jbrowse-plugin-msaview 2.7.1 → 2.7.2

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js

@@ -1,5 +1,4 @@
 import React, { useState } from 'react';
-import { useLocalStorage } from '@jbrowse/core/util';
 import SettingsIcon from '@mui/icons-material/Settings';
 import { IconButton } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
@@ -9,6 +8,7 @@ import NCBIBlastMethodSelector from './NCBIBlastMethodSelector';
 import NCBIBlastRIDPanel from './NCBIBlastRIDPanel';
 import NCBISettingsDialog from './NCBISettingsDialog';
 import { BASE_BLAST_URL } from './consts';
+import { useLocalStorage } from '../../../utils/useLocalStorage';
 const useStyles = makeStyles()({
     settingsButton: {
         float: 'right',

package/dist/LaunchMsaView/components/calculateProteinSequence.d.ts

@@ -1,14 +1,15 @@
 import type { Feat } from './types';
 import type { Feature } from '@jbrowse/core/util';
-export declare function stitch(subfeats: Feat[], sequence: string): string;
-export declare function calculateProteinSequence({ cds, sequence, }: {
+export declare function calculateProteinSequence({ cds, sequence, geneticCodeId, }: {
     cds: Feat[];
     sequence: string;
+    geneticCodeId?: number;
 }): string;
 export declare function revlist(list: Feat[], seqlen: number): {
     start: number;
     end: number;
     type?: string;
+    phase?: number;
 }[];
 export declare function getProteinSequenceFromFeature({ feature, seq, }: {
     seq: string;

package/dist/LaunchMsaView/components/calculateProteinSequence.js

@@ -1,18 +1,25 @@
-import { dedupe, defaultCodonTable, generateCodonTable, revcom, } from '@jbrowse/core/util';
-// pure constant: the standard codon table never varies, so build it once rather
-// than on every translation (which runs on every panel re-render)
-const codonTable = generateCodonTable(defaultCodonTable);
-export function stitch(subfeats, sequence) {
-    return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
-}
-export function calculateProteinSequence({ cds, sequence, }) {
-    const str = stitch(cds, sequence);
-    let protein = '';
-    for (let i = 0; i < str.length; i += 3) {
-        // use & symbol for undefined codon, or partial slice
-        protein += codonTable[str.slice(i, i + 3)] ?? '&';
-    }
-    return protein;
+import { dedupe, revcom } from '@jbrowse/core/util';
+import { convertCodingSequenceToPeptides } from '@jbrowse/core/util/convertCodingSequenceToPeptides';
+import { getGeneticCode, parseTranslTable } from './geneticCodes';
+// `@jbrowse/core/util/convertCodingSequenceToPeptides` is a deep path, so unlike
+// the `@jbrowse/core/util` barrel it is absent from ReExports and gets bundled
+// rather than resolved out of the host's JBrowseExports. That is what makes
+// reusing core's translation safe across every host a config names: this module
+// previously built its codon table at module scope from the barrel's
+// `defaultCodonTable`, and a core build that dropped that export turned it into
+// `Object.keys(undefined)` while the UMD was still evaluating -- the plugin
+// global was never assigned and PluginLoader error-paged the whole app.
+export function calculateProteinSequence({ cds, sequence, geneticCodeId, }) {
+    // `starts` is deliberately not passed: @jbrowse/core 4.3.0's signature has no
+    // such parameter, so alternative initiators (GTG under table 11, ATA under
+    // table 2) render as their internal residue rather than M. Core main added it;
+    // pass it here when msaview's @jbrowse/core floor reaches that release.
+    const { codonTable } = getGeneticCode(geneticCodeId);
+    return convertCodingSequenceToPeptides({
+        cds,
+        sequence,
+        codonTable,
+    });
 }
 export function revlist(list, seqlen) {
     return list
@@ -33,8 +40,17 @@ export function getProteinSequenceFromFeature({ feature, seq, }) {
         end: sub.end - start,
     }))
         .filter(subfeature => subfeature.type === 'CDS') ?? [], feat => `${feat.start}-${feat.end}`);
+    // a mitochondrial gene declares e.g. transl_table=2, so it translates with
+    // NCBI table 2 rather than the standard code. GFF3 usually carries the
+    // attribute on the CDS rather than the transcript, so check both.
+    const cdsSubfeature = feature
+        .get('subfeatures')
+        ?.find((f) => f.get('type')?.toLowerCase() === 'cds');
+    const geneticCodeId = parseTranslTable(feature.get('transl_table')) ??
+        parseTranslTable(cdsSubfeature?.get('transl_table'));
     return calculateProteinSequence({
         cds: strand === -1 ? revlist(cds, seq.length) : cds,
         sequence: strand === -1 ? revcom(seq) : seq,
+        geneticCodeId,
     });
 }

package/dist/LaunchMsaView/components/geneticCodes.d.ts

@@ -0,0 +1,15 @@
+export interface NcbiGeneticCode {
+    id: number;
+    name: string;
+    ncbieaa: string;
+    sncbieaa: string;
+}
+export declare const ncbiGeneticCodes: NcbiGeneticCode[];
+export interface GeneticCode {
+    id: number;
+    name: string;
+    codonTable: Record<string, string>;
+    starts: string[];
+}
+export declare function getGeneticCode(id?: number): GeneticCode;
+export declare function parseTranslTable(value: unknown): number | undefined;

package/dist/LaunchMsaView/components/geneticCodes.js

@@ -0,0 +1,227 @@
+export const ncbiGeneticCodes = [
+    {
+        id: 1,
+        name: 'Standard',
+        ncbieaa: 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '---M------**--*----M---------------M----------------------------',
+    },
+    {
+        id: 2,
+        name: 'Vertebrate Mitochondrial',
+        ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG',
+        sncbieaa: '----------**--------------------MMMM----------**---M------------',
+    },
+    {
+        id: 3,
+        name: 'Yeast Mitochondrial',
+        ncbieaa: 'FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '----------**----------------------MM---------------M------------',
+    },
+    {
+        id: 4,
+        name: 'Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma',
+        ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '--MM------**-------M------------MMMM---------------M------------',
+    },
+    {
+        id: 5,
+        name: 'Invertebrate Mitochondrial',
+        ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG',
+        sncbieaa: '---M------**--------------------MMMM---------------M------------',
+    },
+    {
+        id: 6,
+        name: 'Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear',
+        ncbieaa: 'FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '--------------*--------------------M----------------------------',
+    },
+    {
+        id: 9,
+        name: 'Echinoderm Mitochondrial; Flatworm Mitochondrial',
+        ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG',
+        sncbieaa: '----------**-----------------------M---------------M------------',
+    },
+    {
+        id: 10,
+        name: 'Euplotid Nuclear',
+        ncbieaa: 'FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '----------**-----------------------M----------------------------',
+    },
+    {
+        id: 11,
+        name: 'Bacterial, Archaeal and Plant Plastid',
+        ncbieaa: 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '---M------**--*----M------------MMMM---------------M------------',
+    },
+    {
+        id: 12,
+        name: 'Alternative Yeast Nuclear',
+        ncbieaa: 'FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '----------**--*----M---------------M----------------------------',
+    },
+    {
+        id: 13,
+        name: 'Ascidian Mitochondrial',
+        ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG',
+        sncbieaa: '---M------**----------------------MM---------------M------------',
+    },
+    {
+        id: 14,
+        name: 'Alternative Flatworm Mitochondrial',
+        ncbieaa: 'FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG',
+        sncbieaa: '-----------*-----------------------M----------------------------',
+    },
+    {
+        id: 15,
+        name: 'Blepharisma Macronuclear',
+        ncbieaa: 'FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '----------*---*--------------------M----------------------------',
+    },
+    {
+        id: 16,
+        name: 'Chlorophycean Mitochondrial',
+        ncbieaa: 'FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '----------*---*--------------------M----------------------------',
+    },
+    {
+        id: 21,
+        name: 'Trematode Mitochondrial',
+        ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG',
+        sncbieaa: '----------**-----------------------M---------------M------------',
+    },
+    {
+        id: 22,
+        name: 'Scenedesmus obliquus Mitochondrial',
+        ncbieaa: 'FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '------*---*---*--------------------M----------------------------',
+    },
+    {
+        id: 23,
+        name: 'Thraustochytrium Mitochondrial',
+        ncbieaa: 'FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '--*-------**--*-----------------M--M---------------M------------',
+    },
+    {
+        id: 24,
+        name: 'Rhabdopleuridae Mitochondrial',
+        ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG',
+        sncbieaa: '---M------**-------M---------------M---------------M------------',
+    },
+    {
+        id: 25,
+        name: 'Candidate Division SR1 and Gracilibacteria',
+        ncbieaa: 'FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '---M------**-----------------------M---------------M------------',
+    },
+    {
+        id: 26,
+        name: 'Pachysolen tannophilus Nuclear',
+        ncbieaa: 'FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '----------**--*----M---------------M----------------------------',
+    },
+    {
+        id: 27,
+        name: 'Karyorelict Nuclear',
+        ncbieaa: 'FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '--------------*--------------------M----------------------------',
+    },
+    {
+        id: 28,
+        name: 'Condylostoma Nuclear',
+        ncbieaa: 'FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '----------**--*--------------------M----------------------------',
+    },
+    {
+        id: 29,
+        name: 'Mesodinium Nuclear',
+        ncbieaa: 'FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '--------------*--------------------M----------------------------',
+    },
+    {
+        id: 30,
+        name: 'Peritrich Nuclear',
+        ncbieaa: 'FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '--------------*--------------------M----------------------------',
+    },
+    {
+        id: 31,
+        name: 'Blastocrithidia Nuclear',
+        ncbieaa: 'FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '----------**-----------------------M----------------------------',
+    },
+    {
+        id: 32,
+        name: 'Balanophoraceae Plastid',
+        ncbieaa: 'FFLLSSSSYY*WCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+        sncbieaa: '---M------*---*----M------------MMMM---------------M------------',
+    },
+    {
+        id: 33,
+        name: 'Cephalodiscidae Mitochondrial',
+        ncbieaa: 'FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG',
+        sncbieaa: '---M-------*-------M---------------M---------------M------------',
+    },
+];
+// The codon order shared by every NCBI table -- the Base1/Base2/Base3 comment
+// rows in gc.prt. codon i = BASE1[i] + BASE2[i] + BASE3[i].
+const BASE1 = 'TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG';
+const BASE2 = 'TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG';
+const BASE3 = 'TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG';
+const CODONS = Array.from({ length: 64 }, (_, i) => BASE1[i] + BASE2[i] + BASE3[i]);
+const ncbiCodeById = new Map(ncbiGeneticCodes.map(t => [t.id, t]));
+// Expand an uppercase codon map so every case combination of a triplet resolves,
+// which is what callers reading raw sequence need.
+function caseExpand(table) {
+    const out = {};
+    for (const [codon, aa] of Object.entries(table)) {
+        const cases = (i) => {
+            const n = codon.charAt(i);
+            return [n.toUpperCase(), n.toLowerCase()];
+        };
+        for (const n0 of cases(0)) {
+            for (const n1 of cases(1)) {
+                for (const n2 of cases(2)) {
+                    out[n0 + n1 + n2] = aa;
+                }
+            }
+        }
+    }
+    return out;
+}
+function buildGeneticCode(id) {
+    const def = ncbiCodeById.get(id);
+    if (!def && id !== 1) {
+        console.warn(`Unknown genetic code (transl_table=${id}); using standard code`);
+    }
+    const { id: resolvedId, name, ncbieaa, sncbieaa, } = def ?? ncbiCodeById.get(1);
+    const table = {};
+    const starts = [];
+    for (const [i, codon] of CODONS.entries()) {
+        table[codon] = ncbieaa[i];
+        if (sncbieaa[i] === 'M') {
+            starts.push(codon);
+        }
+    }
+    return { id: resolvedId, name, codonTable: caseExpand(table), starts };
+}
+const geneticCodeCache = new Map();
+// Resolves the codon map + start set for an NCBI translation-table id, falling
+// back to the standard code (1) for an unrecognized id. Memoized: there are only
+// ~27 tables and each result is immutable.
+export function getGeneticCode(id = 1) {
+    let code = geneticCodeCache.get(id);
+    if (!code) {
+        code = buildGeneticCode(id);
+        geneticCodeCache.set(id, code);
+    }
+    return code;
+}
+// Parses a GFF/GenBank `transl_table` attribute value into an NCBI table id. The
+// GFF adapter yields a string (or an array if the attribute repeated), so this
+// normalizes both; returns undefined for a missing or non-positive-integer value
+// so callers fall back to their default code.
+export function parseTranslTable(value) {
+    const raw = Array.isArray(value) ? value[0] : value;
+    const n = Number(raw);
+    return Number.isInteger(n) && n > 0 ? n : undefined;
+}

package/dist/LaunchMsaView/components/types.d.ts

@@ -2,6 +2,7 @@ export interface Feat {
     start: number;
     end: number;
     type?: string;
+    phase?: number;
 }
 export interface SeqState {
     seq: string;

package/dist/LaunchMsaView/index.js

@@ -4,6 +4,7 @@ import LaunchMsaViewDialog from './components/LaunchMsaViewDialog';
 function isDisplay(elt) {
     return elt.name === 'LinearBasicDisplay';
 }
+const GENE_LIKE_TYPES = new Set(['gene', 'mRNA', 'transcript']);
 function extendStateModel(stateModel) {
     return stateModel.views((self) => {
         const superContextMenuItems = self.contextMenuItems;
@@ -11,35 +12,40 @@ function extendStateModel(stateModel) {
             contextMenuItems() {
                 const track = getContainingTrack(self);
                 const session = getSession(track);
+                const launch = (feature) => {
+                    session.queueDialog(handleClose => [
+                        LaunchMsaViewDialog,
+                        { model: track, handleClose, feature },
+                    ]);
+                };
                 const info = self.contextMenuInfo;
-                const showMsaMenuItem = info && self.isGeneLike;
+                const fetchFullFeature = self.fetchFullFeature;
+                const legacyFeature = self.contextMenuFeature;
+                const onClick = info && fetchFullFeature && self.isGeneLike
+                    ? () => {
+                        fetchFullFeature(info.item.featureId, info.displayedRegionIndex)
+                            .then(feature => {
+                            if (feature) {
+                                launch(feature);
+                            }
+                            else {
+                                session.notify('Could not load feature for MSA view', 'warning');
+                            }
+                        })
+                            .catch((e) => {
+                            session.notifyError(`${e}`, e);
+                        });
+                    }
+                    : legacyFeature &&
+                        GENE_LIKE_TYPES.has(String(legacyFeature.get('type')))
+                        ? () => {
+                            launch(legacyFeature);
+                        }
+                        : undefined;
                 return [
                     ...superContextMenuItems(),
-                    ...(showMsaMenuItem
-                        ? [
-                            {
-                                label: 'Launch MSA view',
-                                icon: AddIcon,
-                                onClick: () => {
-                                    self
-                                        .fetchFullFeature(info.item.featureId, info.displayedRegionIndex)
-                                        .then(feature => {
-                                        if (feature) {
-                                            session.queueDialog(handleClose => [
-                                                LaunchMsaViewDialog,
-                                                { model: track, handleClose, feature },
-                                            ]);
-                                        }
-                                        else {
-                                            session.notify('Could not load feature for MSA view', 'warning');
-                                        }
-                                    })
-                                        .catch((e) => {
-                                        session.notifyError(`${e}`, e);
-                                    });
-                                },
-                            },
-                        ]
+                    ...(onClick
+                        ? [{ label: 'Launch MSA view', icon: AddIcon, onClick }]
                         : []),
                 ];
             },