jbrowse-plugin-msaview 3.3.0 → 3.4.0

package/dist/MsaViewPanel/components/JobLink.js

@@ -2,12 +2,18 @@ import React from 'react';
 import { Typography } from '@mui/material';
 import ExternalLink from '../../components/ExternalLink';
 import { ebiBlastResultUrl } from '../../utils/ebiBlast';
+import { isPhmmerJobId, phmmerResultUrl } from '../../utils/phmmer';
 function JobLink({ jobId }) {
+    // read off the job id rather than the launch params, so a link rebuilt for an
+    // old cached job still points at the tool that actually ran it
+    const url = isPhmmerJobId(jobId)
+        ? phmmerResultUrl(jobId)
+        : ebiBlastResultUrl(jobId);
     return (React.createElement(Typography, null,
         "Job ",
         jobId,
         " (",
-        React.createElement(ExternalLink, { href: ebiBlastResultUrl(jobId) }, "see status"),
+        React.createElement(ExternalLink, { href: url }, "see status"),
         ")"));
 }
 export default JobLink;

package/dist/MsaViewPanel/components/LaunchProgress.d.ts

@@ -0,0 +1,17 @@
+import React from 'react';
+import type { JBrowsePluginMsaViewModel } from '../model';
+/**
+ * What a view shows while it is still building its alignment, and what it shows
+ * when that fails.
+ *
+ * Every launch that resolves something leaves its request on the model until it
+ * succeeds -- `blastParams`, `orthologParams`, `init` -- so one still being
+ * there IS "no alignment yet", and the error a failed launch records is only
+ * readable here. This used to key on `blastParams` alone, which left an ortholog
+ * launch rendering an empty MSAView for the minutes its alignment takes and, on
+ * failure, forever: the error was set and nothing drew it.
+ */
+declare const LaunchProgress: ({ model, }: {
+    model: JBrowsePluginMsaViewModel;
+}) => React.JSX.Element;
+export default LaunchProgress;

package/dist/MsaViewPanel/components/LaunchProgress.js

@@ -0,0 +1,41 @@
+import React from 'react';
+import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+import { Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import JobLink from './JobLink';
+const useStyles = makeStyles()({
+    margin: {
+        padding: 20,
+    },
+});
+/**
+ * What a view shows while it is still building its alignment, and what it shows
+ * when that fails.
+ *
+ * Every launch that resolves something leaves its request on the model until it
+ * succeeds -- `blastParams`, `orthologParams`, `init` -- so one still being
+ * there IS "no alignment yet", and the error a failed launch records is only
+ * readable here. This used to key on `blastParams` alone, which left an ortholog
+ * launch rendering an empty MSAView for the minutes its alignment takes and, on
+ * failure, forever: the error was set and nothing drew it.
+ */
+const LaunchProgress = observer(function LaunchProgress2({ model, }) {
+    const { blastParams, orthologParams, progress, rid, error } = model;
+    const { classes } = useStyles();
+    const message = blastParams
+        ? 'Running EBI BLAST'
+        : orthologParams
+            ? 'Building ortholog alignment'
+            : 'Loading alignment';
+    return (React.createElement("div", { className: classes.margin }, error ? (React.createElement(React.Fragment, null,
+        React.createElement(Typography, { variant: "h5" },
+            message,
+            " failed"),
+        rid ? React.createElement(JobLink, { jobId: rid }) : null,
+        React.createElement(ErrorMessage, { error: error }))) : (React.createElement(React.Fragment, null,
+        React.createElement(LoadingEllipses, { message: message, variant: "h5" }),
+        rid ? React.createElement(JobLink, { jobId: rid }) : null,
+        React.createElement(Typography, null, progress || 'Initializing')))));
+});
+export default LaunchProgress;

package/dist/MsaViewPanel/components/MsaViewPanel.js

@@ -4,7 +4,7 @@ import { observer } from 'mobx-react';
 import { MSAView } from 'react-msaview';
 import { makeStyles } from 'tss-react/mui';
 import { ErrorBoundary } from './ErrorBoundary';
-import LoadingBLAST from './LoadingBLAST';
+import LaunchProgress from './LaunchProgress';
 const useStyles = makeStyles()({
     loadingContainer: {
         padding: 20,
@@ -12,9 +12,12 @@ const useStyles = makeStyles()({
 });
 const MsaViewPanel = observer(function MsaViewPanel2({ model, }) {
     const { classes } = useStyles();
-    const { blastParams, loadingStoredData } = model;
+    const { blastParams, orthologParams, init, loadingStoredData } = model;
+    // an unresolved launch request means there is no alignment to draw yet, so all
+    // three gate the same panel -- see LaunchProgress
+    const launching = !!(blastParams ?? orthologParams ?? init);
     return (React.createElement(ErrorBoundary, null,
-        React.createElement("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model })) : loadingStoredData ? (React.createElement("div", { className: classes.loadingContainer },
+        React.createElement("div", null, launching ? (React.createElement(LaunchProgress, { model: model })) : loadingStoredData ? (React.createElement("div", { className: classes.loadingContainer },
             React.createElement(LoadingEllipses, { message: "Loading MSA data", variant: "h6" }))) : (React.createElement(MSAView, { model: model })))));
 });
 export default MsaViewPanel;

package/dist/MsaViewPanel/components/MsaViewPanel.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/MsaViewPanel/components/MsaViewPanel.test.js

@@ -0,0 +1,68 @@
+// @vitest-environment jsdom
+import React from 'react';
+import { cleanup, render, screen } from '@testing-library/react';
+import { afterEach, expect, test, vi } from 'vitest';
+import MsaViewPanel from './MsaViewPanel';
+// react-msaview's MSAView is the "nothing is launching" branch and wants a real
+// MST model; a marker is enough to say the panel reached it
+vi.mock('react-msaview', () => ({
+    MSAView: () => React.createElement("div", null, "the alignment"),
+}));
+function panel(model) {
+    return render(React.createElement(MsaViewPanel, { model: model }));
+}
+afterEach(() => {
+    cleanup();
+});
+test('an alignment with no pending launch draws itself', () => {
+    panel({ progress: '' });
+    expect(screen.getByText('the alignment')).toBeTruthy();
+});
+test('a running BLAST shows its progress, not an empty alignment', () => {
+    panel({
+        blastParams: { proteinSequence: 'MKV' },
+        progress: 'Submitting query',
+    });
+    expect(screen.queryByText('the alignment')).toBeNull();
+    expect(screen.getByText(/Running EBI BLAST/)).toBeTruthy();
+    expect(screen.getByText('Submitting query')).toBeTruthy();
+});
+// the bug this file was written for: an ortholog launch sets orthologParams
+// rather than blastParams, and the panel keyed on blastParams alone -- so it
+// rendered an empty MSAView for the minutes the alignment takes, and drew
+// nothing at all when the launch failed
+test('a running ortholog launch shows its progress', () => {
+    panel({
+        orthologParams: { taxId: 9606 },
+        progress: 'Resolving orthologs',
+    });
+    expect(screen.queryByText('the alignment')).toBeNull();
+    expect(screen.getByText(/Building ortholog alignment/)).toBeTruthy();
+    expect(screen.getByText('Resolving orthologs')).toBeTruthy();
+});
+test('a failed ortholog launch shows why', () => {
+    panel({
+        orthologParams: { taxId: 9606 },
+        progress: '',
+        error: new Error('Only 1 ortholog(s) found for this gene'),
+    });
+    expect(screen.getByText(/Only 1 ortholog\(s\) found/)).toBeTruthy();
+});
+test('a failed init shows why', () => {
+    panel({
+        init: { msaName: 'ENST00000288602' },
+        progress: '',
+        error: new Error('No alignment named ENST00000288602 in msa.fa.gz'),
+    });
+    expect(screen.queryByText('the alignment')).toBeNull();
+    expect(screen.getByText(/No alignment named ENST00000288602/)).toBeTruthy();
+});
+test('a running job links out to it', () => {
+    panel({
+        blastParams: { proteinSequence: 'MKV' },
+        progress: 'Re-checking BLAST status in... 7',
+        rid: 'ncbiblast-R20260826-123456-0001-abc',
+    });
+    const link = screen.getByRole('link');
+    expect(link.getAttribute('href')).toContain('jobId=ncbiblast-R20260826-123456-0001-abc');
+});

package/dist/MsaViewPanel/doLaunchBlast.d.ts

@@ -2,7 +2,7 @@ import type { JBrowsePluginMsaViewModel } from './model';
 export declare function doLaunchBlast({ self, }: {
     self: JBrowsePluginMsaViewModel;
 }): Promise<{
-    treeMetadata: string;
     msa: string;
     tree: string;
+    treeMetadata: string;
 }>;

package/dist/MsaViewPanel/doLaunchBlast.js

@@ -2,29 +2,72 @@ import { makeId, strip } from '../LaunchMsaView/components/util';
 import { cleanProteinSequence } from '../LaunchMsaView/util';
 import { saveBlastResult } from '../utils/blastCache';
 import { queryEbiBlast } from '../utils/ebiBlast';
-import { launchMSA } from '../utils/msa';
+import { launchMSA, launchTree } from '../utils/msa';
+import { buildPhmmerMsa, buildRowMetadata } from '../utils/msaRows';
+import { queryPhmmer } from '../utils/phmmer';
 import { fetchTaxonomyInfo } from '../utils/taxonomyNames';
 export async function doLaunchBlast({ self, }) {
-    const { blastDatabase, msaAlgorithm, proteinSequence, selectedTranscript } = self.blastParams;
-    const cleanedSeq = cleanProteinSequence(proteinSequence);
+    // kept whole rather than destructured: the database's type depends on
+    // searchProgram, and pulling the two apart loses the link between them
+    const params = self.blastParams;
+    const { selectedTranscript } = params;
+    const cleanedSeq = cleanProteinSequence(params.proteinSequence);
     const onProgress = (arg) => {
         self.setProgress(arg);
     };
+    // publish the job id before the first poll so the view can link out while the
+    // job is still running
+    const onRid = (r) => {
+        self.setRid(r);
+    };
+    const { msa, tree, treeMetadata, rid } = params.searchProgram === 'phmmer'
+        ? await runPhmmer({
+            query: cleanedSeq,
+            database: params.blastDatabase,
+            onProgress,
+            onRid,
+        })
+        : await runBlast({
+            query: cleanedSeq,
+            blastDatabase: params.blastDatabase,
+            msaAlgorithm: params.msaAlgorithm,
+            onProgress,
+            onRid,
+        });
+    const treeMetadataJson = JSON.stringify(treeMetadata);
+    await saveBlastResult({
+        proteinSequence: cleanedSeq,
+        blastDatabase: params.blastDatabase,
+        msaAlgorithm: params.msaAlgorithm,
+        searchProgram: params.searchProgram,
+        msa,
+        tree,
+        treeMetadata: treeMetadataJson,
+        rid,
+        geneId: selectedTranscript?.get('parentId'),
+        transcriptId: selectedTranscript?.id(),
+        transcriptName: selectedTranscript?.get('name') ?? selectedTranscript?.get('id'),
+        geneName: selectedTranscript?.get('gene_name') ??
+            selectedTranscript?.get('parentId'),
+    });
+    return { msa, tree, treeMetadata: treeMetadataJson };
+}
+/**
+ * BLAST returns each hit already aligned to the query, but pairwise and one hit
+ * at a time, so the alignments are stripped back off and every hit is realigned
+ * together by a dedicated aligner.
+ */
+async function runBlast({ query, blastDatabase, msaAlgorithm, onProgress, onRid, }) {
     const { hits, rid } = await queryEbiBlast({
-        query: cleanedSeq,
+        query,
         blastDatabase,
         onProgress,
-        // publish the job id before the first poll so the view can link out while
-        // the job is still running
-        onRid: r => {
-            self.setRid(r);
-        },
+        onRid,
     });
-    self.setProgress('Fetching species taxonomy info...');
-    const taxids = hits
+    onProgress('Fetching species taxonomy info...');
+    const taxonomyInfo = await fetchTaxonomyInfo(hits
         .map(h => h.description[0]?.taxid)
-        .filter((t) => t !== undefined);
-    const taxonomyInfo = await fetchTaxonomyInfo(taxids);
+        .filter((t) => t !== undefined));
     const treeMetadata = {};
     const sequences = hits.map(h => {
         const desc = h.description[0] ?? {
@@ -33,52 +76,41 @@ export async function doLaunchBlast({ self, }) {
             sciname: 'unknown',
         };
         const rowName = makeId(desc, taxonomyInfo);
-        const seq = strip(h.hsps[0]?.hseq ?? '');
         treeMetadata[rowName] = buildRowMetadata(desc, taxonomyInfo);
-        return `>${rowName}\n${seq}`;
+        return `>${rowName}\n${strip(h.hsps[0]?.hseq ?? '')}`;
     });
     const result = await launchMSA({
         algorithm: msaAlgorithm,
-        sequence: [`>QUERY\n${cleanedSeq}`, ...sequences].join('\n'),
+        sequence: [`>QUERY\n${query}`, ...sequences].join('\n'),
         onProgress,
     });
-    const treeMetadataJson = JSON.stringify(treeMetadata);
-    await saveBlastResult({
-        proteinSequence: cleanedSeq,
-        blastDatabase,
-        msaAlgorithm,
-        msa: result.msa,
-        tree: result.tree,
-        treeMetadata: treeMetadataJson,
-        rid,
-        geneId: selectedTranscript?.get('parentId'),
-        transcriptId: selectedTranscript?.id(),
-        transcriptName: selectedTranscript?.get('name') ?? selectedTranscript?.get('id'),
-        geneName: selectedTranscript?.get('gene_name') ??
-            selectedTranscript?.get('parentId'),
+    return { ...result, treeMetadata, rid };
+}
+/**
+ * phmmer aligns every hit to a profile of the query as it searches, so its own
+ * output is the MSA and there is no realignment step — the hits keep the
+ * placement HMMER gave them, and the query row is derived from the alignment's
+ * match columns rather than being aligned back in afterwards. That leaves no
+ * aligner run to take a tree from, so the tree is built from this alignment.
+ */
+async function runPhmmer({ query, database, onProgress, onRid, }) {
+    const { rows, queryRow, rid } = await queryPhmmer({
+        query,
+        database,
+        onProgress,
+        onRid,
+    });
+    onProgress('Fetching species taxonomy info...');
+    const taxonomyInfo = await fetchTaxonomyInfo(rows.map(r => r.taxid).filter((t) => t !== undefined));
+    const { msa, treeMetadata } = buildPhmmerMsa({
+        rows,
+        queryRow,
+        taxonomyInfo,
     });
     return {
-        ...result,
-        treeMetadata: treeMetadataJson,
+        msa,
+        tree: await launchTree({ alignment: msa, onProgress }),
+        treeMetadata,
+        rid,
     };
 }
-function buildRowMetadata(desc, taxonomyInfo) {
-    const metadata = {};
-    const taxInfo = desc.taxid ? taxonomyInfo.get(desc.taxid) : undefined;
-    if (taxInfo?.sciname) {
-        metadata['Scientific name'] = taxInfo.sciname;
-    }
-    if (taxInfo?.commonName) {
-        metadata['Common name'] = taxInfo.commonName;
-    }
-    if (desc.accession) {
-        metadata.Accession = desc.accession;
-    }
-    if (desc.id) {
-        metadata.ID = desc.id;
-    }
-    if (desc.title) {
-        metadata.Description = desc.title;
-    }
-    return metadata;
-}

package/dist/MsaViewPanel/doLaunchOrthologs.test.js

@@ -1,9 +1,9 @@
 import { beforeEach, describe, expect, test, vi } from 'vitest';
-import { doLaunchOrthologs } from './doLaunchOrthologs';
 import { launchMSA } from '../utils/msa';
 import { defaultMaxSpecies, fetchOrthologRows, fetchProteinForGene, resolveGeneId, } from '../utils/ncbiOrthologs';
 import { fetchPantherOrthologs } from '../utils/pantherOrthologs';
 import { fetchTaxonomyInfo } from '../utils/taxonomyNames';
+import { doLaunchOrthologs } from './doLaunchOrthologs';
 // Every network call is mocked and nothing else is. What is under test is the
 // argument shaping either side of those calls -- which species get asked for,
 // what becomes the QUERY row, and whether the row earns the Accession that

package/dist/MsaViewPanel/genomeToMSA.js

@@ -1,9 +1,11 @@
 import { getSession } from '@jbrowse/core/util';
-import { hasHoverPosition } from './util';
+import { hasHoverPosition, hasQueryRow } from './util';
 export function genomeToMSA({ model }) {
     const { hovered } = getSession(model);
     const { querySeqName, transcriptToMsaMap, connectedView, mafRegion } = model;
-    if (!connectedView?.initialized || !hasHoverPosition(hovered)) {
+    if (!connectedView?.initialized ||
+        !hasHoverPosition(hovered) ||
+        !hasQueryRow(model)) {
         return undefined;
     }
     const { coord, refName } = hovered.hoverPosition;

package/dist/MsaViewPanel/genomeToMSA.test.js

@@ -19,6 +19,7 @@ describe('genomeToMSA', () => {
         });
         const model = {
             querySeqName: 'hg38.chr1',
+            rows: [['hg38.chr1', 'ACGTACGTAC']],
             transcriptToMsaMap: undefined,
             mafRegion: {
                 refName: 'chr1',
@@ -38,6 +39,7 @@ describe('genomeToMSA', () => {
         });
         const model = {
             querySeqName: 'hg38.chr1',
+            rows: [['hg38.chr1', 'ACGTACGTAC']],
             transcriptToMsaMap: undefined,
             mafRegion: {
                 refName: 'chr1',
@@ -62,6 +64,7 @@ describe('genomeToMSA', () => {
             const mockSeqPosToVisibleCol = vi.fn().mockReturnValue(5);
             const model = {
                 querySeqName: 'hg38.chr1',
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -90,6 +93,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -116,6 +120,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -142,6 +147,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -167,6 +173,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -195,6 +202,7 @@ describe('genomeToMSA', () => {
             const mockSeqPosToVisibleCol = vi.fn().mockReturnValue(10);
             const model = {
                 querySeqName: 'QUERY',
+                rows: [['QUERY', 'MKVLTAEEK']],
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     // g2p is keyed by 0-based genome position, the hover coord is 1-based
@@ -220,6 +228,7 @@ describe('genomeToMSA', () => {
             const mockSeqPosToVisibleCol = vi.fn();
             const model = {
                 querySeqName: 'QUERY',
+                rows: [['QUERY', 'MKVLTAEEK']],
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     g2p: { 1004: 10 },
@@ -240,6 +249,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'QUERY',
+                rows: [['QUERY', 'MKVLTAEEK']],
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     g2p: { 1000: 0 }, // No entry for 1004
@@ -261,6 +271,7 @@ describe('genomeToMSA', () => {
         });
         const model = {
             querySeqName: 'QUERY',
+            rows: [['QUERY', 'MKVLTAEEK']],
             transcriptToMsaMap: undefined,
             mafRegion: undefined,
             connectedView: { initialized: true },
@@ -269,4 +280,27 @@ describe('genomeToMSA', () => {
         const result = genomeToMSA({ model });
         expect(result).toBeUndefined();
     });
+    // seqPosToVisibleCol answers 0 for a row name it does not know, so without a
+    // guard an alignment whose query row is missing -- the default 'QUERY' on an
+    // uploaded file, or the empty name the manual panel leaves when it matches
+    // nothing -- lights column 0 on every genome hover
+    test('returns undefined when querySeqName names no row here', () => {
+        mockGetSession.mockReturnValue({
+            hovered: {
+                hoverFeature: {},
+                hoverPosition: { coord: 1005, refName: 'chr1' },
+            },
+        });
+        const seqPosToVisibleCol = vi.fn(() => 0);
+        const model = {
+            querySeqName: 'QUERY',
+            rows: [['some_other_row', 'MKVLTAEEK']],
+            transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 3 } },
+            mafRegion: undefined,
+            connectedView: { initialized: true },
+            seqPosToVisibleCol,
+        };
+        expect(genomeToMSA({ model })).toBeUndefined();
+        expect(seqPosToVisibleCol).not.toHaveBeenCalled();
+    });
 });

package/dist/MsaViewPanel/model.d.ts

@@ -1,6 +1,6 @@
 export type { MSAFormat } from 'msa-parsers';
+import type { BlastDatabase, MsaAlgorithm, PhmmerDatabase } from '../LaunchMsaView/components/BlastQuery/consts';
 import type { MafRegion, MsaViewInitState } from './types';
-import type { BlastDatabase, MsaAlgorithm } from '../LaunchMsaView/components/BlastQuery/consts';
 import type { Feature } from '@jbrowse/core/util';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
@@ -11,12 +11,31 @@ export interface IRegion {
     start: number;
     end: number;
 }
-export interface BlastParams {
-    blastDatabase: BlastDatabase;
-    msaAlgorithm: MsaAlgorithm;
+/**
+ * A search to run, discriminated by the program that runs it: the two arms
+ * differ in which databases they name and in whether an aligner runs at all, so
+ * splitting them is what lets doLaunchBlast read the database without asserting
+ * whose it is.
+ *
+ * The field is still `blastDatabase` rather than `database`: it is persisted in
+ * session snapshots and in the IndexedDB result cache, so renaming it would
+ * orphan every row already written.
+ */
+export type BlastParams = {
     selectedTranscript?: Feature;
     proteinSequence: string;
-}
+} & ({
+    /** absent on params written before phmmer existed, which were all blastp */
+    searchProgram?: 'blastp';
+    blastDatabase: BlastDatabase;
+    msaAlgorithm: MsaAlgorithm;
+} | {
+    searchProgram: 'phmmer';
+    /** phmmer names its databases its own way: `swissprot`, not `uniprotkb_swissprot` */
+    blastDatabase: PhmmerDatabase;
+    /** phmmer aligns as it searches, so there is no aligner to choose */
+    msaAlgorithm?: undefined;
+});
 /**
  * Where the ortholog set comes from. NCBI's sets cover vertebrates and
  * insects; PANTHER's span its 144 reference proteomes, human to yeast to
@@ -66,7 +85,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-}, "height" | "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth"> & {
+}, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -80,7 +99,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "height" | "id" | "type" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & {
+}, "id" | "type" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -486,10 +505,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         setTreeMetadata(treeMetadata?: string): void;
         setGFF(gff?: string): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
-        tree: string | undefined;
-        msa: string | undefined;
-        treeMetadata: string | undefined;
-        gff: string | undefined;
+        [k: string]: string | undefined;
     }>, [undefined]>;
     featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -559,6 +575,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     highlightedColumns: number[] | undefined;
     minimapHeight: number;
     conservationTrackHeight: number;
+    sequenceLogoTrackHeight: number;
     marginLeft: number;
     error: unknown;
     annotations: import("msa-parsers").Annotation[];
@@ -655,6 +672,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }[];
     readonly colClustalX: Record<string, string>[];
     readonly conservation: number[];
+    readonly alphabetMaxBits: number;
     readonly propertyConservation: number[];
     readonly hierarchy: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIdsAndLength>;
     readonly totalHeight: number;
@@ -669,6 +687,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly dataInitialized: boolean;
     readonly blocksX: number[];
     readonly blocksY: number[];
+    readonly visibleMsaHeight: number;
 } & {
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
@@ -704,6 +723,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }): void;
 } & {
     readonly labelWidthMap: Map<string, number>;
+    readonly labelWidthScale: number;
     readonly labelsWidth: number;
     readonly secondaryStructureConsensus: string | undefined;
     readonly seqConsensus: string | undefined;
@@ -770,6 +790,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     setHeaderHeight(arg: number): void;
     setConservationTrackHeight(arg: number): void;
+    setSequenceLogoTrackHeight(arg: number): void;
     reset(): void;
     exportSVG(opts: {
         theme: import("@mui/material").Theme;

package/dist/MsaViewPanel/observeProteinHighlights.test.js

@@ -18,6 +18,7 @@ function makeModel({ highlightColumns } = {}) {
     const calls = [];
     const model = {
         querySeqName: 'query',
+        rows: [['query', 'MKVLTAEEK']],
         connectedViewId: CONNECTED,
         // g2p is indexed by genome coord; identity keeps the arithmetic out of the way
         transcriptToMsaMap: {
@@ -195,6 +196,16 @@ describe('scope and redundant writes', () => {
         run();
         expect(calls).toEqual([]);
     });
+    // seqPosToGlobalCol answers 0 for a row name it does not know, so without a
+    // guard a structure hover would light column 0 of whatever row is first
+    test('a query row this alignment does not have contributes no column', () => {
+        const { model, calls } = makeModel();
+        Object.assign(model, { rows: [['some_other_row', 'MKVLTAEEK']] });
+        const run = observeProteinHighlights(model);
+        session({ hover: [{ start: 10, end: 12 }] });
+        run();
+        expect(calls).toEqual([]);
+    });
     test('nothing happens until the view is connected and mapped', () => {
         const { calls } = makeModel();
         const bare = {

package/dist/MsaViewPanel/syncGenomeHoverToMsaColumn.test.js

@@ -21,6 +21,7 @@ function makeModel() {
     const calls = [];
     const model = {
         querySeqName: 'hg38.chr1',
+        rows: [['hg38.chr1', 'ACGTACGTAC']],
         transcriptToMsaMap: undefined,
         mafRegion,
         connectedView: { initialized: true, assemblyNames: ['hg38'] },