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* What the panel and the drawer know before anything runs.
*
* Assembled on the **main thread**, from what the reader already sent when the
* file was opened, and deliberately not by asking the worker for it. Three
* things read this — `appliesTo`, which decides whether a task row exists at
* all; the form, which fills its four entry dropdowns; and `estimate`, which
* prices a run before the reader commits to it — and every one of them happens
* while somebody is looking at a list. A round trip to price a row nobody has
* clicked is a round trip that makes the panel feel slow for no result.
*
* The one number here that is derived rather than reported is `startBin`. It is
* the §3.3 arithmetic — a fixed-bin file's `chrom_offset` is the running sum of
* `ceil(length / binsize)` — and it is recomputed here rather than shipped
* because the reader has never had a reason to send it and adding a field to
* `OpenResult` for a panel is the wrong direction. Where the two could disagree
* they cannot: this is the same expression `metacooler/coords.ts` evaluates, and
* `test/unit/analysis-context.test.ts` checks it against a real file's offsets.
*/
import type { AnnotationEntry } from '../annotations/types'
import type { LayoutKind } from '../types'
import type {
AnalysisContext,
AnalysisFraming,
ContextContig,
ContextGenome,
Params,
} from './types'
/** The parts of an open file this needs, named so nothing imports `Session`. */
export interface ContextInput {
uri: string
/** See {@link AnalysisContext.memoryKey}. */
memoryKey?: string
layout: LayoutKind
binsize: number
nBins: number
hasGenomes: boolean
hasWeights: boolean
scoreColumns: string[]
/** The `/contigs` table, flattened, as the reader sends it. */
contigs: { length: number; columns: string[]; data: Record<string, string[] | Float64Array> } | null
/** The `/genomes` table, likewise; `null` for a plain cooler. */
genomes: { length: number; columns: string[]; data: Record<string, string[] | Float64Array> } | null
/** Which genome rows may be shown. `__unbinned__` is not among them (§7.4). */
displayGenomes: Int32Array | null
entries: readonly AnnotationEntry[]
framing: AnalysisFraming | null
blockLoaded: boolean
blockBytes: number
/** Cells in a single-cell container (§3.8); absent or `0` for every other file. */
cells?: number
/** How many of them are ticked; absent means all of them. */
activeCells?: number
/** The ticked cells by name, where fewer than all of them are. */
selectedCells?: readonly string[]
/** The other maps of a deck, for a task that compares two files (§16). */
peers?: Array<{ label: string; uri: string; binsize: number }>
/** The resolution ladder in bp, finest first; absent or empty without one. */
resolutions?: number[]
/** The sequences declared circular, and the declared origins (§8.15). */
circular?: readonly string[]
origins?: Readonly<Record<string, number>>
/** The `.pairs` the map was binned from on open, where it was (§3.7). */
binnedFrom?: { name: string; orientation: boolean }
}
function strings(
table: ContextInput['contigs'],
column: string,
): string[] | null {
const value = table?.data[column]
return Array.isArray(value) ? value : null
}
function numbers(table: ContextInput['contigs'], column: string): Float64Array | null {
const value = table?.data[column]
return value instanceof Float64Array ? value : null
}
/**
* Bins one sequence occupies, at this bin size.
*
* `ceil`, because the last bin of a contig is partial — a sequence length is not
* a multiple of the bin size — and the partial bin is a bin. Rounding down here
* would shift `startBin` for every contig after the first and put every
* subsequent estimate, region default and gate on the wrong sequence.
*/
export function binsForLength(length: number, binsize: number): number {
if (!(binsize > 0) || !(length > 0)) return 0
return Math.ceil(length / binsize)
}
/**
* The same sequences, in the same order, each cut from its first base into bins
* of `binsize` — the grid a vector at a bin size of its own is laid out over.
*
* Base composition is the task that makes one (§18.8): it reads at the map's
* resolution unless told otherwise, and at 10 kb with no map, and a lane or a
* file laid out over the map's grid at any other size gives every sequence after
* the first the values of the one before it. A sequence with no length has no
* bins, as on the session's own grid.
*/
export function gridAt(
contigs: ReadonlyArray<{ name: string; length: number }>,
binsize: number,
): Array<{ name: string; startBin: number; bins: number; length: number }> {
const out: Array<{ name: string; startBin: number; bins: number; length: number }> = []
let startBin = 0
for (const contig of contigs) {
const bins = binsForLength(contig.length, binsize)
if (bins === 0) continue
out.push({ name: contig.name, startBin, bins, length: contig.length })
startBin += bins
}
return out
}
/** Assemble the context. Pure, so a test can build one without a worker. */
export function buildAnalysisContext(input: ContextInput): AnalysisContext {
const names = strings(input.contigs, 'name') ?? []
const lengths = numbers(input.contigs, 'length')
const genomeIds = numbers(input.contigs, 'genome_id')
const contigs: ContextContig[] = []
let startBin = 0
for (let i = 0; i < names.length; i++) {
const length = lengths === null ? 0 : (lengths[i] ?? 0)
const bins = binsForLength(length, input.binsize)
contigs.push({
name: names[i],
length,
startBin,
bins,
genome: genomeIds === null ? -1 : (genomeIds[i] ?? -1),
})
startBin += bins
}
const genomes = genomesOf(input, contigs)
return {
uri: input.uri,
...(input.memoryKey === undefined ? {} : { memoryKey: input.memoryKey }),
layout: input.layout,
hasGenomes: input.hasGenomes,
hasWeights: input.hasWeights,
scoreColumns: input.scoreColumns,
binsize: input.binsize,
nBins: input.nBins,
hasMap: input.binsize > 0 && input.nBins > 0,
contigs,
genomes,
entries: input.entries,
framing: input.framing,
blockLoaded: input.blockLoaded,
blockBytes: input.blockBytes,
...(input.resolutions === undefined || input.resolutions.length === 0
? {}
: { resolutions: [...input.resolutions] }),
// Absent rather than empty where nothing is declared, as on a framing.
...(input.circular === undefined || input.circular.length === 0
? {}
: { circular: [...input.circular] }),
...(input.origins === undefined || Object.keys(input.origins).length === 0
? {}
: { origins: { ...input.origins } }),
// Absent rather than zero on a file with no cells, so that a task asking
// `(context.cells ?? 0) > 0` reads the same on an old stored context as on a
// fresh one.
...(input.cells === undefined || input.cells === 0
? {}
: {
cells: input.cells,
activeCells: input.activeCells ?? input.cells,
...(input.selectedCells === undefined || input.selectedCells.length === 0
? {}
: { selectedCells: input.selectedCells }),
}),
...(input.peers === undefined || input.peers.length === 0 ? {} : { peers: input.peers }),
...(input.binnedFrom === undefined ? {} : { binnedFrom: { ...input.binnedFrom } }),
}
}
/**
* The genomes a task may be offered, with their bin extents.
*
* Built from the *contigs* rather than from a column of the genomes table,
* because the extent of a genome is where its contigs are and §3.3's
* `genome-then-length` ordering is what makes that one contiguous run. A genome
* with no contigs in the table is dropped rather than given an empty extent —
* an entry a task could select and then find nothing in is worse than one that
* is not offered.
*
* `__unbinned__` never appears, and it is excluded by the reader's own
* `display` list rather than by matching the name a second time here. §7.4 is
* emphatic that it is matched by name in exactly one place; this is not that
* place.
*/
function genomesOf(input: ContextInput, contigs: ContextContig[]): ContextGenome[] | null {
if (!input.hasGenomes || input.genomes === null) return null
const names = strings(input.genomes, 'name') ?? []
const allowed =
input.displayGenomes === null ? null : new Set(Array.from(input.displayGenomes))
const spans = new Map<number, { from: number; to: number; contigs: number }>()
for (const contig of contigs) {
if (contig.genome < 0 || contig.bins === 0) continue
const held = spans.get(contig.genome)
if (held === undefined) {
spans.set(contig.genome, {
from: contig.startBin,
to: contig.startBin + contig.bins,
contigs: 1,
})
} else {
held.from = Math.min(held.from, contig.startBin)
held.to = Math.max(held.to, contig.startBin + contig.bins)
held.contigs++
}
}
const out: ContextGenome[] = []
for (const [id, span] of [...spans.entries()].sort((a, b) => a[1].from - b[1].from)) {
if (allowed !== null && !allowed.has(id)) continue
const name = names[id]
if (name === undefined) continue
out.push({ name, extent: [span.from, span.to], contigs: span.contigs })
}
return out
}
/**
* The sequences a `kind: 'sequences'` parameter names, as rows of the table.
*
* **Never answered is every one of them**, which is the convention
* `SequencesParam` states and the one the runners already read with
* `Array.isArray`: the form ticks them all on the way in, so a value that is not
* an array is a job that never went through a form — a stored session, or a
* `chromosomix` line with no `--sequences` — and what those mean is the whole
* file. An **empty array** is a different answer and not a narrower one: it is a
* reader who pressed *None*, and it prices as nothing to read.
*
* A ticked name this file has not got is dropped rather than counted, because a
* deck holds files of different assemblies on purpose and a batch asks every
* panel of it for one reader's list (§5.9). What is priced is what this file can
* answer.
*/
export function tickedContigs(
context: AnalysisContext,
params: Params,
key: string,
): ContextContig[] {
const value = params[key]
if (!Array.isArray(value)) return [...context.contigs]
const names = new Set(value.filter((name): name is string => typeof name === 'string'))
return context.contigs.filter((contig) => names.has(contig.name))
}
/**
* The bin extent a set of sequences spans, for the *is the block enough* question.
*
* The outer bounds rather than a list of runs, which is what `framingCovers`
* takes and is the conservative reading of it: a framing that covers the span
* from the first ticked sequence to the last covers every one in between, and
* one that does not cannot be used for any of them.
*/
export function extentOf(contigs: readonly ContextContig[]): [number, number] {
let from = Number.POSITIVE_INFINITY
let to = 0
for (const contig of contigs) {
from = Math.min(from, contig.startBin)
to = Math.max(to, contig.startBin + contig.bins)
}
return Number.isFinite(from) ? [from, to] : [0, 0]
}
/** The contig of that name, or `undefined`. */
export function contigNamed(
context: AnalysisContext,
name: string,
): ContextContig | undefined {
return context.contigs.find((contig) => contig.name === name)
}
/**
* Whether the framing already covers `extent`, so a task can use the block.
*
* Both axes, and both must be on-diagonal-or-wider: a task that wants
* `chrIV × chrIV` cannot take it from a block showing `chrIV × chrXII`, and the
* cheapest way to get that wrong is to check the rows and assume the columns.
*/
export function framingCovers(
framing: AnalysisFraming | null,
extent: readonly [number, number],
): boolean {
if (framing === null) return false
return (
framing.rows[0] <= extent[0] &&
framing.rows[1] >= extent[1] &&
framing.cols[0] <= extent[0] &&
framing.cols[1] >= extent[1]
)
}
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