Merge pull request #1329 from nextstrain/feat/default-cds

packages_rs/nextclade-cli/src/dataset/dataset_download.rs

@@ -233,8 +233,8 @@ pub fn dataset_individual_files_load(
               rest_files: BTreeMap::default(),
               other: serde_json::Value::default(),
             },
-            default_gene: None,
-            gene_order_preference: vec![],
+            default_cds: None,
+            cds_order_preference: vec![],
             mut_labels: LabelledMutationsConfig::default(),
             primers: vec![],
             qc: None,

packages_rs/nextclade-web/src/components/GeneMap/GeneMap.tsx

@@ -4,7 +4,7 @@ import React, { useCallback, useEffect, useMemo, useState } from 'react'
 import { ReactResizeDetectorDimensions, withResizeDetector } from 'react-resize-detector'
 import { useRecoilValue, useSetRecoilState } from 'recoil'
 import { ErrorInternal } from 'src/helpers/ErrorInternal'
-import { isInNucleotideViewAtom, viewedGeneAtom } from 'src/state/seqViewSettings.state'
+import { isInNucleotideViewAtom, viewedCdsAtom } from 'src/state/seqViewSettings.state'
 import styled from 'styled-components'
 import { BASE_MIN_WIDTH_PX } from 'src/constants'
 import type { Cds, CdsSegment } from 'src/types'
@@ -88,7 +88,7 @@ export function CdsSegmentView({
   const { t } = useTranslationSafe()
   const [showTooltip, setShowTooltip] = useState(false)
 
-  const setViewedGene = useSetRecoilState(viewedGeneAtom)
+  const setViewedGene = useSetRecoilState(viewedCdsAtom)
 
   const [hovered, setHovered] = useState(false)
   const [timeoutId, setTimeoutId] = useState<number | undefined>(undefined)
@@ -224,7 +224,7 @@ export type GeneMapProps = ReactResizeDetectorDimensions
 export function GeneMapUnsized({ width = 0, height = 0 }: GeneMapProps) {
   const cdsesAll = useRecoilValue(cdsesAtom)
   const genomeSize = useRecoilValue(genomeSizeAtom)
-  const viewedGene = useRecoilValue(viewedGeneAtom)
+  const viewedGene = useRecoilValue(viewedCdsAtom)
   const isInNucView = useRecoilValue(isInNucleotideViewAtom)
 
   const { viewBox, cdsSegViews, geneMapHeight } = useMemo(() => {

packages_rs/nextclade-web/src/components/GeneMap/GeneMapAxis.tsx

@@ -3,7 +3,7 @@ import { range } from 'lodash'
 import { XAxis, ComposedChart, ResponsiveContainer } from 'recharts'
 import { useRecoilValue } from 'recoil'
 import { cdsesAtom, genomeSizeAtom } from 'src/state/results.state'
-import { viewedGeneAtom } from 'src/state/seqViewSettings.state'
+import { viewedCdsAtom } from 'src/state/seqViewSettings.state'
 import { getAxisLength } from './getAxisLength'
 
 const MARGIN = {}
@@ -26,7 +26,7 @@ export function getTickSize(axisLength: number) {
 export function GeneMapAxis() {
   const genomeSize = useRecoilValue(genomeSizeAtom)
   const cdses = useRecoilValue(cdsesAtom)
-  const viewedGene = useRecoilValue(viewedGeneAtom)
+  const viewedGene = useRecoilValue(viewedCdsAtom)
 
   const { ticks, domain } = useMemo(() => {
     const length = getAxisLength(genomeSize, viewedGene, cdses)

packages_rs/nextclade-web/src/components/GeneMap/getAxisLength.ts

@@ -1,11 +1,11 @@
 import type { Cds } from 'src/types'
-import { GENE_OPTION_NUC_SEQUENCE } from 'src/constants'
+import { CDS_OPTION_NUC_SEQUENCE } from 'src/constants'
 import { cdsCodonLength } from 'src/types'
 
 /** Retrieves length of the axis to draw: Genome size in case of nuc sequence, or gene length on case of gene */
 export function getAxisLength(genomeSize: number, viewedGene: string, cdses: Cds[]) {
   let length = genomeSize
-  if (viewedGene !== GENE_OPTION_NUC_SEQUENCE) {
+  if (viewedGene !== CDS_OPTION_NUC_SEQUENCE) {
     const cds = cdses?.find((cds) => cds.name === viewedGene)
     if (cds) {
       length = Math.round(cdsCodonLength(cds))

packages_rs/nextclade-web/src/components/Results/ResultsTable.tsx

@@ -4,7 +4,7 @@ import { useTranslationSafe as useTranslation } from 'src/helpers/useTranslation
 import { FixedSizeList as FixedSizeListBase, FixedSizeListProps } from 'react-window'
 import AutoSizerBase from 'react-virtualized-auto-sizer'
 import { useRecoilCallback, useRecoilValue } from 'recoil'
-import { viewedGeneAtom } from 'src/state/seqViewSettings.state'
+import { viewedCdsAtom } from 'src/state/seqViewSettings.state'
 import styled from 'styled-components'
 
 import { SortCategory, SortDirection } from 'src/helpers/sortResults'
@@ -78,7 +78,7 @@ export function ResultsTable() {
   const aaMotifsDescs = useRecoilValue(aaMotifsDescsAtom)
 
   const isResultsFilterPanelCollapsed = useRecoilValue(isResultsFilterPanelCollapsedAtom)
-  const viewedGene = useRecoilValue(viewedGeneAtom)
+  const viewedGene = useRecoilValue(viewedCdsAtom)
 
   const rowData: TableRowDatum[] = useMemo(() => {
     return seqIndices.map((seqIndex) => ({

packages_rs/nextclade-web/src/components/Results/ResultsTableRowResult.tsx

@@ -26,7 +26,7 @@ import {
 } from 'src/components/Results/ResultsTableStyle'
 import { PeptideView } from 'src/components/SequenceView/PeptideView'
 import { SequenceView } from 'src/components/SequenceView/SequenceView'
-import { GENE_OPTION_NUC_SEQUENCE } from 'src/constants'
+import { CDS_OPTION_NUC_SEQUENCE } from 'src/constants'
 import { analysisResultAtom } from 'src/state/results.state'
 import { ColumnCoverage } from 'src/components/Results/ColumnCoverage'
 import { ColumnAaMotifs } from 'src/components/Results/ColumnAaMotifs'
@@ -185,7 +185,7 @@ export function ResultsTableRowResult({
 
       <TableCell basis={columnWidthsPx.sequenceView} grow={1} shrink={0}>
         <Suspense fallback={null}>
-          {viewedGene === GENE_OPTION_NUC_SEQUENCE ? (
+          {viewedGene === CDS_OPTION_NUC_SEQUENCE ? (
             <SequenceView key={seqName} sequence={analysisResult} />
           ) : (
             <PeptideView key={seqName} sequence={analysisResult} viewedGene={viewedGene} warnings={warnings} />

packages_rs/nextclade-web/src/components/SequenceView/ListOfAminoacidDeletions.tsx

@@ -8,7 +8,7 @@ import { useTranslationSafe } from 'src/helpers/useTranslationSafe'
 import { splitToRows } from 'src/components/Results/splitToRows'
 import { TableSlim } from 'src/components/Common/TableSlim'
 import { AminoacidMutationBadge } from 'src/components/Common/MutationBadge'
-import { geneOrderPreferenceAtom } from 'src/state/dataset.state'
+import { cdsOrderPreferenceAtom } from 'src/state/dataset.state'
 import { sortByCdsName } from './sortByCdsName'
 
 export interface ListOfAminoacidDeletionsProps {
@@ -18,7 +18,7 @@ export interface ListOfAminoacidDeletionsProps {
 export function ListOfAminoacidDeletions({ aminoacidDeletions }: ListOfAminoacidDeletionsProps) {
   const { t } = useTranslationSafe()
 
-  const geneOrderPreference = useRecoilValue(geneOrderPreferenceAtom)
+  const geneOrderPreference = useRecoilValue(cdsOrderPreferenceAtom)
 
   const totalDeletions = aminoacidDeletions.length
   const maxRows = 6

packages_rs/nextclade-web/src/components/SequenceView/ListOfAminoacidSubstitutions.tsx

@@ -3,7 +3,7 @@ import { useRecoilValue } from 'recoil'
 import copy from 'fast-copy'
 
 import type { AaSub } from 'src/types'
-import { geneOrderPreferenceAtom } from 'src/state/dataset.state'
+import { cdsOrderPreferenceAtom } from 'src/state/dataset.state'
 import { formatAAMutation } from 'src/helpers/formatMutation'
 import { useTranslationSafe } from 'src/helpers/useTranslationSafe'
 import { splitToRows } from 'src/components/Results/splitToRows'
@@ -18,7 +18,7 @@ export interface ListOfAminoacidMutationsProps {
 export function ListOfAminoacidSubstitutions({ aminoacidSubstitutions }: ListOfAminoacidMutationsProps) {
   const { t } = useTranslationSafe()
 
-  const geneOrderPreference = useRecoilValue(geneOrderPreferenceAtom)
+  const geneOrderPreference = useRecoilValue(cdsOrderPreferenceAtom)
 
   const totalMutations = aminoacidSubstitutions.length
   const maxRows = Math.min(8, totalMutations)

packages_rs/nextclade-web/src/components/SequenceView/SequenceSelector.tsx

@@ -10,9 +10,9 @@ import { Badge as BadgeBase } from 'reactstrap'
 import { ButtonFilter } from 'src/components/Results/ButtonFilter'
 import { notUndefinedOrNull } from 'src/helpers/notUndefined'
 import styled from 'styled-components'
-import { viewedGeneAtom } from 'src/state/seqViewSettings.state'
+import { viewedCdsAtom } from 'src/state/seqViewSettings.state'
 import { useRecoilState, useRecoilValue } from 'recoil'
-import { GENE_OPTION_NUC_SEQUENCE } from 'src/constants'
+import { CDS_OPTION_NUC_SEQUENCE } from 'src/constants'
 import { useTranslationSafe } from 'src/helpers/useTranslationSafe'
 import { genesAtom } from 'src/state/results.state'
 import { ensureNumber } from 'src/helpers/number'
@@ -30,23 +30,23 @@ export interface Option {
 
 export function SequenceSelector() {
   const genes = useRecoilValue(genesAtom)
-  const [viewedGene, setViewedGene] = useRecoilState(viewedGeneAtom)
+  const [viewedGene, setViewedGene] = useRecoilState(viewedCdsAtom)
 
   const { options, defaultOption } = useMemo(() => {
     return prepareOptions(genes)
   }, [genes])
 
   const option = useMemo((): Option => {
-    if (viewedGene === GENE_OPTION_NUC_SEQUENCE) {
-      return { value: GENE_OPTION_NUC_SEQUENCE }
+    if (viewedGene === CDS_OPTION_NUC_SEQUENCE) {
+      return { value: CDS_OPTION_NUC_SEQUENCE }
     }
     return options.find((option) => option.cds?.name === viewedGene) ?? defaultOption
   }, [defaultOption, options, viewedGene])
 
   const onChange = useCallback(
     (option: Option | null) => {
-      if (option?.value === GENE_OPTION_NUC_SEQUENCE) {
-        setViewedGene(GENE_OPTION_NUC_SEQUENCE)
+      if (option?.value === CDS_OPTION_NUC_SEQUENCE) {
+        setViewedGene(CDS_OPTION_NUC_SEQUENCE)
       }
 
       if (option?.cds?.name) {
@@ -135,7 +135,7 @@ function OptionLabel(option: Option, meta: FormatOptionLabelMeta<Option>) {
     return <OptionLabelProtein protein={option.protein} isMenu={meta.context === 'menu'} />
   }
 
-  if (option.value === GENE_OPTION_NUC_SEQUENCE) {
+  if (option.value === CDS_OPTION_NUC_SEQUENCE) {
     return <OptionLabelFullGenome isMenu={meta.context === 'menu'} />
   }
 
@@ -224,7 +224,7 @@ const Indent = styled.div<{ indent?: number | boolean }>`
 `
 
 function prepareOptions(genes: Gene[]) {
-  const options: Option[] = [{ value: GENE_OPTION_NUC_SEQUENCE }]
+  const options: Option[] = [{ value: CDS_OPTION_NUC_SEQUENCE }]
 
   if (isEmpty(genes)) {
     return { options, defaultOption: options[0] }
@@ -276,7 +276,7 @@ function prepareOptions(genes: Gene[]) {
 }
 
 const checkSearchCandidateEntry = (candidate: FilterOptionOption<Option>, searchTerm: string): boolean => {
-  if (candidate.value === GENE_OPTION_NUC_SEQUENCE) {
+  if (candidate.value === CDS_OPTION_NUC_SEQUENCE) {
     return true
   }
 

packages_rs/nextclade-web/src/constants.ts

@@ -80,4 +80,4 @@ export const ANY = '.' as const
 export const AMINOACID_UNKNOWN = 'X' as const as Aminoacid
 export const AMINOACID_GAP = '-' as const as Aminoacid
 
-export const GENE_OPTION_NUC_SEQUENCE = 'Sequence' // Show nucleotide sequence in sequence view (as opposed to a gene)
+export const CDS_OPTION_NUC_SEQUENCE = 'Sequence' // Show nucleotide sequence in sequence view (as opposed to a gene)

packages_rs/nextclade-web/src/hooks/useRunAnalysis.ts

@@ -4,12 +4,12 @@ import { changeColorBy } from 'auspice/src/actions/colors'
 import { useRouter } from 'next/router'
 import { useDispatch } from 'react-redux'
 import { useRecoilCallback } from 'recoil'
-import { viewedGeneAtom } from 'src/state/seqViewSettings.state'
+import { viewedCdsAtom } from 'src/state/seqViewSettings.state'
 import { AlgorithmGlobalStatus } from 'src/types'
 import { sanitizeError } from 'src/helpers/sanitizeError'
 import { auspiceStartClean, treeFilterByNodeType } from 'src/state/auspice/auspice.actions'
 import { createAuspiceState } from 'src/state/auspice/createAuspiceState'
-import { datasetCurrentAtom, geneOrderPreferenceAtom } from 'src/state/dataset.state'
+import { datasetCurrentAtom, cdsOrderPreferenceAtom } from 'src/state/dataset.state'
 import { globalErrorAtom } from 'src/state/error.state'
 import {
   geneMapInputAtom,
@@ -48,8 +48,8 @@ export function useRunAnalysis() {
         set(showNewRunPopupAtom, false)
 
         reset(analysisResultsAtom)
-        reset(viewedGeneAtom)
-        reset(geneOrderPreferenceAtom)
+        reset(viewedCdsAtom)
+        reset(cdsOrderPreferenceAtom)
 
         const numThreads = getPromise(numThreadsAtom)
         const datasetCurrent = getPromise(datasetCurrentAtom)
@@ -71,8 +71,8 @@ export function useRunAnalysis() {
           onInitialData({
             geneMap,
             genomeSize,
-            defaultGene,
-            geneOrderPreference,
+            defaultCds,
+            cdsOrderPreference,
             cladeNodeAttrKeyDescs,
             phenotypeAttrDescs,
             aaMotifsDescs,
@@ -85,12 +85,12 @@ export function useRunAnalysis() {
             set(cdsesAtom, cdses)
             set(genomeSizeAtom, genomeSize)
 
-            if (defaultGene) {
-              set(viewedGeneAtom, defaultGene)
+            if (defaultCds) {
+              set(viewedCdsAtom, defaultCds)
             }
 
-            if (geneOrderPreference) {
-              set(geneOrderPreferenceAtom, geneOrderPreference)
+            if (cdsOrderPreference) {
+              set(cdsOrderPreferenceAtom, cdsOrderPreference)
             }
 
             // FIXME: This type is duplicated. One comes from handwritten Auspice typings,

packages_rs/nextclade-web/src/state/dataset.state.ts

@@ -2,9 +2,7 @@ import { isNil } from 'lodash'
 import { atom, DefaultValue, selector } from 'recoil'
 
 import type { Dataset, MinimizerIndexVersion } from 'src/types'
-// import { GENE_OPTION_NUC_SEQUENCE } from 'src/constants'
 import { persistAtom } from 'src/state/persist/localStorage'
-// import { viewedGeneAtom } from 'src/state/seqViewSettings.state'
 import { isDefaultValue } from 'src/state/utils/isDefaultValue'
 import { areDatasetsEqual } from 'src/types'
 
@@ -46,8 +44,8 @@ export const datasetUpdatedAtom = atom<Dataset | undefined>({
   default: undefined,
 })
 
-export const geneOrderPreferenceAtom = atom<string[]>({
-  key: 'geneOrderPreference',
+export const cdsOrderPreferenceAtom = atom<string[]>({
+  key: 'cdsOrderPreferenceAtom',
   default: [],
 })
 

packages_rs/nextclade-web/src/state/seqViewSettings.state.ts

@@ -1,5 +1,5 @@
 import { atom, selector } from 'recoil'
-import { GENE_OPTION_NUC_SEQUENCE } from 'src/constants'
+import { CDS_OPTION_NUC_SEQUENCE } from 'src/constants'
 import { ErrorInternal } from 'src/helpers/ErrorInternal'
 
 import { persistAtom } from 'src/state/persist/localStorage'
@@ -93,18 +93,18 @@ export const maxNucMarkersAtom = atom<number>({
   effects: [persistAtom],
 })
 
-export const viewedGeneAtom = atom<string>({
-  key: 'viewedGene',
-  default: GENE_OPTION_NUC_SEQUENCE,
+export const viewedCdsAtom = atom<string>({
+  key: 'viewedCdsAtom',
+  default: CDS_OPTION_NUC_SEQUENCE,
 })
 
 export const isInNucleotideViewAtom = selector<boolean>({
   key: 'isInNucleotideView',
-  get: ({ get }) => get(viewedGeneAtom) === GENE_OPTION_NUC_SEQUENCE,
+  get: ({ get }) => get(viewedCdsAtom) === CDS_OPTION_NUC_SEQUENCE,
 })
 
 export const switchToNucleotideViewAtom = selector({
   key: 'switchToNucleotideView',
   get: () => undefined,
-  set: ({ set }) => set(viewedGeneAtom, GENE_OPTION_NUC_SEQUENCE),
+  set: ({ set }) => set(viewedCdsAtom, CDS_OPTION_NUC_SEQUENCE),
 })

packages_rs/nextclade/src/analyze/virus_properties.rs

@@ -41,10 +41,10 @@ pub struct VirusProperties {
 
   pub files: DatasetFiles,
 
-  pub default_gene: Option<String>,
+  pub default_cds: Option<String>,
 
   #[serde(default, skip_serializing_if = "Vec::is_empty")]
-  pub gene_order_preference: Vec<String>,
+  pub cds_order_preference: Vec<String>,
 
   #[serde(default)]
   pub mut_labels: LabelledMutationsConfig,

packages_rs/nextclade/src/run/nextclade_wasm.rs

@@ -85,9 +85,9 @@ pub struct AnalysisInitialData<'a> {
   pub genome_size: usize,
   pub gene_map: GeneMap,
   #[serde(default, skip_serializing_if = "Option::is_none")]
-  pub default_gene: Option<String>,
+  pub default_cds: Option<String>,
   #[serde(default, skip_serializing_if = "Vec::is_empty")]
-  pub gene_order_preference: Vec<String>,
+  pub cds_order_preference: Vec<String>,
   pub clade_node_attr_key_descs: &'a [CladeNodeAttrKeyDesc],
   pub phenotype_attr_descs: &'a [PhenotypeAttrDesc],
   pub aa_motifs_descs: &'a [AaMotifsDesc],
@@ -241,8 +241,8 @@ impl Nextclade {
     AnalysisInitialData {
       gene_map: self.gene_map.clone(),
       genome_size: self.ref_seq.len(),
-      default_gene: self.virus_properties.default_gene.clone(),
-      gene_order_preference: self.virus_properties.gene_order_preference.clone(),
+      default_cds: self.virus_properties.default_cds.clone(),
+      cds_order_preference: self.virus_properties.cds_order_preference.clone(),
       clade_node_attr_key_descs: &self.clade_attr_descs,
       phenotype_attr_descs: &self.phenotype_attr_descs,
       aa_motifs_descs: &self.aa_motifs_descs,