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* The worker message protocol — the shared vocabulary between the main thread
* and the reader worker.
*
* The worker owns *all* I/O (HDF5 mounts, range requests, the sidecar edge-list
* `fetch`), so no user gesture on the main thread can ever block on a byte that
* has not arrived. Everything crossing the boundary is therefore either plain
* data or a transferable buffer.
*
* Two things need explicit care at this boundary:
*
* 1. **Errors.** A structured clone of an `Error` subclass loses the subclass:
* `ViewerError` arrives on the other side as a bare `Error` with no `code`
* and no `detail`, which would collapse every named refusal of spec §10 into
* "something went wrong". They are serialised and revived explicitly.
* 2. **Tables.** {@link Table} carries methods (`get`, `strings`, `numbers`),
* and methods do not survive structured cloning. Tables travel as
* {@link TablePayload} and are rehydrated by {@link tableFromPayload}.
*/
import { ViewerError, type ErrorCode } from '../errors'
import type { ReferenceEdit } from '../genome/edit'
import type { FileCorner } from '../edit/corners'
import type { GridLayout } from '../edit/grid'
import type { WindowRead } from '../edit/paint'
import type { RefinedPoint, RefinePoint } from '../edit/refine'
import type { Expected } from '../edit/method'
import type { SequenceEvidence } from '../edit/sequenceEvidence'
import type { Suggested } from '../edit/suggest'
import type { PictureContacts } from '../metacooler/picture'
import type { NameContext, NameMatch } from '../genome/naming'
import type { S3Credential } from '../s3/sigv4'
import type { Column, Extent, Info, Layout, ParsedRange, SourceStats, Table } from '../types'
import type { Census, ResampleMode } from '../metacooler/resample'
import type { PairStats } from '../pairs/stats'
// ---------------------------------------------------------------------------
// Byte sources
// ---------------------------------------------------------------------------
/** Which of the two byte-source implementations to build (spec §6.1). */
export type SourceKind = 'local' | 'remote'
/**
* How to obtain the bytes. A `File` is structured-cloneable, so a dropped file
* is handed to the worker by reference — it is never read into a buffer on the
* main thread and it never leaves the browser (spec §11).
*
* A remote source may carry the credential that signs it. It travels *with the
* URL* rather than being configured on the worker, and the two properties that
* follow are both wanted:
*
* - The worker holds no credential store and cannot enumerate one. It is handed
* the single key the URL it was given needs, for as long as that open lasts.
* - `localStorage` does not exist in a worker, so a worker-side lookup was never
* available anyway — the shape the platform forces is also the better one.
*
* Absent means an unsigned request, which is the whole of the public path: the
* demo bucket is read with no `Authorization` header, no preflight, and no
* credential ever reaching this message.
*/
/**
* Where a file's bytes are, and — for the one format that is two files — where
* its other half's are.
*
* `bins` is the HiC-Pro pair (§3.9), and it is the same shape as the thing it
* hangs off because it is the same question asked twice: a bin file may be a
* local drop or a URL exactly as its matrix may. It is not a sidecar index in
* the §8.11 sense — the matrix is unreadable without it rather than merely
* slower — so its absence is a refusal rather than a fallback.
*/
export type SourceSpec = SourceLocation & {
bins?: SourceLocation
/**
* How to read this file, when the default is known to be wrong for it.
*
* Absent is the default, and is what every file takes. It is set only by the
* shell re-issuing an open with the reader's answer to a load gate, and it
* doubles as the token that says the gate has been answered — which is why it
* sits out here rather than on the remote arm: §3.8's gate is about round
* trips and fires only over the network, but §3.9's is about parsing and
* memory and fires on a local file just the same.
*
* - `whole` — one `GET` of the entire object, then everything is instant.
* The only answer a HiC-Pro pair has, since it is read whole regardless.
* - `fine` — small chunks, little bandwidth, many round trips. An `.scool`
* only (§3.8); nothing else has a scattered-metadata problem to trade against.
*/
reading?: 'whole' | 'fine'
}
type SourceLocation =
| { kind: 'local'; file: File; index?: File }
| {
kind: 'remote'
url: string
credential?: S3Credential
/**
* The sidecar index named beside the URL — `<url>#index=<url>` split at
* the door — for the one question the shell asks the annotations worker
* about a remote file before opening it as a genome: a FASTA's assembly
* is read from its `.fai` (§8.8), and a name the reader gave must reach
* that question and not only the track loaded afterwards.
*/
index?: string
/**
* Static headers put on **every** request for this URL (SPECS §24.7).
*
* The other kind of credential, and it travels for the same reason the
* first one does: a Google API key and a bearer token are read from
* `localStorage` and from a registry that exist only on the main thread,
* so the worker is handed the headers the URL it was given needs rather
* than a way to work them out.
*
* Unlike the signature, they are *static* — the same on the `HEAD`, the
* probe, every ranged read and the whole-object fallback — because they
* are a statement about who is asking rather than about what is being
* asked. `sources/access.ts` is the one place the two are merged, in the
* one order that works.
*/
headers?: Record<string, string>
}
/**
* How a `.pairs` file is turned into a map (§3.7).
*
* Present only on the second `open` of one: the first is refused with
* `pairs-binning-needed`, because a contact list declares no resolution and
* there is nothing to open it *at* until a reader has chosen one.
*/
export interface PairsBinning {
/** Bin size of the finest rung, in base pairs. */
base: number
/** How many rungs the ladder has, base included. */
rungs: number
/** Positions are 1-based, per the 4DN spec. */
oneBased?: boolean
/** Hand the written `.mcool` to the browser as soon as it is built. */
download?: boolean
}
/** What a probe of a `.pairs` learned, for the dialog that picks a resolution. */
export interface PairsProbeResult {
contigs: Array<{ name: string; length: number }>
genomeLength: number
/** Exact when the file is indexed, `null` otherwise. */
records: number | null
indexed: boolean
assembly: string | null
sorted: string | null
sourceBytes: number
/** The base resolution the dialog opens on. */
suggestedBase: number
}
// ---------------------------------------------------------------------------
// Wire-safe tables
// ---------------------------------------------------------------------------
/**
* A {@link Table} flattened for structured cloning: column order preserved,
* every numeric column narrowed to `Float64Array` (int64 columns arrive as
* `BigInt64Array`, and mixing `BigInt` with `Number` throws at *runtime*, so
* the narrowing happens once, here — spec §6.2).
*/
export interface TablePayload {
length: number
columns: string[]
data: Record<string, string[] | Float64Array>
}
/** `true` when a decoded column holds strings rather than numbers. */
function isStringColumn(column: Column): column is string[] {
return Array.isArray(column) && (column.length === 0 || typeof column[0] === 'string')
}
/**
* Flatten a {@link Table} for transfer. Numeric columns become `Float64Array`.
*
* Every numeric column is **copied**, even one that is already a
* `Float64Array`. {@link transfersFor} moves the buffers it finds rather than
* cloning them, and moving a buffer detaches it: handing over the reader's own
* `/contigs/length` array would leave the still-open `MetaCooler` reading from
* a zero-length view on the next query.
*/
export function tableToPayload(table: Table): TablePayload {
const data: Record<string, string[] | Float64Array> = {}
for (const name of table.columns) {
const column = table.data[name]
if (column === undefined) continue
if (isStringColumn(column)) {
// Strings are structured-cloned, not transferred, so sharing is safe.
data[name] = column
} else if (column instanceof BigInt64Array) {
data[name] = Float64Array.from(column, Number)
} else {
data[name] = Float64Array.from(column as ArrayLike<number>)
}
}
return { length: table.length, columns: [...table.columns], data }
}
/**
* Rebuild a usable {@link Table} from a payload. The column *set* is whatever
* the file had — nothing here knows the names of `/genomes`' optional metadata
* columns, which is what lets the genomes table render them generically (§5.1).
*/
export function tableFromPayload(payload: TablePayload): Table {
const data = payload.data as Record<string, Column>
return {
length: payload.length,
columns: payload.columns,
data,
get(column: string, row: number): string | number | undefined {
const col = payload.data[column]
if (col === undefined || row < 0 || row >= payload.length) return undefined
return col[row]
},
strings(column: string): string[] {
const col = payload.data[column]
if (col === undefined) throw new Error(`no such column: ${column}`)
if (!Array.isArray(col)) throw new Error(`column ${column} is not a string column`)
return col
},
numbers(column: string): number[] {
const col = payload.data[column]
if (col === undefined) throw new Error(`no such column: ${column}`)
if (Array.isArray(col)) throw new Error(`column ${column} is not a numeric column`)
return Array.from(col)
},
}
}
/** `true` when a payload column should be treated as text by the UI. */
export function payloadColumnIsText(column: string[] | Float64Array): column is string[] {
return Array.isArray(column)
}
// ---------------------------------------------------------------------------
// Reader-side statistics that the UI displays but does not compute
// ---------------------------------------------------------------------------
/**
* Re-exported from the reader so the wire types cannot drift from what the
* reader actually produces. These are *type-only* re-exports: they are erased
* at build time, so importing them here does not drag `MetaCooler` — and with
* it h5wasm — into the main-thread bundle.
*
* `UnassignedStats` is the single retained `__unbinned__` number (§7.4): a
* read-only QC statistic for the info panel that opens nothing and selects
* nothing. `DeepValidation` is the outcome of the opt-in full check (§6.3).
*/
export type { DeepValidation, UnassignedStats } from '../metacooler/MetaCooler'
import type { DeepValidation, UnassignedStats } from '../metacooler/MetaCooler'
// ---------------------------------------------------------------------------
// Results
// ---------------------------------------------------------------------------
/** The `.mcool` an import was written to, ready to be handed to the browser. */
export interface McoolExport {
/** The file's bytes. Transferred rather than copied — see `reader.worker.ts`. */
bytes: Uint8Array
/** What to call it in the download. */
filename: string
/** Rungs it carries, finest first. */
rungs: number[]
}
/** A map lifted through an edit of the reference (§27.8): its bytes, and what was left out. */
export interface LiftedExport extends McoolExport {
/** Contacts written at the finest rung. */
contacts: number
/** Rungs of the file not written, finest first, and why. */
skipped: Array<{ rung: number; why: string }>
}
/** What an import actually did, for the info panel and the status line. */
export interface PairsImportSummary {
base: number
rungs: number[]
records: number
nnz: number
indexed: boolean
/** Records naming a contig the header did not declare. */
skippedUnknownContig: number
/** Records whose position column did not hold a number. */
skippedBadPosition: number
/** Records whose position ran past the declared contig length. */
clampedPosition: number
/** `true` when the file was not `bin1`-ordered and a merge pass ran. */
requiredMerge: boolean
/** `true` when the file ended mid-member or without a BGZF end-of-file marker. */
truncated: boolean
/** Declared sequences with nothing on their own diagonal. */
sequencesWithoutCisContacts: string[]
/** Whether the caller asked for the `.mcool` to be built and downloaded. */
download: boolean
/**
* The four orientation-resolved decay curves, where the file carried strands.
*
* Accumulated in the import's own pass (`pairs/bin.ts`), so it costs two more
* fields off each record and no second read. Carried here rather than fetched
* because the records are gone once the pass ends: the map is the pixel table
* from then on, and this is the one reading that cannot be recovered from it.
*
* `null` for a file with no `strand1`/`strand2` columns, which is a fact about
* the file rather than a failure.
*/
orientation: OrientationSummary | null
/**
* What `pairtools stats` counts over the same records (`pairs/stats.ts`),
* counted in the same pass and carried for the same reason: the records are
* gone once the pass ends, and every one of these numbers is about records.
*/
stats: PairStats | null
/** The binning that produced this map, so a second mount can reproduce it. */
binning: PairsBinning
}
/** {@link PairsImportSummary.orientation}, as plain arrays that cross a worker. */
export interface OrientationSummary {
edges: Float64Array
counts: [Float64Array, Float64Array, Float64Array, Float64Array]
total: number
}
export interface OpenResult {
uri: string
layout: Layout
info: Info
metadata: Record<string, unknown>
binsize: number | null
shape: [number, number]
nGenomes: number
nContigs: number
nBins: number
unassigned: UnassignedStats | null
/**
* The bins a whole-file picture may draw: everything but `__unbinned__`.
*
* `[0, nBins]` for a cooler and for a metacool written with
* `drop_unassigned`. Elsewhere it is the range with the unassigned contigs
* left out — they are not a genome, are shown nowhere else (§7.4), and on a
* real metagenome are the largest thing in the picture.
*/
displayExtent: Extent
/**
* Sibling names of the enclosing collection; `[]` for a plain file. The other
* maps of an mmetacool (§3.4), or the other resolutions of an mcool (§9).
*/
entries: string[]
/** The group they live under: `entries` (mmetacool) or `resolutions` (mcool). */
entryGroup: string
/**
* Every cell of an `.scool`, in file order; `[]` for every other container.
*
* Separate from {@link entries} on purpose, though both are sibling coolers
* in one file. An mcool's resolutions are *rungs of the same map* and belong
* in the breadcrumb's picker beside it; an scool's cells are the map's
* **subject**, thousands of them, sorted and filtered and ticked — a table,
* not a drop-down. Folding them into one list would put four thousand entries
* in a menu and lose the columns that make them choosable.
*
* Paid for at open, and it is the one thing an scool costs: the names come
* from walking the container's HDF5 link storage, which writers scatter
* across the whole file (§12).
*/
cells: string[]
/**
* The cells the open map is currently summing, in file order.
*
* Equal to {@link cells} for a file opened with nothing chosen, which is what
* dropping one means: an scool with no selection is the pseudo-bulk of
* everything in it. `[]` for every other container.
*/
activeCells: string[]
/**
* Stored pixels across {@link activeCells}; `null` for every other container.
*
* The cost forecast the whole-file gate asks for, and an scool is the one
* file where the root's own `nnz` cannot answer it: a standard container does
* not write one (it has no pixels of its own) and a flat one writes nothing
* at all. What the reader would otherwise conclude is "this file declares no
* cost", and the read it then starts unwarned is a pass over every pixel of
* every selected cell — the most expensive thing the format can be asked for.
*
* Recomputed whenever the set changes, because it is a property of the set:
* one cell of a 3,882-cell file is four orders of magnitude cheaper than all
* of them, and a gate quoting the file's total would fire on both.
*/
cellNnz: number | null
/** `false` for a plain cooler, which has no genome layer to browse. */
hasGenomes: boolean
/** `true` when `/bins/weight` exists, so balanced counts can be offered. */
hasWeights: boolean
/**
* The `/pixels` value columns, `count` first — what the score picker lists.
*
* On the info rather than fetched on demand because it is one group listing
* taken while the file is being opened anyway, and because every view that
* offers the picker would otherwise ask for it separately.
*/
scoreColumns: string[]
/** Byte size of the source — the remote overview gate is a byte threshold (§7.3). */
sourceBytes: number
/**
* The contacts the file says it holds (§6.5): cooler's `attrs['sum']`, a pairs
* import's records — what the *contacts* box shows before anything is typed
* in it. `null` where the file does not say exactly, a `.hic` among them, and
* a `contacts` request then counts them.
*/
contacts: number | null
/** Present only when this map was imported from a `.pairs` (§3.7). */
pairs?: PairsImportSummary
/**
* What became of the edit the open asked for (§27.7): `null` where the map is
* drawn through it, the reason where it is not — an edit made on another
* assembly, or a container it is not yet drawn on. Absent where none was asked.
*/
edit?: { refusal: string | null }
sourceKind: SourceKind
}
export interface GenomesResult {
table: TablePayload
/**
* Row indices of `table` that may be displayed. `__unbinned__` is absent with
* no toggle (§7.4), and nothing is renumbered to achieve that — the omitted
* row keeps its index, its `genome_id` and all of its bins.
*/
display: Int32Array
/**
* `bin1_offset[hi] − bin1_offset[lo]` per genome row: the number of non-zero
* pixels whose *row* bin falls inside the genome (§4). Free, from an index
* already in memory. **Not a contact count** — the column is labelled as a
* proxy wherever it is shown.
*/
density: Float64Array
}
export interface ContigsResult {
table: TablePayload
}
/**
* The cells table (§5.1's sibling for an `.scool`).
*
* One row per cell, and the columns are **discovered**, exactly as the genomes
* table's are: `name`, `nnz` and `sum` are guaranteed because every cooler
* writes them, and anything else a writer put on its cells that actually
* *differs* between them comes through as a column of its own.
*
* Attributes that are the same on every cell are dropped rather than shown.
* They describe the file — its bin size, its storage mode, the cooler that
* wrote it — and a column repeating one value four thousand times is a column
* that cannot be sorted, cannot be filtered, and pushes the two that can off
* the side of the screen. The info panel is where a file-level fact belongs.
*/
export interface CellsResult {
table: TablePayload
/** Row indices currently summed into the map, as offsets into `table`. */
selected: Int32Array
}
/** What changed when a reader ticked a different set of cells. */
export interface CellsSelectedResult {
/** The resolved set, in file order — deduplicated and validated. */
names: string[]
/** Stored pixels the new set will walk; the read-cost forecast. */
nnz: number
/** Value columns every cell of the new set offers. */
scoreColumns: string[]
}
/**
* The `/bins` columns a file carries — names and kinds, never a value (§8.12).
*
* Names and dtypes only, which is what makes it safe to ask while a file is
* being opened for a drop-down that may never be opened: §3.3's rule is that
* `/bins` is never *read*, and a group listing reads nothing. `[]` for a file
* with no `/bins` group at all, which is every `.hic`.
*/
export interface BinColumnsResult {
columns: Array<{ name: string; text: boolean }>
}
/** One `/bins` column over the bin range that was asked for. */
export interface BinColumnResult {
column: string
/** The half-open bin range these values cover, clamped to the file. */
from: number
to: number
/** One of the two, according to what is on disk. */
values?: Float64Array
text?: string[]
}
/** One labelled run along an axis of a rendered block, in block-local offsets. */
export interface AxisGroup {
/**
* Every sequence in this stretch of the axis, where a cell holds more than
* one.
*
* A cell is at most a capacity of bins and never part of one sequence beside
* anything else — but sequences too small to fill a cell do share, and then
* the axis is labelled with the first of them and the rest are invisible. This
* is where they are: the readout names them, and the sequence list beside the
* map offers all of them rather than every other one.
*
* Absent for the ordinary group, which is one sequence however many cells it
* spans. A sequence longer than the capacity has several, and listing it once
* per cell is how it came to appear twice in a list of names.
*/
merged?: Array<{ label: string; unitLength: number }>
label: string
/** First row/column of the group within the block. */
start: number
/** One past the last row/column of the group within the block. */
end: number
/**
* Absolute bin index at which this group's contig (or genome) *itself*
* begins, which is not in general the bin the block begins at.
*
* `start` is block-local, so `(offset - start) * binsize` measures from the
* left edge of the picture. That is the same thing as a position in the
* contig only when the block starts on a contig boundary — true for a genome
* view and for a whole contig, false for `contig:start-end`, where the block
* begins at `chrom_offset[c] + floor(start / binsize)` and the readout
* restarted at zero. A base-pair position is
* `(rowExtent[0] + offset - unitStart) * binsize`.
*
* Absent above bin level, where a cell *is* a whole contig or genome and has
* no position inside anything.
*/
unitStart?: number
/**
* The absolute bin this group's contig begins at, as an **identity**.
*
* Distinct from {@link unitStart}, which is an arithmetic *origin*, and the
* two are only the same number on a dense block. A coarsened axis is measured
* in cells anchored to the contig, so its origin depends on where that axis's
* own block opens — which makes it useless for the one other question an
* axis run is asked, "is the other axis the same sequence as this one".
* `contig × the same contig` over two different windows gets two different
* origins and one `unitBin`, and the genomic distance across such a cell is
* exactly what needs to tell them apart (`ui/blockAxes.separationOf`).
*
* A number rather than the name because a metagenome may hold two `contig_1`s
* in two MAGs. Absent above bin level, where a cell is a whole sequence.
*/
unitBin?: number
/**
* Length of this group's contig in base pairs, where it is a contig.
*
* Only the reader knows it, and only it can answer the question a selection
* asks at the end of a sequence: the last bin of a contig is usually partial,
* so `bins * binsize` overshoots the sequence — by up to one bin — and a
* region built from that arithmetic is refused as out of bounds by the very
* parser that would open it. Sent so the UI can clamp to the truth rather
* than to a multiple of the bin size.
*/
unitLength?: number
}
export interface MatrixResult {
nrows: number
ncols: number
/**
* Names this read answered that this file does not itself write (§5.9).
*
* A ticked selection resolves its names the same way a region does, and it
* has to *report* the same way too: a selection view drawn from names matched
* across conventions and saying nothing is precisely the silent rename the
* region path was built to prevent. Absent — not empty — where nothing was
* matched, which is every read of a file in its own vocabulary.
*/
matched?: NameMatch[]
/** Row-major, `nrows * ncols` long. Transferred, not copied. */
values: Float32Array
rowExtent: Extent
colExtent: Extent
/** Contig (or genome) runs along each axis, for separators and tick labels. */
rowGroups: AxisGroup[]
colGroups: AxisGroup[]
/**
* The genome each stretch of the axis belongs to — the coarser structure over
* {@link rowGroups}, in the same offset space.
*
* Two levels of structure exist in a contig × contig picture and both are
* wanted at once, which is why this does not replace `rowGroups`: the pointer
* is over a contig, and that contig is in a genome, and a reader looking at a
* whole metagenome needs to be told which.
*
* Present only where the axis *is* contigs of a file that has genomes. Absent
* for a plain cooler, and absent when the axis is already genomes.
*/
rowGenomes?: AxisGroup[]
colGenomes?: AxisGroup[]
/**
* Whether the genome runs above are the boundaries to *draw*.
*
* Naming and drawing are separate decisions, and two pictures want both,
* because in both the subject is genomes. The whole-metagenome overview: there
* 20,000 contig hairlines over 4,000 genome blocks is a grey wash that hides
* the block structure the view exists to show, so the genome runs become the
* separators and the axis labels. And a **selection of several genomes**,
* which is the same picture of a chosen few — ticking four MAGs asks for four
* blocks, and their two thousand contigs are the wash again.
*
* Everywhere else the genome is a fact for the tooltip and the contigs keep
* the lines: a whole-genome view of a metacool is still read contig by contig,
* a selection of *contigs* is a picture of the contigs that were ticked, and
* one genome on its own has nothing coarser than its own contigs to show.
*/
genomeBoundaries?: boolean
level: 'bin' | 'contig' | 'genome'
/**
* The sequence this block was read round, where it was read round one.
*
* Present only on a wrapped read (see the `matrix` request's `wrap`), and it is
* what tells the view that `rowExtent` and `colExtent` are **unwrapped** — that
* they may run off either end of the sequence, and that a bin of them is a bin
* of the file only after being taken modulo this. In bins of the open map, like
* the extents beside it.
*
* The axis runs need no such warning, because they already carry the answer:
* a run's `unitStart` is shifted a lap per revolution, which is what makes the
* second stretch of a junction-crossing block say *this is the beginning of the
* sequence, one lap along* rather than *this is somewhere past its end*.
*/
wrapped?: Extent
/**
* Bins summed into one cell, where the block was read at a coarser bin size
* than the file stores (`metacooler/pooling.ts`). Absent, or 1, for the
* ordinary read.
*
* The axes are then *bins of that coarser grid*: a cell is `binsPerCell` bins
* of one contig, a run of cells is that contig, and every coordinate the UI
* computes is right if it multiplies the file's bin size by this. Reported
* rather than assumed, so the picture and the summary above it cannot claim
* two different resolutions.
*/
binsPerCell?: number
/**
* The bin size of the map this block was actually read from, where that is
* not the open one.
*
* Present only for a cross-rung read (`WorkerRequest`'s `rung`). The effective
* resolution on screen is this times {@link binsPerCell}, and a caller that
* assumed the open map's bin size would label a 5 kb picture as a 1 kb one —
* which is the one number a methods section quotes.
*/
binsize?: number
/**
* The window that was asked for, in bins of the map that is **open**.
*
* Present only for a cross-rung read, and present because bin indices are not
* comparable across levels: `rowExtent` describes the block on the rung's own
* grid — which is what the axes, the runs and every coordinate on screen are
* built from — while a caller deciding *what to ask for next* is working in
* the space it asked in. Without this the two silently disagree, and a zoom
* that had just read a coarse rung would compute its next window against that
* rung's indices as though they were the open map's.
*/
source?: { rows: Extent; cols: Extent }
/**
* Whole sequences summed into one cell, where the axis had more of them than
* the picture has pixels. Absent, or 1, for every axis with room for a cell
* per sequence — which is every cooler and most assemblies.
*
* Above 1 the axis is no longer one of positions: a cell is a named set of
* sequences, `binsPerCell` says nothing about it, and the view labels it as
* sequences rather than as base pairs. A cell still never holds part of a
* sequence, which is the property that makes the picture readable at all
* (`metacooler/pooling.ts`).
*/
contigsPerCell?: number
/**
* Sequences on each axis, as against cells.
*
* The two part company exactly when {@link contigsPerCell} is above one: an
* axis run is one *cell's* name, so counting runs then counts cells, and a
* summary saying "4,885 bins across 2,441 contigs" of a 4,882-contig genome
* reports the pooling as though it were the assembly.
*/
rowContigs?: number
colContigs?: number
}
export interface OverviewResult {
/** Whether the axes are genomes or contigs. */
level: 'genome' | 'contig'
/** Axis names, `__unbinned__` and its contigs excluded (§7.3, §7.4). */
labels: string[]
/**
* The genome each axis entry belongs to, at contig level only.
*
* A contig × contig picture of a whole metagenome is read *by genome* — the
* question is which bins hold together — so the boundaries worth drawing are
* the genome ones, not one per contig. The labels stay per contig, because
* that is what the pointer is over.
*/
groups?: string[]
/**
* The plain name of the unit each slot *starts* at.
*
* Distinct from {@link labels}, which carries the "+15" that tells a reader a
* row is pooled. This one is what a click resolves to — a real contig or
* genome the app can open — so the display string and the navigation target
* never have to be recovered from one another by parsing.
*/
unitNames: string[]
/** Row-major `n × n`. */
values: Float32Array
n: number
/** Whether the numbers came from a full pixel scan or a sidecar edge list. */
source: 'scan' | 'edge-list'
/**
* `true` when consecutive units share an axis slot.
*
* Note what this is *not*: units are never dropped. Every displayable unit
* contributes to exactly one slot, so a pooled overview is a coarser picture
* of the whole file rather than a sharp picture of part of it. The field it
* replaces, `restricted`, meant the opposite — that the axis had been cut to
* the densest few and the rest discarded.
*/
pooled: boolean
/** Mean units per slot; `1` when nothing is pooled. */
unitsPerSlot: number
/** Displayable units at this level — the number actually represented. */
totalUnits: number
}
/**
* What a map was drawn to (§6.5).
*
* `total` is the contacts the file holds, counted by the census — the number the
* box shows as the map's own once one has been taken, where the file's own
* claim ({@link OpenResult.contacts}) may be absent or rounded. The census rides
* along so the analysis worker's mount of the same map is handed it rather than
* walking every pixel a second time.
*/
export interface ResampleResult {
mode: ResampleMode
/** The total asked for, or `null` for the file as stored. */
contacts: number | null
/** Contacts in the file, counted; `null` before any census. */
total: number | null
census: Census | null
}
/**
* The stage's whole-genome picture (§27.9): every contact of a map at up to
* 16,384 cells a side, one byte a cell, in the file's order — see
* `metacooler/picture.ts` for how it is read and what a byte means.
*/
export interface PictureResult {
/** The rung it was read from, as `OpenResult.entries` names it; `null` for the open map. */
rung: string | null
/** Base pairs a cell a side: the rung's bin size times {@link stride}. */
binsize: number
/** Bins of that rung a cell a side. */
stride: number
/** Cells a side. */
n: number
/** The sequences, in file order, each with the cells it spans. */
sequences: Array<{ name: string; length: number; firstCell: number; cells: number }>
/** The picture and the pyramid over it, finest first: upper triangles. */
levels: Array<{ n: number; cells: Uint8Array }>
/** The base-10 logs bytes `1` and `255` stand for. */
low: number
high: number
/** The range the picture opens at, in base-10 logs. */
vmin: number
vmax: number
/** Whether the values are balanced, or the raw column. */
balanced: boolean
/** Stored pixels walked. */
pixels: number
/**
* The finest bins, in base pairs, this map is deep enough to show, from the
* picture's rung (`metacooler/picture.ts`, `depthFloor`): a window is never
* read finer (§27.9).
*/
least?: number
/**
* What the method that proposes edits weighs (§27.5), from the same pass: the
* contacts as numbers, what the map is expected to hold, and the corners of
* the file in its own order. Absent where the request did not ask for them.
*/
method?: { contacts: PictureContacts; expected: Expected; corners: FileCorner[] }
/**
* Where the request asked the worker to **keep** what the method weighs
* rather than send it: the picture's id, which a `suggest` request names —
* tens of megabytes held where the suggestions are counted, off the stage's
* thread (§27.12), in place of {@link method}.
*/
methodKept?: number
}
/** One side of a stage window: where it begins and ends in the edited assembly. */
export interface StageWindowSide {
from: { sequence: string; bp: number }
to: { sequence: string; bp: number }
}
/**
* Where one genome's contigs, and the contigs of the others, belong by their
* contacts (§27.10): a pass over every stored pixel of a metagenome, raw
* counts, a contig's contacts with itself left out.
*/
export interface GenomeLinksResult {
/**
* Each contig of the genome's edit: its contacts with every other contig,
* with the edit's own, and with the genomes the most of the rest are with,
* most first — `__unbinned__` among them, by that name.
*/
inside: Array<{ contig: string; total: number; own: number; partners: Array<{ genome: string; contacts: number }> }>
/**
* Contigs of other genomes, and of none, in contact with the edit's: the
* contacts with it and with every contig, the largest share first, at most
* a hundred.
*/
outside: Array<{ contig: string; genome: string; length: number; contacts: number; total: number }>
/** Stored pixels walked. */
pixels: number
}
export interface StatsResult {
/** Everything the byte source has fetched since the file was opened. */
total: SourceStats
/** Delta across the most recent matrix/aggregate/overview request (§12). */
lastOp: SourceStats
/** Number of worker requests served. */
calls: number
}
/** Every request kind, mapped to what it resolves with. */
export interface ResultMap {
open: OpenResult
genomes: GenomesResult
contigs: ContigsResult
cells: CellsResult
selectCells: CellsSelectedResult
binColumns: BinColumnsResult
binColumn: BinColumnResult
range: ParsedRange
matrix: MatrixResult
aggregate: MatrixResult
selection: MatrixResult
overview: OverviewResult
overviewSidecar: OverviewResult
validateDeep: DeepValidation
stats: StatsResult
exportMcool: McoolExport
exportLifted: LiftedExport
resample: ResampleResult
contacts: { total: number | null }
picture: PictureResult
stageWindow: WindowRead | null
suggest: Suggested
refine: Array<RefinedPoint | null>
genomeLinks: GenomeLinksResult
cancel: null
close: null
}
export type RequestKind = keyof ResultMap
// ---------------------------------------------------------------------------
// Requests
// ---------------------------------------------------------------------------
export type WorkerRequest =
| {
id: number
kind: 'open'
uri: string
source: SourceSpec
binning?: PairsBinning
/**
* Whether the multi-genome containers are read — the page's *dev
* features* switch (§29), stamped on every open by the client, since a
* worker cannot read the page's address. Absent reads them.
*/
metacool?: boolean
/**
* An edit of the reference to draw the map through (§27.7): the file is
* opened as it is, then presented as the edited assembly — its sequences,
* its bins, its pixels carried to where they land (`metacooler/lens.ts`) —
* and so is every rung opened for a zoom after it. Sent only while the dev
* features are on (§29), and only for an edit that changes something.
*/
edit?: ReferenceEdit
}
// Build the `.mcool` for the pairs import this session was opened from.
// Separate from `open` because it is a second long job with its own
// progress and its own cancel, and because a reader who cancelled the
// download still has the map.
| { id: number; kind: 'exportMcool' }
/** The open map lifted through an edit of its reference, every rung, as an `.mcool` (§27.8). */
| { id: number; kind: 'exportLifted'; edit: ReferenceEdit }
| { id: number; kind: 'genomes' }
| { id: number; kind: 'contigs' }
| { id: number; kind: 'cells' }
/**
* Change which cells the open map sums (§3.8).
*
* A cell set is not part of the URI — `file.scool::/cells/one` addresses one
* cell as a plain cooler, and there is no group path that means *these eight*
* — so it is state on the open map, swapped here rather than by re-opening.
* The swap costs one small index read per cell and no re-mount.
*
* `null` is every cell, which is what an scool with nothing ticked shows.
*/
| { id: number; kind: 'selectCells'; names: string[] | null }
| { id: number; kind: 'binColumns' }
// One `/bins` column over the bins a picture actually covers (§8.12). The
// range is the caller's because the caller is the side that knows what is on
// screen; it is clamped here, so a block that runs past the last bin asks for
// a slice rather than an error.
| { id: number; kind: 'binColumn'; column: string; from: number; to: number }
| {
id: number
kind: 'range'
range: string
rung?: string
/**
* The naming context of the file the range string came **out of**.
*
* Two booleans, and they travel because a name cannot carry them: `X` is
* chromosome ten in a file counting `I`…`XVI` and the sex chromosome
* everywhere else, and only the list it was written in can say which
* (§5.9). A companion following a lead of another nomenclature is the
* whole reason this field exists; a session of one file never sets it.
*/
naming?: NameContext
/**
* Sequences the reader has declared circular, in **this file's** spelling
* (§8.15).
*
* Sent because nothing in a `.cool` can say it and this worker therefore
* cannot know it: the declaration is the reader's, made in the Chromosomes
* table and kept per file on the main thread. It changes exactly one
* answer here — a range whose end is below its start is a typo on a line
* and the window across the origin on a circle — so it travels with the
* range rather than being mounted with the file, and a request that omits
* it gets cooler's own refusal.
*/
circular?: readonly string[]
}
// `balance` multiplies each cell by its two bin weights, which is cooler's
// own definition of a balanced matrix (§6.4). Off by default, matching
// `metacooler show`, and offered only when the file carries the column.
// `genomes` asks for the genome each stretch of the axes belongs to, for the
// tooltip. Off by default: it costs a walk over the block's bins and a run
// encoding, and every view but the whole-genome one already knows the answer
// from the view it is — a genome view is one genome, a region view is one
// contig of one.
// `binsPerCell` reads the block at a coarser bin size: every N consecutive
// bins of a contig summed into one cell, accumulated from the stored pixels
// rather than from a block that would have to exist first
// (`metacooler/pooling.ts`). 1 or absent is the ordinary dense read. The
// caller chooses it because the caller is what has to label the axes in the
// matching units, and one number cannot be derived twice and agree.
| {
id: number
kind: 'matrix'
/**
* Read from a **sibling rung** of the collection this file is in, rather
* than from the map that is open (§3.4, §9).
*
* The entry's own name — `2000` under `/resolutions`, whatever an
* `.mmetacool` calls it under `/entries` — as `OpenResult.entries` lists
* them. Absent is the open map, which is every request that is not a
* zoom-driven one.
*
* `rows` and `cols` stay **bins of the open map** even when this is set,
* and the worker converts. That is not a convenience: bin indices are not
* comparable across rungs — each level has its own `chrom_offset` and its
* own short last bin per sequence — so a caller converting for itself
* would need every rung's tables, which is the reader's side of the wall.
* Converting here means one round trip and one implementation.
*
* A coarse rung is read rather than pooled for two reasons, and the second
* is the one that matters: it walks fewer stored pixels for the same
* picture, and its balanced values are *balanced at that resolution*
* rather than summed — which is what `cooler zoomify --balance` produces
* and what summing a fine level cannot approximate (§6.4).
*/
rung?: string
rows: Extent
cols?: Extent
/**
* Read `rows` and `cols` as positions on a **circle** whose bins are this
* extent (SPECS §8.15).
*
* With it, the two extents are *unwrapped*: they may run off either end of
* the sequence and are resolved modulo it, so a window across the junction
* is up to four stored blocks assembled into one — see `worker/wrap.ts` for
* the two coordinate spaces and why the request is written in the one that
* runs off the ends.
*
* The sequence's own extent, in bins of the **open** map, exactly as `rows`
* and `cols` are: the worker converts both together when a rung is named.
* Absent is every ordinary read, and a window that happens to fall entirely
* inside the sequence takes the ordinary path whether this is set or not —
* same bins, same block, same grid.
*/
wrap?: Extent
balance?: boolean
/** `/pixels` column the values come from; `count` when absent. */
value?: string
budgetBytes?: number
genomes?: boolean
binsPerCell?: number
contigsPerCell?: number
/**
* A read nobody is looking at yet — the circularity check's (§8.15). It
* waits until the views' own reads have been answered (§12).
*/
background?: boolean
}
| {
id: number
kind: 'aggregate'
rows: Extent
cols?: Extent
level: 'contig' | 'genome'
balance?: boolean
/** `/pixels` column the values come from; `count` when absent. */
value?: string
budgetBytes?: number
genomes?: boolean
}
// One map of several chosen sequences: their own maps on the diagonal and
// everything between them off it. Named rather than given as bin extents,
// because the names are what the URL carries and what the axis is labelled
// with — resolving them in the worker keeps one answer to "which bins is
// `MAG_7`", the reader's.
| {
id: number
kind: 'selection'
unit: 'genome' | 'contig'
names: string[]
/**
* The naming context of the file the names came out of — see the `range`
* request, which carries it for the same reason. A ticked selection is a
* shared view exactly as a region is, so it has to cross nomenclatures
* exactly as one does (§5.9).
*/
naming?: NameContext
balance?: boolean
/** `/pixels` column the values come from; `count` when absent. */
value?: string
binsPerCell?: number
contigsPerCell?: number
/**
* Ceiling on the dense block this read may build, as `matrix` takes one.
*
* A selection is already capped at `POOLED_CELL_CAP²` cells whatever the
* file's size, so this is not what stops a runaway read — it is what lets a
* *deck* divide that ceiling. Six panels each entitled to the whole cap is
* six times the one block the guard was written for (§16.7), and the
* selection path was the one request kind with no way to say so.
*/
budgetBytes?: number
}
| { id: number; kind: 'overview'; level?: 'genome' | 'contig'; maxUnits?: number }
| { id: number; kind: 'overviewSidecar'; url: string }
| { id: number; kind: 'validateDeep' }
/**
* Draw the open map to `contacts` contacts, or back to the file as stored
* (`null`) — §6.5. Every read after it, of this map and of any rung of it,
* is of the drawn map; reads already queued behind it wait for the census.
*/
| { id: number; kind: 'resample'; contacts: number | null; seed?: number; alpha?: number }
/**
* Count the contacts the open map holds, where the file does not say (§6.5):
* a census of the **coarsest** rung of its ladder, which holds every contact
* in the fewest pixels, or of the map itself where it has no ladder.
*/
| { id: number; kind: 'contacts' }
| { id: number; kind: 'stats' }
/**
* The stage's whole-genome picture (§27.9), at the finest rung of the ladder
* that fits `cells` a side — pooled a few bins a cell where none does.
*/
| {
id: number
kind: 'picture'
cells?: number
balance?: boolean
value?: string
method?: boolean
/**
* The sequences to draw, by name, where not all of them: one genome of a
* metagenome and the contigs brought into it (§27.10). The rest of the
* file is left out of the picture and of what the method weighs.
*/
contigs?: string[]
/**
* Keep what the method weighs here, for `suggest` requests, rather than
* send it (`PictureResult.methodKept`). The last picture kept is the one
* kept.
*/
keep?: boolean
}
/**
* A window of the stage's map read finer than its picture (§27.9): the rung
* whose bins are about `binsize`, drawn through `edit`, over the stretch of
* the edited assembly each side names. `key` names the edit, so the map
* drawn through it is kept while the edit stands. Answered `null` where no
* rung is finer than `coarser`, the picture's own cell.
*/
| {
id: number
kind: 'stageWindow'
edit: ReferenceEdit
key: string
binsize: number
coarser: number
rows: StageWindowSide
cols: StageWindowSide
balance: boolean
}
/**
* A suggestion's points placed again at the finer rungs (§27.5): each read
* around, through the stage's edit, at every rung from the picture's `cell`
* down to `least`, the finest bin the map is deep enough to show. One answer
* a point, in order: `null` where the first rung already could not.
*/
| {
id: number
kind: 'refine'
edit: ReferenceEdit
points: RefinePoint[]
cell: number
least: number
balance: boolean
}
/**
* The suggestions for an edit (§27.5), counted here against what the method
* weighs of the picture `picture` names — kept by its read — so the stage's
* thread stays with the hand (§27.12).
*/
| {
id: number
kind: 'suggest'
picture: number
edit: ReferenceEdit
layout: GridLayout
weights?: number[]
evidence?: SequenceEvidence
}
| {
id: number
kind: 'genomeLinks'
/** The contigs of one genome's edit, by name (§27.10). */
contigs: string[]
}
| { id: number; kind: 'cancel'; target: number }
| { id: number; kind: 'close' }
/** The request payload for a kind, before the client stamps an id on it. */
export type RequestOf<K extends RequestKind> = Omit<Extract<WorkerRequest, { kind: K }>, 'id'>
// ---------------------------------------------------------------------------
// Responses
// ---------------------------------------------------------------------------
/**
* A `ViewerError` flattened for the wire. `code` and `detail` are what the UI
* switches on (spec §10), so losing them to structured clone is not acceptable.
*/
export interface SerialisedError {
name: string
code: ErrorCode | null
message: string
detail: Record<string, unknown>
stack?: string
}
export type WorkerResponse =
| { type: 'result'; id: number; kind: RequestKind; payload: unknown }
| { type: 'error'; id: number; error: SerialisedError }
| { type: 'progress'; id: number; done: number; total: number; note?: string }
// Unsolicited, and the only message here that answers no request: the worker
// saying how busy it has been. It carries no id because there is nothing to
// correlate it with — the status bar's CPU figure is about the thread, not
// about any one read (see `perf/busy.ts`).
| { type: 'busy'; fraction: number }
/** Progress callbacks receive the same numbers the worker emits. */
export type ProgressHandler = (done: number, total: number, note?: string) => void
// ---------------------------------------------------------------------------
// Error serialisation
// ---------------------------------------------------------------------------
/**
* Reduce a value to something structured-clone-safe. `detail` is built by the
* reader and may legitimately contain a `Map`, a typed array or a `BigInt`;
* a single un-cloneable value in there would fail the whole `postMessage` and
* turn a precise refusal into a silent hang.
*/
function plain(value: unknown): unknown {
if (value === null || value === undefined) return null
switch (typeof value) {
case 'string':
case 'number':
case 'boolean':
return value
case 'bigint':
return Number(value)
case 'object': {
if (Array.isArray(value)) return value.map(plain)
if (ArrayBuffer.isView(value)) return Array.from(value as unknown as ArrayLike<number>)
if (value instanceof Map) {
const out: Record<string, unknown> = {}
for (const [k, v] of value) out[String(k)] = plain(v)
return out
}
const out: Record<string, unknown> = {}
for (const [k, v] of Object.entries(value as Record<string, unknown>)) out[k] = plain(v)
return out
}
default:
return String(value)
}
}
/** Flatten any thrown value into a {@link SerialisedError}. */
export function serialiseError(err: unknown): SerialisedError {
if (err instanceof ViewerError) {
return {
name: err.name,
code: err.code,
message: err.message,
detail: plain(err.detail) as Record<string, unknown>,
stack: err.stack,
}
}
if (err instanceof Error) {
return { name: err.name, code: null, message: err.message, detail: {}, stack: err.stack }
}
return { name: 'Error', code: null, message: String(err), detail: {} }
}
/**
* Rebuild an error on the receiving side. A `code` means the refusal was one of
* spec §10's named cases, so it comes back as a real `ViewerError` and the UI's
* `switch (err.code)` keeps working across the worker boundary.
*/
export function reviveError(serialised: SerialisedError): Error {
if (serialised.code !== null) {
const err = new ViewerError(serialised.code, serialised.message, serialised.detail)
err.name = serialised.name
if (serialised.stack) err.stack = serialised.stack
return err
}
const err = new Error(serialised.message)
err.name = serialised.name
if (serialised.stack) err.stack = serialised.stack
return err
}
// ---------------------------------------------------------------------------
// Transfers
// ---------------------------------------------------------------------------
/**
* Collect the buffers in a result that should move rather than be copied.
*
* A genome's matrix is up to a few million `Float32` cells; copying it across
* the boundary would double both the peak footprint and the latency for no
* benefit, since the worker has no further use for it.
*/
export function transfersFor(payload: unknown): Transferable[] {
const out: Transferable[] = []
const seen = new Set<ArrayBufferLike>()
const visit = (value: unknown): void => {
if (value === null || typeof value !== 'object') return
if (ArrayBuffer.isView(value)) {
const buffer = value.buffer
if (buffer instanceof ArrayBuffer && !seen.has(buffer)) {
seen.add(buffer)
out.push(buffer)
}
return
}
if (Array.isArray(value)) {
// A table's string column is 154,468 entries, and a string cannot hold a
// buffer — so recursing into one was 1.5 M `typeof` checks per contigs
// response looking for something that cannot be there.
if (value.length === 0 || typeof value[0] !== 'object') return
for (const item of value) visit(item)
return
}
for (const item of Object.values(value as Record<string, unknown>)) visit(item)
}
visit(payload)
return out
}
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