jbrowse-plugin-msaview 3.5.0 → 3.7.0

package/README.md

@@ -14,6 +14,14 @@ MSAView plugin running in JBrowse 2
 
 ## Demo
 
+[p53 across vertebrates, linked to the genome and the structure](https://jbrowse.org/code/jb2/main/?config=https://jbrowse.org/ucsc/hg38/config.json&session=spec-{%22views%22:[{%22type%22:%22LinearGenomeView%22,%22id%22:%22lgv1%22,%22assembly%22:%22hg38%22,%22loc%22:%22chr17:7,661,779-7,687,538%22,%22tracks%22:[%22hg38-ncbiRefSeqSelect%22,%22hg38-clinvarMain%22]},{%22type%22:%22MsaView%22,%22displayName%22:%22p53%20across%20vertebrates%22,%22msaFileLocation%22:{%22uri%22:%22https://gmod.org/JBrowseMSA/demo/data/p53/p53-vertebrates.afa%22},%22treeFileLocation%22:{%22uri%22:%22https://gmod.org/JBrowseMSA/demo/data/p53/p53-vertebrates.nh%22},%22querySeqName%22:%22Human%22,%22relativeTo%22:%22Human%22,%22connectedViewId%22:%22lgv1%22,%22connectedTranscript%22:%22NM_000546.6%22,%22placement%22:%22splitRight%22,%22colorSchemeName%22:%22clustalx_protein_dynamic%22,%22highlights%22:[{%22row%22:%22Human%22,%22start%22:102,%22end%22:292,%22label%22:%22DNA-binding%22,%22color%22:%22rgba%28255,140,0,0.15%29%22},{%22row%22:%22Human%22,%22start%22:175,%22end%22:175,%22label%22:%22R175%22},{%22row%22:%22Human%22,%22start%22:245,%22end%22:245,%22label%22:%22G245%22},{%22row%22:%22Human%22,%22start%22:248,%22end%22:248,%22label%22:%22R248%22},{%22row%22:%22Human%22,%22start%22:249,%22end%22:249,%22label%22:%22R249%22},{%22row%22:%22Human%22,%22start%22:273,%22end%22:273,%22label%22:%22R273%22},{%22row%22:%22Human%22,%22start%22:282,%22end%22:282,%22label%22:%22R282%22}],%22columnTracks%22:[{%22id%22:%22clinvar%22,%22name%22:%22ClinVar%20pathogenic%20missense%22,%22kind%22:%22bar%22,%22row%22:%22Human%22,%22color%22:%22%23c0392b%22,%22height%22:60,%22max%22:8,%22values%22:[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,1,0,0,2,4,3,0,6,0,0,0,0,0,0,0,0,0,0,1,2,1,5,0,0,2,2,3,1,1,4,0,0,2,0,0,2,0,3,0,0,0,1,0,0,0,6,2,0,0,1,1,3,6,2,0,1,0,2,1,1,0,0,2,0,0,2,1,3,0,3,3,1,3,5,1,3,0,0,0,0,0,0,0,0,1,0,0,4,3,1,1,1,0,1,0,0,0,0,0,3,0,0,0,0,0,0,0,3,2,1,1,0,1,0,3,0,0,0,0,0,0,0,0,0,0,0,3,0,4,0,2,4,6,2,3,5,2,0,4,5,4,1,6,2,1,2,0,1,3,0,0,0,2,1,0,0,0,0,0,2,3,3,0,1,4,1,3,6,0,2,1,1,3,0,3,8,3,1,0,2,2,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,1,0,0,5,0,0,0,1,1,0,2,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]},{%22id%22:%22alphamissense%22,%22name%22:%22AlphaMissense%20mean%20%28x100%29%22,%22kind%22:%22bar%22,%22row%22:%22Human%22,%22color%22:%22%231565c0%22,%22height%22:60,%22max%22:100,%22values%22:[49,27,19,11,12,14,18,10,12,14,28,17,40,57,73,65,65,68,95,29,30,72,95,21,24,60,39,21,18,17,18,16,17,12,11,13,14,13,14,21,22,20,17,20,16,16,15,14,17,17,15,13,37,29,11,19,16,11,11,12,14,20,14,12,11,20,13,19,15,14,12,13,15,17,14,17,15,19,20,17,15,15,22,22,19,22,20,24,17,23,67,41,46,66,63,37,90,98,63,35,36,20,76,15,99,13,58,48,98,26,81,57,97,43,17,64,87,68,90,98,96,92,73,81,98,91,95,23,13,81,56,97,84,97,98,87,86,81,91,84,94,93,89,66,81,57,77,26,20,13,90,69,17,52,70,49,91,98,87,88,94,87,95,89,48,54,52,76,76,68,92,87,98,78,99,100,98,97,100,96,85,50,38,52,32,74,52,32,83,87,71,47,99,95,89,95,91,96,95,81,20,25,69,48,98,24,64,93,17,23,84,56,99,92,91,93,70,89,76,91,77,27,92,87,57,92,58,35,54,68,75,87,85,87,74,93,96,100,95,98,99,100,94,100,100,98,97,100,99,93,93,59,91,91,87,92,93,99,87,22,21,94,24,76,83,99,98,36,61,97,93,93,99,95,100,97,100,100,99,100,100,97,84,60,98,96,47,62,13,18,56,34,17,17,11,9,9,16,11,15,13,18,20,17,81,75,26,26,23,13,12,14,16,18,18,14,15,15,47,54,46,19,13,34,24,50,56,88,36,87,48,93,63,98,73,40,89,90,45,60,88,51,36,81,77,55,79,75,87,31,54,67,23,18,17,16,25,22,13,15,15,16,20,18,15,20,25,13,15,56,21,47,45,21,16,16,15,21,16,20,66,47,13,26,19,66,13,28,18,16,47,54,66]},{%22id%22:%22mavedb%22,%22name%22:%22MaveDB%20nutlin-3,%20p53WT%22,%22kind%22:%22bar%22,%22row%22:%22Human%22,%22color%22:%22%232e7d32%22,%22height%22:60,%22max%22:2,%22values%22:[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.6,0,0.1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.1,0,0,0.2,0.4,0,0,0,0,0.1,0,0.8,0,0.7,0.3,1.6,0.1,1.4,0.1,1.3,0,0,0,0.1,0,0.1,0.5,0.2,0.4,0.4,0.8,0.8,1.4,1.5,0.1,0.1,1.2,1,1.7,1.1,1.4,1.3,0.8,0.5,0.5,0.8,0.4,1.2,0.4,1.4,0.7,1.2,0.6,1.1,0.5,0.4,0.6,1.5,1.3,0,0.7,1.3,0.3,1.4,1,1.4,0.8,1.4,0.8,1.8,0.8,0.3,0,0.2,0.8,0.4,0,0.6,0.7,1.7,1,1.2,2,1.1,0.6,2,0.8,0.7,0.3,0.1,0.4,0.2,0.3,0.1,0.1,0.5,0.8,0.1,0.1,1.4,1.6,1.4,0.7,1.3,0.1,0.1,0,0,0,0.9,0.3,1.8,0,0,1,0,0.1,0.9,0.7,1.2,1.1,1.5,1.4,0.6,1.3,0.5,1.5,0.4,0.3,0.6,0.3,0.1,0.4,0.3,0.2,0.7,0.5,0.6,1.4,0.5,1.4,0.6,1.7,1.1,1.9,0.8,1.3,1.3,1.7,0.9,1.7,2.2,2,0.9,1.5,2.1,1,1.4,0.3,1.3,1.2,1.4,0.8,1.4,1.4,0.9,0.5,0.5,0.7,0.5,0.5,0.8,1.6,1,0.9,0.8,1.5,1.3,1.5,1.5,1.7,1.8,0.5,0.4,2,0,0.9,0.6,1,0,0,1,1.8,0,0.1,0.2,0.1,0.2,0,0.1,0.4,0.4,0.3,0.4,0.6,0.4,0.6,0.5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]}],%22region%22:{%22row%22:%22Human%22,%22start%22:170,%22end%22:290}},{%22type%22:%22ProteinView%22,%22uniprotId%22:%22P04637%22,%22transcriptId%22:%22NM_000546.6%22,%22connectedViewId%22:%22lgv1%22,%22connectedView%22:{%22assembly%22:%22hg38%22,%22loc%22:%22chr17:7,661,779-7,687,538%22,%22tracks%22:[%22hg38-ncbiRefSeqSelect%22]}}]}):
+TP53 in hg38 with ClinVar, a vertebrate p53 alignment carrying ClinVar,
+AlphaMissense and MaveDB per-residue tracks, and the AlphaFold model of P04637.
+Hovering a codon, a column or a residue lights the other two views. See
+[DEVELOPERS.md](DEVELOPERS.md#demo-p53-variant-evidence) for how the link is
+built.
+
+An older shared session:
 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/index.js

@@ -3,9 +3,9 @@ import { getSession } from '@jbrowse/core/util';
 import { isMsaView } from '../MsaViewPanel/model';
 import HighlightComponents from './HighlightComponents';
 export default function AddHighlightComponentsModelF(pluginManager) {
-    pluginManager.addToExtensionPoint('LinearGenomeView-TracksContainerComponent', 
-    // @ts-expect-error
-    (rest, { model }) => {
+    pluginManager.addToExtensionPoint(
+    // @ts-expect-error v4 hosts have no contributeToExtensionPoint
+    'LinearGenomeView-TracksContainerComponent', (rest, { model }) => {
         // Quick check: don't add any components if no MSA view exists
         const { views } = getSession(model);
         const hasMsaView = views.some(v => isMsaView(v) && v.connectedViewId === model.id);

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.d.ts

@@ -3,8 +3,14 @@ import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAda
 export default class BgzipFastaMsaAdapter extends BaseAdapter {
     configureP: Promise<BaseFeatureDataAdapter> | undefined;
     refNamesP: Promise<string[]> | undefined;
-    configurePre(): Promise<BaseFeatureDataAdapter>;
-    configure(): Promise<BaseFeatureDataAdapter>;
+    configurePre(): Promise<BaseFeatureDataAdapter<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+        setSubschema(slotName: string, data: Record<string, unknown>): any;
+        setSlot(slotName: string, value: unknown): void;
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>>>;
+    configure(): Promise<BaseFeatureDataAdapter<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+        setSubschema(slotName: string, data: Record<string, unknown>): any;
+        setSlot(slotName: string, value: unknown): void;
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>>>;
     getMSARefs(): Promise<string[]>;
     getMsaRegex(): RegExp;
     refNameToMsaId(refName: string): string;

package/dist/BgzipFastaMsaAdapter/configSchema.d.ts

@@ -1,7 +1,7 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    msaRegex: {
-        type: string;
-        defaultValue: string;
+    readonly msaRegex: {
+        readonly type: "string";
+        readonly defaultValue: "_";
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration").AnyConfigurationSchemaType, undefined>>;

package/dist/BgzipFastaMsaAdapter/configSchema.js

@@ -7,6 +7,6 @@ export default function configSchemaF(pluginManager) {
             defaultValue: '_',
         },
     }, {
-        baseConfiguration: base?.configSchema,
+        baseConfiguration: base.configSchema,
     });
 }

package/dist/LaunchMsaView/cleanProteinSequence.test.d.ts

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

package/dist/LaunchMsaView/cleanProteinSequence.test.js

@@ -0,0 +1,77 @@
+import { SimpleFeature } from '@jbrowse/core/util';
+import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
+import { describe, expect, test } from 'vitest';
+import { transcriptPosToVisibleCol } from '../MsaViewPanel/util';
+import { getProteinSequenceFromFeature } from './components/calculateProteinSequence';
+import { findQueryRow } from './detectQueryRow';
+import { cleanProteinSequence } from './util';
+describe('cleanProteinSequence', () => {
+    test('drops the stop and a trailing partial codon', () => {
+        expect(cleanProteinSequence('MAWK*')).toBe('MAWK');
+        expect(cleanProteinSequence('MAWK&')).toBe('MAWK');
+    });
+    test('keeps a residue for every other codon', () => {
+        expect(cleanProteinSequence('&MAWK*')).toBe('XMAWK');
+        expect(cleanProteinSequence('MA*WK*')).toBe('MAXWK');
+        expect(cleanProteinSequence('MA&WK')).toBe('MAXWK');
+    });
+});
+// what the genome view hovers is a codon, and what lights is the query row's
+// residue at g2p's number for that codon, so the two have to count alike
+describe('a launched query row read through g2p', () => {
+    function rowResidueUnder(genomePos, json) {
+        const seq = json.seq;
+        const feature = new SimpleFeature(json);
+        const row = cleanProteinSequence(getProteinSequenceFromFeature({ seq, feature }));
+        const { g2p } = genomeToTranscriptSeqMapping(feature.toJSON());
+        const col = transcriptPosToVisibleCol({
+            querySeqName: 'QUERY',
+            querySeqOffset: 0,
+            seqPosToVisibleCol: (_, p) => (p < row.length ? p : row.length),
+            visibleColToSeqPos: (_, c) => (c < row.length ? c : undefined),
+        }, g2p[genomePos]);
+        return row[col];
+    }
+    function transcript(seq, cds) {
+        return {
+            uniqueId: 't1',
+            refName: 'chr1',
+            start: 0,
+            end: seq.length,
+            strand: 1,
+            type: 'mRNA',
+            seq,
+            subfeatures: [
+                { uniqueId: 'c1', refName: 'chr1', start: 0, end: seq.length, ...cds },
+            ],
+        };
+    }
+    test('after a partial first codon', () => {
+        // G | ATG GCC TGG AAA TAA: base 4 opens GCC, alanine
+        const json = transcript('GATGGCCTGGAAATAA', { type: 'CDS', phase: 1 });
+        expect(rowResidueUnder(4, json)).toBe('A');
+        expect(rowResidueUnder(10, json)).toBe('K');
+    });
+    test('after an internal stop', () => {
+        // ATG TGA GCC TGG TAA: a selenocysteine GENCODE does not annotate
+        const json = transcript('ATGTGAGCCTGGTAA', { type: 'CDS' });
+        expect(rowResidueUnder(6, json)).toBe('A');
+    });
+});
+describe('query row detection', () => {
+    test('matches a row a search launch built from a partial transcript', () => {
+        const msa = '>QUERY\nXMAWK\n>other\nMAWR-';
+        expect(findQueryRow(msa, '&MAWK*').match).toMatchObject({
+            name: 'QUERY',
+            quality: 'exact',
+            offset: 0,
+        });
+    });
+    test('still places a row that starts at the first whole codon', () => {
+        const msa = '>Query_1\nMAWK\n>other\nMAWR';
+        expect(findQueryRow(msa, '&MAWK*').match).toMatchObject({
+            name: 'Query_1',
+            offset: 1,
+        });
+    });
+});

package/dist/LaunchMsaView/codingFeature.d.ts

@@ -0,0 +1,14 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function isGeneLikeType(type: unknown): boolean;
+export declare function isCodingFeature(feature: Feature): boolean;
+/**
+ * Whether the feature is known not to code for anything.
+ *
+ * Not simply `!isCodingFeature`: a feature that arrived with no subfeatures at
+ * all says nothing either way, and a host is free to hand one over that way.
+ * Reading that as "no protein here" takes the menu item off a perfectly
+ * ordinary gene, silently, which is worse than opening a dialog that then has
+ * nothing to translate.
+ */
+export declare function isKnownNonCoding(feature: Feature): boolean;
+export declare function geneLikeRoot(feature: Feature): Feature;

package/dist/LaunchMsaView/codingFeature.js

@@ -0,0 +1,38 @@
+// Copied from @jbrowse/core's featureTypes rather than imported: the barrel
+// only exports it from v5, and a bundle resolving it on a v4 host reads
+// undefined.
+const GENE_LIKE_TYPE = /gene(_segment)?$|rna$|transcript/;
+// `unknown` rather than `string | undefined`, because the type comes off a
+// host's hit-test item and nothing here built it.
+export function isGeneLikeType(type) {
+    return typeof type === 'string' && GENE_LIKE_TYPE.test(type.toLowerCase());
+}
+function isCDS(feature) {
+    return feature.get('type')?.toLowerCase() === 'cds';
+}
+// The feature itself counts: a viral polyprotein hangs its cleavage products
+// off its CDS rather than off further CDSs.
+export function isCodingFeature(feature) {
+    return isCDS(feature) || !!feature.get('subfeatures')?.some(isCodingFeature);
+}
+/**
+ * Whether the feature is known not to code for anything.
+ *
+ * Not simply `!isCodingFeature`: a feature that arrived with no subfeatures at
+ * all says nothing either way, and a host is free to hand one over that way.
+ * Reading that as "no protein here" takes the menu item off a perfectly
+ * ordinary gene, silently, which is worse than opening a dialog that then has
+ * nothing to translate.
+ */
+export function isKnownNonCoding(feature) {
+    return !!feature.get('subfeatures')?.length && !isCodingFeature(feature);
+}
+// The outermost gene-like ancestor, so a click on an isoform opens the dialog
+// on the gene with every transcript to choose from, as the canvas host does.
+export function geneLikeRoot(feature) {
+    let root = feature;
+    for (let parent = root.parent?.(); parent && isGeneLikeType(parent.get('type')); parent = parent.parent?.()) {
+        root = parent;
+    }
+    return root;
+}

package/dist/LaunchMsaView/codingFeature.test.d.ts

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

package/dist/LaunchMsaView/codingFeature.test.js

@@ -0,0 +1,75 @@
+import { SimpleFeature } from '@jbrowse/core/util';
+import { describe, expect, it } from 'vitest';
+import { geneLikeRoot, isCodingFeature, isGeneLikeType, isKnownNonCoding, } from './codingFeature';
+function feature(type, subfeatures = []) {
+    return new SimpleFeature({
+        uniqueId: `${type}-${Math.random()}`,
+        refName: 'chr1',
+        start: 0,
+        end: 100,
+        type,
+        subfeatures: subfeatures.map(s => s.toJSON()),
+    });
+}
+describe('isGeneLikeType', () => {
+    it('accepts the SO spellings of gene, transcript and RNA', () => {
+        for (const t of [
+            'gene',
+            'mRNA',
+            'transcript',
+            'ncRNA_gene',
+            'protein_coding_gene',
+            'V_gene_segment',
+            'primary_transcript',
+            'pseudogenic_transcript',
+            'lnc_RNA',
+        ]) {
+            expect(isGeneLikeType(t)).toBe(true);
+        }
+    });
+    it('rejects regions, matches and CDS', () => {
+        for (const t of ['intergenic_region', 'cDNA_match', 'CDS', 'exon']) {
+            expect(isGeneLikeType(t)).toBe(false);
+        }
+        expect(isGeneLikeType(undefined)).toBe(false);
+    });
+});
+describe('isCodingFeature', () => {
+    it('finds a CDS anywhere below the feature', () => {
+        const gene = feature('gene', [
+            feature('mRNA', [feature('exon'), feature('CDS')]),
+        ]);
+        expect(isCodingFeature(gene)).toBe(true);
+    });
+    it('is false for a transcript with exons only', () => {
+        const lnc = feature('lnc_RNA', [feature('exon'), feature('exon')]);
+        expect(isCodingFeature(lnc)).toBe(false);
+    });
+    it('counts the feature itself', () => {
+        expect(isCodingFeature(feature('CDS'))).toBe(true);
+    });
+});
+describe('isKnownNonCoding', () => {
+    it('is true for a transcript whose subfeatures are all exons', () => {
+        expect(isKnownNonCoding(feature('lnc_RNA', [feature('exon'), feature('exon')]))).toBe(true);
+    });
+    // a host is free to hand over a bare record, and reading that as "no protein
+    // here" takes the menu item off an ordinary gene without a word
+    it('is false for a feature that arrived with no subfeatures at all', () => {
+        expect(isKnownNonCoding(feature('gene'))).toBe(false);
+    });
+    it('is false when a CDS is somewhere below', () => {
+        expect(isKnownNonCoding(feature('gene', [feature('mRNA', [feature('CDS')])]))).toBe(false);
+    });
+});
+describe('geneLikeRoot', () => {
+    it('climbs from an isoform to its gene', () => {
+        const gene = feature('gene', [feature('mRNA', [feature('CDS')])]);
+        const mrna = gene.get('subfeatures')[0];
+        expect(geneLikeRoot(mrna)).toBe(gene);
+    });
+    it('stays put with no gene-like parent', () => {
+        const mrna = feature('mRNA', [feature('CDS')]);
+        expect(geneLikeRoot(mrna)).toBe(mrna);
+    });
+});

package/dist/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.d.ts

@@ -1,9 +1,11 @@
 import React from 'react';
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-declare const BlastAutomaticPanel: ({ handleClose, feature, model, children, }: {
+declare const BlastAutomaticPanel: ({ handleClose, feature, model, children, preferredTranscriptId, }: {
     model: AbstractTrackModel;
     feature: Feature;
     handleClose: () => void;
     children: React.ReactNode;
+    /** the isoform the user right-clicked, preselected in the picker */
+    preferredTranscriptId?: string;
 }) => React.JSX.Element;
 export default BlastAutomaticPanel;

package/dist/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.js

@@ -6,24 +6,24 @@ import { makeStyles } from 'tss-react/mui';
 import TextField2 from '../../../components/TextField2';
 import { getBlastViewTitle, getGeneIdentifiers, getLinearGenomeView, } from '../../util';
 import LaunchPanelContent from '../LaunchPanelContent';
+import SequenceStatusMessage from '../SequenceStatus';
 import SubmitCancelActions from '../SubmitCancelActions';
 import TranscriptSelector from '../TranscriptSelector';
+import { builtAlignmentLook, launchConnectedView, useLaunchSubmit, } from '../launchConnectedView';
 import { useTranscriptSelection } from '../useTranscriptSelection';
 import CachedBlastResults from './CachedBlastResults';
 import MsaAlgorithmSelect from './MsaAlgorithmSelect';
-import { blastLaunchView } from './blastLaunchView';
-import { databaseOptionsFor, defaultMaxHits, defaultSearchFor, searchPrograms, } from './consts';
+import { databaseLabel, databaseOptionsFor, defaultMaxHits, defaultSearchFor, searchProgramLabels, searchPrograms, } from './consts';
 import { useStoredMsaAlgorithm, useStoredSearchChoice, } from './searchChoiceStorage';
 import { useCachedBlastResults } from './useCachedBlastResults';
 const useStyles = makeStyles()({
     selectField: {
         width: 150,
     },
-    // wider than the rest because the values are what the user came to read, and
-    // `uniprotkb_swissprot` is 19 characters — at 150 the field showed
-    // `uniprotkb_swis…`, which does not distinguish it from `uniprotkb_trembl`
+    // wider than the rest because the collection names are what the user came to
+    // read, and truncating them does not distinguish Swiss-Prot from TrEMBL
     databaseField: {
-        width: 230,
+        width: 260,
     },
     cachedResultsAccordion: {
         marginTop: 20,
@@ -32,10 +32,10 @@ const useStyles = makeStyles()({
         marginTop: 20,
     },
 });
-const BlastAutomaticPanel = observer(function ({ handleClose, feature, model, children, }) {
+const BlastAutomaticPanel = observer(function ({ handleClose, feature, model, children, preferredTranscriptId, }) {
     const { classes } = useStyles();
     const view = getLinearGenomeView(model);
-    const [launchViewError, setLaunchViewError] = useState();
+    const { launchError, submit } = useLaunchSubmit(handleClose);
     // one piece of state, not two: a program and a database that program does not
     // have is a 400 from EBI minutes after Submit, and holding them apart is what
     // would let them drift into that
@@ -47,9 +47,13 @@ const BlastAutomaticPanel = observer(function ({ handleClose, feature, model, ch
     const isPhmmer = search.program === 'phmmer';
     const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature]);
     const { results: cachedResults, error: cachedResultsError } = useCachedBlastResults(geneIds);
-    const transcriptSelection = useTranscriptSelection({ feature, view });
-    const { selectedTranscript, proteinSequence } = transcriptSelection;
-    const e = transcriptSelection.error ?? launchViewError ?? cachedResultsError;
+    const transcriptSelection = useTranscriptSelection({
+        feature,
+        view,
+        preferredTranscriptId,
+    });
+    const { selectedTranscript, proteinSequence, sequenceStatus } = transcriptSelection;
+    const e = transcriptSelection.error ?? launchError ?? cachedResultsError;
     return (React.createElement(React.Fragment, null,
         React.createElement(LaunchPanelContent, { error: e },
             children,
@@ -58,69 +62,57 @@ const BlastAutomaticPanel = observer(function ({ handleClose, feature, model, ch
                     // program replaces the database rather than keeping a name the new
                     // one has never heard of
                     setSearch(defaultSearchFor(event.target.value));
-                } }, searchPrograms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
+                } }, searchPrograms.map(val => (React.createElement(MenuItem, { value: val, key: val }, searchProgramLabels[val])))),
             React.createElement(TextField2, { variant: "outlined", label: "Database", className: classes.databaseField, select: true, value: search.database, onChange: event => {
                     setSearch({
                         program: search.program,
                         database: event.target.value,
                     });
-                } }, databaseOptionsFor(search.program).map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
+                } }, databaseOptionsFor(search.program).map(val => (React.createElement(MenuItem, { value: val, key: val }, databaseLabel(val))))),
             isPhmmer ? null : (React.createElement(MsaAlgorithmSelect, { className: classes.selectField, value: selectedMsaAlgorithm, onChange: setSelectedMsaAlgorithm })),
             React.createElement(TextField2, { variant: "outlined", label: "Hits", className: classes.selectField, type: "number", value: maxHits, onChange: event => {
                     setMaxHits(event.target.value);
                 }, error: !hitCountValid, helperText: "best-scoring sequences to keep" }),
             React.createElement(TranscriptSelector, { feature: feature, ...transcriptSelection }),
-            React.createElement(Typography, { className: classes.infoText },
+            React.createElement(Typography, { variant: "body2", className: classes.infoText },
                 isPhmmer
-                    ? `phmmer searches UniProtKB with a profile HMM built from the query,
-               so it aligns the hits as it finds them and that alignment is used
-               directly — nothing is realigned afterwards. The tree is then built
-               from it in the browser. A hit matching the query in more than one
-               place appears once per matched region. rp15 spreads the hits
-               across all of life; swissprot keeps to the curated set.`
-                    : `This panel will automatically submit a blastp query to EBI, which
-               searches UniProtKB. swissprot returns curated sequences that align
-               more cleanly than the many near-identical entries a TrEMBL search
-               brings back. After completion, all the hits will be run through
-               the chosen aligner; "in browser" needs no second EBI job.`,
+                    ? 'phmmer aligns the hits as it finds them, so nothing is realigned afterwards.'
+                    : 'The hits come back from EBI and are then run through the chosen aligner.',
                 ' ',
-                "EBI's queue is the wait, and it varies from seconds to many minutes. For a homolog panel with no job at all, the Orthologs tab's UniRef source is a lookup. Searching NCBI's nr needs the manual approach: NCBI no longer lets a browser read responses from Blast.cgi."),
+                "The EBI queue is the wait, and it runs from seconds to many minutes."),
             cachedResults.length > 0 ? (React.createElement(Accordion, { className: classes.cachedResultsAccordion },
                 React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, null) },
                     React.createElement(Typography, null, "Previous BLAST Results")),
                 React.createElement(AccordionDetails, null,
                     React.createElement(CachedBlastResults, { model: model, handleClose: handleClose, feature: feature })))) : null),
-        React.createElement(SubmitCancelActions, { model: model, submitDisabled: !proteinSequence || !hitCountValid, onSubmit: () => {
-                try {
-                    if (selectedTranscript) {
-                        setLaunchViewError(undefined);
-                        blastLaunchView({
-                            feature: selectedTranscript,
+        React.createElement(SubmitCancelActions, { model: model, hint: React.createElement(SequenceStatusMessage, { status: sequenceStatus }), submitDisabled: !proteinSequence || !hitCountValid, onSubmit: placement => {
+                if (selectedTranscript) {
+                    const blastParams = search.program === 'phmmer'
+                        ? {
+                            searchProgram: 'phmmer',
+                            blastDatabase: search.database,
+                            maxHits: hitCount,
+                            selectedTranscript: selectedTranscript.toJSON(),
+                            proteinSequence,
+                        }
+                        : {
+                            searchProgram: 'blastp',
+                            blastDatabase: search.database,
+                            msaAlgorithm: selectedMsaAlgorithm,
+                            maxHits: hitCount,
+                            selectedTranscript: selectedTranscript.toJSON(),
+                            proteinSequence,
+                        };
+                    submit(() => {
+                        launchConnectedView({
                             view,
-                            newViewTitle: getBlastViewTitle(feature, selectedTranscript),
-                            blastParams: search.program === 'phmmer'
-                                ? {
-                                    searchProgram: 'phmmer',
-                                    blastDatabase: search.database,
-                                    maxHits: hitCount,
-                                    selectedTranscript: selectedTranscript.toJSON(),
-                                    proteinSequence,
-                                }
-                                : {
-                                    searchProgram: 'blastp',
-                                    blastDatabase: search.database,
-                                    msaAlgorithm: selectedMsaAlgorithm,
-                                    maxHits: hitCount,
-                                    selectedTranscript: selectedTranscript.toJSON(),
-                                    proteinSequence,
-                                },
+                            feature: selectedTranscript,
+                            placement,
+                            displayName: getBlastViewTitle(feature, selectedTranscript),
+                            ...builtAlignmentLook,
+                            blastParams,
                         });
-                        handleClose();
-                    }
-                }
-                catch (e) {
-                    console.error(e);
-                    setLaunchViewError(e);
+                    });
                 }
             }, onCancel: handleClose })));
 });

package/dist/LaunchMsaView/components/BlastQuery/BlastManualPanel.d.ts

@@ -11,10 +11,12 @@ import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
  * button -- leaving them to find the Manual upload tab, re-pick the transcript
  * they had already chosen here, and hand-type the row name.
  */
-declare const BlastManualPanel: ({ handleClose, feature, model, children, }: {
+declare const BlastManualPanel: ({ handleClose, feature, model, children, preferredTranscriptId, }: {
     children: React.ReactNode;
     model: AbstractTrackModel;
     feature: Feature;
     handleClose: () => void;
+    /** the isoform the user right-clicked, preselected in the picker */
+    preferredTranscriptId?: string;
 }) => React.JSX.Element;
 export default BlastManualPanel;

package/dist/LaunchMsaView/components/BlastQuery/BlastManualPanel.js

@@ -8,10 +8,10 @@ import TextField2 from '../../../components/TextField2';
 import { useQueryRowName } from '../../useQueryRowName';
 import { cleanProteinSequence, getGeneDisplayName, getLinearGenomeView, } from '../../util';
 import LaunchPanelContent from '../LaunchPanelContent';
-import { launchView } from '../ManualMSALoader/launchView';
 import QueryRowSelector from '../QueryRowSelector';
 import SubmitCancelActions from '../SubmitCancelActions';
 import TranscriptSelector from '../TranscriptSelector';
+import { launchConnectedView, useLaunchSubmit } from '../launchConnectedView';
 import { useTranscriptSelection } from '../useTranscriptSelection';
 import { BASE_BLAST_URL } from './consts';
 const useStyles = makeStyles()({
@@ -43,13 +43,17 @@ const useStyles = makeStyles()({
  * button -- leaving them to find the Manual upload tab, re-pick the transcript
  * they had already chosen here, and hand-type the row name.
  */
-const BlastManualPanel = observer(function ({ handleClose, feature, model, children, }) {
+const BlastManualPanel = observer(function ({ handleClose, feature, model, children, preferredTranscriptId, }) {
     const { classes } = useStyles();
     const view = getLinearGenomeView(model);
-    const [launchViewError, setLaunchViewError] = useState();
+    const { launchError, submit } = useLaunchSubmit(handleClose);
     const [msaText, setMsaText] = useState('');
     const [treeText, setTreeText] = useState('');
-    const transcriptSelection = useTranscriptSelection({ feature, view });
+    const transcriptSelection = useTranscriptSelection({
+        feature,
+        view,
+        preferredTranscriptId,
+    });
     const { proteinSequence, selectedTranscript, error } = transcriptSelection;
     const queryRow = useQueryRowName(msaText, proteinSequence);
     const s2 = cleanProteinSequence(proteinSequence);
@@ -58,7 +62,7 @@ const BlastManualPanel = observer(function ({ handleClose, feature, model, child
     const link = `${BASE_BLAST_URL}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${s2}`;
     const link2 = `${BASE_BLAST_URL}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${shorten2(s2, 10)}`;
     return (React.createElement(React.Fragment, null,
-        React.createElement(LaunchPanelContent, { error: launchViewError ?? error },
+        React.createElement(LaunchPanelContent, { error: launchError ?? error },
             children,
             React.createElement(TranscriptSelector, { feature: feature, ...transcriptSelection }),
             React.createElement("div", { className: classes.step },
@@ -79,24 +83,19 @@ const BlastManualPanel = observer(function ({ handleClose, feature, model, child
                             setTreeText(event.target.value);
                         } }),
                     React.createElement(QueryRowSelector, { ...queryRow })))),
-        React.createElement(SubmitCancelActions, { model: model, submitDisabled: !selectedTranscript || !msaText.trim(), onSubmit: () => {
-                try {
-                    if (selectedTranscript) {
-                        setLaunchViewError(undefined);
-                        launchView({
-                            newViewTitle: getGeneDisplayName(selectedTranscript),
+        React.createElement(SubmitCancelActions, { model: model, submitDisabled: !selectedTranscript || !msaText.trim(), onSubmit: placement => {
+                if (selectedTranscript) {
+                    submit(() => {
+                        launchConnectedView({
                             view,
                             feature: selectedTranscript,
+                            placement,
+                            displayName: getGeneDisplayName(selectedTranscript),
                             querySeqName: queryRow.querySeqName,
                             querySeqOffset: queryRow.querySeqOffset,
                             data: { msa: msaText, tree: treeText },
                         });
-                        handleClose();
-                    }
-                }
-                catch (e) {
-                    console.error(e);
-                    setLaunchViewError(e);
+                    });
                 }
             }, onCancel: handleClose })));
 });

package/dist/LaunchMsaView/components/BlastQuery/BlastPanel.d.ts

@@ -1,23 +1,27 @@
 import React from 'react';
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
 declare const panelMap: {
-    readonly automatic: ({ handleClose, feature, model, children, }: {
+    readonly automatic: ({ handleClose, feature, model, children, preferredTranscriptId, }: {
         model: AbstractTrackModel;
         feature: Feature;
         handleClose: () => void;
         children: React.ReactNode;
+        preferredTranscriptId?: string;
     }) => React.JSX.Element;
-    readonly manual: ({ handleClose, feature, model, children, }: {
+    readonly manual: ({ handleClose, feature, model, children, preferredTranscriptId, }: {
         children: React.ReactNode;
         model: AbstractTrackModel;
         feature: Feature;
         handleClose: () => void;
+        preferredTranscriptId?: string;
     }) => React.JSX.Element;
 };
 export type BlastLookupMethod = keyof typeof panelMap;
-export default function BlastPanel({ handleClose, model, feature, }: {
+export default function BlastPanel({ handleClose, model, feature, preferredTranscriptId, }: {
     handleClose: () => void;
     model: AbstractTrackModel;
     feature: Feature;
+    /** the isoform the user right-clicked, preselected in the picker */
+    preferredTranscriptId?: string;
 }): React.JSX.Element;
 export {};

package/dist/LaunchMsaView/components/BlastQuery/BlastPanel.js

@@ -1,6 +1,6 @@
 import React, { useState } from 'react';
 import SettingsIcon from '@mui/icons-material/Settings';
-import { IconButton } from '@mui/material';
+import { IconButton, Tooltip } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import { DEFAULT_EBI_EMAIL, EBI_EMAIL_STORAGE_KEY, } from '../../../utils/ebiJobDispatcher';
 import { useLocalStorage } from '../../../utils/useLocalStorage';
@@ -17,18 +17,19 @@ const panelMap = {
     automatic: BlastAutomaticPanel,
     manual: BlastManualPanel,
 };
-export default function BlastPanel({ handleClose, model, feature, }) {
+export default function BlastPanel({ handleClose, model, feature, preferredTranscriptId, }) {
     const [lookupMethod, setLookupMethod] = useState('automatic');
     const [ebiEmail, setEbiEmail] = useLocalStorage(EBI_EMAIL_STORAGE_KEY, DEFAULT_EBI_EMAIL);
     const [settingsOpen, setSettingsOpen] = useState(false);
     const { classes } = useStyles();
     const Panel = panelMap[lookupMethod];
     return (React.createElement(React.Fragment, null,
-        React.createElement(IconButton, { className: classes.settingsButton, size: "small", onClick: () => {
-                setSettingsOpen(true);
-            } },
-            React.createElement(SettingsIcon, null)),
-        React.createElement(Panel, { model: model, feature: feature, handleClose: handleClose },
+        React.createElement(Tooltip, { title: `EBI settings — jobs are submitted with ${ebiEmail}` },
+            React.createElement(IconButton, { className: classes.settingsButton, "aria-label": "EBI settings", size: "small", onClick: () => {
+                    setSettingsOpen(true);
+                } },
+                React.createElement(SettingsIcon, null))),
+        React.createElement(Panel, { model: model, feature: feature, handleClose: handleClose, preferredTranscriptId: preferredTranscriptId },
             React.createElement(BlastMethodSelector, { lookupMethod: lookupMethod, setLookupMethod: setLookupMethod })),
         settingsOpen ? (React.createElement(BlastSettingsDialog, { ebiEmail: ebiEmail, handleClose: settings => {
                 if (settings) {