jbrowse-plugin-msaview 1.0.17 → 2.0.0

package/CHANGELOG.md

@@ -1,3 +1,7 @@
+# v1.0.18
+
+- Fix clicking on node labels
+
 # v1.0.17
 
 - Avoid Link redirection at react-msaview importform
@@ -16,7 +20,8 @@
 
 # v1.0.13
 
-- Factor out code into the react-msaview package on NPM, and make the plugin more of a wrapper around this module
+- Factor out code into the react-msaview package on NPM, and make the plugin
+  more of a wrapper around this module
 
 # v1.0.12
 
@@ -45,7 +50,8 @@
 
 # v1.0.6
 
-- Use postversion to run build so that the accurate version is encoded into the release binary
+- Use postversion to run build so that the accurate version is encoded into the
+  release binary
 
 # v1.0.5
 
@@ -76,8 +82,8 @@
   as a newick tree embedded in stockholm metadata
 - View metadata about alignment from MSA headers (e.g. stockholm)
 - Collapse subtrees with click action on branches
-- The collapse subtree action hides gaps that were introduced by that subtree
-  in the rest of the alignment
+- The collapse subtree action hides gaps that were introduced by that subtree in
+  the rest of the alignment
 - Allows "zooming out" by setting tiny rowHeight/colWidth settings
 - Allows changing color schemes, with jalview, clustal, and other color schemes
 - Allows toggling the branch length rendering for the phylogenetic tree

package/README.md

@@ -1,18 +1,20 @@
 # jbrowse-plugin-msaview
 
-This plugin packages https://github.com/gmod/react-msaview for usage inside of JBrowse 2
+This plugin packages https://github.com/gmod/react-msaview for usage inside of
+JBrowse 2
 
-See the docs for the react-msaview for more info https://github.com/GMOD/react-msaview/blob/main/docs/user_guide.md
+See the docs for the react-msaview for more info
+https://github.com/GMOD/react-msaview/blob/main/docs/user_guide.md
 
 ## Gallery
 
 ![](img/1.png)
 
-MSAView plugin running in v1.5.0 of JBrowse web
+MSAView plugin running in JBrowse 2
 
 ## Demo
 
-https://s3.amazonaws.com/jbrowse.org/code/jb2/main/index.html?config=https://unpkg.com/jbrowse-plugin-msaview/dist/config.json&session=share-BVmmEYAoAv&password=SuQaN
+https://jbrowse.org/code/jb2/main/index.html?config=https://unpkg.com/jbrowse-plugin-msaview/dist/config.json&session=share-BVmmEYAoAv&password=SuQaN
 
 ## Features
 

package/dist/AddHighlightModel/GenomeMouseoverHighlight.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+declare const GenomeMouseoverHighlight: ({ model, }: {
+    model: LinearGenomeViewModel;
+}) => React.JSX.Element | null;
+export default GenomeMouseoverHighlight;

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js

@@ -0,0 +1,30 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { getSession } from '@jbrowse/core/util';
+import { useStyles } from './util';
+const GenomeMouseoverHighlight = observer(function GenomeMouseoverHighlight2({ model, }) {
+    const { hovered } = getSession(model);
+    return hovered &&
+        typeof hovered === 'object' &&
+        'hoverPosition' in hovered ? (React.createElement(HoverHighlight, { model: model })) : null;
+});
+const HoverHighlight = observer(function HoverHighlight2({ model, }) {
+    const { classes } = useStyles();
+    const session = getSession(model);
+    if (session.views.some(s => s.type === 'MsaView')) {
+        const { hovered } = session;
+        const { offsetPx } = model;
+        // @ts-expect-error
+        const { coord, refName } = hovered.hoverPosition;
+        const s = model.bpToPx({ refName, coord: coord - 1 });
+        const e = model.bpToPx({ refName, coord: coord });
+        if (s && e) {
+            const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4);
+            const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx;
+            return React.createElement("div", { className: classes.highlight, style: { left, width } });
+        }
+    }
+    return null;
+});
+export default GenomeMouseoverHighlight;
+//# sourceMappingURL=GenomeMouseoverHighlight.js.map

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map

@@ -0,0 +1 @@
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package/dist/AddHighlightModel/HighlightComponents.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+type LGV = LinearGenomeViewModel;
+declare const HighlightComponents: ({ model, }: {
+    model: LGV;
+}) => React.JSX.Element;
+export default HighlightComponents;

package/dist/AddHighlightModel/HighlightComponents.js

@@ -0,0 +1,12 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+// locals
+import MsaToGenomeHighlight from './MsaToGenomeHighlight';
+import GenomeMouseoverHighlight from './GenomeMouseoverHighlight';
+const HighlightComponents = observer(function HighlightComponents2({ model, }) {
+    return (React.createElement(React.Fragment, null,
+        React.createElement(MsaToGenomeHighlight, { model: model }),
+        React.createElement(GenomeMouseoverHighlight, { model: model })));
+});
+export default HighlightComponents;
+//# sourceMappingURL=HighlightComponents.js.map

package/dist/AddHighlightModel/HighlightComponents.js.map

@@ -0,0 +1 @@
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package/dist/AddHighlightModel/MsaToGenomeHighlight.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+type LGV = LinearGenomeViewModel;
+declare const MsaToGenomeHighlight: ({ model, }: {
+    model: LGV;
+}) => React.JSX.Element | null;
+export default MsaToGenomeHighlight;

package/dist/AddHighlightModel/MsaToGenomeHighlight.js

@@ -0,0 +1,26 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { getSession } from '@jbrowse/core/util';
+import { useStyles } from './util';
+function getCanonicalName(assembly, s) {
+    return assembly.getCanonicalRefName(s) ?? s;
+}
+const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, }) {
+    const { classes } = useStyles();
+    const { assemblyManager, views } = getSession(model);
+    const p = views.find(f => f.type === 'MsaView');
+    const assembly = assemblyManager.get(model.assemblyNames[0]);
+    return assembly ? (React.createElement(React.Fragment, null, p?.connectedHighlights.map((r, idx) => {
+        const refName = getCanonicalName(assembly, r.refName);
+        const s = model.bpToPx({ refName, coord: r.start });
+        const e = model.bpToPx({ refName, coord: r.end });
+        if (s && e) {
+            const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4);
+            const left = Math.min(s.offsetPx, e.offsetPx) - model.offsetPx;
+            return (React.createElement("div", { key: `${JSON.stringify(r)}-${idx}`, className: classes.highlight, style: { left, width } }));
+        }
+        return null;
+    }))) : null;
+});
+export default MsaToGenomeHighlight;
+//# sourceMappingURL=MsaToGenomeHighlight.js.map

package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map

@@ -0,0 +1 @@
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package/dist/AddHighlightModel/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function AddHighlightComponentsModelF(pluginManager: PluginManager): void;

package/dist/AddHighlightModel/index.js

@@ -0,0 +1,14 @@
+import React from 'react';
+// locals
+import HighlightComponents from './HighlightComponents';
+export default function AddHighlightComponentsModelF(pluginManager) {
+    pluginManager.addToExtensionPoint('LinearGenomeView-TracksContainerComponent', 
+    // @ts-expect-error
+    (rest = [], { model }) => {
+        return [
+            ...rest,
+            React.createElement(HighlightComponents, { key: "highlight_protein_viewer_msaview", model: model }),
+        ];
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/AddHighlightModel/index.js.map

@@ -0,0 +1 @@
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package/dist/AddHighlightModel/util.d.ts

@@ -0,0 +1,9 @@
+export declare const useStyles: (params: void, muiStyleOverridesParams?: {
+    props: Record<string, unknown>;
+    ownerState?: Record<string, unknown> | undefined;
+} | undefined) => {
+    classes: Record<"highlight", string>;
+    theme: import("@mui/material").Theme;
+    css: import("tss-react").Css;
+    cx: import("tss-react").Cx;
+};

package/dist/AddHighlightModel/util.js

@@ -0,0 +1,14 @@
+import { makeStyles } from 'tss-react/mui';
+export const useStyles = makeStyles()({
+    highlight: {
+        height: '100%',
+        background: 'rgba(255,255,0,0.2)',
+        border: '1px solid rgba(50,50,0,0.2)',
+        position: 'absolute',
+        zIndex: 1000,
+        textAlign: 'center',
+        pointerEvents: 'none',
+        overflow: 'hidden',
+    },
+});
+//# sourceMappingURL=util.js.map

package/dist/AddHighlightModel/util.js.map

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

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

package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js

@@ -0,0 +1,20 @@
+import React, { useState } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { Box, Tab, Tabs } from '@mui/material';
+// locals
+import { CustomTabPanel, a11yProps } from './TabUtils';
+import NewNcbiBlastQueryPanel from './NewNCBIBlastQuery';
+import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel';
+export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
+    const [value, setValue] = useState(0);
+    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch MSA view", onClose: () => handleClose(), open: true },
+        React.createElement(Box, { sx: { borderBottom: 1, borderColor: 'divider' } },
+            React.createElement(Tabs, { value: value, onChange: (_, val) => setValue(val) },
+                React.createElement(Tab, { label: "NCBI BLAST query", ...a11yProps(0) }),
+                React.createElement(Tab, { label: "UCSC 100-way dataset", ...a11yProps(1) }))),
+        React.createElement(CustomTabPanel, { value: value, index: 0 },
+            React.createElement(NewNcbiBlastQueryPanel, { handleClose: handleClose, feature: feature, model: model })),
+        React.createElement(CustomTabPanel, { value: value, index: 1 },
+            React.createElement(PreLoadedMSA, { model: model, feature: feature, handleClose: handleClose }))));
+}
+//# sourceMappingURL=LaunchMsaViewDialog.js.map

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

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
+declare const NcbiBlastPanel: ({ handleClose, feature, model, }: {
+    model: AbstractTrackModel;
+    feature: Feature;
+    handleClose: () => void;
+}) => React.JSX.Element;
+export default NcbiBlastPanel;

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

@@ -0,0 +1,76 @@
+import React, { useState } from 'react';
+import { observer } from 'mobx-react';
+import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { getContainingView, } from '@jbrowse/core/util';
+import { ErrorMessage } from '@jbrowse/core/ui';
+// locals
+import { getId, getTranscriptDisplayName, getTranscriptFeatures, getGeneDisplayName, } from '../../util';
+import { getProteinSequence } from './calculateProteinSequence';
+import { useFeatureSequence } from './useFeatureSequence';
+import TextField2 from '../../../TextField2';
+import { ncbiBlastLaunchView } from './ncbiBlastLaunchView';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+});
+const NcbiBlastPanel = observer(function NcbiBlastPanel2({ handleClose, feature, model, }) {
+    const { classes } = useStyles();
+    const view = getContainingView(model);
+    const [blastDatabase, setBlastDatabase] = useState('nr');
+    const [msaAlgorithm, setMsaAlgorithm] = useState('clustalo');
+    const options = getTranscriptFeatures(feature);
+    const [userSelection, setUserSelection] = useState(getId(options[0]));
+    const selectedTranscript = options.find(val => getId(val) === userSelection);
+    const { sequence, error } = useFeatureSequence({
+        view,
+        feature: selectedTranscript,
+    });
+    const proteinSequence = sequence && !('error' in sequence)
+        ? getProteinSequence({
+            seq: sequence.seq,
+            selectedTranscript,
+        })
+        : '';
+    const blastDatabaseOptions = ['nr', 'nr_cluster_seq'];
+    const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'];
+    return (React.createElement(DialogContent, { className: classes.dialogContent },
+        error ? React.createElement(ErrorMessage, { error: error }) : null,
+        React.createElement(TextField2, { value: blastDatabase, onChange: event => setBlastDatabase(event.target.value), label: "BLAST blastDatabase", select: true }, blastDatabaseOptions.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
+        React.createElement(TextField2, { value: msaAlgorithm, onChange: event => setMsaAlgorithm(event.target.value), label: "MSA Algorithm", select: true }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
+        React.createElement(TextField2, { value: userSelection, onChange: event => setUserSelection(event.target.value), label: "Choose isoform to BLAST", select: true }, options.map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() },
+            getGeneDisplayName(feature),
+            " - ",
+            getTranscriptDisplayName(val))))),
+        React.createElement(TextField2, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, fullWidth: true, value: !proteinSequence
+                ? 'Loading...'
+                : `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`, InputProps: {
+                readOnly: true,
+                classes: {
+                    input: classes.textAreaFont,
+                },
+            } }),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
+                    const newView = ncbiBlastLaunchView({
+                        feature: selectedTranscript,
+                        view,
+                        newViewTitle: `NCBI BLAST - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)} - ${msaAlgorithm}`,
+                    });
+                    newView.setBlastParams({
+                        blastProgram: 'blastp',
+                        blastDatabase,
+                        msaAlgorithm,
+                        selectedTranscript,
+                        proteinSequence,
+                    });
+                    handleClose();
+                }, disabled: !proteinSequence }, "Submit"),
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => handleClose() }, "Cancel"))));
+});
+export default NcbiBlastPanel;
+//# sourceMappingURL=NcbiBlastPanel.js.map

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

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.d.ts

@@ -0,0 +1,26 @@
+import { Feature } from '@jbrowse/core/util';
+export interface Feat {
+    start: number;
+    end: number;
+    type: string;
+}
+export declare function stitch(subfeats: Feat[], sequence: string): string;
+export declare function calculateProteinSequence({ cds, sequence, codonTable, }: {
+    cds: Feat[];
+    sequence: string;
+    codonTable: Record<string, string>;
+}): string;
+export declare function revlist(list: {
+    start: number;
+    end: number;
+    type: string;
+}[], seqlen: number): {
+    start: number;
+    end: number;
+    type: string;
+}[];
+export declare function dedupe(list: Feat[]): Feat[];
+export declare function getProteinSequence({ selectedTranscript, seq, }: {
+    seq: string;
+    selectedTranscript: Feature;
+}): string;

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

@@ -0,0 +1,48 @@
+import { 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,
+    }))
+        .sort((a, b) => a.start - b.start);
+}
+// filter items if they have the same "ID" or location
+function getItemId(feat) {
+    return `${feat.start}-${feat.end}`;
+}
+// filters if successive elements share same start/end
+export function dedupe(list) {
+    return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
+}
+export function getProteinSequence({ selectedTranscript, seq, }) {
+    // @ts-expect-error
+    const f = selectedTranscript.toJSON();
+    const cds = dedupe(f.subfeatures
+        .sort((a, b) => a.start - b.start)
+        .map(sub => ({
+        ...sub,
+        start: sub.start - f.start,
+        end: sub.end - f.start,
+    }))
+        .filter(f => f.type === 'CDS'));
+    return calculateProteinSequence({
+        cds: f.strand === -1 ? revlist(cds, seq.length) : cds,
+        sequence: f.strand === -1 ? revcom(seq) : seq,
+        codonTable: generateCodonTable(defaultCodonTable),
+    });
+}
+//# sourceMappingURL=calculateProteinSequence.js.map

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

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.d.ts

@@ -0,0 +1,2 @@
+import NcbiBlastPanel from './NcbiBlastPanel';
+export default NcbiBlastPanel;

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js

@@ -0,0 +1,3 @@
+import NcbiBlastPanel from './NcbiBlastPanel';
+export default NcbiBlastPanel;
+//# sourceMappingURL=index.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/index.tsx"],"names":[],"mappings":"AAAA,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,eAAe,cAAc,CAAA"}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.d.ts

@@ -0,0 +1,8 @@
+import { Feature } from '@jbrowse/core/util';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import { JBrowsePluginMsaViewModel } from '../../../MsaViewPanel/model';
+export declare function ncbiBlastLaunchView({ newViewTitle, view, feature, }: {
+    newViewTitle: string;
+    view: LinearGenomeViewModel;
+    feature: Feature;
+}): JBrowsePluginMsaViewModel;

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.js

@@ -0,0 +1,17 @@
+import { getSession } from '@jbrowse/core/util';
+export function ncbiBlastLaunchView({ newViewTitle, view, feature, }) {
+    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',
+    });
+}
+//# sourceMappingURL=ncbiBlastLaunchView.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ncbiBlastLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAKxD,MAAM,UAAU,mBAAmB,CAAC,EAClC,YAAY,EACZ,IAAI,EACJ,OAAO,GAKR;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,aAAa,EAAE,GAAG;QAClB,SAAS,EAAE,GAAG;QACd,eAAe,EAAE,IAAI;QACrB,gBAAgB,EAAE,IAAI;QACtB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,eAAe,EAAE,0BAA0B;KAC5C,CAA8B,CAAA;AACjC,CAAC"}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.d.ts

@@ -0,0 +1,20 @@
+import { Feature } from '@jbrowse/core/util';
+export interface SeqState {
+    seq: string;
+    upstream?: string;
+    downstream?: string;
+}
+export interface ErrorState {
+    error: string;
+}
+export declare function useFeatureSequence({ view, feature, upDownBp, forceLoad, }: {
+    view: {
+        assemblyNames?: string[];
+    } | undefined;
+    feature: Feature;
+    upDownBp?: number;
+    forceLoad?: boolean;
+}): {
+    sequence: SeqState | ErrorState | undefined;
+    error: unknown;
+};

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.js

@@ -0,0 +1,64 @@
+import { useEffect, useState } from 'react';
+import { getSession } from '@jbrowse/core/util';
+import { getConf } from '@jbrowse/core/configuration';
+const BPLIMIT = 500_000;
+export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = true, }) {
+    const [sequence, setSequence] = useState();
+    const [error, setError] = useState();
+    useEffect(() => {
+        if (view) {
+            const { assemblyManager, rpcManager } = getSession(view);
+            const [assemblyName] = view?.assemblyNames || [];
+            async function fetchSeq(start, end, refName) {
+                const assembly = await assemblyManager.waitForAssembly(assemblyName);
+                if (!assembly) {
+                    throw new Error('assembly not found');
+                }
+                const sessionId = 'getSequence';
+                const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
+                    adapterConfig: getConf(assembly, ['sequence', 'adapter']),
+                    sessionId,
+                    regions: [
+                        {
+                            start,
+                            end,
+                            refName: assembly.getCanonicalRefName(refName),
+                            assemblyName,
+                        },
+                    ],
+                });
+                const [feat] = feats;
+                return feat?.get('seq') || '';
+            }
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            ;
+            (async () => {
+                try {
+                    setError(undefined);
+                    setSequence(undefined);
+                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                    const { start, end, refName } = feature.toJSON();
+                    if (!forceLoad && end - start > BPLIMIT) {
+                        setSequence({
+                            error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
+                        });
+                    }
+                    else {
+                        const b = start - upDownBp;
+                        const e = end + upDownBp;
+                        const seq = await fetchSeq(start, end, refName);
+                        const up = await fetchSeq(Math.max(0, b), start, refName);
+                        const down = await fetchSeq(end, e, refName);
+                        setSequence({ seq, upstream: up, downstream: down });
+                    }
+                }
+                catch (e) {
+                    console.error(e);
+                    setError(e);
+                }
+            })();
+        }
+    }, [feature, view, upDownBp, forceLoad]);
+    return { sequence, error };
+}
+//# sourceMappingURL=useFeatureSequence.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"useFeatureSequence.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE3C,OAAO,EAAW,UAAU,EAAE,MAAM,oBAAoB,CAAA;AACxD,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AAWrD,MAAM,OAAO,GAAG,OAAO,CAAA;AAEvB,MAAM,UAAU,kBAAkB,CAAC,EACjC,IAAI,EACJ,OAAO,EACP,QAAQ,GAAG,CAAC,EACZ,SAAS,GAAG,IAAI,GAMjB;IACC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAyB,CAAA;IACjE,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,IAAI,EAAE,CAAC;YACT,MAAM,EAAE,eAAe,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YACxD,MAAM,CAAC,YAAY,CAAC,GAAG,IAAI,EAAE,aAAa,IAAI,EAAE,CAAA;YAChD,KAAK,UAAU,QAAQ,CAAC,KAAa,EAAE,GAAW,EAAE,OAAe;gBACjE,MAAM,QAAQ,GAAG,MAAM,eAAe,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;gBACpE,IAAI,CAAC,QAAQ,EAAE,CAAC;oBACd,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBACvC,CAAC;gBACD,MAAM,SAAS,GAAG,aAAa,CAAA;gBAC/B,MAAM,KAAK,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;oBAChE,aAAa,EAAE,OAAO,CAAC,QAAQ,EAAE,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC;oBACzD,SAAS;oBACT,OAAO,EAAE;wBACP;4BACE,KAAK;4BACL,GAAG;4BACH,OAAO,EAAE,QAAQ,CAAC,mBAAmB,CAAC,OAAO,CAAC;4BAC9C,YAAY;yBACb;qBACF;iBACF,CAAC,CAAA;gBAEF,MAAM,CAAC,IAAI,CAAC,GAAG,KAAkB,CAAA;gBACjC,OAAQ,IAAI,EAAE,GAAG,CAAC,KAAK,CAAwB,IAAI,EAAE,CAAA;YACvD,CAAC;YAED,mEAAmE;YACnE,CAAC;YAAA,CAAC,KAAK,IAAI,EAAE;gBACX,IAAI,CAAC;oBACH,QAAQ,CAAC,SAAS,CAAC,CAAA;oBACnB,WAAW,CAAC,SAAS,CAAC,CAAA;oBACtB,8DAA8D;oBAC9D,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,MAAM,EAAS,CAAA;oBAEvD,IAAI,CAAC,SAAS,IAAI,GAAG,GAAG,KAAK,GAAG,OAAO,EAAE,CAAC;wBACxC,WAAW,CAAC;4BACV,KAAK,EAAE,gCAAgC,OAAO,wCAAwC;yBACvF,CAAC,CAAA;oBACJ,CAAC;yBAAM,CAAC;wBACN,MAAM,CAAC,GAAG,KAAK,GAAG,QAAQ,CAAA;wBAC1B,MAAM,CAAC,GAAG,GAAG,GAAG,QAAQ,CAAA;wBACxB,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,KAAK,EAAE,GAAG,EAAE,OAAO,CAAC,CAAA;wBAC/C,MAAM,EAAE,GAAG,MAAM,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,OAAO,CAAC,CAAA;wBACzD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,GAAG,EAAE,CAAC,EAAE,OAAO,CAAC,CAAA;wBAC5C,WAAW,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,EAAE,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAA;oBACtD,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;oBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;gBACb,CAAC;YACH,CAAC,CAAC,EAAE,CAAA;QACN,CAAC;IACH,CAAC,EAAE,CAAC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAC,CAAA;IACxC,OAAO,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;AAC5B,CAAC"}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/util.d.ts

@@ -0,0 +1,5 @@
+export declare function makeId(h: {
+    accession: string;
+    sciname: string;
+}): string;
+export declare function strip(s: string): string;

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/util.js

@@ -0,0 +1,7 @@
+export function makeId(h) {
+    return `${h.accession}-${h.sciname.replaceAll(' ', '_')}`;
+}
+export function strip(s) {
+    return s.replace('-', '');
+}
+//# sourceMappingURL=util.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/util.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,MAAM,CAAC,CAAyC;IAC9D,OAAO,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,CAAA;AAC3D,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,CAAS;IAC7B,OAAO,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;AAC3B,CAAC"}

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
+declare const PreLoadedMSA: ({ model, feature, handleClose, }: {
+    model: AbstractTrackModel;
+    feature: Feature;
+    handleClose: () => void;
+}) => React.JSX.Element;
+export default PreLoadedMSA;