+    const { proteinSequence, error } = useFeatureSequence({
+        view,
+        feature: selectedTranscript,
+    });
+    const s2 = proteinSequence.replaceAll('*', '').replaceAll('&', '');
+    const link = `${baseUrl}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${s2}`;
+    const link2 = `${baseUrl}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${shorten2(s2, 10)}`;
+    return (React.createElement(React.Fragment, null,
+        React.createElement(DialogContent, { className: classes.dialogContent },
+            children,
+            error ? React.createElement(ErrorMessage, { error: error }) : null,
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscriptId: userSelection, onTranscriptChange: setUserSelection, proteinSequence: proteinSequence }),
+            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(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;
+//# sourceMappingURL=NCBIBlastManualPanel.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"NCBIBlastManualPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,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,uBAAuB,CAAA;AAChD,OAAO,EAAE,KAAK,EAAE,qBAAqB,EAAE,MAAM,YAAY,CAAA;AACzD,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,kBAAkB,EAAE,MAAM,uBAAuB,CAAA;AAK1D,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,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrE,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,aAAa,CAAE,CAAA;IAC7E,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,kBAAkB,CAAC;QACpD,IAAI;QACJ,OAAO,EAAE,kBAAkB;KAC5B,CAAC,CAAA;IAEF,MAAM,EAAE,GAAG,eAAe,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;IAClE,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,oBAAoB,EAAE,aAAa,EACnC,kBAAkB,EAAE,gBAAgB,EACpC,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"}

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

@@ -0,0 +1,5 @@
+import React from 'react';
+export default function NCBIBlastMethodSelector({ lookupMethod, setLookupMethod, }: {
+    lookupMethod: string;
+    setLookupMethod: (method: string) => void;
+}): React.JSX.Element;

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

@@ -0,0 +1,11 @@
+import React from 'react';
+import { FormControl, FormControlLabel, Radio, RadioGroup } from '@mui/material';
+export default function NCBIBlastMethodSelector({ lookupMethod, setLookupMethod, }) {
+    return (React.createElement(FormControl, { component: "fieldset" },
+        React.createElement(RadioGroup, { row: true, value: lookupMethod, onChange: event => {
+                setLookupMethod(event.target.value);
+            } },
+            React.createElement(FormControlLabel, { value: "automatic", control: React.createElement(Radio, null), label: "Run NCBI BLAST and load results automatically" }),
+            React.createElement(FormControlLabel, { value: "manual", control: React.createElement(Radio, null), label: "Link to NCBI BLAST and import results manually" }))));
+}
+//# sourceMappingURL=NCBIBlastMethodSelector.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"NCBIBlastMethodSelector.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,WAAW,EAAE,gBAAgB,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAEhF,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,EAC9C,YAAY,EACZ,eAAe,GAIhB;IACC,OAAO,CACL,oBAAC,WAAW,IAAC,SAAS,EAAC,UAAU;QAC/B,oBAAC,UAAU,IACT,GAAG,QACH,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,eAAe,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YACrC,CAAC;YAED,oBAAC,gBAAgB,IACf,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,+CAA+C,GACrD;YACF,oBAAC,gBAAgB,IACf,KAAK,EAAC,QAAQ,EACd,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,gDAAgD,GACtD,CACS,CACD,CACf,CAAA;AACH,CAAC"}

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

@@ -0,0 +1,7 @@
+import React from 'react';
+import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
+export default function NCBIBlastPanel({ handleClose, model, feature, }: {
+    handleClose: () => void;
+    model: AbstractTrackModel;
+    feature: Feature;
+}): React.JSX.Element;

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

@@ -0,0 +1,30 @@
+import React, { useState } from 'react';
+import { useLocalStorage } from '@jbrowse/core/util';
+import SettingsIcon from '@mui/icons-material/Settings';
+import { IconButton } from '@mui/material';
+import NCBIBlastAutomaticPanel from './NCBIBlastAutomaticPanel';
+import NCBIBlastManualPanel from './NCBIBlastManualPanel';
+import NCBIBlastMethodSelector from './NCBIBlastMethodSelector';
+import NCBISettingsDialog from './NCBISettingsDialog';
+import { BASE_BLAST_URL } from './consts';
+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);
+    return (React.createElement(React.Fragment, null,
+        React.createElement(IconButton, { style: { float: 'right' }, size: "small", onClick: () => {
+                setSettingsOpen(true);
+            } },
+            React.createElement(SettingsIcon, null)),
+        lookupMethod === 'automatic' ? (React.createElement(NCBIBlastAutomaticPanel, { model: model, feature: feature, handleClose: handleClose, baseUrl: baseUrl },
+            React.createElement(NCBIBlastMethodSelector, { lookupMethod: lookupMethod, setLookupMethod: setLookupMethod }))) : null,
+        lookupMethod === 'manual' ? (React.createElement(NCBIBlastManualPanel, { model: model, feature: feature, handleClose: handleClose, baseUrl: baseUrl },
+            React.createElement(NCBIBlastMethodSelector, { lookupMethod: lookupMethod, setLookupMethod: setLookupMethod }))) : null,
+        settingsOpen ? (React.createElement(NCBISettingsDialog, { baseUrl: baseUrl, handleClose: arg => {
+                if (arg) {
+                    setBaseUrl(arg);
+                }
+                setSettingsOpen(false);
+            } })) : null));
+}
+//# sourceMappingURL=NCBIBlastPanel.js.map

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

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.d.ts

@@ -0,0 +1,5 @@
+import React from 'react';
+export default function NCBISettingsDialog({ handleClose, baseUrl, }: {
+    handleClose: (arg?: string) => void;
+    baseUrl: string;
+}): React.JSX.Element;

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

@@ -0,0 +1,26 @@
+import React, { useState } from 'react';
+import { Button, Dialog, DialogActions, DialogContent, DialogTitle, } from '@mui/material';
+import { BASE_BLAST_URL } from './consts';
+import TextField2 from '../../../TextField2';
+export default function NCBISettingsDialog({ handleClose, baseUrl, }) {
+    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 => {
+                    setTempBaseUrl(e.target.value);
+                } }),
+            React.createElement(Button, { variant: "contained", onClick: () => {
+                    setTempBaseUrl(BASE_BLAST_URL);
+                } }, "Reset")),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
+            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
+                    handleClose(tempBaseUrl);
+                } }, "Save"))));
+}
+//# sourceMappingURL=NCBISettingsDialog.js.map

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

@@ -0,0 +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;AAEtB,OAAO,EAAE,cAAc,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,UAAU,MAAM,qBAAqB,CAAA;AAE5C,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,WAAW,EACX,OAAO,GAIR;IACC,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,KAAK,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,EAC5B,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/{NewNCBIBlastQuery/ncbiBlastLaunchView.d.ts → NCBIBlastQuery/blastLaunchView.d.ts}

@@ -1,8 +1,9 @@
 import { Feature } from '@jbrowse/core/util';
 import type { JBrowsePluginMsaViewModel } from '../../../MsaViewPanel/model';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function ncbiBlastLaunchView({ newViewTitle, view, feature, }: {
+export declare function blastLaunchView({ newViewTitle, view, feature, blastParams, }: {
     newViewTitle: string;
     view: LinearGenomeViewModel;
     feature: Feature;
+    blastParams: Record<string, unknown>;
 }): JBrowsePluginMsaViewModel;

package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/ncbiBlastLaunchView.js → NCBIBlastQuery/blastLaunchView.js}

@@ -1,17 +1,14 @@
 import { getSession } from '@jbrowse/core/util';
-export function ncbiBlastLaunchView({ newViewTitle, view, feature, }) {
+export function blastLaunchView({ newViewTitle, view, feature, blastParams, }) {
     return getSession(view).addView('MsaView', {
         type: 'MsaView',
         displayName: newViewTitle,
         connectedViewId: view.id,
         connectedFeature: feature.toJSON(),
-        treeAreaWidth: 250,
-        treeWidth: 100,
         drawNodeBubbles: true,
-        labelsAlignRight: true,
         colWidth: 10,
         rowHeight: 12,
-        colorSchemeName: 'percent_identity_dynamic',
+        blastParams,
     });
 }
-//# sourceMappingURL=ncbiBlastLaunchView.js.map
+//# sourceMappingURL=blastLaunchView.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"blastLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAKxD,MAAM,UAAU,eAAe,CAAC,EAC9B,YAAY,EACZ,IAAI,EACJ,OAAO,EACP,WAAW,GAMZ;IACC,OAAO,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QACzC,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,CAA8B,CAAA;AACjC,CAAC"}

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

@@ -0,0 +1 @@
+export declare const BASE_BLAST_URL = "https://blast.ncbi.nlm.nih.gov/Blast.cgi";

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

@@ -0,0 +1,2 @@
+export const BASE_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi';
+//# sourceMappingURL=consts.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"consts.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/consts.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,cAAc,GAAG,0CAA0C,CAAA"}

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

@@ -1,12 +1,15 @@
 import React, { useEffect, useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { getContainingView, getSession, } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, MenuItem, TextField, Typography, } from '@mui/material';
+import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import { fetchGeneList } from './fetchGeneList';
 import { preCalculatedLaunchView } from './preCalculatedLaunchView';
-import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
+import ExternalLink from '../../../ExternalLink';
+import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util';
+import TranscriptSelector from '../TranscriptSelector';
+import { useFeatureSequence } from '../useFeatureSequence';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -16,7 +19,7 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
     const session = getSession(model);
     const view = getContainingView(model);
     const { classes } = useStyles();
-    const [error, setError] = useState();
+    const [error1, setError] = useState();
     const [geneNameList, setGeneNameList] = useState();
     useEffect(() => {
         // eslint-disable-next-line @typescript-eslint/no-floating-promises
@@ -38,27 +41,25 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
             }
         })();
     }, [feature]);
-    const set = new Set(geneNameList);
+    const validSet = new Set(geneNameList);
     const options = getTranscriptFeatures(feature);
-    const ret = options.find(val => set.has(getId(val)));
+    const ret = options.find(val => validSet.has(getId(val)));
     const [userSelection, setUserSelection] = useState(getId(options[0]));
+    const selectedTranscript = options.find(val => getId(val) === userSelection);
+    const { proteinSequence, error: error2 } = useFeatureSequence({
+        view,
+        feature: selectedTranscript,
+    });
+    const e = error1 ?? error2;
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
+            e ? React.createElement(ErrorMessage, { error: e }) : null,
             React.createElement(Typography, null,
                 "The source data for these multiple sequence alignments is from",
                 ' ',
-                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,
+                React.createElement(ExternalLink, { href: "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/alignments/" }, "knownCanonical.multiz100way.protAA.fa.gz")),
             geneNameList && !ret ? (React.createElement(Typography, { color: "error" }, "No MSA data for this gene found")) : null,
-            React.createElement(TextField, { select: true, label: "Choose isoform to view MSA for", value: userSelection, onChange: event => {
-                    setUserSelection(event.target.value);
-                } }, options.map(val => {
-                const inSet = set.has(getId(val));
-                return (React.createElement(MenuItem, { value: getId(val), key: val.id(), disabled: !inSet },
-                    getTranscriptDisplayName(val),
-                    " ",
-                    inSet ? ' (has data)' : ''));
-            }))),
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscriptId: userSelection, onTranscriptChange: setUserSelection, proteinSequence: proteinSequence, validSet: validSet })),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
                     // eslint-disable-next-line @typescript-eslint/no-floating-promises

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

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/TranscriptSelector.d.ts

@@ -0,0 +1,10 @@
+import React from 'react';
+import { Feature } from '@jbrowse/core/util';
+export default function TranscriptSelector({ feature, options, selectedTranscriptId, onTranscriptChange, proteinSequence, validSet, }: {
+    feature: Feature;
+    options: Feature[];
+    selectedTranscriptId: string;
+    onTranscriptChange: (transcriptId: string) => void;
+    proteinSequence: string | undefined;
+    validSet?: Set<string>;
+}): React.JSX.Element;

package/dist/LaunchMsaView/components/TranscriptSelector.js

@@ -0,0 +1,45 @@
+import React, { useState } from 'react';
+import { Button, MenuItem } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import ReadOnlyTextField2 from '../../ReadOnlyTextField2';
+import TextField2 from '../../TextField2';
+import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptLength, } from '../util';
+const useStyles = makeStyles()({
+    flex: {
+        display: 'flex',
+    },
+    minWidth: {
+        minWidth: 300,
+    },
+});
+export default function TranscriptSelector({ feature, options, selectedTranscriptId, onTranscriptChange, proteinSequence, validSet, }) {
+    const { classes } = useStyles();
+    const [showSequence, setShowSequence] = useState(false);
+    const selectedTranscript = options.find(val => getId(val) === selectedTranscriptId);
+    return (React.createElement(React.Fragment, null,
+        React.createElement("div", { className: classes.flex },
+            React.createElement(TextField2, { variant: "outlined", label: `Choose isoform of ${getGeneDisplayName(feature)}`, select: true, className: classes.minWidth, value: selectedTranscriptId, onChange: event => {
+                    onTranscriptChange(event.target.value);
+                } }, options
+                .toSorted((a, b) => getTranscriptLength(b).len - getTranscriptLength(a).len)
+                .map(val => {
+                const inSet = validSet ? validSet.has(getId(val)) : true;
+                const { len, mod } = getTranscriptLength(val);
+                return (React.createElement(MenuItem, { value: getId(val), key: val.id(), disabled: !inSet },
+                    getTranscriptDisplayName(val),
+                    " (",
+                    len,
+                    " aa)",
+                    ' ',
+                    mod ? ` (possible fragment)` : '',
+                    validSet ? (inSet ? ' (has data)' : ' (no data)') : ''));
+            })),
+            React.createElement("div", { style: { alignContent: 'center', marginLeft: 20 } },
+                React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
+                        setShowSequence(!showSequence);
+                    } }, showSequence ? 'Hide sequence' : 'Show sequence'))),
+        showSequence && (React.createElement(ReadOnlyTextField2, { value: proteinSequence
+                ? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
+                : 'Loading...' }))));
+}
+//# sourceMappingURL=TranscriptSelector.js.map

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

@@ -0,0 +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;AAGvC,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAChD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,kBAAkB,MAAM,0BAA0B,CAAA;AACzD,OAAO,UAAU,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,mBAAmB,GACpB,MAAM,SAAS,CAAA;AAEhB,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,oBAAoB,EACpB,kBAAkB,EAClB,eAAe,EACf,QAAQ,GAQT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACvD,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CACrC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,oBAAoB,CAC1C,CAAA;IAEF,OAAO,CACL;QACE,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,qBAAqB,kBAAkB,CAAC,OAAO,CAAC,EAAE,EACzD,MAAM,QACN,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC,IAEA,OAAO;iBACL,QAAQ,CACP,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,mBAAmB,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,mBAAmB,CAAC,CAAC,CAAC,CAAC,GAAG,CAClE;iBACA,GAAG,CAAC,GAAG,CAAC,EAAE;gBACT,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;gBACxD,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,CACO;YACb,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"}

package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/calculateProteinSequence.d.ts → calculateProteinSequence.d.ts}

@@ -11,8 +11,7 @@ export declare function revlist(list: Feat[], seqlen: number): {
     end: number;
     type?: string;
 }[];
-export declare function dedupe(list: Feat[]): Feat[];
-export declare function getProteinSequence({ selectedTranscript, seq, }: {
+export declare function getProteinSequenceFromFeature({ selectedTranscript, seq, }: {
     seq: string;
     selectedTranscript: Feature;
 }): string;

package/dist/LaunchMsaView/components/calculateProteinSequence.js

@@ -0,0 +1,39 @@
+import { dedupe, defaultCodonTable, generateCodonTable, revcom, } from '@jbrowse/core/util';
+export function stitch(subfeats, sequence) {
+    return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
+}
+export function calculateProteinSequence({ cds, sequence, codonTable, }) {
+    const str = stitch(cds, sequence);
+    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)] ?? '&';
+    }
+    return protein;
+}
+export function revlist(list, seqlen) {
+    return list
+        .map(sub => ({
+        ...sub,
+        start: seqlen - sub.end,
+        end: seqlen - sub.start,
+    }))
+        .toSorted((a, b) => a.start - b.start);
+}
+export function getProteinSequenceFromFeature({ selectedTranscript, seq, }) {
+    const { subfeatures, start, strand } = selectedTranscript.toJSON();
+    const cds = dedupe(subfeatures
+        ?.toSorted((a, b) => a.start - b.start)
+        .map(sub => ({
+        ...sub,
+        start: sub.start - start,
+        end: sub.end - start,
+    }))
+        .filter(subfeature => subfeature.type === 'CDS') ?? [], feat => `${feat.start}-${feat.end}`);
+    return calculateProteinSequence({
+        cds: strand === -1 ? revlist(cds, seq.length) : cds,
+        sequence: strand === -1 ? revcom(seq) : seq,
+        codonTable: generateCodonTable(defaultCodonTable),
+    });
+}
+//# sourceMappingURL=calculateProteinSequence.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"calculateProteinSequence.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/calculateProteinSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,MAAM,EACN,iBAAiB,EACjB,kBAAkB,EAClB,MAAM,GACP,MAAM,oBAAoB,CAAA;AAK3B,MAAM,UAAU,MAAM,CAAC,QAAgB,EAAE,QAAgB;IACvD,OAAO,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACzE,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,GAAG,EACH,QAAQ,EACR,UAAU,GAKX;IACC,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IACjC,IAAI,OAAO,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACvC,qDAAqD;QACrD,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG,CAAA;IACnD,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,IAAY,EAAE,MAAc;IAClD,OAAO,IAAI;SACR,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,MAAM,GAAG,GAAG,CAAC,GAAG;QACvB,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC,KAAK;KACxB,CAAC,CAAC;SACF,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAA;AAC1C,CAAC;AAED,MAAM,UAAU,6BAA6B,CAAC,EAC5C,kBAAkB,EAClB,GAAG,GAIJ;IACC,MAAM,EAAE,WAAW,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,kBAAkB,CAAC,MAAM,EAAE,CAAA;IAClE,MAAM,GAAG,GAAG,MAAM,CAChB,WAAW;QACT,EAAE,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;SACtC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,GAAG,CAAC,KAAK,GAAG,KAAK;QACxB,GAAG,EAAE,GAAG,CAAC,GAAG,GAAG,KAAK;KACrB,CAAC,CAAC;SACF,MAAM,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,KAAK,KAAK,CAAC,IAAI,EAAE,EACxD,IAAI,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CACpC,CAAA;IAED,OAAO,wBAAwB,CAAC;QAC9B,GAAG,EAAE,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG;QACnD,QAAQ,EAAE,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG;QAC3C,UAAU,EAAE,kBAAkB,CAAC,iBAAiB,CAAC;KAClD,CAAC,CAAA;AACJ,CAAC"}

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

@@ -0,0 +1 @@
+{"version":3,"file":"fetchSeq.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/fetchSeq.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AAIrD,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAC,EAC7B,KAAK,EACL,GAAG,EACH,OAAO,EACP,OAAO,EACP,YAAY,GAOb;IACC,MAAM,EAAE,eAAe,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;IAC/C,MAAM,QAAQ,GAAG,MAAM,eAAe,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;IACpE,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;IACvC,CAAC;IACD,MAAM,SAAS,GAAG,aAAa,CAAA;IAC/B,MAAM,KAAK,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;QACjE,aAAa,EAAE,OAAO,CAAC,QAAQ,EAAE,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC;QACzD,SAAS;QACT,OAAO,EAAE;YACP;gBACE,KAAK;gBACL,GAAG;gBACH,OAAO,EAAE,QAAQ,CAAC,mBAAmB,CAAC,OAAO,CAAC;gBAC9C,YAAY;aACb;SACF;KACF,CAAC,CAAc,CAAA;IAChB,OAAQ,KAAK,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,CAAwB,IAAI,EAAE,CAAA;AAC3D,CAAC"}

package/dist/LaunchMsaView/components/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/types.ts"],"names":[],"mappings":""}

package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/useFeatureSequence.d.ts → useFeatureSequence.d.ts}

@@ -1,5 +1,5 @@
-import type { Feature } from '@jbrowse/core/util';
 import type { SeqState } from './types';
+import type { Feature } from '@jbrowse/core/util';
 export interface ErrorState {
     error: string;
 }
@@ -11,6 +11,7 @@ export declare function useFeatureSequence({ view, feature, upDownBp, forceLoad,
     upDownBp?: number;
     forceLoad?: boolean;
 }): {
+    proteinSequence: string;
     sequence: SeqState | ErrorState | undefined;
     error: unknown;
 };

package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/useFeatureSequence.js → useFeatureSequence.js}

@@ -1,5 +1,6 @@
 import { useEffect, useState } from 'react';
 import { getSession } from '@jbrowse/core/util';
+import { getProteinSequenceFromFeature } from './calculateProteinSequence';
 import { fetchSeq } from './fetchSeq';
 const BPLIMIT = 500_000;
 export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = true, }) {
@@ -59,6 +60,16 @@ export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = tr
             })();
         }
     }, [feature, view, upDownBp, assemblyName, forceLoad]);
-    return { sequence, error };
+    const proteinSequence = sequence && !('error' in sequence)
+        ? getProteinSequenceFromFeature({
+            seq: sequence.seq,
+            selectedTranscript: feature,
+        })
+        : '';
+    return {
+        proteinSequence,
+        sequence,
+        error,
+    };
 }
 //# sourceMappingURL=useFeatureSequence.js.map