jbrowse-plugin-msaview 3.10.0 → 5.0.0

package/dist/LaunchMsaView/launchTarget.test.js

@@ -1,132 +1,40 @@
 import { SimpleFeature } from '@jbrowse/core/util';
 import { describe, expect, test } from 'vitest';
-import { isGeneLikeType, launchTarget } from './launchTarget';
-function feature(type, subfeatures = ['CDS']) {
-    return new SimpleFeature({
-        uniqueId: type,
+import { launchTarget } from './launchTarget';
+const host = (type) => ({
+    contextMenuItems: () => [],
+    contextMenuInfo: { item: { featureId: 'f1', type }, displayedRegionIndex: 0 },
+    fetchFullFeature: (featureId) => Promise.resolve(new SimpleFeature({
+        uniqueId: featureId,
         refName: 'chr1',
         start: 0,
         end: 100,
-        type,
-        subfeatures: subfeatures.map((t, i) => ({
-            uniqueId: `${type}-${i}`,
-            refName: 'chr1',
-            start: 0,
-            end: 100,
-            type: t,
-        })),
-    });
-}
-const modernHost = (type) => ({
-    contextMenuItems: () => [],
-    contextMenuInfo: { item: { featureId: 'f1', type }, displayedRegionIndex: 0 },
-    fetchFullFeature: (featureId) => Promise.resolve(feature(`fetched:${featureId}`)),
-});
-const legacyHost = (feat) => ({
-    contextMenuItems: () => [],
-    contextMenuFeature: feat,
-});
-async function fetched(target) {
-    return target && 'fetchFeature' in target
-        ? await target.fetchFeature()
-        : undefined;
-}
-describe('isGeneLikeType', () => {
-    test.each(['gene', 'mRNA', 'transcript', 'lnc_RNA', 'protein_coding_gene'])('accepts %s', type => {
-        expect(isGeneLikeType(type)).toBe(true);
-    });
-    test.each(['CDS', 'exon', 'match', 'SNV', undefined, null, 42])('rejects %s', type => {
-        expect(isGeneLikeType(type)).toBe(false);
-    });
+        type: `fetched:${featureId}`,
+    })),
 });
 describe('launchTarget', () => {
     test('resolves the clicked feature through fetchFullFeature', async () => {
-        const target = launchTarget(modernHost('mRNA'));
-        expect(await fetched(target)).toBeDefined();
-        expect((await fetched(target))?.get('type')).toBe('fetched:f1');
+        const feature = await launchTarget(host('mRNA'))?.fetchFeature();
+        expect(feature?.get('type')).toBe('fetched:f1');
     });
     test('offers nothing for a non-gene click', () => {
-        expect(launchTarget(modernHost('CDS'))).toBeUndefined();
-        expect(launchTarget(modernHost(undefined))).toBeUndefined();
+        expect(launchTarget(host('CDS'))).toBeUndefined();
+        expect(launchTarget(host(undefined))).toBeUndefined();
     });
     test('offers nothing when nothing was clicked', () => {
-        expect(launchTarget({ contextMenuItems: () => [] })).toBeUndefined();
-    });
-    // v4.3.0 and earlier have contextMenuFeature and nothing else; dropping this
-    // fallback once took "Launch MSA view" off every host in the wild.
-    test('falls back to a synchronous contextMenuFeature', () => {
-        const target = launchTarget(legacyHost(feature('mRNA')));
-        expect(target && 'feature' in target && target.feature.get('type')).toBe('mRNA');
-    });
-    test('applies the same gene test on both host shapes', () => {
-        expect(launchTarget(legacyHost(feature('lnc_RNA')))).toBeDefined();
-        expect(launchTarget(legacyHost(feature('exon')))).toBeUndefined();
-    });
-    // gene-like is not enough: an lncRNA translates to nothing, and offering the
-    // item opened a dialog whose Submit never left grey
-    test('declines a gene-like feature with no CDS below it', () => {
-        expect(launchTarget(legacyHost(feature('lnc_RNA', ['exon'])))).toBeUndefined();
-    });
-    // a legacy host can hand over a bare record whose children are a separate
-    // query, and declining it takes the item off an ordinary gene with no word
-    test('offers the item for a gene that arrived with no subfeatures', () => {
-        expect(launchTarget(legacyHost(feature('gene', [])))).toBeDefined();
-    });
-    // a click on an isoform should open the dialog on the gene, so every
-    // transcript is there to pick from
-    test('climbs to the gene from a clicked isoform', () => {
-        const gene = new SimpleFeature({
-            uniqueId: 'gene',
-            refName: 'chr1',
-            start: 0,
-            end: 100,
-            type: 'gene',
-            subfeatures: [
-                {
-                    uniqueId: 'mrna',
-                    refName: 'chr1',
-                    start: 0,
-                    end: 100,
-                    type: 'mRNA',
-                    subfeatures: [
-                        {
-                            uniqueId: 'cds',
-                            refName: 'chr1',
-                            start: 0,
-                            end: 100,
-                            type: 'CDS',
-                        },
-                    ],
-                },
-            ],
-        });
-        const mrna = gene.get('subfeatures')[0];
-        const target = launchTarget(legacyHost(mrna));
-        expect(target && 'feature' in target && target.feature).toBe(gene);
-        // the gene is what the dialog opens on, but the picker still opens on the
-        // isoform the click landed on -- on a v4 host that click is the only place
-        // the choice is ever stated
-        expect(target?.preferredTranscriptId).toBe(mrna.id());
+        expect(launchTarget({ ...host('mRNA'), contextMenuInfo: undefined })).toBeUndefined();
     });
     // the canvas host names the clicked isoform beside the gene it fetches, as
     // its own Collapse introns dialog reads it
-    test('carries the isoform a canvas click landed on', () => {
-        const host = modernHost('gene');
+    test('carries the isoform a click landed on', () => {
+        const h = host('gene');
         const target = launchTarget({
-            ...host,
+            ...h,
             contextMenuInfo: {
-                ...host.contextMenuInfo,
+                ...h.contextMenuInfo,
                 subfeature: { featureId: 'mrna-2' },
             },
         });
         expect(target?.preferredTranscriptId).toBe('mrna-2');
     });
-    // a host that has both shapes must not fall through to the legacy branch and
-    // launch on a stale feature when the click was not on a gene
-    test('a non-gene click on a host carrying both shapes offers nothing', () => {
-        expect(launchTarget({
-            ...modernHost('CDS'),
-            ...legacyHost(feature('mRNA')),
-        })).toBeUndefined();
-    });
 });

package/dist/LaunchMsaViewExtensionPoint/index.js

@@ -1,4 +1,3 @@
-import { expandSpec } from 'react-msaview';
 import { launchMsaView } from '../utils/launchMsaView';
 /**
  * `msa` and `tree` onto the plugin's own sources, so a url still goes through
@@ -23,7 +22,7 @@ function withLongSources({ msa, tree, ...args }) {
     };
 }
 export default function LaunchMsaViewExtensionPointF(pluginManager) {
-    pluginManager.addToExtensionPoint('LaunchView-MsaView', (args) => {
+    pluginManager.addToExtensionPoint('LaunchView-MsaView', async (args) => {
         const { session, query, data, msaFileLocation, msaIndexedLocation, msaName, treeFileLocation, querySeqName, searchParams, ...rest } = withLongSources(args);
         // `orthologParams` and `searchParams` name no alignment at all — the
         // view builds one at launch, which is the dialog's Orthologs and BLAST
@@ -49,7 +48,8 @@ export default function LaunchMsaViewExtensionPointF(pluginManager) {
             msaName,
             querySeqName,
         };
-        launchMsaView(session, {
+        const { expandSpec } = await import('react-msaview');
+        await launchMsaView(session, {
             ...expandSpec({ ...rest, query }),
             ...(searchParams ? { blastParams: searchParams } : {}),
             data,

package/dist/LaunchMsaViewExtensionPoint/index.test.js

@@ -1,6 +1,6 @@
 import { expect, test } from 'vitest';
 import LaunchMsaViewExtensionPointF from './index';
-function launch(args) {
+async function launch(args) {
     let run;
     LaunchMsaViewExtensionPointF({
         addToExtensionPoint(_name, cb) {
@@ -9,20 +9,20 @@ function launch(args) {
     });
     const added = [];
     const session = {
-        addView(_type, snapshot) {
+        async launchView(_type, snapshot) {
             added.push(snapshot);
             return { id: 'view-1' };
         },
     };
-    run({ session, ...args });
+    await run({ session, ...args });
     return added[0];
 }
-test('inline data carries no init, which the panel would read as a launch in flight', () => {
-    const snapshot = launch({ data: { msa: '>a\nMEEP' } });
+test('inline data carries no init, which the panel would read as a launch in flight', async () => {
+    const snapshot = await launch({ data: { msa: '>a\nMEEP' } });
     expect('init' in snapshot).toBe(false);
 });
-test('a file location travels through init', () => {
-    const snapshot = launch({
+test('a file location travels through init', async () => {
+    const snapshot = await launch({
         msaFileLocation: { uri: 'http://example.com/a.fa' },
     });
     expect(snapshot.init).toEqual({
@@ -32,8 +32,8 @@ test('a file location travels through init', () => {
         querySeqName: undefined,
     });
 });
-test('searchParams is a source, stored under the name the dialog uses', () => {
-    const snapshot = launch({
+test('searchParams is a source, stored under the name the dialog uses', async () => {
+    const snapshot = await launch({
         searchParams: {
             searchProgram: 'phmmer',
             blastDatabase: 'rp15',
@@ -50,13 +50,13 @@ test('searchParams is a source, stored under the name the dialog uses', () => {
     expect('searchParams' in snapshot).toBe(false);
     expect(snapshot.connectedTranscript).toBe('NM_000546.6');
 });
-test('a launch naming no source at all is refused', () => {
-    expect(() => launch({ connectedViewId: 'lgv1' })).toThrow(/searchParams/);
+test('a launch naming no source at all is refused', async () => {
+    await expect(launch({ connectedViewId: 'lgv1' })).rejects.toThrow(/searchParams/);
 });
-test('region and the data-layer keys reach the view as snapshot properties', () => {
+test('region and the data-layer keys reach the view as snapshot properties', async () => {
     const region = { row: 'Human', start: 245, end: 249 };
     const clades = [{ mrca: ['Human', 'Mouse'], tips: 2, mark: 'bracket' }];
-    const snapshot = launch({
+    const snapshot = await launch({
         data: { msa: '>Human\nMEEP' },
         region,
         clades,
@@ -68,8 +68,11 @@ test('region and the data-layer keys reach the view as snapshot properties', ()
     expect(snapshot.relativeTo).toBe('Human');
     expect(snapshot.gffFilehandle).toEqual({ uri: 'http://example.com/a.gff' });
 });
-test('one field set is enough to need init', () => {
-    const snapshot = launch({ data: { msa: '>a\nMEEP' }, querySeqName: 'QUERY' });
+test('one field set is enough to need init', async () => {
+    const snapshot = await launch({
+        data: { msa: '>a\nMEEP' },
+        querySeqName: 'QUERY',
+    });
     expect(snapshot.init).toEqual({
         msaUrl: undefined,
         msaIndexedLocation: undefined,
@@ -77,8 +80,8 @@ test('one field set is enough to need init', () => {
         querySeqName: 'QUERY',
     });
 });
-test('msa and tree urls reach the plugin sources, query the query row', () => {
-    const snapshot = launch({
+test('msa and tree urls reach the plugin sources, query the query row', async () => {
+    const snapshot = await launch({
         msa: 'https://example.com/p53.afa',
         tree: 'https://example.com/p53.nh',
         query: 'Human',
@@ -94,13 +97,13 @@ test('msa and tree urls reach the plugin sources, query the query row', () => {
     expect(snapshot.relativeTo).toBe('Human');
     expect('msa' in snapshot || 'query' in snapshot).toBe(false);
 });
-test('inline msa and newick text become inline data', () => {
-    const snapshot = launch({ msa: '>a\nMEEP\n>b\nMEEP', tree: '(a,b);' });
+test('inline msa and newick text become inline data', async () => {
+    const snapshot = await launch({ msa: '>a\nMEEP\n>b\nMEEP', tree: '(a,b);' });
     expect(snapshot.data).toEqual({ msa: '>a\nMEEP\n>b\nMEEP', tree: '(a,b);' });
     expect('init' in snapshot).toBe(false);
 });
-test('highlights, region and column tracks expand onto the query row', () => {
-    const snapshot = launch({
+test('highlights, region and column tracks expand onto the query row', async () => {
+    const snapshot = await launch({
         msa: 'https://example.com/p53.afa',
         query: 'Human',
         highlights: ['102-292 DNA-binding', 175],

package/dist/MsaViewPanel/index.js

@@ -1,13 +1,13 @@
 import { lazy } from 'react';
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
-import stateModelFactory from './model';
-// lazies
 const MsaViewPanel = lazy(() => import('./components/MsaViewPanel'));
 export default function MsaViewF(pluginManager) {
     pluginManager.addViewType(() => {
         return new ViewType({
             name: 'MsaView',
-            stateModel: stateModelFactory(),
+            // a thunk, so react-msaview loads with the first view rather than with
+            // the plugin; addView refuses the type until then, hence launchView
+            stateModel: () => import('./model').then(m => m.default()),
             ReactComponent: MsaViewPanel,
         });
     });

package/dist/MsaViewPanel/isMsaView.d.ts

@@ -0,0 +1,4 @@
+import type { JBrowsePluginMsaViewModel } from './model';
+export declare function isMsaView(view: {
+    type: string;
+}): view is JBrowsePluginMsaViewModel;

package/dist/MsaViewPanel/isMsaView.js

@@ -0,0 +1,3 @@
+export function isMsaView(view) {
+    return view.type === 'MsaView';
+}

package/dist/MsaViewPanel/model.d.ts

@@ -498,16 +498,16 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Clade, import("react-msaview").Clade, import("react-msaview").Clade>>, [undefined]>;
     encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>>, [undefined]>;
     rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>>, [undefined]>;
-}, "init" | "querySeqName" | "querySeqOffset" | "zoomToBaseLevel" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
+}, "init" | "querySeqName" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
     connectedTranscript: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
     orthologParams: import("@jbrowse/mobx-state-tree").IType<OrthologParams | undefined, OrthologParams | undefined, OrthologParams | undefined>;
-    querySeqName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-    querySeqOffset: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    querySeqName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    querySeqOffset: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     uniprotId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     init: import("@jbrowse/mobx-state-tree").IType<MsaViewInitState | undefined, MsaViewInitState | undefined, MsaViewInitState | undefined>;
     dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     launchCompleted: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -1509,16 +1509,16 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Clade, import("react-msaview").Clade, import("react-msaview").Clade>>, [undefined]>;
     encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>>, [undefined]>;
     rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>>, [undefined]>;
-}, "init" | "querySeqName" | "querySeqOffset" | "zoomToBaseLevel" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
+}, "init" | "querySeqName" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
     connectedTranscript: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
     orthologParams: import("@jbrowse/mobx-state-tree").IType<OrthologParams | undefined, OrthologParams | undefined, OrthologParams | undefined>;
-    querySeqName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-    querySeqOffset: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    querySeqName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    querySeqOffset: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     uniprotId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     init: import("@jbrowse/mobx-state-tree").IType<MsaViewInitState | undefined, MsaViewInitState | undefined, MsaViewInitState | undefined>;
     dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     launchCompleted: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -1803,6 +1803,3 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 export type JBrowsePluginMsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type JBrowsePluginMsaViewModel = Instance<JBrowsePluginMsaViewStateModel>;
 export { type MafRegion, type MsaViewInitState } from './types';
-export declare function isMsaView(view: {
-    type: string;
-}): view is JBrowsePluginMsaViewModel;

package/dist/MsaViewPanel/model.js

@@ -51,12 +51,7 @@ export default function stateModelFactory() {
         /**
          * #property
          */
-        // Plain defaults, not types.stripDefault: that postdates the
-        // mobx-state-tree every released core exposes (present only on main), and
-        // the missing function throws while this model is being built, which
-        // error-pages the whole app rather than just this view. Restore
-        // stripDefault once a release ships it.
-        querySeqName: 'QUERY',
+        querySeqName: types.stripDefault(types.string, 'QUERY'),
         /**
          * #property
          * transcript residues before the query row's first residue, so a
@@ -66,8 +61,7 @@ export default function stateModelFactory() {
          * transcript's first residue put every click off by the trimmed
          * amount. Negative when the row runs past the transcript's start.
          */
-        // see querySeqName above re: types.stripDefault
-        querySeqOffset: 0,
+        querySeqOffset: types.stripDefault(types.number, 0),
         /**
          * #property
          */
@@ -75,8 +69,7 @@ export default function stateModelFactory() {
         /**
          * #property
          */
-        // see querySeqName above re: types.stripDefault
-        zoomToBaseLevel: false,
+        zoomToBaseLevel: types.stripDefault(types.boolean, false),
         /**
          * #property
          */
@@ -513,6 +506,3 @@ export default function stateModelFactory() {
         },
     }));
 }
-export function isMsaView(view) {
-    return view.type === 'MsaView';
-}

package/dist/MsaViewPanel/resolveConnectedTranscript.js

@@ -50,13 +50,7 @@ async function findTranscript(self, transcriptId) {
     const tracks = transcriptTracks(view.tracks);
     for (const regions of searchWindows(view)) {
         for (const track of tracks) {
-            // a named object keeps sessionId, which v4 hosts read from the args
-            const args = {
-                adapterConfig: getConf(track, 'adapter'),
-                sessionId,
-                regions,
-            };
-            const feats = await session.rpcManager.call(sessionId, 'CoreGetFeatures', args);
+            const feats = await session.rpcManager.call(sessionId, 'CoreGetFeatures', { adapterConfig: getConf(track, 'adapter'), regions });
             for (const feat of feats) {
                 const hit = getTranscriptFeatures(feat).find(t => transcriptMatches(t, transcriptId));
                 if (hit) {

package/dist/chunks/AboutDialog-WT6GXMXU.js

@@ -0,0 +1,2 @@
+import{a as i}from"./chunk-DNFD5II2.js";import{a as m}from"./chunk-BX4Z274Q.js";import{a}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(a(),1),o=r(i(),1),t=r(m(),1);var l="8.4.1";function c({onClose:n}){return e.default.createElement(o.Dialog,{open:!0,title:"About",onClose:()=>{n()}},e.default.createElement(t.DialogContent,null,e.default.createElement(t.Typography,null,"MSAView ",l," (",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/gmod/react-msaview"},"Github"),")"),e.default.createElement("ul",null,e.default.createElement("li",null,e.default.createElement(t.Typography,null,"We use some color schemes from the"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite"},"biotite")," ","project, and their license is reproduced"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some information on jalview colorings"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.jalview.org/help/html/colourSchemes/"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some info on the clustal, cinema, maeditor, and lesk color schemes"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"http://www.bioinformatics.nl/~berndb/aacolour.html"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this paper about the flower color scheme"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/"},"here"))))))}export{c as default};
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package/dist/chunks/AboutDialog-WT6GXMXU.js.map

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+{
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+  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_35cd7d1fa06820f3dff395dec9803110/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx", "../../node_modules/.pnpm/react-msaview@8.4.1_35cd7d1fa06820f3dff395dec9803110/node_modules/react-msaview/src/version.ts"],
+  "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { DialogContent, Link, Typography } from '@mui/material'\n\nimport { version } from '../../version.ts'\n\nexport default function AboutDialog({ onClose }: { onClose: () => void }) {\n  return (\n    <Dialog\n      open\n      title=\"About\"\n      onClose={() => {\n        onClose()\n      }}\n    >\n      <DialogContent>\n        <Typography>\n          MSAView {version} (\n          <Link\n            target=\"_blank\"\n            rel=\"noopener\"\n            href=\"https://github.com/gmod/react-msaview\"\n          >\n            Github\n          </Link>\n          )\n        </Typography>\n\n        <ul>\n          <li>\n            <Typography>\n              We use some color schemes from the{' '}\n              <Link\n                target=\"_blank\"\n                rel=\"noopener\"\n                href=\"https://github.com/biotite-dev/biotite\"\n              >\n                biotite\n              </Link>{' '}\n              project, and their license is reproduced{' '}\n              <Link\n                target=\"_blank\"\n                rel=\"noopener\"\n                href=\"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst\"\n              >\n                here\n              </Link>\n            </Typography>\n          </li>\n          <li>\n            <Typography>\n              See this page for some information on jalview colorings{' '}\n              <Link\n                target=\"_blank\"\n                rel=\"noopener\"\n                href=\"https://www.jalview.org/help/html/colourSchemes/\"\n              >\n                here\n              </Link>\n            </Typography>\n          </li>\n          <li>\n            <Typography>\n              See this page for some info on the clustal, cinema, maeditor, and\n              lesk color schemes{' '}\n              <Link\n                target=\"_blank\"\n                rel=\"noopener\"\n                href=\"http://www.bioinformatics.nl/~berndb/aacolour.html\"\n              >\n                here\n              </Link>\n            </Typography>\n          </li>\n          <li>\n            <Typography>\n              See this paper about the flower color scheme{' '}\n              <Link\n                target=\"_blank\"\n                rel=\"noopener\"\n                href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/\"\n              >\n                here\n              </Link>\n            </Typography>\n          </li>\n        </ul>\n      </DialogContent>\n    </Dialog>\n  )\n}\n", "export const version = '8.4.1'\n"],
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+  "names": ["import_react", "import_ui", "import_material", "version", "AboutDialog", "onClose", "React", "version"]
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package/dist/chunks/AnnotationFileDialog-34R7LFHB.js

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package/dist/chunks/AnnotationFileDialog-34R7LFHB.js.map

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+  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_35cd7d1fa06820f3dff395dec9803110/node_modules/react-msaview/src/components/dialogs/AnnotationFileDialog.tsx"],
+  "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog, ErrorMessage } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  FormControl,\n  FormControlLabel,\n  Radio,\n  RadioGroup,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport {\n  annotationsToGFF,\n  interProScanResponseToAnnotations,\n} from 'msa-parsers'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { InterProScanResponse } from 'msa-parsers'\n\n// GFF3 as the CLI writes it, or the JSON an InterProScan run returns. 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