jbrowse-plugin-msaview 3.9.0 → 3.10.0

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.d.ts

@@ -3,14 +3,8 @@ 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<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>>>;
+    configurePre(): Promise<BaseFeatureDataAdapter<import("@jbrowse/core/configuration").AnyConfigurationModel>>;
+    configure(): Promise<BaseFeatureDataAdapter<import("@jbrowse/core/configuration").AnyConfigurationModel>>;
     getMSARefs(): Promise<string[]>;
     getMsaRegex(): RegExp;
     refNameToMsaId(refName: string): string;

package/dist/BgzipFastaMsaAdapter/configSchema.d.ts

@@ -1,7 +1,14 @@
 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: "_";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration").AnyConfigurationSchemaType, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<any, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;

package/dist/LaunchMsaView/cleanProteinSequence.test.js

@@ -1,8 +1,8 @@
 import { SimpleFeature } from '@jbrowse/core/util';
+import { translateTranscript } from '@jbrowse/core/util/translateTranscript';
 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', () => {
@@ -22,7 +22,7 @@ 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 row = cleanProteinSequence(translateTranscript({ transcript: feature, seq })?.protein ?? '');
         const { g2p } = genomeToTranscriptSeqMapping(feature.toJSON());
         const col = transcriptPosToVisibleCol({
             querySeqName: 'QUERY',
@@ -52,6 +52,40 @@ describe('a launched query row read through g2p', () => {
         expect(rowResidueUnder(4, json)).toBe('A');
         expect(rowResidueUnder(10, json)).toBe('K');
     });
+    test('on the reverse strand, across an intron, after a partial first codon', () => {
+        // sense G | ATG GCC <intron> TGG AAA TAA, stored as the reverse complement
+        const json = {
+            uniqueId: 't1',
+            refName: 'chr1',
+            start: 0,
+            end: 24,
+            strand: -1,
+            type: 'mRNA',
+            seq: 'TTATTTCCACTACTTACGGCCATC',
+            subfeatures: [
+                {
+                    uniqueId: 'c1',
+                    refName: 'chr1',
+                    type: 'CDS',
+                    start: 17,
+                    end: 24,
+                    phase: 1,
+                },
+                {
+                    uniqueId: 'c2',
+                    refName: 'chr1',
+                    type: 'CDS',
+                    start: 0,
+                    end: 9,
+                    phase: 0,
+                },
+            ],
+        };
+        expect(rowResidueUnder(22, json)).toBe('M');
+        expect(rowResidueUnder(18, json)).toBe('A');
+        expect(rowResidueUnder(7, json)).toBe('W');
+        expect(rowResidueUnder(4, 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' });

package/dist/LaunchMsaView/components/useFeatureSequence.js

@@ -1,6 +1,6 @@
 import { getSession } from '@jbrowse/core/util';
+import { translateTranscript } from '@jbrowse/core/util/translateTranscript';
 import { useFetch } from '../../utils/useFetch';
-import { getProteinSequenceFromFeature } from './calculateProteinSequence';
 import { fetchSeq } from './fetchSeq';
 export function useFeatureSequence({ view, feature, }) {
     const assemblyName = view?.assemblyNames?.[0];
@@ -18,11 +18,8 @@ export function useFeatureSequence({ view, feature, }) {
     });
     return {
         proteinSequence: sequence && feature
-            ? getProteinSequenceFromFeature({
-                seq: sequence.seq,
-                feature,
-                assemblyGeneticCodeId: sequence.assemblyGeneticCodeId,
-            })
+            ? (translateTranscript({ transcript: feature, ...sequence })?.protein ??
+                '')
             : '',
         sequence,
         error,

package/dist/LaunchMsaView/launchTarget.test.js

@@ -52,7 +52,7 @@ describe('launchTarget', () => {
     test('offers nothing when nothing was clicked', () => {
         expect(launchTarget({ contextMenuItems: () => [] })).toBeUndefined();
     });
-    // v3.7.0 hosts have contextMenuFeature and nothing else; dropping this
+    // 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')));