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* The genome-wide view: the whole matrix, at whatever resolution it can be
* drawn at.
*
* SPECS §9 used to rule this out for cool files, on the grounds that a
* eukaryotic cooler reintroduces the streaming problem §2 exists to avoid. That
* is true of a *human* cooler and false of the genomes this viewer is most
* often pointed at: yeast is 12 Mb, which at 1 kb is 12,100 bins and the single
* most useful picture of the file.
*
* It used to ask for that picture one file bin per cell, and there is a size
* past which that cannot be done at all: the values are one `Float32Array`, a
* browser serves at most 2 GiB in one, and a whole yeast genome at 500 bp is
* 24,228 bins and 2.3 GB. It was offered, computed, and then refused — for a
* block nothing was going to show, since the renderer pools any raster to
* `RASTER_MAX_DIM` per axis and 24,228 rows were always going to be drawn as
* about 4,000 pixels.
*
* So the block is read **at the resolution it will be drawn at**
* (`metacooler/pooling.ts`): every `stride` consecutive bins of a chromosome
* summed into one cell, in the worker, from the stored pixels. The read is
* bounded at 4096² cells whatever the file's bin count, so this view no longer
* has a size that defeats it — and because the stride restarts at each
* chromosome, what arrives is an ordinary block one bin size up. The panel is
* told that bin size and every coordinate, tick, tooltip and selection is right
* without knowing pooling happened.
*
* What it costs is the pass over the stored pixels, which is the same pass it
* always cost and is what {@link WHOLE_VIEW_GATE_PIXELS} asks about first. The
* whole-metagenome scan is gated for that reason and this is now gated for the
* same one; the shell keeps whichever of the two it built, so coming back is
* free.
*/
import { WHOLE_VIEW_GATE_PIXELS, WHOLE_VIEW_GATE_BINS } from '../constants'
import { IDENTITY_PLAN, POOLED_CELL_CAP, poolPlan, type PoolPlan } from '../metacooler/pooling'
import type { MatrixResult } from '../worker/protocol'
import type { Extent } from '../types'
import { isCancellation, type Cancellable, type ReaderClient } from '../worker/client'
import { ViewerError, isAllocationFailure } from '../errors'
import { typedLociToRegions } from '../genome/assembly'
import { button, el, fmt, titleWhenCut } from './dom'
import { resolutionLabel } from '../units'
import type { PanelSeed, ScaleState } from './GenomeView'
import {
MatrixPanel,
type AnnotationContext,
type DerivePresentation,
type TurnPresentation,
type FigureSubject} from './MatrixPanel'
import { axisRegion } from './mapSelection'
import { blockSummary, poolingNote } from './mapSummary'
import { REMOTE_SCAN_BYTE_LIMIT, overviewTarget } from './Overview'
import { presentationOf, secondBlock, type CompareRead, type LowerRead } from './compare'
import type { LowerPresentation } from './LowerReading'
import { attachRefine, rungsOf, type BlockLadder } from './refine'
import { scoreChoices, scoreFor, type ScoreChoice } from './scores'
import { SearchBox, featureSuggestions, locusPlaceholder } from './SearchBox'
export interface WholeViewProps {
client: ReaderClient
binsize: number
/** Sibling rungs of a laddered file (§3.4); absent for a plain one. */
rungs?: readonly string[]
/**
* Bins of this map summed into one drawn cell, because the reader asked for a
* resolution the file does not store (§3.4).
*
* The factor, not the bin size: a 10 kb rung derived from a 2 kb map is `5`,
* and the effective resolution on screen is this map's bin size times it. The
* base rung is the map that is *open* — picking a derived resolution navigates
* to it — so every read here is an ordinary one carrying an explicit plan,
* and the worker snaps that plan to each sequence's own grid so the cells hold
* the same sums wherever the reader pans (`worker/reader.worker.ts`).
*
* Absent, or 1, is every view of every file until somebody adds one.
*/
binsPerCell?: number
/**
* Open the file at another rung, by entry name — the gate's second button.
*
* A whole-genome view pools the fine rung into cells hundreds of bins wide,
* and a coarser rung of the same file draws the same cells from a fraction
* of the pixels. Absent where the shell cannot switch rung, and the gate
* then offers only the read.
*/
onOpenRung?(entry: string): void
/**
* Present when this view is the `bin × bin` level of a metagenome's whole-file
* picker (§7.3) rather than a view of its own.
*
* Four things follow from it, and they are one thing said four ways — *this
* picture is of the whole metagenome*:
*
* - the picker is in the General column's Genomes card, at every level, or
* there is no way back to the other two (`Session.paintLevel`);
* - the read is asked about first whatever the pixel count, because it is the
* landing level now and §7.3's rule is that a full pass is never automatic;
* - the axis is labelled and divided by **genome**, which is what the other
* two levels do and what makes the three one picture at three depths;
* - and so a label click opens a genome, since a genome name is not a region.
*
* Passed in rather than derived: this view does not know which of the three
* levels it is, and the shell does.
*/
wholeFileLevel?: {
/** An axis label — a genome name here — was clicked. */
onOpenGenome(genome: string): void
/**
* A cell between two genomes was clicked.
*
* The other half of {@link onOpenGenome}, and it is what makes this level
* agree with the two beside it: on the contig × contig and genome × genome
* pictures a click has always resolved to a *genome* — its own square on
* the diagonal, the pair off it (`ui/Overview.ts`) — and here it resolved
* to a contig, so the same gesture on the same file went somewhere else
* depending on which of three levels the reader had chosen.
*/
onOpenPair(rowGenome: string, colGenome: string): void
}
/** Total bins in the file, for the counts a selection is measured against. */
nBins: number
/**
* The bins this view draws: everything but `__unbinned__` (§7.4).
*
* Not `[0, nBins)`. The unassigned contigs are not a genome, are absent from
* every table and every other view, and on a real metagenome are the largest
* thing in the file — drawing them here put a band across the picture and,
* being among the drawn pixels, set the colour scale for everything else.
*/
displayExtent: Extent
/**
* Stored pixels in the file, when it says. The read walks all of them, so
* this is what it costs and what the gate asks about; `null` where the file
* declares no `nnz`, and then nothing is asked.
*/
nnz: number | null
/**
* The sequences to draw, when it is not all of them.
*
* A selection and the whole file are the same picture asked for two ways —
* this view is "the map of what you chose", and choosing everything is what
* it did before there was a way to choose less. So it is one class: the
* selection changes which read is made and what the heading says, and nothing
* else about the view knows.
*/
selection?: { kind: 'genome' | 'contig'; names: string[]; bins: number; contigs: number }
/**
* Total sequences — the second number the grid is planned against.
*
* A plan needs both: `n / cap` bins per cell is only achievable while the
* sequences are fewer than the cells, because every sequence starts a cell of
* its own (`metacooler/pooling.ts`). Planning from the bin count alone is what
* produced a block above the cap that the renderer then pooled a second time,
* contig-blind, two cells to a pixel.
*/
nContigs: number
level: 'bin' | 'contig'
scale: PanelSeed
balance: boolean
/** Whether the file carries a weight column at all. */
hasWeights: boolean
/**
* The `/pixels` column the reads take; `count` when absent.
*
* Resolved by the session rather than derived here from {@link score}, so the
* fallback for a hash naming a column this file does not have is decided in
* one place — see `Session.valueOf`.
*/
value?: string
/** Value columns this file carries, for the score picker (`ui/scores.ts`). */
scoreColumns?: readonly string[]
/** The picker's current choice, by id; `count` when absent. */
score?: string
/** What one axis unit is called here: a chromosome, or a contig. */
noun: string
/**
* The assembly's first sequence name, for the locus box's example (§26.6).
*
* Absent on a file whose sequences this view has not been told about, and then
* the builder writes the neutral word instead.
*/
first?: string
/**
* Where the pixels come from, and how many bytes of them there are.
*
* The gate priced the read in stored pixels and said nothing about the
* download, while the metagenome's gate next to it quoted the bytes and said
* nothing about the pixels — and over a network the cost a lab pays is the
* download (§7.3, §18.6). Both gates state both figures now, and this view
* had neither of them.
*/
sourceKind?: 'local' | 'remote'
sourceBytes?: number
/**
* Ask the reader which genome each contig belongs to, for the tooltip.
*
* This is the one view where the answer is not already known from the view
* itself: a genome view is one genome and a region view is one contig of one,
* but here the axes run over the whole file and a contig's genome is exactly
* the thing that is not on screen. False for a plain cooler, which has none.
*/
namesGenomes: boolean
onScoreChange(choice: ScoreChoice): void
/**
* The derived-values presentation (`render/derive.ts`), built by the session.
*
* Passed through rather than assembled here: four views mount the same panel,
* and a default decided in each is a default that comes to differ.
*/
derive?: DerivePresentation
/** The 45° turn (`render/rotate.ts`), built by the session like `derive`. */
turn?: TurnPresentation
onScaleChange(scale: ScaleState): void
/** A cell was clicked: open that sequence, or the block between two. */
onOpenRegion(region: string, region2?: string): void
/**
* An axis label was clicked and that label is a **genome** name.
*
* Only reached where the axis is divided and labelled by genome, which for
* this view means a selection of several of them ({@link selection}); the
* whole-file picker has its own, beside the two other destinations it opens
* ({@link wholeFileLevel}). Both go to the same place, and the split is only
* that the picker hands over three callbacks and a selection needs one.
*
* Absent leaves the label opening as a *region*, which is not a broken path —
* `parseMetacoolerRange` takes a bare genome name and the region view offers
* the genome view from there. It is one screen longer than the gesture meant,
* which is why this exists.
*/
onOpenGenome?(genome: string): void
onError(err: unknown): void
/**
* The bin-level read could not be given the memory it needs (§7.3).
*
* Handed to the shell rather than shown here, because the answer is another
* level — the shell's to route — and a level this machine has just refused is
* one the picker should stop offering. Absent, the failure is an ordinary
* error.
*/
onOutOfMemory?(): void
/**
* Start the read at once, past the gate: the reader has already agreed to a
* pass over every pixel, at the level that just ran out of memory.
*/
start?: boolean
/**
* Annotations to draw beside and on the map (spec §8).
*
* Every view that mounts a panel takes this now. It used to be this view and
* the region view alone, on the grounds that a `.metacool` carries no
* annotations (§8.5) and the genome, pair and overview views are reachable
* only on files that have genomes — true of *files*, and no longer true of
* annotations: a metacool's own columns are ones it cannot misplace (§8.12),
* so the three views a metagenome is actually read in are exactly the ones
* that had no way to draw them.
*/
annotations?: AnnotationContext
/**
* The sequence a name typed into the box means, as the file names it, or
* `null` (`findContig`'s ladder: `chr4`, `4` and `IV` alike). With genes on
* offer the box lists it first, so `IV` opens chromosome IV and not IVY1.
*/
sequenceNamed?(text: string): string | null
/**
* A second cooler in the lower-left triangle (`render/compare.ts`).
*
* Read with the same request, after the first — sequentially rather than in
* parallel, because both are full passes over their file's pixels and running
* two at once would double the peak memory of the operation this view already
* asks permission for.
*/
compare?: CompareRead
/**
* The lower triangle in a reading of its own (§5.10), for the map's second
* tab; absent beside a second file and in a deck.
*/
lower?: LowerPresentation
/**
* The second read that reading needs where its score is another column or
* the balancing the other way — the same requests as the first, asked of the
* same file again (`ui/compare.ts`). Never beside {@link compare}.
*/
lowerRead?: LowerRead
/** File and genome context for the exported figure's caption. */
caption?: FigureSubject
}
export class WholeView {
readonly el: HTMLElement
/**
* The view's own controls, mounted by the shell in the right-hand column
* rather than inside this element — see `App.showContent`.
*/
readonly sideEl: HTMLElement
/**
* The heatmap panel, exposed so the shell can reach it.
*
* The manual-annotation card lives in the sidebar and the plot lives in
* whichever view is mounted, so "click the map to place a mark" has to cross
* that gap. The shell forwards to this; the view itself stays unaware.
*/
readonly panel: MatrixPanel
private readonly summary: HTMLElement
private readonly problem: HTMLElement
/** Where a contig or a range is typed; the `/` key puts the caret here. */
private readonly search: SearchBox
/** The ask-first screen, and the map it stands in front of. */
private readonly gate: HTMLElement
private readonly panelHost: HTMLElement
/**
* Fixed for the life of this view: the level is view state, and the shell
* builds one of these per level rather than asking it to change its mind.
*/
private readonly level: 'bin' | 'contig'
/**
* Bins summed into one cell: `1` at contig level, where a cell is a whole
* sequence, and at bin level whatever brings the axes down to what the
* renderer draws.
*
* Decided here rather than in the worker because the panel has to be built
* with the matching bin size *before* the read returns — a cell of six 500 bp
* bins is a 3 kb bin, and every coordinate on screen is that multiplication.
*/
private readonly plan: PoolPlan
/** The bar, the count and the cancel — the whole-metagenome scan's, verbatim. */
private readonly progressBar = el('progress', { class: 'progress' })
private readonly progressText = el('span', { class: 'progress-text' })
private readonly progressBox: HTMLElement
/** The read in flight, so it can be called off. */
private running: Cancellable<MatrixResult> | null = null
private disposed = false
/**
* The zoom's own reader, once the gated pass has produced a picture.
*
* This is the view the whole feature is for: a whole file arrives pooled
* — the note under it says by how much — and until now the only way to
* sharpen it was to leave and open something smaller. The gate is
* untouched: the full pass still runs once, on an explicit action, and
* what the ladder adds is *bounded* reads inside the picture it produced,
* never another pass over every pixel.
*/
private ladder: BlockLadder | null = null
/**
* Whether the axis on screen is divided and labelled by **genome** — and so
* whether an axis label is a genome name or a contig one.
*
* A fact about the block rather than about the view, because two views arrive
* at it by different routes: the whole-file level sets the flag itself
* ({@link byGenome}), and a map of several ticked genomes has it set by the
* reader, which is the half that knows what was ticked. A boolean rather than
* the block it is read off, so nothing here outlives the panel's own copy.
*/
private axisIsGenomes = false
constructor(private readonly props: WholeViewProps) {
this.level = props.level
// A selection is pooled against *its own* size: four MAGs are a small
// picture however large the file they came out of is, and pooling them by
// the file's stride would throw away the detail they were chosen for.
const fitted =
props.level === 'bin'
? poolPlan(
props.selection?.bins ?? props.displayExtent[1] - props.displayExtent[0],
props.selection?.contigs ?? props.nContigs,
POOLED_CELL_CAP,
)
: IDENTITY_PLAN
// **The reader's declared resolution is a floor, never a ceiling** (§3.4).
// A whole genome at 10 kb is a picture; a whole genome at the 3 kb somebody
// added for a locus view is a hundred thousand cells a side, which is not a
// picture and which this view's own plan exists to refuse. So the coarser of
// the two wins, the summary says which, and a reader who came here from a
// 3 kb region view is told *cells of about 40 kb* rather than handed a
// number that was quietly ignored.
this.plan =
fitted.contigsPerCell > 1
? fitted
: { ...fitted, binsPerCell: Math.max(fitted.binsPerCell, props.binsPerCell ?? 1) }
this.summary = el('p', { class: 'summary' })
// One line under the title, with the whole of it in a tooltip where it is cut.
titleWhenCut(this.summary)
this.problem = el('p', { class: 'inline-error hidden' })
const store = props.annotations?.store
this.search = new SearchBox({
// The shared builder (§26.6). Spelled out as a list of nouns, this one
// came to 46 characters — `chromosome, chromosome:start-end, or a gene` —
// in a box about 260 pixels wide, so it was cut mid-word at exactly the
// clause that says a gene name works here, which is the clause a reader of
// a whole-genome picture most wants.
placeholder: locusPlaceholder({
first: props.first,
accepts: { sequence: true, gene: store !== undefined },
}),
go: true,
title:
`Open one ${props.noun} or a range within it` +
(store === undefined
? ', or two with × between them for the block where they meet. '
: ', two with × between them for the block where they meet, or a gene from the starred model. ') +
'The same box the / key opens.',
// 1-based inclusive in, the machine form out (§26.1): what a reader types
// here is what they read off the map, and the region reader behind this
// takes cooler's half-open interval.
onSubmit: (text) => {
if (text === '') return
// One window, or two for the block between them (§5.4).
const typed = typedLociToRegions(text)
props.onOpenRegion(typed.region, typed.region2)
},
// What the comment on the title bar promises: a whole-genome map of a
// mammal is three pixels per chromosome arm, so "go to MYC" has to be
// answerable by typing.
// `display`, for the reason the sequence bar's box takes it: this box
// reads what it shows back through `typedLocusToRegion`.
...(store === undefined
? {}
: {
suggest: (text: string) => featureSuggestions(store, text, 'display'),
...(props.sequenceNamed === undefined
? {}
: { sequence: (text: string) => props.sequenceNamed?.(text) ?? null }),
}),
})
this.gate = el('div', { class: 'gate hidden' })
this.progressBar.max = 1
this.progressBox = el(
'div',
{ class: 'progress-box hidden' },
this.progressBar,
this.progressText,
button('cancel', () => this.cancel(), { class: 'btn btn-quiet' }),
)
this.panelHost = el('div', { class: 'whole-host' })
this.panel = new MatrixPanel({
// The bin size of the grid actually on screen. Pooling is not a mode the
// panel has to know about: a block of 3 kb cells is a block of 3 kb bins.
binsize: props.binsize * this.plan.binsPerCell,
...(props.caption === undefined ? {} : { caption: props.caption }),
...(props.annotations === undefined ? {} : { annotations: props.annotations }),
...(presentationOf(props.compare) === undefined
? {}
: { compare: presentationOf(props.compare) }),
...(props.lower === undefined ? {} : { lower: props.lower }),
detachedControls: true,
hideTitle: true,
initial: { ...props.scale, level: props.level },
balance: props.balance,
onScaleChange: (scale) => props.onScaleChange(scale),
...(props.derive === undefined ? {} : { derive: props.derive }),
...(props.turn === undefined ? {} : { turn: props.turn }),
scores: {
choices: scoreChoices(props),
current: scoreFor(scoreChoices(props), props).id,
onChange: (choice) => props.onScoreChange(choice),
},
// Reported, not acted on. Both of these change *what is read*, so they go
// out to the URL and the shell brings back a view built for the answer —
// which is also what decides whether the new read is one to ask about
// first. Loading here as well was the second of two reads for one click.
onCellClick: (_cell, groups, genomes) => {
if (groups.row === undefined) return
// **The whole-metagenome picture answers with a genome**, which is what
// the two levels above it have always answered with (`ui/Overview.ts`).
// Its cells are bins and its runs are contigs, but the thing a reader
// is pointing at is a MAG — the axis is divided and labelled by genome
// at this level — and a contig of a metagenome is rarely the question
// and is one click further in.
//
// Through `overviewTarget`, so all three levels of the whole-file
// picker decide by one rule: same genome on both axes is that genome's
// own map, two genomes are the block between them, and no genome at all
// — a cooler, which has none — falls through to the sequence, which is
// what this view has always done.
const whole = props.wholeFileLevel
const target =
whole === undefined
? null
: overviewTarget({
level: 'contig',
rowLabel: groups.row.label,
colLabel: groups.col?.label ?? groups.row.label,
...(genomes?.row === undefined ? {} : { rowGenome: genomes.row }),
...(genomes?.col === undefined ? {} : { colGenome: genomes.col }),
})
if (whole !== undefined && target !== null && target.kind === 'genome') {
whole.onOpenGenome(target.genome)
return
}
if (whole !== undefined && target !== null && target.kind === 'pair') {
whole.onOpenPair(target.rowGenome, target.colGenome)
return
}
if (groups.col !== undefined && groups.col.label !== groups.row.label) {
props.onOpenRegion(groups.row.label, groups.col.label)
return
}
props.onOpenRegion(groups.row.label)
},
// A label is a contig, except where the axis is divided by genome — the
// whole-file level, and a map of several ticked genomes — and there it is
// a genome name, which the genome view is the answer to.
//
// Dispatched on **what the axis is** rather than on which of the two
// views this is (`labelTarget`). The old test asked the second question
// and so had one answer for the picker and another for everything else,
// which is how a picture divided and labelled by genome came to open its
// labels as regions — a genome name is a legal range, so the click landed
// one screen short of where it meant to go rather than failing.
onLabelClick: (_axis, name) => {
const whole = props.wholeFileLevel
const opensGenomes = whole !== undefined || props.onOpenGenome !== undefined
if (labelTarget({ axisIsGenomes: this.axisIsGenomes, opensGenomes }) === 'region') {
props.onOpenRegion(name)
return
}
// Called on their objects rather than through a lifted reference: these
// are callbacks a caller wrote, and detaching one is a `this` a caller
// did not agree to.
if (whole !== undefined) whole.onOpenGenome(name)
else props.onOpenGenome?.(name)
},
// On the diagonal a box is one region; anywhere else it is the rectangle
// between two windows — of two chromosomes in the trans corner, or of one
// chromosome against itself above its own diagonal, which is a picture
// this view can show and a single region cannot.
onSelectRegion: (selection) =>
selection.diagonal
? props.onOpenRegion(axisRegion(selection.rows))
: props.onOpenRegion(axisRegion(selection.rows), axisRegion(selection.cols)),
})
this.panelHost.appendChild(this.panel.el)
this.el = el(
'section',
{ class: 'view view-whole' },
el(
'header',
{ class: 'view-head' },
el(
'div',
{ class: 'title-bar' },
el('h2', { text: this.heading() }),
// The box `/` reaches, and the only way to leave this picture by
// typing rather than by aiming: a whole-genome map of a mammal is
// three pixels per chromosome arm, so "go to MYC" is a question this
// view has to be able to answer without a click on a 3-pixel target.
this.search.el,
),
this.summary,
this.problem,
),
this.gate,
this.progressBox,
this.panelHost,
)
this.sideEl = el(
'aside',
{ class: 'side' },
...this.panel.cards,
)
// There is no longer a size that defeats this view, so there are two
// answers rather than three: this is worth asking about first, or it opens.
if (this.gated()) {
// The scan view's sentence, in the scan view's place, because at this
// level the two are the same screen: a heading, what the read costs, and
// the button that starts it.
if (props.wholeFileLevel !== undefined) {
this.summary.textContent =
'One pass over every non-zero pixel, at the level chosen in the Genomes card.'
}
if (props.start === true) void this.load(Number.POSITIVE_INFINITY)
else this.renderGate()
} else void this.load()
}
/**
* Adopt a colour scale the URL moved to (a shared link, the back button).
*
* Delegated to the panel, which repaints without echoing the change back out.
* Its existence is what lets `App.render` treat a colour-only state change as
* a repaint rather than as a reason to rebuild this view and re-read its
* matrix.
*/
applyScale(scale: ScaleState): void {
this.panel.applyScale(scale)
}
/** The `/` key. */
focusSearch(): void {
this.search.focus()
}
destroy(): void {
this.disposed = true
this.running?.cancel()
this.running = null
this.ladder?.destroy()
this.ladder = null
this.panel.destroy()
}
/**
* Call the read off and go back to the gate.
*
* Cancellation is cooperative and therefore late — the worker stops at the
* next window — so what makes it *look* immediate is putting the gate back
* now. A result that arrives afterwards is dropped by {@link running} having
* been cleared, the same way the overview's generation counter drops one.
*/
private cancel(): void {
this.running?.cancel()
this.running = null
this.progressBox.classList.add('hidden')
this.panelHost.classList.add('hidden')
this.panel.setBusy(false)
this.renderGate()
}
/**
* Whether to ask before reading.
*
* The cost of every level is the same pass over the same pixels — the roll-up
* and the pooled read differ only in what they add them into — so the question
* is asked at any of them. What is no longer asked is anything about the
* *block*: it is bounded now, and a bounded block is not a decision.
*
* Unconditional at the whole-file level, whatever the file declares. That one
* is the landing view of a metagenome (§7.3), and the rule there is not "warn
* when it looks expensive" but "a pass over every pixel never starts on its
* own" — a threshold would make the rule hold on large files and lapse on the
* small ones, which is the same as not having it. Everywhere else the
* threshold stands: a bounded read nobody waits for is not worth a click.
*/
private gated(): boolean {
const { nnz, wholeFileLevel } = this.props
if (wholeFileLevel !== undefined) return true
// A coarser rung that draws the same cells is read instead of the open
// one's every pixel ({@link rungRead}), and that is a bounded read.
if (this.rungRead() !== null) return false
// A file that states no pixel count is measured by its bins instead — a
// `.hic` at 1 kb walks every block of the file whatever it declares.
if (nnz === null) return this.props.nBins > WHOLE_VIEW_GATE_BINS
return nnz > WHOLE_VIEW_GATE_PIXELS
}
/**
* The coarsest rung of this file whose bins still fit in one drawn cell.
*
* That rung draws the picture this view is about to pool the fine one into,
* from far fewer pixels. `null` for a file with no ladder, and for one whose
* open rung is already the coarsest that fits.
*/
/**
* The rung to read the whole picture from instead of the open map, and its
* cells in that rung's bins — or `null` to read the open map.
*
* A file with a ladder already holds this picture at a coarse rung, balanced
* at that resolution, in a fraction of the pixels: on a 5 GB `.mcool` opened
* at 25 kb, the 500 kb rung's few million pixels against the open rung's
* three hundred million, which was a gate asking to download the whole file.
* So the view reads it there, as the zoom already reads coarse windows
* (`ui/refine.ts`), and the open rung stays what it is: the finest a zoom
* inside the picture goes to. Only the plain whole-genome picture: a selection
* and a second file have their own grids to agree with, and a metagenome's
* whole-file level is a scan by definition (§7.3).
*/
private rungRead(): { name: string; binsPerCell: number } | null {
if (this.level !== 'bin' || this.props.selection !== undefined) return null
if (this.props.wholeFileLevel !== undefined || this.props.compare !== undefined) return null
const rung = this.cheaperRung()
if (rung === null) return null
const cell = this.props.binsize * this.plan.binsPerCell
return { name: rung.name, binsPerCell: Math.max(1, Math.floor(cell / rung.binsize)) }
}
private cheaperRung(): { name: string; binsize: number } | null {
const cell = this.props.binsize * this.plan.binsPerCell
const fits = rungsOf(this.props.rungs ?? []).filter(
(rung) => rung.binsize > this.props.binsize && rung.binsize <= cell,
)
return fits.length === 0 ? null : fits[fits.length - 1]
}
/**
* The ask-first screen: what the read costs, and the button that starts it.
*
* Stated in pixels and in the resolution they will be summed into, because
* those are the two things a reader cannot see from here and would want:
* how long this will take, and what the picture will be. The metagenome's
* gate says the same two things in its own units.
*
* The count is dropped where the file does not declare one — the gate is
* unconditional at the whole-file level and a file with no `nnz` still gets
* it, so the sentence has to work without the number rather than the screen
* going missing when it is absent.
*/
private renderGate(): void {
const { nnz, sourceBytes, sourceKind } = this.props
const counted = nnz === null ? '' : ` — ${fmt.int(nnz)} of them —`
// **And the bytes.** A remote cooler was offered `compute whole genome` with
// its pixel count and no mention of the download, while the metagenome's
// gate beside it quoted the bytes and nothing else: over a network the cost
// a lab actually pays is the download, and the gate that was about to fetch
// eighteen megabytes did not say so (§7.3, §18.6).
const priced =
sourceBytes === undefined
? ''
: ` — ${fmt.bytes(sourceBytes)} ${sourceKind === 'remote' ? 'downloaded' : 'read'}`
const rung = this.props.onOpenRung === undefined ? null : this.cheaperRung()
const lines: HTMLElement[] = [
el(
'p',
{},
el('strong', {
// `resolutionLabel`, not `fmt.bp`: a bin size is a round number by
// construction (§26.2), and this sentence said `at 1.0 kb` under a
// resolution chip saying `1 kb` and beside a File card saying
// `1,000 bp` — three spellings of one number on one screen.
text: `${this.wholeName()} at ${resolutionLabel(this.props.binsize)} reads every stored pixel of the file`,
}),
`${counted} and sums them into ${this.resolutionPhrase()}${priced}. Once per file; the ` +
'picture is kept while it is open.' +
// A selection reads the whole file too: the sequences it wants are
// scattered through the pixels, so there is no smaller span to walk.
(this.props.selection === undefined
? ''
: ' A selection costs the same pass: its sequences are spread through the file.'),
),
]
if (sourceKind === 'remote' && sourceBytes !== undefined && sourceBytes > REMOTE_SCAN_BYTE_LIMIT) {
// The warning the metagenome's gate has always given, on the gate that
// reads the same pixels of the same file. A caution with a way through, so
// `--warn` and not `--danger` (§26.5) — the button is right below it.
lines.push(
el('p', {
class: 'hint gate-warn',
text:
`Reading this file over HTTP means downloading all ${fmt.bytes(sourceBytes)} of it, ` +
`which is past the ${fmt.bytes(REMOTE_SCAN_BYTE_LIMIT)} this page starts on a click.`,
}),
)
}
if (rung !== null) {
lines.push(
el(
'p',
{},
el('strong', {
text: `Opening the file at ${resolutionLabel(rung.binsize)} draws the same picture`,
}),
` from far fewer pixels — the cells are ${this.resolutionPhrase().replace(/^cells of /, '')} ` +
'either way, and every region after it opens quicker too.',
),
)
}
this.gate.replaceChildren(
...lines,
el(
'div',
{ class: 'whole-gate-actions' },
...(rung === null
? []
: [
button(`open at ${resolutionLabel(rung.binsize)} instead`, () => this.props.onOpenRung?.(rung.name), {
class: 'btn btn-primary',
}),
]),
button(`compute ${this.wholeName().toLowerCase()}`, () => this.compute(), { class: 'btn' }),
),
)
this.gate.classList.remove('hidden')
this.panelHost.classList.add('hidden')
// What the page's report of a finished picture says in place of `drawn`:
// nothing is read until the reader agrees to the cost (§7.3).
this.panel.noteRendered('gated', `${this.wholeName()} waits for its button`)
}
/**
* What the whole file is called: a metagenome's is the whole *meta*genome,
* which is what its crumb, its palette entry and its other two levels say.
*/
private wholeName(): string {
return this.props.wholeFileLevel === undefined ? 'Whole genome' : 'Whole metagenome'
}
/** The gate was accepted. */
private compute(): void {
void this.load(Number.POSITIVE_INFINITY)
}
/**
* What this view is of: everything, or the sequences that were ticked.
*
* Named rather than counted while there are few enough to read — `II × VII`
* is the picture, and "2 chromosomes" is a fact about it.
*/
private heading(): string {
const selection = this.props.selection
if (selection === undefined) return this.wholeName()
const noun = selection.kind === 'genome' ? 'genomes' : `${this.props.noun}s`
return selection.names.length <= 3
? selection.names.join(' × ')
: `${fmt.int(selection.names.length)} ${noun}`
}
/**
* `cells of about 3.0 kb`, or `cells of 2 contigs` where a cell is whole
* sequences.
*
* The gate's half of what the summary says once the read is done — a sentence
* fragment rather than the summary's phrase, because it is read inside "sums
* them into …". It works from the plan rather than from a result, being the
* thing said *before* anything has been read.
*
* Hence *about*. The plan is a bound the reader may coarsen: it divides the
* bin count by the cell budget, and the reader then has to fit whole contigs
* into whole cells without straddling a genome, which on a fragmented
* assembly costs cells and buys them back by widening. On the reference
* metagenome that is 41 kb planned against 50 kb read — a number the gate
* used to state flatly, on a screen the reader then compared with the summary
* a moment later.
*/
private resolutionPhrase(): string {
if (this.plan.contigsPerCell > 1) {
return `cells of ${fmt.int(this.plan.contigsPerCell)} ${this.props.noun}s`
}
// A bin size takes `resolutionLabel` (§26.2). `fmt.bp` wrote `cells of
// about 3.0 kb` beside a chip reading `1 kb`, and a reader looks for a
// difference between `3.0 kb` and `3 kb` that is not there.
return `cells of about ${resolutionLabel(this.props.binsize * this.plan.binsPerCell)}`
}
/**
* The plan on the wire, with the identity left off.
*
* Both numbers are optional in the protocol and absent means one, so an
* unpooled read carries nothing rather than two ones — which is also what
* keeps the request a caller can read.
*/
private wire(): { binsPerCell?: number; contigsPerCell?: number } {
return {
...(this.plan.binsPerCell > 1 ? { binsPerCell: this.plan.binsPerCell } : {}),
...(this.plan.contigsPerCell > 1 ? { contigsPerCell: this.plan.contigsPerCell } : {}),
}
}
private async load(budgetBytes?: number): Promise<void> {
const { client, balance, namesGenomes } = this.props
const rows: Extent = this.props.displayExtent
const budget = budgetBytes === undefined ? {} : { budgetBytes }
const genomes = namesGenomes ? { genomes: true } : {}
// Whatever stood in front of the map — the gate, or a refusal that has just
// been overridden — this is the read it was waiting for.
this.gate.classList.add('hidden')
this.panelHost.classList.remove('hidden')
this.panel.setBusy(true)
this.panel.noteRendered(null)
this.problem.replaceChildren()
this.problem.classList.add('hidden')
this.progressBar.value = 0
this.progressText.textContent = 'starting…'
this.progressBox.classList.remove('hidden')
// Cancellable, and watched, because it is the same pass over every pixel the
// whole-metagenome scan makes — see `metacooler/matrix.ts`. The task is held
// so `cancel` can reach it and so a result that arrives *after* a cancel can
// be told apart from the one being waited for.
// The denominator is named by whoever counted it. A read of a cell set is
// counted in *cells* — it is one bounded read repeated per cell — and a bar
// that called those pixels would report three hundred pixels for a map with
// a million in it.
const onProgress = (done: number, total: number, note?: string): void => {
this.progressBar.value = total === 0 ? 0 : done / total
const unit = note === 'summing cells' ? 'cells' : 'pixels'
this.progressText.textContent = `${fmt.int(done)} of ${fmt.int(total)} ${unit}`
}
// Three kinds, one shape: each resolves to a `MatrixResult` and each walks
// the same pixels. Written as separate calls rather than one over a union
// because a request type is a discriminated union and narrowing it through
// a ternary argument loses the discriminant.
const selection = this.props.selection
const fromRung = this.rungRead()
const task: Cancellable<MatrixResult> =
selection !== undefined && this.level === 'bin'
? client.cancellable<'selection'>(
{
kind: 'selection',
unit: selection.kind,
names: selection.names,
balance,
...this.wire(),
},
onProgress,
)
: this.level === 'bin'
? client.cancellable<'matrix'>(
{
kind: 'matrix',
rows,
balance,
// An identity plan asks for the ordinary dense read; above that
// the block comes back on the coarser grid the panel was built
// for — from a coarser rung where one draws it ({@link rungRead}),
// its cells counted in that rung's bins.
...(fromRung === null
? this.wire()
: {
rung: fromRung.name,
...(fromRung.binsPerCell > 1 ? { binsPerCell: fromRung.binsPerCell } : {}),
}),
...budget,
...genomes,
},
onProgress,
)
: client.cancellable<'aggregate'>(
{ kind: 'aggregate', rows, level: 'contig', balance, ...budget, ...genomes },
onProgress,
)
this.running = task
try {
const result = await task.promise
if (this.disposed || this.running !== task) return
// The same three shapes, against the other file. Written out for the
// reason the reads above are: a request type is a discriminated union and
// narrowing it through a ternary argument loses the discriminant.
const second = await secondBlock(this.props.compare ?? this.props.lowerRead, (other) =>
selection !== undefined && this.level === 'bin'
? other.request<'selection'>({
kind: 'selection',
unit: selection.kind,
names: selection.names,
balance,
...this.wire(),
})
: this.level === 'bin'
? other.request<'matrix'>({
kind: 'matrix',
rows,
balance,
...this.wire(),
...budget,
...genomes,
})
: other.request<'aggregate'>({
kind: 'aggregate',
rows,
level: 'contig',
balance,
...budget,
...genomes,
}),
)
if (this.disposed || this.running !== task) return
// The reader may have planned a coarser grid than the file's bins — a
// whole chromosome at 10 kb is more cells than any picture holds — and
// every coordinate on screen is the bin size times a cell offset, so the
// panel is told before it is given the block.
// The bin size of the map that answered: a rung's, where one was read.
this.panel.setResolution((result.binsize ?? this.props.binsize) * (result.binsPerCell ?? 1))
this.panel.setData(this.byGenome(result), this.wholeName(), second)
this.summary.replaceChildren(...this.summarise(result))
this.armRefine(rows, result, budget)
} catch (err) {
// `disposed` covers the case the others need a guard for: closing the map
// puts the reader down, which rejects this read after the browser has
// been mounted in this view's place.
if (this.disposed || this.running !== task) return
// A cancel is an answer, not a failure: `cancel` has already put the gate
// back, so there is nothing to say here.
if (isCancellation(err)) return
// Too big is a fact about this machine, not a broken file: say it here,
// above a level control that offers the version which does fit, rather
// than on an error screen that offers a way back to the file picker.
if (err instanceof ViewerError && err.code === 'dense-too-large') {
this.panel.setBusy(false)
this.showRefusal(err)
return
}
// The browser refused the block's memory. A coarser level is the answer,
// and the shell is what routes levels (`Session.binRefused`).
if (
isAllocationFailure(err) &&
this.level === 'bin' &&
this.props.selection === undefined &&
this.props.onOutOfMemory !== undefined
) {
this.panel.setBusy(false)
this.props.onOutOfMemory()
return
}
this.props.onError(err)
} finally {
if (this.running === task) {
this.running = null
this.progressBox.classList.add('hidden')
}
}
}
/**
* Let the zoom read inside the whole-file picture.
*
* Three things this deliberately does *not* do. It is not armed at contig
* level or over a selection: a cell there is a whole sequence and there is no
* finer grid under it. It does not send `this.wire()` — the plan this view
* chose for the *whole file* is the answer to a different question, and a
* window inside it deserves the finest grid its own cell count allows. (The
* reader's **declared** resolution is not that plan and does travel, as the
* `floor` below; it is a number somebody typed rather than one this view fitted,
* and the worker snaps it to each sequence's own grid so panning holds it
* still.) And it does not run another full pass: every read it makes is a
* bounded window inside the extent the gate already allowed.
*/
private armRefine(
ceiling: Extent,
result: MatrixResult,
budget: { budgetBytes?: number },
): void {
this.ladder?.destroy()
this.ladder = null
if (this.level !== 'bin' || this.props.selection !== undefined) return
if ((result.contigsPerCell ?? 1) > 1) return
const { client, balance, namesGenomes } = this.props
const genomes = namesGenomes ? { genomes: true } : {}
this.ladder = attachRefine({
panel: this.panel,
ceiling: { rows: ceiling, cols: ceiling },
binsize: this.props.binsize,
rungs: rungsOf(this.props.rungs ?? []),
floor: () => this.props.binsPerCell ?? 1,
budget: () => budget.budgetBytes,
read: (rows, cols, rung, binsPerCell) => {
const own = client.cancellable<'matrix'>({
kind: 'matrix',
...(rung === undefined ? {} : { rung }),
...(binsPerCell === undefined ? {} : { binsPerCell }),
rows,
cols,
balance,
...budget,
...genomes,
})
return {
cancel: own.cancel,
promise: own.promise.then(async (block) => {
const other = await secondBlock(this.props.compare ?? this.props.lowerRead, (client2) =>
client2.request<'matrix'>({
kind: 'matrix',
...(rung === undefined ? {} : { rung }),
...(binsPerCell === undefined ? {} : { binsPerCell }),
rows,
cols,
balance,
...budget,
...genomes,
}),
)
const primary = this.byGenome(block)
return other === undefined ? { result: primary } : { result: primary, second: other }
}),
}
},
onInstalled: (block) => this.summary.replaceChildren(...this.summarise(block)),
onError: (err) => {
if (err instanceof ViewerError) this.showRefusal(err)
},
})
// A block read at a rung is held by the extent it was asked for, in bins
// of the open map, which is the unit the ladder counts in.
this.ladder.adopt(this.byGenome(result), ...(result.binsize === undefined ? [] : [ceiling, ceiling]))
}
/**
* Mark the block's genome runs as the axis, where this is the whole-file
* level.
*
* A presentation flag and not a second read: the reader already returns
* `rowGenomes`/`colGenomes` for this block (it is asked for them by
* `namesGenomes`, for the tooltip), and `separatorsFor` promotes them to the
* drawn boundaries *and* the labels when this is set. So the change is which
* of two run lists the picture is divided by, decided by the view that knows
* what it is a picture of.
*
* Left off everywhere else on purpose. A whole-genome map of a cooler has no
* genomes, and a map of a chosen handful of *contigs* is a picture of the
* choice — its axis names what was ticked, which is the answer to "what did I
* pick" and would be lost by coarsening to the genomes those contigs came
* from. A selection of *genomes* is that same rule the other way up and the
* reader decides it there, on the read that knows what was ticked
* (`handleSelection`): the flag arrives set and this method passes it through.
*/
private byGenome(result: MatrixResult): MatrixResult {
const block =
this.props.wholeFileLevel !== undefined &&
result.rowGenomes !== undefined &&
result.colGenomes !== undefined
? { ...result, genomeBoundaries: true }
: result
// Recorded here because this is the one place every block this view installs
// passes through — the gated read, each rung of the ladder, and the block it
// adopts — and because the question it answers, "what is a label here", is
// the same question this method decides.
this.axisIsGenomes = block.genomeBoundaries === true
return block
}
/**
* The line under the heading: what is on screen, and at what resolution.
*
* The resolution is the part that is new and the part a reader cannot get any
* other way. It used to say "1 bin is 1 pixel" or, past the raster's cap, that
* the *picture* was pooled and zooming would not sharpen it — a caveat about
* the drawing. Now the pooling is in the data, so the sentence is about the
* data: these cells are this many base pairs, and that is the map you are
* reading. `poolingNote` still speaks for the raster, which pools again above
* 4096 cells and, at this cap, never does.
*/
private summarise(result: MatrixResult): Array<string | HTMLElement> {
const raster = this.level === 'bin' ? poolingNote(result.nrows, result.ncols) : null
return [
...blockSummary(this.props.binsize, result, this.props.noun),
...(raster === null ? [] : [` · ${raster.phrase}`]),
' · ',
this.panel.viewNote,
]
}
/**
* A refusal, said where the map would have been, with what to do instead.
*
* Shared by the read and by the pre-flight, so the sentence a user meets
* before clicking and the one they would have met after are the same
* sentence.
*/
private showRefusal(err: ViewerError): void {
const { noun } = this.props
// Only the *budget* refusal is overridable, and after the gate there is
// nothing left to override: the confirmation already set the budget aside.
// The CLI-parity limit, the single-array ceiling and a real allocation
// failure are not opinions about this machine, so they get no button.
const estimate = err.detail['bytes']
const needed =
err.detail['where'] === 'browser' && typeof estimate === 'number' ? estimate : null
// "Switch to level" is a real escape hatch now. It used to be a false one:
// the roll-up loaded the same bin-level block before summing it, so it was
// refused by the same guard for the same reason. It accumulates from the
// stored pixels instead, and its cost is the *output* size — one cell per
// sequence pair, which always fits.
this.problem.replaceChildren(
el('span', {
text:
`${err.message} The ${noun}-level view of the same selection is one cell per ` +
`${noun} and always fits; a coarser resolution of this file, if it has one, or a ` +
`single ${noun} from the table, will too.`,
}),
...(needed === null
? []
: [
button(`load anyway (${fmt.bytes(needed)})`, () => void this.load(needed), {
class: 'btn',
title:
'Ignore the estimated memory budget for this read. The tab may become ' +
'unresponsive while the block loads, and may run out of memory.',
}),
]),
)
this.problem.classList.remove('hidden')
this.summary.textContent = ''
this.gate.classList.add('hidden')
this.panelHost.classList.add('hidden')
this.panel.noteRendered('error', this.problem.textContent ?? '')
}
}
/**
* Where a clicked axis label leads.
*
* One rule for both pictures that are divided by genome — the whole-file picker
* and a map of several ticked genomes — because a label means the same thing in
* both and a reader clicking one is asking the same question. It used to be
* decided by which view was asking, which is how the two came to disagree.
*
* `opensGenomes` is the second half and not a formality: a view with nowhere to
* take a genome name falls back to the region, which the range parser accepts
* (§5.4's first rule) and the region view then offers the genome view from. A
* label that did nothing would be worse than a label one screen from home.
*
* Exported for the test that pins it, beside the selection helpers below
* `MatrixPanel` and for the same reason: the rule is arithmetic and the view it
* is read in needs a canvas.
*/
export function labelTarget(axis: {
/** The axis is divided and labelled by genome (`MatrixResult.genomeBoundaries`). */
axisIsGenomes: boolean
/** This view has somewhere to take a genome name. */
opensGenomes: boolean
}): 'genome' | 'region' {
return axis.axisIsGenomes && axis.opensGenomes ? 'genome' : 'region'
}
|