Press n or j to go to the next uncovered block, b, p or k for the previous block.
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24x 24x 24x 24x 24x 24x 24x 2x | /**
* The stage where the reader edits the reference (SPECS §27.3, §27.4).
*
* The third caller of the stage dialog, after the enlarged model and a
* figure's *customise*: the picture, a sidebar of what is done to it, the grip
* between them. **One map and its tracks** — the file's whole-genome picture
* (§27.9), drawn through the edit, with a pieces bar along its top and its left
* and the lanes placed on the map under it, drawn through the same lens — and
* never a deck.
*
* Every act is a step on the file's {@link EditStore}, so the stage holds no
* edit of its own: it draws what the store folds into, and a step made here is
* a step the heading's chip counts and a workspace carries. What the stage does
* hold is the hand: the view, the selection, the drag, and the preview a drag
* draws — the map rearranged under the pointer through the edit it would make,
* with nothing kept until the drop.
*
* **Escape never closes it.** It cancels, innermost first — a drag, then the
* selection — and the stage is closed by its ✕. Its keys are live only while it
* is open, and printed on the controls that perform them (§26.4).
*/
import type { GroupSettings } from '../annotations/groups'
import type { ManualStore } from '../annotations/manual'
import type { MapId } from '../annotations/placement'
import type { AnnotationStore } from '../annotations/store'
import type { AnnotationClient } from '../annotations/worker/client'
import { EditedAssembly, isGap, lengthsOf, wholeOriginal, type AsideReason, type EditStep, type Piece, type ReferenceEdit } from '../genome/edit'
import { formatLocus, formatPosition } from '../genome/assembly'
import { bpAt } from '../render/locus'
import { Scale } from '../render/scale'
import type { EditStore } from '../state/referenceEdit'
import { AnnotationLanes, type LaneGeometry } from '../ui/AnnotationLanes'
import { el } from '../ui/dom'
import { TAB_WALKS, tabStep } from '../ui/tabWalk'
import { icon, iconButton } from '../ui/icons'
import { closeMenu, openMenu, type MenuItem } from '../ui/Menu'
import type { Modal } from '../ui/Modal'
import { stageDialog } from '../ui/StageDialog'
import { fmt } from '../units'
import type { GenomeLinksResult, PictureResult, StageWindowSide } from '../worker/protocol'
import { BAR_NAMES, BAR_THICKNESS, drawBar, drawOverlay, readInk, type StageInk } from './draw'
import {
dropPlace,
dropStep,
endTargets,
isWholeSequence,
landed,
partStretch,
sequenceStretch,
shiftStep,
snapUnit,
stretchBetween,
stretchUnits,
type Snapped,
type SnapTarget,
type Stretch,
} from './gestures'
import { LensGrid, type GridLayout } from './grid'
import { adjustableEnds, adjustSuggestion } from './adjust'
import { pointKey, pointsOf, refinedSuggestion, type RefinedPoint, type RefinePoint } from './refine'
import { LiveDotplot } from './LiveDotplot'
import { sequenceSets } from './dotplotLines'
import { ExportCard, type ExportCardProps } from './ExportCard'
import { readSequenceEvidence, type SequenceEvidence } from './sequenceEvidence'
import { drawSuggestions, markSpots, type MarkedSuggestion } from './marks'
import { paintPicture, paintWindow, pictureColours, windowSide, type WindowRead } from './paint'
import { Rail, type RailItem } from './rail'
import { INITIAL_WEIGHTS, learn, suggest, type Suggested, type Suggestion } from './suggest'
import { stepText } from './words'
import type { Learned } from '../state/referenceEdit'
import { recall, remember } from '../state/UiMemory'
/** The lanes the stage draws, as the map they were placed on has them. */
export interface StageLanes {
store: AnnotationStore
map?: MapId
manual?: ManualStore
client?: AnnotationClient
groups?: GroupSettings
}
/** A read of the picture in flight, and the way to stop it. */
export interface PictureRequest {
promise: Promise<PictureResult>
cancel(): void
}
export interface EditStageProps {
/** The file's own name, for the heading. */
title: string
memoryKey: () => string
store: EditStore
/**
* Start reading the whole-genome picture, reporting progress as it goes —
* of these sequences of the map alone, where they are given: one genome of a
* metagenome and the contigs it may bring in (§27.10).
*/
readPicture(onProgress: (done: number, total: number, note?: string) => void, contigs?: string[], cells?: number): PictureRequest
/**
* On one genome of a metagenome (§27.10): read every contact of the file for
* where the genome's contigs, and the others, belong — without being asked
* where `auto`, as on a file small enough to read in a moment.
*/
genomeLinks?: {
read(contigs: string[], onProgress: (done: number, total: number) => void): { promise: Promise<GenomeLinksResult>; cancel(): void }
auto: boolean
}
/**
* Count the suggestions for an edit off the stage's thread (§27.12), against
* what the method weighs of the picture — kept where it was read, under the
* picture's id (`PictureResult.methodKept`). Absent, a picture that carries
* the method's data is weighed here.
*/
suggest?(input: SuggestRequest): { promise: Promise<Suggested>; cancel(): void }
/**
* Read the window on screen finer than the picture (§27.9): a rung whose
* bins are about a pixel, through the stage's edit. Absent, a zoom past the
* picture's cell shows the cell enlarged.
*/
readWindow?(request: WindowRequest): { promise: Promise<WindowRead | null>; cancel(): void }
/**
* Place a suggestion's points again at the finer rungs (§27.5), through the
* stage's edit, off its thread: one answer a point, `null` where no finer
* rung could. Absent, a suggestion is placed to the picture's cell.
*/
refine?(request: RefineRequest): { promise: Promise<Array<RefinedPoint | null>>; cancel(): void }
/** The map lifted through an edit, every rung, as an `.mcool` (§27.8). */
liftContacts?: ExportCardProps['liftContacts']
/** On a metagenome: the contig → MAG table every genome's edit makes (§27.10). */
binning?: ExportCardProps['binning']
/** The file's sequences the reader declared circular (§8.15), whose origin the stage may set (§27.4). */
circular?: () => readonly string[]
/** The map's colours, as its Map card has them. */
colormap: string
lanes?: StageLanes
onClose(): void
}
/** What a finer read of the window on screen is asked for (§27.9). */
export interface WindowRequest {
edit: ReferenceEdit
/** Names the edit, so the map drawn through it is kept while it stands. */
key: string
/** Base pairs a pixel: the rung wanted is the coarsest no coarser. */
binsize: number
/** The picture's cell, which a rung must be finer than to be worth reading. */
coarser: number
rows: StageWindowSide
cols: StageWindowSide
balance: boolean
}
/** What a count of the suggestions off the stage's thread is asked for. */
export interface RefineRequest {
edit: ReferenceEdit
points: RefinePoint[]
/** The picture's cell, in base pairs: where the method placed them. */
cell: number
/** The finest bin the map is deep enough to show. */
least: number
balance: boolean
}
export interface SuggestRequest {
picture: number
edit: ReferenceEdit
layout: GridLayout
weights?: number[]
evidence?: SequenceEvidence
}
/** What is selected: a stretch on the diagonal, or a box of two off it. */
type Selection = { kind: 'stretch'; stretch: Stretch } | { kind: 'box'; rows: Stretch; cols: Stretch }
/** A drag in progress. */
type Drag =
| { kind: 'pan'; x: number; y: number }
| { kind: 'along'; anchor: number; x: number; y: number; moved: boolean }
| { kind: 'box'; ax: number; ay: number; x: number; y: number; moved: boolean }
/** An end of a suggestion dragged to adjust it (§27.6): which suggestion, which end. */
| { kind: 'adjust'; key: string; end: 0 | 1; x: number; y: number; moved: boolean }
| {
kind: 'move'
stretch: Stretch
units: [number, number]
/** Where along the stretch it was taken hold of, in units. */
grip: number
x: number
y: number
moved: boolean
strand: 1 | -1
copy: boolean
/** ⇧ held: at an edge between two sequences it goes into one, joined to its end, rather than between them (§27.4). */
fuse: boolean
/** Pressed on what was selected already: a press that does not travel widens it to its sequence, or narrows it back. */
again: boolean
/** Where it would go is between two sequences: ⇧ would join it instead. */
between?: boolean
step: EditStep | null
/** The unit the stretch would start at, before the step. */
mark: number | null
}
/** The fewest contacts a contig's links say anything with, on a genome's card (§27.10). */
const LEAST_LINKS = 5
/** The share of a contig's contacts with a genome from which it is offered to it. */
const BELONGS = 0.4
/** Pixels within which the pointer snaps along an axis (§27.4). */
const SNAP_PX = 8
/** Pixels from the diagonal within which a drag selects along it. */
const DIAGONAL_PX = 12
/** Travel, in pixels, before a press becomes a drag. */
const DRAG_PX = 4
/**
* How wide a picture cell must be on screen, in pixels, before the window is
* read again finer than the picture (§27.9): below it the picture shows as
* much as a pixel can.
*/
const WINDOW_CELL_PX = 2
/**
* What a value of a window read at `binsize` is multiplied by to be on the
* picture's scale (§27.9). A picture cell is the sum of `stride²` pixels of
* its rung; a pixel of a rung `k` times coarser than the window's holds, raw,
* the sum of `k²` of the window's — and, balanced, about `k` of them, since
* balancing sets each rung's rows to the same total over `k` times fewer bins.
*/
export function windowScale(picture: Pick<PictureResult, 'binsize' | 'stride' | 'balanced'>, binsize: number): number {
const k = picture.binsize / picture.stride / binsize
return picture.stride * picture.stride * (picture.balanced ? k : k * k)
}
/** The picture's sizes a reader may choose, cells a side, the finest first (§27.9). */
const PICTURE_CELL_CHOICES: readonly number[] = [16_384, 8_192, 4_096, 2_048]
/** Where the picture's size is kept for a file. */
const PICTURE_CELLS_SCOPE = 'map:edit-cells'
/** The fewest cells a view may show a side. */
const MIN_SPAN = 12
/** Pixels within which the pointer snaps to a corner, measured in the plane (§27.4). */
const CORNER_PX = 10
/** The rail's width, beside the map. */
const RAIL_WIDTH = 150
/** The confidence auto mode applies at and above (§27.6). */
const AUTO_THRESHOLD = 0.5
/**
* The least confidence a suggestion is offered at: one a curator would take one
* time in seven or less is noise on the map, drawn where the reader is judging.
* Still ranked — an answer about another can raise it — and still listed among
* those turned down, to be offered again.
*/
const OFFER_FLOOR = 0.15
/** The most steps one run of auto mode makes. */
const AUTO_MOST = 40
/** The most suggestions, best first, whose points are placed at the finer rungs after a count (§27.5). */
const PLACE_MOST = 24
/** Who presses accept (§27.6). */
type Mode = 'manual' | 'review' | 'auto'
/** A confidence, as the stage writes it. */
function percent(confidence: number): string {
return `${Math.round(confidence * 100)}%`
}
/** A suggestion's kind, in a word. */
const KIND_WORD: Record<Suggestion['kind'], string> = { split: 'split', turn: 'turn', move: 'move', join: 'join' }
const REASONS: Array<{ why: AsideReason; label: string; title: string }> = [
{ why: 'debris', label: 'debris', title: 'Short, unplaceable sequence the assembler left over' },
{ why: 'contaminant', label: 'contaminant', title: 'Not this organism’s: a vector, a bacterium, a sample from next door' },
{ why: 'haplotig', label: 'haplotig', title: 'The other copy of a stretch already in the assembly' },
{ why: 'unplaced', label: 'unplaced', title: 'Belongs to this genome, but the map cannot say where' },
]
export class EditStage {
private readonly props: EditStageProps
private readonly modal: Modal
private readonly root: HTMLElement
private readonly side: HTMLElement
private readonly plot: HTMLElement
private readonly readoutEl: HTMLElement
private readonly statusEl: HTMLElement
private readonly pictureCanvas: HTMLCanvasElement
private readonly overlayCanvas: HTMLCanvasElement
private readonly topBar: HTMLCanvasElement
private readonly leftBar: HTMLCanvasElement
/** A band per lane stack, lighting the selection on the tracks as on the map. */
private readonly laneBands: Record<'top' | 'right' | 'bottom' | 'left', HTMLElement>
private readonly lanes: AnnotationLanes | null
private readonly undoButton: HTMLButtonElement
private readonly redoButton: HTMLButtonElement
private readonly selectionCard: HTMLElement
private readonly historyCard: HTMLElement
private readonly sequencesCard: HTMLElement
private readonly pictureCard: HTMLElement
private readonly suggestionsCard: HTMLElement
/** On one genome of a metagenome: where its contigs and the others belong (§27.10). */
private readonly genomeCard: HTMLElement
private readonly exportCard: ExportCard
private readonly modes: Record<Mode, HTMLButtonElement>
private readonly modesEl: HTMLElement
/** The corner dot plot against another reference, where the session holds one (§27.3). */
private readonly dotplot: LiveDotplot | null
private readonly rail: Rail
private readonly reviewBar: HTMLElement
private request: PictureRequest | null = null
private picture: PictureResult | null = null
private colours: Uint32Array | null = null
private layout: GridLayout | null = null
private grid: LensGrid | null = null
/** The grid a drag is previewing, and where its stretch is in it. */
private preview: { grid: LensGrid; units: [number, number] | null } | null = null
private readonly sx = new Scale([0, 1], 1)
private readonly sy = new Scale([0, 1], 1)
private size = 0
private dpr = 1
private image: ImageData | null = null
private pictureDirty = true
private frame = 0
private selection: Selection | null = null
private hover: { x: Snapped; y: Snapped; px: number; py: number } | null = null
private drag: Drag | null = null
private space = false
private alt = false
private ink: StageInk | null = null
/** Where the map sits in the plot, for the bands over the lanes around it. */
private mapAt: { x: number; y: number } = { x: 0, y: 0 }
/** The grid the lanes were last pointed at. */
private lanesGrid: LensGrid | null = null
/** What the method weighs, read with the picture (§27.5) — here, or kept where it was read under the picture's id. */
private method: NonNullable<PictureResult['method']> | null = null
private methodKept: number | null = null
/** A count of the suggestions in flight off the stage's thread. */
private recountRequest: { cancel(): void } | null = null
/** Auto mode applying, one suggestion and one count at a time. */
private autoRunning = false
/** Suggestions whose ends the hand has dragged, by key, until the edit changes (§27.6). */
private readonly adjustments = new Map<string, Suggestion>()
/**
* Where the finer rungs placed the points of the suggestions offered, for
* the edit as it stands (§27.5), by point — `null` where they could not —
* and the suggestions as they make them, until the placements change.
*/
private readonly placements = new Map<string, RefinedPoint | null>()
private placedMemo = new WeakMap<Suggestion, Suggestion>()
/** The placement being read; the count it was for, which a newer one drops; and the whole run, which auto mode waits on. */
private refineRequest: { cancel(): void } | null = null
private refineRound = 0
private refining: Promise<void> | null = null
/** Names this stage's edits to the reader's worker, a new one each time the edit changes (§27.9). */
private readonly token = Math.random().toString(36).slice(2)
private editVersion = 0
/** The window on screen read finer than the picture, for the edit `key` names; the read in flight; its timer. */
private windowRead: { key: string; read: WindowRead; view: [number, number, number, number]; asked: number } | null = null
private windowRequest: { cancel(): void } | null = null
private windowTimer = 0
/** The sequence whose name is being typed, on the sequences card; and a line about the last name refused. */
private renaming: string | null = null
private sequencesNote = ''
/** The sequences the picture was read of, where not the whole map. */
private drawn: Set<string> | null = null
/** Where a genome's contigs and the others belong, read for the contigs `linksOf` names. */
private links: GenomeLinksResult | null = null
private linksOf = ''
private linksRequest: { cancel(): void } | null = null
private linksDone: number | null = null
/** What the session's sequence says about the assembly (§27.5), once read; `null` until then or without one. */
private evidence: SequenceEvidence | null = null
/** Whether the sequence is being read for it. */
private readingEvidence = false
/** The suggestions for the edit as it stands, and a recount pending. */
private suggested: Suggested | null = null
private suggesting = 0
/** What the reader's answers have taught the stage about this file (§27.6). */
private learned: Learned
/** The stretch a line hovered in the corner dot plot lies along, lit on the map (§27.3). */
private linked: Stretch | null = null
/** The suggestion lit — hovered on the map, the rail or the list — by key. */
private lit: string | null = null
private mode: Mode = 'manual'
/** The suggestion review mode is on, by key. */
private current: string | null = null
/** Space held in review mode: the map as it would be with the current suggestion done. */
private previewing = false
/** What the rail was last painted from, so a frame that changes none of it leaves it be. */
private railSignature = ''
/** A move begun on a pieces bar: where the press was, on the page, until it travels. */
private barPress: { x: number; y: number } | null = null
private closed = false
private readonly stopStore: () => void
private readonly observer: ResizeObserver | null
private readonly onKey: (event: KeyboardEvent) => void
private readonly onKeyUp: (event: KeyboardEvent) => void
private readonly onBlur: () => void
constructor(props: EditStageProps) {
this.props = props
this.pictureCanvas = el('canvas', { class: 'edit-picture' })
this.overlayCanvas = el('canvas', { class: 'edit-overlay', attrs: { tabindex: '0', 'aria-label': 'The edited map' } })
this.topBar = el('canvas', { class: 'edit-bar edit-bar-top' })
this.leftBar = el('canvas', { class: 'edit-bar edit-bar-left' })
this.laneBands = {
top: el('div', { class: 'edit-lane-band hidden' }),
right: el('div', { class: 'edit-lane-band hidden' }),
bottom: el('div', { class: 'edit-lane-band hidden' }),
left: el('div', { class: 'edit-lane-band hidden' }),
}
this.statusEl = el('div', { class: 'edit-status' })
this.plot = el(
'div',
{ class: 'edit-plot' },
this.topBar,
this.leftBar,
this.pictureCanvas,
this.overlayCanvas,
this.statusEl,
)
this.lanes =
props.lanes === undefined
? null
: new AnnotationLanes({
store: props.lanes.store,
...(props.lanes.map === undefined ? {} : { map: props.lanes.map }),
...(props.lanes.manual === undefined ? {} : { manual: props.lanes.manual }),
...(props.lanes.client === undefined ? {} : { client: props.lanes.client }),
...(props.lanes.groups === undefined ? {} : { groups: props.lanes.groups }),
onChange: () => this.schedule(),
})
if (this.lanes !== null) {
for (const canvas of Object.values(this.lanes.canvases)) {
canvas.classList.add('edit-lane')
this.plot.append(canvas)
}
}
this.plot.append(...Object.values(this.laneBands))
this.rail = new Rail({ hover: (key) => this.setLit(key), pick: (key) => this.pick(key) })
this.plot.append(this.rail.element)
this.learned = props.store.learned
this.readoutEl = el('div', { class: 'edit-readout', attrs: { 'aria-live': 'polite' } })
const fitButton = iconButton('maximize', 'Show the whole assembly (0, or a double click)', () => this.fit(), {
class: 'btn btn-icon',
size: 15,
})
const zoomOut = iconButton('zoom-out', 'Zoom out (−)', () => this.zoomBy(2), { class: 'btn btn-icon', size: 15 })
const zoomIn = iconButton('zoom-in', 'Zoom in (+)', () => this.zoomBy(0.5), { class: 'btn btn-icon', size: 15 })
this.undoButton = iconButton('undo-2', 'Undo the last step (⌘Z)', () => props.store.undo(), {
class: 'btn btn-icon',
size: 15,
})
this.redoButton = iconButton('redo-2', 'Redo it (⇧⌘Z)', () => props.store.redo(), {
class: 'btn btn-icon',
size: 15,
})
const toolbar = el(
'div',
{ class: 'edit-toolbar' },
el('div', { class: 'edit-tools' }, fitButton, zoomOut, zoomIn),
this.readoutEl,
el('div', { class: 'edit-tools' }, this.undoButton, this.redoButton),
)
this.reviewBar = el('div', { class: 'edit-review hidden', attrs: { 'aria-live': 'polite' } })
this.root = el('div', { class: 'edit-stage' }, toolbar, this.reviewBar, this.plot)
this.selectionCard = el('section', { class: 'edit-card' })
this.historyCard = el('section', { class: 'edit-card' })
this.sequencesCard = el('section', { class: 'edit-card edit-sequences-card' })
this.pictureCard = el('section', { class: 'edit-card edit-picture-card' })
this.suggestionsCard = el('section', { class: 'edit-card edit-suggestions-card' })
this.genomeCard = el('section', { class: 'edit-card edit-genome-card' })
this.exportCard = new ExportCard({
title: props.title,
store: props.store,
...(props.lanes === undefined
? {}
: { annotations: { store: props.lanes.store, ...(props.lanes.client === undefined ? {} : { client: props.lanes.client }) } }),
...(props.liftContacts === undefined ? {} : { liftContacts: props.liftContacts }),
...(props.binning === undefined ? {} : { binning: props.binning }),
})
const mode = (name: Mode, title: string): HTMLButtonElement =>
el('button', {
class: 'btn btn-toggle',
text: name,
title,
attrs: { type: 'button', 'aria-pressed': String(name === 'manual') },
on: { click: () => this.setMode(name) },
})
this.modes = {
manual: mode('manual', 'The suggestions are guides — drawn, labelled, snapped to — and never apply themselves'),
review: mode('review', 'Work through the suggestions, best first: Y takes one, N turns it down, and every answer teaches the ranking'),
auto: mode('auto', `Apply every suggestion at ${percent(AUTO_THRESHOLD)} or more, best first — each a step to undo like any other`),
}
this.modesEl = el('div', { class: 'edit-modes', attrs: { role: 'group', 'aria-label': 'Who presses accept' } }, ...Object.values(this.modes))
this.side = el('div', { class: 'edit-side-body' })
this.arrangeSide()
this.wireCanvas()
this.wireBar(this.topBar, 'top')
this.wireBar(this.leftBar, 'left')
// The assembly against another reference the session holds, through the
// edit, in the map's corner (§27.3).
const lanes = props.lanes
this.dotplot =
lanes?.client === undefined
? null
: LiveDotplot.of({
store: lanes.store,
client: lanes.client,
assembly: () => this.props.store.assembly,
framing: () => ({
uri: props.title,
rows: [0, 0],
cols: [0, 0],
binsize: 0,
binsPerCell: 1,
balance: false,
value: 'count',
normalise: null,
level: 'bin',
label: `${props.title} · sequences, no contact map`,
}),
say: (text) => {
if (text === null) this.paintReadout()
else this.readoutEl.textContent = text
},
frame: (sequence, from, to) => {
const units = this.grid === null ? null : stretchUnits(this.grid, { sequence, from, to })
if (units !== null) this.frameUnits(units[0], units[1])
},
light: (stretch) => {
this.linked = stretch
this.schedule()
},
memoryKey: props.memoryKey(),
})
if (this.dotplot !== null) this.plot.append(this.dotplot.element)
this.onKey = (event) => this.key(event)
this.onKeyUp = (event) => this.keyUp(event)
this.onBlur = () => this.letGo()
window.addEventListener('keydown', this.onKey, true)
window.addEventListener('keyup', this.onKeyUp, true)
window.addEventListener('blur', this.onBlur)
this.stopStore = props.store.subscribe(() => this.edited())
this.modal = stageDialog({
// One genome of a metagenome is edited on its own (§27.10), and says so.
title: props.store.edit.original.genome === undefined ? `Edit the reference · ${props.title}` : `Edit ${props.store.edit.original.genome} · ${props.title}`,
variant: 'modal-edit',
stage: this.root,
stageClass: 'edit-stage-body',
side: this.side,
sideClass: 'edit-side',
memoryKey: props.memoryKey,
scope: 'edit:side',
onResize: () => this.resized(),
onEscape: () => this.escape(),
onClose: () => this.teardown(),
})
this.observer =
typeof ResizeObserver === 'undefined' ? null : new ResizeObserver(() => this.resized())
this.observer?.observe(this.plot)
this.paintSide()
this.read()
requestAnimationFrame(() => this.resized())
}
/** Close the stage, as its ✕ does. */
close(): void {
this.modal.close()
}
// -------------------------------------------------------------------------
// The picture
// -------------------------------------------------------------------------
/**
* The picture's size, chosen: a coarser picture is read faster over a slow
* link and weighed faster, and a zoom past its cell reads the window on
* screen finer anyway (§27.9).
*/
private cellsChoice(): HTMLElement {
const select = el('select', {
class: 'select edit-cells-select',
attrs: { 'aria-label': 'Cells a side of the picture' },
on: { change: () => this.setCells(Number(select.value)) },
}) as HTMLSelectElement
for (const cells of PICTURE_CELL_CHOICES) {
select.append(el('option', { text: `${cells.toLocaleString('en-US')}${cells === PICTURE_CELL_CHOICES[0] ? ' (the finest)' : ''}`, attrs: { value: String(cells) } }))
}
select.value = String(this.cells())
select.disabled = this.request !== null
return el('label', { class: 'edit-cells' }, el('span', { text: 'cells a side' }), select)
}
private read(): void {
this.request?.cancel()
const genome = this.props.store.edit.original.genome
const reading = genome === undefined ? 'reading the whole map for the stage' : `reading ${genome}’s contigs for the stage`
this.showStatus(`${reading}…`, 0, true)
const contigs = this.drawnContigs()
// What the pass reads, as the worker says it on the way in (§27.12): the
// stored pixels and the resolution, so a long read is a known one.
let what = ''
const request = this.props.readPicture(
(done, total, note) => {
if (note !== undefined) what = note
if (this.request === request && total > 0) this.showStatus(what === '' ? `${reading}…` : `${reading}: ${what}…`, done / total, true)
},
contigs,
this.cells(),
)
this.request = request
request.promise
.then((picture) => {
if (this.closed || this.request !== request) return
this.request = null
this.picture = picture
this.drawn = contigs === undefined ? null : new Set(contigs)
this.method = picture.method ?? null
this.methodKept = picture.methodKept ?? null
this.dropPlacements()
this.layout = { binsize: picture.binsize, sequences: picture.sequences }
this.colours = pictureColours(this.props.colormap, { low: picture.low, high: picture.high }, picture.vmin, picture.vmax)
this.hideStatus()
this.rebuild(true)
this.countNow()
this.paintSide()
void this.readEvidence()
if (this.props.genomeLinks?.auto === true && this.linksOf !== this.linksKey()) this.readLinks()
})
.catch((error: unknown) => {
if (this.closed || this.request !== request) return
this.request = null
const cancelled = error instanceof Error && error.name === 'AbortError'
this.showStatus(
cancelled ? 'The picture was not read.' : `The picture could not be read: ${error instanceof Error ? error.message : String(error)}`,
null,
false,
)
})
}
/**
* The session's sequence read for what it says about the assembly — the
* telomeres at its ends, the gaps of `N` inside it — and the suggestions
* counted again with it (§27.5). Nothing where the session has no sequence.
*
* The file's own sequence, chosen as the corner plot chooses it
* (`sequenceSets`): the set naming the most of the map's sequences, not the
* first one loaded, which may be the other reference the plot sets it
* against.
*/
private async readEvidence(): Promise<void> {
const lanes = this.props.lanes
const client = lanes?.client
const entry = lanes === undefined ? null : sequenceSets(lanes.store.entries).own
const original = this.props.store.edit.original
if (client === undefined || entry === null || this.readingEvidence) return
this.readingEvidence = true
this.paintPicture()
try {
const evidence = await readSequenceEvidence(
entry.source.name,
original.names,
original.lengths,
async (sequence, start, end) => {
const got = await client.request<'bases'>({ kind: 'bases', entry: entry.id, regions: [{ contig: sequence, start, end }] })
return got.regions[0]?.bases ?? null
},
{ cancelled: () => this.closed },
)
if (evidence === null || this.closed) return
this.evidence = evidence
this.countNow()
this.paintSide()
this.schedule()
} catch {
// A sequence that cannot be read is no evidence either way.
} finally {
this.readingEvidence = false
if (!this.closed) this.paintPicture()
}
}
private showStatus(text: string, fraction: number | null, cancellable: boolean): void {
const bar = el('div', { class: 'edit-status-bar' })
if (fraction !== null) bar.append(el('div', { class: 'edit-status-fill', style: { width: `${Math.round(fraction * 100)}%` } }))
const children: HTMLElement[] = [el('div', { class: 'edit-status-text', text: fraction === null ? text : `${text} ${Math.round(fraction * 100)}%` })]
if (fraction !== null) children.push(bar)
if (cancellable) {
children.push(el('button', { class: 'btn', text: 'cancel', attrs: { type: 'button' }, on: { click: () => this.request?.cancel() } }))
} else {
children.push(el('button', { class: 'btn', text: 'read it again', attrs: { type: 'button' }, on: { click: () => this.read() } }))
}
this.statusEl.replaceChildren(...children)
this.statusEl.classList.remove('hidden')
}
private hideStatus(): void {
this.statusEl.classList.add('hidden')
this.statusEl.replaceChildren()
}
// -------------------------------------------------------------------------
// The edit
// -------------------------------------------------------------------------
/** The store changed: a step made, undone or redone. */
private edited(): void {
// An adjusted suggestion was for the edit as it stood; so was a finer read,
// and where the finer rungs placed the points, named as the edit named them.
this.adjustments.clear()
this.dropPlacements()
// The corner dot plot's lines, moved through the edit as it now stands.
this.dotplot?.refresh()
this.editVersion++
this.windowRead = null
this.windowRequest?.cancel()
this.windowRequest = null
// A contig brought in from another genome is not in the picture yet: it
// is read again, with it (§27.10).
const drawn = this.drawn
if (drawn !== null && this.request === null && (this.drawnContigs() ?? []).some((name) => !drawn.has(name))) {
this.read()
return
}
this.rebuild(false)
this.paintSide()
this.scheduleSuggestions()
}
/** The sequences the picture is of, where not the whole map: a genome's contigs and those it may bring in. */
private drawnContigs(): string[] | undefined {
const original = this.props.store.edit.original
if (original.genome === undefined) return undefined
return [...original.names, ...(original.elsewhere ?? []).map((contig) => contig.name)]
}
/** The contigs a genome's links are read for: its own and those brought in. */
private linksKey(): string {
const original = this.props.store.edit.original
const brought = this.props.store.assembly.sequences.flatMap((sequence) => sequence.parts.flatMap((part) => (isGap(part) ? [] : [part.sequence])))
return [...new Set([...original.names, ...brought])].sort().join('\n')
}
/** Read every contact for where the genome's contigs and the others belong (§27.10). */
private readLinks(): void {
const links = this.props.genomeLinks
if (links === undefined || this.closed) return
this.linksRequest?.cancel()
const key = this.linksKey()
this.linksDone = 0
const request = links.read(key.split('\n'), (done, total) => {
if (this.linksRequest !== request || !(total > 0)) return
this.linksDone = done / total
this.paintGenome()
})
this.linksRequest = request
this.paintGenome()
request.promise
.then((result) => {
if (this.closed || this.linksRequest !== request) return
this.links = result
this.linksOf = key
})
.catch(() => {
// Cancelled, or the file would not be read: the card says to read again.
})
.finally(() => {
if (this.linksRequest !== request) return
this.linksRequest = null
this.linksDone = null
if (!this.closed) this.paintGenome()
})
}
/** The grid for the store's assembly, keeping the view where it can be kept. */
private rebuild(first: boolean): void {
if (this.layout === null) return
const before = this.grid
const whole = before === null || (this.sx.domain[0] <= 0 && this.sx.domain[1] >= before.n && this.sy.domain[0] <= 0 && this.sy.domain[1] >= before.n)
this.grid = LensGrid.of(this.props.store.assembly, this.layout)
const n = Math.max(1, this.grid.n)
const x = this.sx.domain
const y = this.sy.domain
this.sx.setFull([0, n])
this.sy.setFull([0, n])
if (!first && !whole) {
this.sx.setDomain(x)
this.sy.setDomain(y)
this.clampView()
}
if (this.selection !== null && !this.selectionFits(this.selection)) this.selection = null
this.pictureDirty = true
this.schedule()
}
private selectionFits(selection: Selection): boolean {
const assembly = this.props.store.assembly
const fits = (stretch: Stretch): boolean => {
const length = assembly.lengthOf(stretch.sequence)
return length !== null && stretch.to <= length && stretch.from < stretch.to
}
return selection.kind === 'stretch' ? fits(selection.stretch) : fits(selection.rows) && fits(selection.cols)
}
/** Make a step, and have the selection follow what it moved. */
private step(step: EditStep): void {
const before = this.props.store.assembly
this.props.store.apply(step)
const after = this.props.store.assembly
const followed = landed(before, after, step)
this.selection = followed === null ? (step.op === 'cut' ? this.selection : null) : { kind: 'stretch', stretch: followed }
if (this.selection !== null && !this.selectionFits(this.selection)) this.selection = null
this.paintSide()
this.schedule()
}
/** Steps made one after another, each named against the assembly the one before left. */
private steps(make: Array<(assembly: EditedAssembly) => EditStep | null>): void {
for (const next of make) {
const step = next(this.props.store.assembly)
if (step !== null) this.props.store.apply(step)
}
this.selection = null
this.paintSide()
this.schedule()
}
// -------------------------------------------------------------------------
// The acts
// -------------------------------------------------------------------------
private turn(stretch: Stretch): void {
this.step({ op: 'invert', sequence: stretch.sequence, from: stretch.from, to: stretch.to })
}
private copy(stretch: Stretch): void {
this.step({ op: 'duplicate', sequence: stretch.sequence, from: stretch.from, to: stretch.to, into: stretch.sequence, at: stretch.to, strand: 1 })
}
private setAside(stretch: Stretch, why: AsideReason): void {
this.step({ op: 'aside', sequence: stretch.sequence, from: stretch.from, to: stretch.to, why })
}
/** The reasons a stretch can be set aside for, as a menu. */
private asideMenu(stretch: Stretch, x: number, y: number): void {
openMenu(x, y, [
{ label: `set aside ${formatLocus({ contig: stretch.sequence, start: stretch.from, end: stretch.to })} as` },
...REASONS.map((reason) => ({ label: reason.label, title: reason.title, run: () => this.setAside(stretch, reason.why) })),
])
}
/** Where the pointer is, as an edited position, when it is on the map. */
private pointerPlace(): { sequence: string; at: number } | null {
const grid = this.grid
const hover = this.hover
if (grid === null || hover === null) return null
const place = grid.place(Math.min(grid.n - 1e-9, Math.max(0, hover.x.unit)))
if (place === null || place.bp <= 0) return null
const length = this.props.store.assembly.lengthOf(place.sequence) ?? 0
const at = Math.round(place.bp)
return at > 0 && at < length ? { sequence: place.sequence, at } : null
}
private cutHere(): void {
const place = this.pointerPlace()
if (place !== null) {
this.step({ op: 'cut', sequence: place.sequence, at: place.at })
return
}
const selection = this.selection
if (selection?.kind !== 'stretch') return
const { sequence, from, to } = selection.stretch
this.steps([
() => ({ op: 'cut', sequence, at: to }),
() => ({ op: 'cut', sequence, at: from }),
])
}
private splitHere(): void {
const place = this.pointerPlace()
if (place !== null) {
this.step({ op: 'split', sequence: place.sequence, at: place.at })
return
}
const selection = this.selection
if (selection?.kind !== 'stretch') return
this.splitOut(selection.stretch)
}
/**
* Whether an edited sequence is a circle (§8.15): declared one by a layout
* it was read from, or every part of it a piece of one sequence of the file
* the reader declared circular, the whole of it — as it is, or started
* elsewhere by an origin already set.
*/
private circularOf(name: string): boolean {
const assembly = this.props.store.assembly
const sequence = assembly.sequence(name)
if (sequence === null) return false
if (sequence.circular === true) return true
const declared = this.props.circular?.() ?? []
if (declared.length === 0 || sequence.parts.some((part) => isGap(part))) return false
const pieces = sequence.parts.filter((part) => !isGap(part)) as Array<{ sequence: string }>
const of = pieces[0]?.sequence
if (of === undefined || !declared.includes(of) || pieces.some((piece) => piece.sequence !== of)) return false
const original = this.props.store.edit.original
const index = original.names.indexOf(of)
return index >= 0 && assembly.lengthOf(name) === original.lengths[index]
}
/**
* `O`: a circle started at the pointer — or at the selection's start — its
* first base there and the rest after it round the circle (§27.4). Said, and
* nothing done, on a sequence that is not one.
*/
private originHere(): void {
const selection = this.selection
const place = this.pointerPlace() ?? (selection?.kind === 'stretch' && selection.stretch.from > 0 ? { sequence: selection.stretch.sequence, at: selection.stretch.from } : null)
if (place === null) return
if (!this.circularOf(place.sequence)) {
this.readoutEl.textContent = `O starts a circle elsewhere, and ${place.sequence} is not one: tick it circular on the Chromosomes table first`
return
}
this.step({ op: 'rotate', sequence: place.sequence, at: place.at })
}
/** A stretch made a sequence of its own: split after it, then before it. */
private splitOut(stretch: Stretch): void {
const index = this.props.store.assembly.sequences.findIndex((sequence) => sequence.name === stretch.sequence)
if (index < 0) return
this.steps([
(assembly) => {
const length = assembly.lengthOf(stretch.sequence) ?? 0
return stretch.to < length ? { op: 'split', sequence: stretch.sequence, at: stretch.to } : null
},
(assembly) => {
// The split may have renamed it: it is at the same place in the order.
const name = assembly.sequences[index]?.name
return name === undefined || stretch.from === 0 ? null : { op: 'split', sequence: name, at: stretch.from }
},
])
}
/** Two stretches of one sequence, each taking the other's place. */
private swap(rows: Stretch, cols: Stretch): void {
if (rows.sequence !== cols.sequence) return
const [first, second] = rows.from <= cols.from ? [rows, cols] : [cols, rows]
if (first.to > second.from) return
const index = this.props.store.assembly.sequences.findIndex((sequence) => sequence.name === first.sequence)
const gap = second.from - first.to
this.steps([
() => ({ op: 'move', sequence: first.sequence, from: second.from, to: second.to, into: first.sequence, at: first.from, strand: 1 }),
(assembly) => {
const name = assembly.sequences[index]?.name
if (name === undefined) return null
const moved = second.to - second.from
const from = first.from + moved
const to = from + (first.to - first.from)
// After the stretch between, where the second one was: measured with
// the first taken out.
return { op: 'move', sequence: name, from, to, into: name, at: from + gap, strand: 1 }
},
])
}
// -------------------------------------------------------------------------
// The view
// -------------------------------------------------------------------------
private resized(): void {
if (this.closed) return
this.layoutPlot()
this.pictureDirty = true
this.schedule()
}
/** Place the map, its bars and its lanes in the plot's box. */
private layoutPlot(): void {
const box = this.plot.getBoundingClientRect()
const thickness = (edge: 'top' | 'right' | 'bottom' | 'left'): number => this.lanes?.thicknessOf(edge) ?? 0
const top = thickness('top')
const right = thickness('right')
const bottom = thickness('bottom')
const left = thickness('left')
// The rail takes the room left of the map and its lanes (§27.3).
const rail = RAIL_WIDTH
const size = Math.max(
160,
Math.floor(Math.min(box.width - rail - left - BAR_THICKNESS - right - 12, box.height - top - BAR_THICKNESS - bottom - 12)),
)
this.size = size
this.dpr = window.devicePixelRatio > 0 ? window.devicePixelRatio : 1
const x = Math.max(0, Math.floor((box.width - (rail + left + BAR_THICKNESS + size + right)) / 2)) + rail + left + BAR_THICKNESS
const y = top + BAR_THICKNESS + 4
const place = (node: HTMLElement, px: number, py: number, width: number, height: number): void => {
node.style.left = `${px}px`
node.style.top = `${py}px`
node.style.width = `${width}px`
node.style.height = `${height}px`
}
for (const canvas of [this.pictureCanvas, this.overlayCanvas]) {
place(canvas, x, y, size, size)
canvas.width = Math.round(size * this.dpr)
canvas.height = Math.round(size * this.dpr)
}
place(this.topBar, x, y - BAR_THICKNESS, size, BAR_THICKNESS)
this.topBar.width = Math.round(size * this.dpr)
this.topBar.height = Math.round(BAR_THICKNESS * this.dpr)
place(this.leftBar, x - BAR_THICKNESS, y, BAR_THICKNESS, size)
this.leftBar.width = Math.round(BAR_THICKNESS * this.dpr)
this.leftBar.height = Math.round(size * this.dpr)
if (this.lanes !== null) {
const canvases = this.lanes.canvases
canvases.top.style.left = `${x}px`
canvases.top.style.top = `${y - BAR_THICKNESS - top}px`
canvases.bottom.style.left = `${x}px`
canvases.bottom.style.top = `${y + size}px`
canvases.left.style.left = `${x - BAR_THICKNESS - left}px`
canvases.left.style.top = `${y}px`
canvases.right.style.left = `${x + size}px`
canvases.right.style.top = `${y}px`
}
this.rail.place(x - BAR_THICKNESS - left - rail, y, rail - 4, size, this.dpr)
this.railSignature = ''
this.mapAt = { x, y }
this.dotplot?.place(x, y, size)
this.sx.setPixels(size)
this.sy.setPixels(size)
this.image = null
}
private fit(): void {
const grid = this.grid
if (grid === null) return
this.sx.setDomain([0, Math.max(1, grid.n)])
this.sy.setDomain([0, Math.max(1, grid.n)])
this.pictureDirty = true
this.schedule()
}
/** Zoom both axes by `factor` about a point, in units — the middle of the view by default. */
private zoomBy(factor: number, about?: { x: number; y: number }): void {
const grid = this.grid
if (grid === null) return
const [x0, x1] = this.sx.domain
const [y0, y1] = this.sy.domain
const span = Math.min(grid.n, Math.max(MIN_SPAN, (x1 - x0) * factor))
const cx = about?.x ?? (x0 + x1) / 2
const cy = about?.y ?? (y0 + y1) / 2
const kx = (cx - x0) / (x1 - x0)
const ky = (cy - y0) / (y1 - y0)
this.sx.setDomain([cx - kx * span, cx - kx * span + span])
this.sy.setDomain([cy - ky * span, cy - ky * span + span])
this.clampView()
this.pictureDirty = true
this.schedule()
}
private clampView(): void {
const n = Math.max(1, this.grid?.n ?? 1)
for (const scale of [this.sx, this.sy]) {
const [d0, d1] = scale.domain
const span = Math.min(n, d1 - d0)
let start = d0
if (start < 0) start = 0
if (start + span > n) start = n - span
scale.setDomain([start, start + span])
}
}
/** Frame a stretch of the axis, with a little room either side. */
private frameUnits(a: number, b: number): void {
const grid = this.grid
if (grid === null) return
const span = Math.min(grid.n, Math.max(MIN_SPAN, (b - a) * 1.25))
const centre = (a + b) / 2
this.sx.setDomain([centre - span / 2, centre + span / 2])
this.sy.setDomain([centre - span / 2, centre + span / 2])
this.clampView()
this.pictureDirty = true
this.schedule()
}
/**
* How many cells a side the picture may have, as the reader set it on the
* picture card (§27.3's settings, the resolution the stage works at): the
* finest rung that fits them is read. Kept per file, beside the edit.
*/
private cells(): number {
const kept = recall<number>(this.props.memoryKey(), PICTURE_CELLS_SCOPE)
return typeof kept === 'number' && PICTURE_CELL_CHOICES.includes(kept) ? kept : PICTURE_CELL_CHOICES[0]
}
private setCells(cells: number): void {
if (cells === this.cells()) return
remember(this.props.memoryKey(), PICTURE_CELLS_SCOPE, cells === PICTURE_CELL_CHOICES[0] ? null : cells)
this.windowRead = null
this.read()
}
/** A picture cell's width on screen, in CSS pixels. */
private cellPx(): number {
const [x0, x1] = this.sx.domain
return this.size / Math.max(1e-9, x1 - x0)
}
private windowKey(): string {
return `${this.token}:${this.editVersion}`
}
/** Once the view has settled, read the window on screen finer than the picture, where it is zoomed past a cell (§27.9). */
private considerWindow(): void {
window.clearTimeout(this.windowTimer)
if (this.props.readWindow === undefined || this.closed) return
this.windowTimer = window.setTimeout(() => this.readWindow(), 200)
}
private readWindow(): void {
const grid = this.grid
const picture = this.picture
const ask = this.props.readWindow
if (grid === null || picture === null || ask === undefined || this.closed || this.preview !== null || this.drag !== null) return
const cellPx = this.cellPx()
if (cellPx < WINDOW_CELL_PX) return
const [x0, x1] = this.sx.domain
const [y0, y1] = this.sy.domain
// A bin a device pixel — finer shows nothing more — and never finer than
// the map is deep enough to show; and only where that is half a cell or
// less, since a read about as coarse as the picture shows the picture.
const bpPerPixel = Math.max(1, Math.floor(picture.binsize / (cellPx * this.dpr)), picture.least ?? 0)
if (2 * bpPerPixel > picture.binsize) return
const key = this.windowKey()
const held = this.windowRead
const inside = (view: readonly number[]): boolean => view[0] <= x0 && view[1] >= x1 && view[2] <= y0 && view[3] >= y1
// Held already: this edit, the view inside it, and as fine as asked or the finest there is.
if (held !== null && held.key === key && inside(held.view) && (held.read.binsize <= 2 * bpPerPixel || held.read.binsize > held.asked)) return
const padX = (x1 - x0) / 3
const padY = (y1 - y0) / 3
const view: [number, number, number, number] = [x0 - padX, x1 + padX, y0 - padY, y1 + padY]
const rows = this.windowSideOf(grid, view[2], view[3])
const cols = this.windowSideOf(grid, view[0], view[1])
if (rows === null || cols === null) return
this.windowRequest?.cancel()
const request = ask({ edit: this.props.store.edit, key, binsize: bpPerPixel, coarser: picture.binsize, rows, cols, balance: picture.balanced })
this.windowRequest = request
request.promise.then(
(read) => {
if (this.closed || this.windowRequest !== request) return
this.windowRequest = null
if (read === null || key !== this.windowKey()) return
this.windowRead = { key, read, view, asked: bpPerPixel }
this.pictureDirty = true
this.schedule()
this.paintPicture()
},
() => {
if (this.windowRequest === request) this.windowRequest = null
},
)
}
/** A stretch of the axis as the places in the edited assembly it begins and ends at. */
private windowSideOf(grid: LensGrid, from: number, to: number): StageWindowSide | null {
const lo = Math.max(0, from)
const hi = Math.min(grid.n, to)
if (!(hi > lo)) return null
const first = grid.place(lo)
const last = grid.place(Math.max(lo, hi - 1e-6))
if (first === null || last === null) return null
return { from: { sequence: first.sequence, bp: Math.max(0, first.bp) }, to: { sequence: last.sequence, bp: Math.max(0, last.bp) } }
}
// -------------------------------------------------------------------------
// Drawing
// -------------------------------------------------------------------------
private schedule(): void {
if (this.frame !== 0 || this.closed) return
this.frame = requestAnimationFrame(() => {
this.frame = 0
this.draw()
})
}
/** The grid on screen: the preview while a drag has one, else the edit's. */
private get shown(): LensGrid | null {
return this.preview?.grid ?? this.grid
}
private draw(): void {
const grid = this.shown
if (this.size === 0) this.layoutPlot()
this.ink ??= readInk(this.root)
const ink = this.ink
const size = this.size
const dpr = this.dpr
const picture = this.picture
if (grid === null || picture === null || this.colours === null) return
if (this.pictureDirty) {
this.pictureDirty = false
const ctx = this.pictureCanvas.getContext('2d')
if (ctx !== null) {
const width = this.pictureCanvas.width
const height = this.pictureCanvas.height
if (this.image === null || this.image.width !== width || this.image.height !== height) {
this.image = ctx.createImageData(width, height)
}
const target = new Uint32Array(this.image.data.buffer)
const [x0, x1] = this.sx.domain
const [y0, y1] = this.sy.domain
paintPicture(target, { x0, x1, y0, y1, width, height }, grid.cellMap, grid.cellMap, picture.levels, this.colours)
// Closer than a cell, the window read finer, where it reaches (§27.9).
const held = this.windowRead
if (held !== null && this.preview === null && held.key === this.windowKey() && this.cellPx() >= WINDOW_CELL_PX) {
const rows = windowSide(grid, y0, y1, height, held.read.rows, held.read.binsize)
const cols = windowSide(grid, x0, x1, width, held.read.cols, held.read.binsize)
paintWindow(target, width, rows, cols, held.read, windowScale(picture, held.read.binsize), { low: picture.low, high: picture.high }, this.colours)
}
ctx.putImageData(this.image, 0, 0)
this.considerWindow()
}
}
const toX = (unit: number): number => this.sx.toPixel(unit)
const toY = (unit: number): number => this.sy.toPixel(unit)
// Where the view is, on the element — as a map says its locus on its own —
// so a script driving the stage can point at a place by its unit.
const [vx0, vx1] = this.sx.domain
const [vy0, vy1] = this.sy.domain
this.overlayCanvas.dataset.cells = String(grid.n)
this.overlayCanvas.dataset.view = [vx0, vx1, vy0, vy1].map((value) => value.toFixed(3)).join(' ')
const overlay = this.overlayCanvas.getContext('2d')
const lit = this.litUnits(grid)
const linked = this.linkedUnits(grid)
// The suggestions are about the edit as it stands: while a drag or a
// preview shows another, they are not drawn over it.
const marks = this.preview === null ? this.marks() : []
if (overlay !== null) {
overlay.setTransform(dpr, 0, 0, dpr, 0, 0)
const box = this.selection?.kind === 'box' && this.drag === null ? this.boxUnits(grid, this.selection) : this.dragBox()
drawOverlay(overlay, {
size,
grid,
toX,
toY,
ink,
under: (ctx) => drawSuggestions(ctx, { size, toX, toY, ink, marks }),
square: box === null ? lit : null,
box,
linked,
cross:
this.hover === null || (this.drag !== null && this.drag.kind === 'move')
? null
: {
x: this.hover.x.unit,
y: this.hover.y.unit,
snappedX: this.hover.x.target !== null,
snappedY: this.hover.y.target !== null,
},
})
}
const mark = this.drag?.kind === 'move' ? this.drag.mark : null
const ticks = marks.flatMap(({ suggestion, lit: shining }) =>
[...suggestion.breaks, ...(suggestion.target === null ? [] : [suggestion.target])].map((unit) => ({ unit, lit: shining })),
)
const top = this.topBar.getContext('2d')
if (top !== null) {
top.setTransform(dpr, 0, 0, dpr, 0, 0)
const cols = this.selection?.kind === 'box' ? this.boxUnits(grid, this.selection)?.cols ?? null : lit
drawBar(top, 'top', size, grid, toX, ink, this.drag?.kind === 'box' ? (this.dragBox()?.cols ?? null) : cols, this.preview === null ? mark : null, ticks, linked)
}
const left = this.leftBar.getContext('2d')
if (left !== null) {
left.setTransform(dpr, 0, 0, dpr, 0, 0)
const rows = this.selection?.kind === 'box' ? this.boxUnits(grid, this.selection)?.rows ?? null : lit
drawBar(left, 'left', size, grid, toY, ink, this.drag?.kind === 'box' ? (this.dragBox()?.rows ?? null) : rows, null, ticks, linked)
}
this.paintRail(marks, toY, ink)
if (this.lanes !== null) {
// The lanes are drawn through whichever grid is on screen, the preview's
// included, so a track moves with the stretch under the hand.
if (this.lanesGrid !== grid) {
this.lanes.setAxes({ rows: grid.axis, cols: grid.axis })
this.lanesGrid = grid
}
this.lanes.draw(this.laneGeometry())
}
this.paintLaneBands(lit, toX, toY)
}
/**
* The selection across the lanes, so a stretch is lit on the tracks as it is
* on the map and the bars (§27.4): along the columns for the stacks above
* and below, along the rows for the stacks either side.
*/
private paintLaneBands(lit: [number, number] | null, toX: (unit: number) => number, toY: (unit: number) => number): void {
const size = this.size
const { x, y } = this.mapAt
for (const edge of ['top', 'right', 'bottom', 'left'] as const) {
const band = this.laneBands[edge]
const thickness = this.lanes?.thicknessOf(edge) ?? 0
if (lit === null || thickness === 0) {
band.classList.add('hidden')
continue
}
const horizontal = edge === 'top' || edge === 'bottom'
const to = horizontal ? toX : toY
const a = Math.max(0, to(lit[0]))
const b = Math.min(size, to(lit[1]))
if (!(b > a)) {
band.classList.add('hidden')
continue
}
const across =
edge === 'top' ? y - BAR_THICKNESS - thickness : edge === 'bottom' ? y + size : edge === 'left' ? x - BAR_THICKNESS - thickness : x + size
band.style.left = `${horizontal ? x + a : across}px`
band.style.top = `${horizontal ? across : y + a}px`
band.style.width = `${horizontal ? b - a : thickness}px`
band.style.height = `${horizontal ? thickness : b - a}px`
band.classList.remove('hidden')
}
}
private laneGeometry(): LaneGeometry {
const size = this.size
const rect = { x: 0, y: 0, width: size, height: size }
const hover =
this.hover === null ? null : { row: Math.floor(this.hover.y.unit), col: Math.floor(this.hover.x.unit) }
return {
plot: rect,
data: rect,
colScale: this.sx,
rowScale: this.sy,
cssWidth: size,
cssHeight: size,
hover,
anchors: null,
crosshair: this.hover !== null,
echo: null,
echoAnchors: null,
laneEcho: null,
guide: null,
border: null,
handles: false,
grip: null,
scaling: null,
palette: { guide: this.ink?.dim ?? '#555', halo: this.ink?.background ?? '#fff', crosshair: this.ink?.accent ?? '#1f5fa9' },
}
}
/** The selection on the diagonal, in units of the grid shown. */
private litUnits(grid: LensGrid): [number, number] | null {
if (this.drag?.kind === 'along') {
const stretch = stretchBetween(grid, this.drag.anchor, this.alongEnd(this.drag.anchor, this.drag.x, this.drag.y))
return stretch === null ? null : stretchUnits(grid, stretch)
}
if (this.drag?.kind === 'move') {
if (this.preview !== null) return this.preview.units
return this.drag.units
}
if (this.selection?.kind !== 'stretch') return null
return stretchUnits(grid, this.selection.stretch)
}
/**
* What the corner dot plot's hovered line lights on the map (§27.3): the
* piece it lies along — the contig, where nothing is edited yet — in units;
* not while a drag or a preview shows another edit than the one it was drawn through.
*/
private linkedUnits(grid: LensGrid): [number, number] | null {
if (this.linked === null || this.preview !== null || this.drag !== null) return null
const units = stretchUnits(grid, this.linked)
if (units === null) return null
const piece = partStretch(grid, (units[0] + units[1]) / 2)
return (piece === null ? null : stretchUnits(grid, piece)) ?? units
}
private boxUnits(
grid: LensGrid,
selection: Extract<Selection, { kind: 'box' }>,
): { rows: [number, number]; cols: [number, number] } | null {
const rows = stretchUnits(grid, selection.rows)
const cols = stretchUnits(grid, selection.cols)
return rows === null || cols === null ? null : { rows, cols }
}
/** The box being drawn, in units, while a box drag is under way. */
private dragBox(): { rows: [number, number]; cols: [number, number] } | null {
const drag = this.drag
if (drag?.kind !== 'box' || !drag.moved) return null
const x = this.snapX(this.sx.toUnit(drag.x)).unit
const y = this.snapY(this.sy.toUnit(drag.y)).unit
return {
rows: [Math.min(drag.ay, y), Math.max(drag.ay, y)],
cols: [Math.min(drag.ax, x), Math.max(drag.ax, x)],
}
}
// -------------------------------------------------------------------------
// The hand
// -------------------------------------------------------------------------
private targets(): SnapTarget[] {
const grid = this.grid
if (grid === null) return []
const out = endTargets(grid)
if (this.selection?.kind === 'stretch') {
const units = stretchUnits(grid, this.selection.stretch)
if (units !== null) out.push({ unit: units[0], kind: 'selection' }, { unit: units[1], kind: 'selection' })
}
// Every point a suggestion names: its breakpoints, and where it would put a stretch.
for (const suggestion of this.open()) {
for (const unit of suggestion.breaks) out.push({ unit, kind: 'suggestion', key: suggestion.key })
if (suggestion.target !== null) out.push({ unit: suggestion.target, kind: 'suggestion', key: suggestion.key })
for (const corner of suggestion.corners) {
out.push({ unit: corner.row, kind: 'suggestion', key: suggestion.key }, { unit: corner.col, kind: 'suggestion', key: suggestion.key })
}
}
return out
}
private snapX(unit: number): Snapped {
return snapUnit(unit, this.targets(), SNAP_PX * this.sx.unitsPerPixel, this.alt)
}
private snapY(unit: number): Snapped {
return snapUnit(unit, this.targets(), SNAP_PX * this.sy.unitsPerPixel, this.alt)
}
/** A pointer position projected onto the diagonal, snapped. */
private alongUnit(px: number, py: number): Snapped {
return this.snapX((this.sx.toUnit(px) + this.sy.toUnit(py)) / 2)
}
/**
* The far end of a drag along the diagonal: snapped, unless it would snap
* onto the very target the drag began at — at the whole-genome scale eight
* pixels are a hundred kilobases, and a stretch that small near a sequence's
* edge would otherwise come out empty however far the hand went.
*/
private alongEnd(anchor: number, px: number, py: number): number {
const snapped = this.alongUnit(px, py).unit
return snapped === anchor ? Math.round((this.sx.toUnit(px) + this.sy.toUnit(py)) / 2) : snapped
}
private wireCanvas(): void {
const canvas = this.overlayCanvas
const local = (event: MouseEvent): { x: number; y: number } => {
const rect = canvas.getBoundingClientRect()
return { x: event.clientX - rect.left, y: event.clientY - rect.top }
}
canvas.addEventListener('pointerdown', (event) => {
if (this.grid === null) return
canvas.focus({ preventScroll: true })
closeMenu()
const { x, y } = local(event)
if (event.button === 1 || (event.button === 0 && this.space)) {
this.drag = { kind: 'pan', x, y }
} else if (event.button === 0 && this.endUnder(x, y) !== null) {
const grab = this.endUnder(x, y) as { key: string; end: 0 | 1 }
this.drag = { kind: 'adjust', ...grab, x, y, moved: false }
} else if (event.button === 0) {
this.alt = event.altKey
const ux = this.sx.toUnit(x)
const uy = this.sy.toUnit(y)
const lit = this.selection?.kind === 'stretch' ? stretchUnits(this.grid, this.selection.stretch) : null
const diagonal = Math.abs(x - y - (this.sx.toPixel(0) - this.sy.toPixel(0))) / Math.SQRT2
if (lit !== null && ux >= lit[0] && ux <= lit[1] && uy >= lit[0] && uy <= lit[1] && this.selection?.kind === 'stretch') {
const along = (ux + uy) / 2
this.drag = {
kind: 'move',
stretch: this.selection.stretch,
units: lit,
grip: along - lit[0],
x,
y,
moved: false,
strand: 1,
copy: event.altKey,
fuse: event.shiftKey,
again: true,
step: null,
mark: null,
}
} else if (diagonal <= DIAGONAL_PX) {
this.drag = { kind: 'along', anchor: this.alongUnit(x, y).unit, x, y, moved: false }
} else {
this.drag = { kind: 'box', ax: this.snapX(ux).unit, ay: this.snapY(uy).unit, x, y, moved: false }
}
} else {
return
}
canvas.setPointerCapture(event.pointerId)
event.preventDefault()
this.schedule()
})
canvas.addEventListener('pointermove', (event) => {
const { x, y } = local(event)
this.alt = event.altKey
this.pointAt(x, y)
const drag = this.drag
if (drag === null) return
if (drag.kind === 'pan') {
this.sx.panByPixels(x - drag.x)
this.sy.panByPixels(y - drag.y)
this.clampView()
drag.x = x
drag.y = y
this.pictureDirty = true
} else {
// Until it has travelled, `x` and `y` are where the press was.
if (!drag.moved && Math.hypot(x - drag.x, y - drag.y) < DRAG_PX) return
drag.moved = true
drag.x = x
drag.y = y
if (drag.kind === 'move') {
drag.copy = event.altKey
drag.fuse = event.shiftKey
this.updateMove(drag)
} else if (drag.kind === 'adjust') {
this.updateAdjust(drag)
}
}
this.schedule()
})
const finish = (event: PointerEvent): void => {
const drag = this.drag
if (drag === null) return
if (canvas.hasPointerCapture(event.pointerId)) canvas.releasePointerCapture(event.pointerId)
this.drag = null
const grid = this.grid
if (grid === null) return
const { x, y } = local(event)
if (drag.kind === 'along') {
const unit = this.alongEnd(drag.anchor, x, y)
const stretch = drag.moved ? stretchBetween(grid, drag.anchor, unit) : partStretch(grid, (this.sx.toUnit(x) + this.sy.toUnit(y)) / 2)
this.selection = stretch === null ? null : { kind: 'stretch', stretch }
} else if (drag.kind === 'box') {
const cx = this.snapX(this.sx.toUnit(x)).unit
const cy = this.snapY(this.sy.toUnit(y)).unit
if (drag.moved) {
const rows = stretchBetween(grid, drag.ay, cy)
const cols = stretchBetween(grid, drag.ax, cx)
this.selection = rows !== null && cols !== null ? { kind: 'box', rows, cols } : null
} else {
// A press on a corner names the stretch between its two ends (§27.4),
// where both are in one sequence; two parts boxed where they are not.
const same = grid.sequenceAt(cx) !== null && grid.sequenceAt(cx) === grid.sequenceAt(cy)
if (same) {
const stretch = stretchBetween(grid, Math.min(cx, cy), Math.max(cx, cy))
this.selection = stretch === null ? null : { kind: 'stretch', stretch }
} else {
const rows = partStretch(grid, this.sy.toUnit(y))
const cols = partStretch(grid, this.sx.toUnit(x))
this.selection = rows !== null && cols !== null ? { kind: 'box', rows, cols } : null
}
}
} else if (drag.kind === 'adjust') {
// Kept as the hand left it, to be answered: nothing is made until it is taken.
this.paintReadout()
} else if (drag.kind === 'move') {
const step = drag.moved ? drag.step : null
this.preview = null
this.pictureDirty = true
if (step !== null) {
this.step(step)
return
}
if (!drag.moved && drag.again) this.widen((this.sx.toUnit(x) + this.sy.toUnit(y)) / 2)
}
this.paintSide()
this.schedule()
}
canvas.addEventListener('pointerup', finish)
canvas.addEventListener('pointercancel', (event) => {
if (canvas.hasPointerCapture(event.pointerId)) canvas.releasePointerCapture(event.pointerId)
this.cancelDrag()
})
canvas.addEventListener('pointerleave', () => {
if (this.drag !== null) return
this.hover = null
this.setLit(null)
this.paintReadout()
this.schedule()
})
canvas.addEventListener('dblclick', (event) => {
event.preventDefault()
this.fit()
})
canvas.addEventListener(
'wheel',
(event) => {
if (this.grid === null) return
event.preventDefault()
const { x, y } = local(event)
if (event.shiftKey || Math.abs(event.deltaX) > Math.abs(event.deltaY)) {
const dx = event.shiftKey ? event.deltaY : event.deltaX
this.sx.panByPixels(-dx)
this.sy.panByPixels(-dx)
this.clampView()
this.pictureDirty = true
this.schedule()
return
}
const factor = Math.exp(event.deltaY * (event.deltaMode === 1 ? 0.05 : 0.002))
this.zoomBy(factor, { x: this.sx.toUnit(x), y: this.sy.toUnit(y) })
},
{ passive: false },
)
canvas.addEventListener('contextmenu', (event) => {
event.preventDefault()
const { x, y } = local(event)
this.pointAt(x, y)
openMenu(event.clientX, event.clientY, this.menuItems(event.clientX, event.clientY))
})
}
/**
* A pieces bar as a handle on the pieces it draws (§27.3, §27.4): a press
* selects the piece under it, or holds the selection where it is inside it,
* and a drag moves what is held — the map's own move, with the pointer set
* on the diagonal at the bar's place, so the ghost, the snapping, the preview
* under the hand, `I` on the way and ⌥ for a copy are the same ones; a
* double click turns the piece; hovering names it and where it came from.
*/
private wireBar(canvas: HTMLCanvasElement, side: 'top' | 'left'): void {
const unitOf = (event: MouseEvent): number => {
const rect = canvas.getBoundingClientRect()
return side === 'top' ? this.sx.toUnit(event.clientX - rect.left) : this.sy.toUnit(event.clientY - rect.top)
}
const onDiagonal = (unit: number): { x: number; y: number } => ({ x: this.sx.toPixel(unit), y: this.sy.toPixel(unit) })
const onNames = (event: MouseEvent): boolean => {
const rect = canvas.getBoundingClientRect()
return (side === 'top' ? event.clientY - rect.top : event.clientX - rect.left) < BAR_NAMES
}
canvas.addEventListener('pointerdown', (event) => {
const grid = this.grid
if (grid === null || event.button !== 0) return
closeMenu()
this.overlayCanvas.focus({ preventScroll: true })
const unit = unitOf(event)
this.dotplot?.focusOn(null)
// The row of names is the sequence's, whole (§27.4); the row of pieces, a piece's.
const onName = onNames(event)
const held = this.selection?.kind === 'stretch' ? this.selection.stretch : null
const lit = held === null ? null : stretchUnits(grid, held)
const whole = onName ? sequenceStretch(grid, unit) : null
const inside = !onName && held !== null && lit !== null && unit >= lit[0] && unit <= lit[1]
const stretch = whole ?? (inside ? held : partStretch(grid, unit))
if (stretch === null) return
const units = inside && lit !== null ? lit : stretchUnits(grid, stretch)
if (!inside) {
this.selection = { kind: 'stretch', stretch }
this.paintSide()
}
if (units !== null) {
this.drag = {
kind: 'move',
stretch,
units,
grip: unit - units[0],
...onDiagonal(unit),
moved: false,
strand: 1,
copy: event.altKey,
fuse: event.shiftKey,
again: inside,
step: null,
mark: null,
}
this.barPress = { x: event.clientX, y: event.clientY }
canvas.setPointerCapture(event.pointerId)
canvas.classList.add('is-dragging')
}
event.preventDefault()
this.schedule()
})
canvas.addEventListener('pointermove', (event) => {
const drag = this.drag
if (drag?.kind === 'move' && this.barPress !== null) {
if (!drag.moved && Math.hypot(event.clientX - this.barPress.x, event.clientY - this.barPress.y) < DRAG_PX) return
drag.moved = true
Object.assign(drag, onDiagonal(unitOf(event)))
drag.copy = event.altKey
drag.fuse = event.shiftKey
this.updateMove(drag)
this.schedule()
return
}
if (this.drag !== null) return
const unit = unitOf(event)
this.describeBar(unit)
// What is under the pointer lit in the corner dot plot (§27.3): over a
// name the sequence whole, over the pieces the piece.
const grid = this.grid
this.dotplot?.focusOn(grid === null ? null : onNames(event) ? sequenceStretch(grid, unit) : partStretch(grid, unit))
})
const finish = (event: PointerEvent): void => {
if (canvas.hasPointerCapture(event.pointerId)) canvas.releasePointerCapture(event.pointerId)
canvas.classList.remove('is-dragging')
const drag = this.drag
this.barPress = null
if (drag?.kind !== 'move') return
this.drag = null
const step = drag.moved ? drag.step : null
this.preview = null
this.pictureDirty = true
if (step !== null) {
this.step(step)
return
}
if (!drag.moved && drag.again) this.widen(unitOf(event))
this.paintReadout()
this.paintSide()
this.schedule()
}
canvas.addEventListener('pointerup', finish)
canvas.addEventListener('pointercancel', (event) => {
if (canvas.hasPointerCapture(event.pointerId)) canvas.releasePointerCapture(event.pointerId)
canvas.classList.remove('is-dragging')
this.barPress = null
this.cancelDrag()
})
canvas.addEventListener('pointerleave', () => {
this.dotplot?.focusOn(null)
if (this.drag === null) this.paintReadout()
})
canvas.addEventListener('dblclick', (event) => {
event.preventDefault()
const grid = this.grid
if (grid === null) return
const stretch = partStretch(grid, unitOf(event))
if (stretch !== null) this.turn(stretch)
})
}
/** The readout over a pieces bar: the piece under the pointer, where it came from, and what the bar does with it. */
private describeBar(unit: number): void {
const grid = this.grid
if (grid === null) return
const place = grid.place(Math.min(grid.n - 1e-9, Math.max(0, unit)))
const stretch = partStretch(grid, unit)
const piece = place?.part.piece ?? null
if (place === null || stretch === null || piece === null) {
this.readoutEl.textContent = place === null ? this.summary() : `${place.sequence} · gap`
return
}
const here = formatLocus({ contig: stretch.sequence, start: stretch.from, end: stretch.to })
const from = formatLocus({ contig: piece.sequence, start: piece.start, end: piece.end })
const origin = from === here && piece.strand === 1 ? '' : ` ← ${from}${piece.strand === -1 ? ', turned' : ''}`
this.readoutEl.textContent = `${here}${origin} · drag to move it, double-click to turn it · its name above, the whole of ${stretch.sequence}`
}
/**
* A press that did not travel, on what was selected already (§27.4): a piece
* — or any stretch short of its sequence — widens to the whole sequence; the
* whole sequence narrows back to the piece under the pointer.
*/
private widen(unit: number): void {
const grid = this.grid
const held = this.selection?.kind === 'stretch' ? this.selection.stretch : null
if (grid === null || held === null) return
const whole = sequenceStretch(grid, unit)
const part = partStretch(grid, unit)
if (whole === null || part === null || whole.sequence !== held.sequence) return
const next = isWholeSequence(this.props.store.assembly, held) ? part : whole
if (next.from === held.from && next.to === held.to) return
this.selection = { kind: 'stretch', stretch: next }
}
/**
* ↑ or ↓ (§27.4): what is selected one place earlier or later — a whole
* sequence in the order, a piece among its sequence's — joining nothing.
* Where it cannot go, the readout says why.
*/
private shiftSelection(delta: -1 | 1): void {
const held = this.selection?.kind === 'stretch' ? this.selection.stretch : null
if (held === null) return
const assembly = this.props.store.assembly
const step = shiftStep(assembly, held, delta)
if (step !== null) {
this.step(step)
const units = this.grid === null || this.selection?.kind !== 'stretch' ? null : stretchUnits(this.grid, this.selection.stretch)
if (units !== null && !this.inView(units)) this.frameUnits(units[0], units[1])
return
}
const whole = isWholeSequence(assembly, held)
const pieces = assembly.piecesIn(held.sequence, 0, assembly.lengthOf(held.sequence) ?? 0).length
this.readoutEl.textContent = whole
? `${held.sequence} is ${delta < 0 ? 'first' : 'last'} already`
: pieces > 1 && assembly.piecesIn(held.sequence, held.from, held.to).length === 1
? `it is the ${delta < 0 ? 'first' : 'last'} piece of ${held.sequence} already: ↑ ↓ never take it out`
: '↑ ↓ move a whole sequence, or a piece among its sequence’s pieces'
}
/** Whether a stretch of the axis is on screen, both of its ends. */
private inView(units: readonly [number, number]): boolean {
const [a, b] = [this.sx.toPixel(units[0]), this.sx.toPixel(units[1])]
return a >= 0 && b <= this.size
}
/**
* The pointer at `(x, y)` on the map, snapped, and said in the readout: to a
* suggestion's corner in the plane where one is within reach (§27.4), else
* along each axis; and a suggestion's mark under it lit, with its label.
*/
private pointAt(x: number, y: number): void {
if (this.grid === null) return
const spots = this.preview === null && this.drag?.kind !== 'move' ? markSpots({ size: this.size, toX: (u) => this.sx.toPixel(u), toY: (u) => this.sy.toPixel(u), marks: this.marks() }) : []
let nearest: (typeof spots)[number] | null = null
let distance = Number.POSITIVE_INFINITY
for (const spot of spots) {
const d = Math.hypot(spot.x - x, spot.y - y)
if (d < distance) {
nearest = spot
distance = d
}
}
const within = nearest !== null && distance <= CORNER_PX ? nearest : null
if (within !== null && within.corner && !this.alt) {
const target = { kind: 'suggestion' as const, key: within.key }
this.hover = { x: { unit: within.col, target: { ...target, unit: within.col } }, y: { unit: within.row, target: { ...target, unit: within.row } }, px: x, py: y }
} else {
this.hover = { x: this.snapX(this.sx.toUnit(x)), y: this.snapY(this.sy.toUnit(y)), px: x, py: y }
}
if (this.drag === null) this.setLit(within?.key ?? this.hover.x.target?.key ?? this.hover.y.target?.key ?? null)
// An end a drag would take hold of says so under the pointer (§27.6).
this.overlayCanvas.classList.toggle('is-on-end', this.drag === null && this.endUnder(x, y) !== null)
this.overlayCanvas.classList.toggle('is-adjusting', this.drag?.kind === 'adjust')
this.paintReadout()
this.schedule()
}
/** Recompute a move's drop and its preview as the pointer travels. */
private updateMove(drag: Extract<Drag, { kind: 'move' }>): void {
const grid = this.grid
if (grid === null) return
const along = (this.sx.toUnit(drag.x) + this.sy.toUnit(drag.y)) / 2
const length = drag.units[1] - drag.units[0]
// Where the stretch's start would go, snapped by whichever of its two ends
// is nearer a target — a stretch is dropped against an edge either way.
const start = along - drag.grip
const reach = SNAP_PX * this.sx.unitsPerPixel
const ends = endTargets(grid)
const byStart = snapUnit(start, ends, reach, this.alt && !drag.copy)
const byEnd = snapUnit(start + length, ends, reach, this.alt && !drag.copy)
const unit =
byEnd.target !== null && (byStart.target === null || Math.abs(byEnd.unit - (start + length)) < Math.abs(byStart.unit - start))
? byEnd.unit - length
: byStart.unit
// Before the step, a start past the stretch is measured with it still in.
const at = unit > drag.units[0] ? unit + length : unit
drag.mark = Math.max(0, Math.min(grid.n, at))
// A copy goes into a sequence, as a join does: only a move has a place between.
const place = dropPlace(grid, drag.mark, along, drag.fuse || drag.copy)
const step = place === null ? null : dropStep(this.props.store.assembly, drag.stretch, place, drag.strand, drag.copy)
drag.between = place !== null && 'before' in place
drag.step = step
if (step === null) {
this.preview = null
} else {
const assembly = this.props.store.assembly
const next = EditedAssembly.of(this.props.store.tentative(step))
const previewGrid = LensGrid.of(next, this.layout as GridLayout)
const where = landed(assembly, next, step)
this.preview = { grid: previewGrid, units: where === null ? null : stretchUnits(previewGrid, where) }
}
this.pictureDirty = true
this.paintReadout()
}
private cancelDrag(): boolean {
if (this.drag === null) return false
this.drag = null
this.preview = null
this.pictureDirty = true
this.paintReadout()
this.schedule()
return true
}
/** Escape: the innermost thing in progress, and never the stage. */
private escape(): void {
closeMenu()
if (this.cancelDrag()) return
if (this.selection !== null) {
this.selection = null
this.paintSide()
this.schedule()
}
}
private key(event: KeyboardEvent): void {
if (this.closed) return
const target = event.target as HTMLElement | null
if (target !== null && (target.tagName === 'INPUT' || target.tagName === 'TEXTAREA' || target.tagName === 'SELECT' || target.isContentEditable)) {
return
}
// Only the dialog on top answers.
const dialogs = document.querySelectorAll('.modal-backdrop')
if (dialogs.length > 0 && !dialogs[dialogs.length - 1].contains(this.root)) return
const mod = event.metaKey || event.ctrlKey
const key = event.key
let handled = true
if (key === 'Alt') {
this.alt = true
handled = false
} else if (key === ' ') {
this.space = true
this.overlayCanvas.classList.add('is-panning')
// In review, held: the map as it would be with the suggestion taken.
if (this.mode === 'review' && !event.repeat) this.startPreview()
} else if (mod && (key === 'z' || key === 'Z')) {
if (event.shiftKey) this.props.store.redo()
else this.props.store.undo()
} else if (mod && (key === 'y' || key === 'Y')) {
this.props.store.redo()
} else if (mod) {
handled = false
} else if (key === 'i' || key === 'I') {
if (this.drag?.kind === 'move') {
this.drag.strand = this.drag.strand === 1 ? -1 : 1
this.updateMove(this.drag)
this.schedule()
} else if (this.selection?.kind === 'stretch') {
this.turn(this.selection.stretch)
} else handled = false
} else if (key === 'c' || key === 'C') {
this.cutHere()
} else if (key === 's' || key === 'S') {
this.splitHere()
} else if (key === 'o' || key === 'O') {
this.originHere()
} else if (key === 'Backspace' || key === 'Delete') {
if (this.selection?.kind === 'stretch') {
const rect = this.overlayCanvas.getBoundingClientRect()
this.asideMenu(this.selection.stretch, rect.left + rect.width / 2, rect.top + rect.height / 2)
} else handled = false
} else if (key === 'y' || key === 'Y' || key === 'n' || key === 'N') {
// Review answers the one it is on; elsewhere, the one lit under the hand.
const suggestion = this.byKey(this.mode === 'review' ? this.current : this.lit)
if (suggestion === null) handled = false
else if (key === 'y' || key === 'Y') this.accept(suggestion)
else this.reject(suggestion)
} else if (this.mode === 'review' && (key === 'ArrowRight' || key === 'ArrowLeft')) {
this.moveCurrent(key === 'ArrowRight' ? 1 : -1)
} else if (key === 'ArrowUp' || key === 'ArrowDown') {
// A sequence's grip on the card moves its own sequence; elsewhere, what is selected.
const grip = target?.closest?.('.edit-sequence-grip') as HTMLElement | null | undefined
const named = grip?.dataset.sequence
if (named !== undefined) this.selectWhole(named)
if (this.selection?.kind === 'stretch') this.shiftSelection(key === 'ArrowUp' ? -1 : 1)
else handled = false
if (named !== undefined) this.focusGrip(this.selection?.kind === 'stretch' ? this.selection.stretch.sequence : named)
} else if (key === 'Shift') {
if (this.drag?.kind === 'move') {
this.drag.fuse = true
this.updateMove(this.drag)
this.schedule()
}
handled = false
} else if (key === '0') {
this.fit()
} else if (key === '+' || key === '=') {
this.zoomBy(0.5)
} else if (key === '-' || key === '_') {
this.zoomBy(2)
} else {
handled = false
}
if (handled) {
event.preventDefault()
event.stopPropagation()
}
}
private keyUp(event: KeyboardEvent): void {
if (event.key === 'Alt') this.alt = false
if (event.key === 'Shift' && this.drag?.kind === 'move') {
this.drag.fuse = false
this.updateMove(this.drag)
this.schedule()
}
if (event.key === ' ') this.letGoOfSpace()
}
/** The window left with keys held: no key-up comes for them, so they are let go of here. */
private letGo(): void {
this.alt = false
this.letGoOfSpace()
}
private letGoOfSpace(): void {
this.space = false
this.overlayCanvas.classList.remove('is-panning')
this.stopPreview()
}
/** The right-click menu: what can be done with what is selected, or here. */
private menuItems(clientX: number, clientY: number): MenuItem[] {
const items: MenuItem[] = []
const selection = this.selection
if (selection?.kind === 'stretch') {
const stretch = selection.stretch
items.push(
{ label: formatLocus({ contig: stretch.sequence, start: stretch.from, end: stretch.to }) },
{ label: 'turn it round', hint: 'I', run: () => this.turn(stretch) },
{ label: 'copy it after itself', run: () => this.copy(stretch) },
{ label: 'make it a sequence of its own', run: () => this.splitOut(stretch) },
{ label: 'set it aside…', hint: 'delete', run: () => this.asideMenu(stretch, clientX, clientY) },
)
}
const place = this.pointerPlace()
if (place !== null) {
items.push(
{ label: formatPosition(place.sequence, place.at) },
{ label: 'cut here', hint: 'C', run: () => this.step({ op: 'cut', sequence: place.sequence, at: place.at }) },
{ label: 'split into two sequences here', hint: 'S', run: () => this.step({ op: 'split', sequence: place.sequence, at: place.at }) },
...(this.circularOf(place.sequence)
? [{ label: 'start the circle here', hint: 'O', run: () => this.step({ op: 'rotate', sequence: place.sequence, at: place.at }) }]
: []),
)
}
return items
}
// -------------------------------------------------------------------------
// Words
// -------------------------------------------------------------------------
/** The line over the map: where the pointer is, or what the drag would do. */
private paintReadout(): void {
const grid = this.grid
const drag = this.drag
if (drag?.kind === 'move' && drag.moved) {
this.readoutEl.textContent =
drag.step === null
? 'drop it here to leave it where it is'
: `${stepText(drag.step)}${drag.between === true ? ' · ⇧ to join it instead' : ''}${drag.copy ? '' : ' · ⌥ to copy'} · I to turn it`
return
}
const hover = this.hover
if (grid === null || hover === null) {
this.readoutEl.textContent = this.summary()
return
}
const describe = (unit: number): string => {
const place = grid.place(Math.min(grid.n - 1e-9, Math.max(0, unit)))
if (place === null) return ''
const here = formatPosition(place.sequence, Math.floor(place.bp))
const piece = place.part.piece
const segment = place.part.segment
if (piece === null || segment === null) return `${here} · gap`
const original = Math.floor(Math.max(piece.start, Math.min(piece.end - 1, bpAt(segment, unit))))
const same = piece.sequence === place.sequence && piece.strand === 1 && original === Math.floor(place.bp)
return same ? here : `${here} ← ${formatPosition(piece.sequence, original)}${piece.strand === -1 ? ', turned' : ''}`
}
const offDiagonal = Math.abs(hover.px - hover.py - (this.sx.toPixel(0) - this.sy.toPixel(0))) > DIAGONAL_PX * Math.SQRT2
const row = offDiagonal ? describe(hover.y.unit) : ''
const edge = hover.x.target?.kind === 'end' ? this.edgeName(grid, hover.x.unit) : null
const col = edge ?? describe(hover.x.unit)
// A suggestion's point names the suggestion: its number, its kind; a corner
// is two points at once.
const onKey = hover.x.target?.kind === 'suggestion' ? hover.x.target.key : hover.y.target?.kind === 'suggestion' ? hover.y.target.key : undefined
const suggestion = onKey === undefined ? null : this.byKey(onKey)
const number = suggestion === null ? 0 : this.open().findIndex((open) => open.key === suggestion.key) + 1
const corner = suggestion !== null && hover.x.target?.kind === 'suggestion' && hover.y.target?.kind === 'suggestion' && offDiagonal
const snapped =
suggestion !== null
? `${corner ? 'corner of' : 'snapped to'} ${number} · ${KIND_WORD[suggestion.kind]} · `
: hover.x.target !== null && edge === null
? 'edit end · '
: this.alt
? 'free · '
: ''
this.readoutEl.textContent = `${snapped}${col}${row === '' ? '' : ` × ${row}`}`
}
/**
* A unit the pointer snapped to, named as the edge between two sequences where
* it is one — the end of one and the start of the next is one place, and the
* readout says both — or `null` for a junction inside a sequence.
*/
private edgeName(grid: LensGrid, unit: number): string | null {
const before = grid.sequenceAt(unit - 0.5)
const after = grid.sequenceAt(unit)
if (before === after) return null
if (before === null && after !== null) return `the start of ${after.name}`
if (after === null && before !== null) return `the end of ${before.name}`
return before !== null && after !== null ? `between ${before.name} and ${after.name}` : null
}
private summary(): string {
const assembly = this.props.store.assembly
const total = assembly.sequences.reduce((sum, sequence) => sum + (assembly.lengthOf(sequence.name) ?? 0), 0)
const steps = this.props.store.applied
return `${assembly.sequences.length.toLocaleString('en-US')} sequences · ${fmt.bp(total)}${steps > 0 ? ` · ${steps} ${steps === 1 ? 'step' : 'steps'}` : ' · as in the file'}`
}
// -------------------------------------------------------------------------
// The sidebar
// -------------------------------------------------------------------------
private paintSide(): void {
this.paintSuggestions()
this.paintReview()
this.paintSelection()
this.paintHistory()
this.paintSequences()
this.paintGenome()
this.paintPicture()
this.paintReadout()
const store = this.props.store
this.undoButton.disabled = !store.canUndo
this.redoButton.disabled = !store.canRedo
for (const [name, button] of Object.entries(this.modes) as Array<[Mode, HTMLButtonElement]>) {
button.setAttribute('aria-pressed', String(name === this.mode))
button.disabled = name !== 'manual' && this.suggested === null
}
}
// -------------------------------------------------------------------------
// Suggestions
// -------------------------------------------------------------------------
/** The suggestions offered: not turned down, and at the floor or above, best first. */
private open(): Suggestion[] {
const rejected = new Set(this.learned.rejected)
return (this.suggested?.list ?? [])
.filter((suggestion) => !rejected.has(suggestion.key) && suggestion.confidence >= OFFER_FLOOR)
.map((suggestion) => this.effective(suggestion))
}
/**
* A suggestion as the hand left it: its ends where they were dragged, the
* confidence and what it rests on the method's latest count's (§27.6).
*/
private effective(suggestion: Suggestion): Suggestion {
const moved = this.adjustments.get(suggestion.key)
return moved === undefined ? this.placed(suggestion) : { ...moved, confidence: suggestion.confidence, features: suggestion.features, gain: suggestion.gain }
}
/** A suggestion with its points where the finer rungs placed them (§27.5), where they have. */
private placed(suggestion: Suggestion): Suggestion {
const grid = this.grid
if (grid === null || this.placements.size === 0) return suggestion
let placed = this.placedMemo.get(suggestion)
if (placed === undefined) {
placed = refinedSuggestion(grid, suggestion, (point) => this.placements.get(pointKey(point)))
this.placedMemo.set(suggestion, placed)
}
return placed
}
/** Let go of where the finer rungs placed the points: the edit, or the picture, they were read for is gone. */
private dropPlacements(): void {
this.refineRequest?.cancel()
this.refineRequest = null
this.refineRound++
this.refining = null
this.placements.clear()
this.placedMemo = new WeakMap()
}
/**
* Place the points of the suggestions offered at the finer rungs (§27.5),
* best first, one suggestion a read, off the stage's thread: each is said in
* the list as it comes in. A newer count, or an edit, drops what is still to
* come; a point placed already is not asked again.
*/
private placeSuggestions(): void {
this.refineRequest?.cancel()
this.refineRequest = null
const round = ++this.refineRound
const ask = this.props.refine
const picture = this.picture
const suggested = this.suggested
if (ask === undefined || picture === null || suggested === null) {
this.refining = null
return
}
const rejected = new Set(this.learned.rejected)
const offered = suggested.list.filter((suggestion) => !rejected.has(suggestion.key) && suggestion.confidence >= OFFER_FLOOR).slice(0, PLACE_MOST)
const edit = this.props.store.edit
const assembly = EditedAssembly.of(edit)
const cell = picture.binsize
const run = async (): Promise<void> => {
for (const suggestion of offered) {
const points = pointsOf(suggestion, assembly, cell, this.evidence).filter((point) => !this.placements.has(pointKey(point)))
if (points.length === 0) continue
const request = ask({ edit, points, cell, least: picture.least ?? 0, balance: picture.balanced })
this.refineRequest = request
this.paintSuggestions()
let placed: Array<RefinedPoint | null>
try {
placed = await request.promise
} catch {
if (this.refineRequest === request) this.refineRequest = null
return
}
if (this.closed || round !== this.refineRound || this.props.store.edit !== edit) return
this.refineRequest = null
points.forEach((point, i) => this.placements.set(pointKey(point), placed[i] ?? null))
this.placedMemo = new WeakMap()
this.railSignature = ''
this.paintSide()
this.schedule()
}
}
const running = run().finally(() => {
if (this.refineRound !== round || this.closed) return
this.refining = null
this.paintSuggestions()
})
this.refining = running
}
/**
* An end of the suggestion review is on within reach of the pointer, that a
* drag would take hold of (§27.6). In review only: there the suggestion is
* the one thing being answered, where in manual its ends sit on the very
* places a selection's square is pressed to move it.
*/
private endUnder(x: number, y: number): { key: string; end: 0 | 1 } | null {
if (this.mode !== 'review' || this.preview !== null) return null
const suggestion = this.byKey(this.current)
if (suggestion === null) return null
const ends = adjustableEnds(suggestion)
for (let i = 0; i < ends.length; i++) {
if (Math.hypot(this.sx.toPixel(ends[i]) - x, this.sy.toPixel(ends[i]) - y) <= CORNER_PX) return { key: suggestion.key, end: i === 0 ? 0 : 1 }
}
return null
}
/** An end of a suggestion followed to where the pointer is, snapped along the diagonal (§27.6). */
private updateAdjust(drag: Extract<Drag, { kind: 'adjust' }>): void {
const grid = this.grid
const suggestion = this.byKey(drag.key)
if (grid === null || suggestion === null) return
const unit = this.alongUnit(drag.x, drag.y).unit
const next = adjustSuggestion(grid, suggestion, drag.end, unit)
if (next !== null) {
this.adjustments.set(drag.key, next)
// Dragged past the other end, it is the other end now.
if (suggestion.stretch !== null && next.stretch !== null) drag.end = unit <= next.stretch[0] ? 0 : 1
}
const number = this.open().findIndex((open) => open.key === drag.key) + 1
this.readoutEl.textContent = `adjusting ${number} · ${(next ?? suggestion).words}${next === null ? ' · not here' : ''}`
this.railSignature = ''
}
/** The ones turned down, which the list strikes through. */
private declined(): Suggestion[] {
const rejected = new Set(this.learned.rejected)
return (this.suggested?.list ?? []).filter((suggestion) => rejected.has(suggestion.key))
}
private byKey(key: string | null | undefined): Suggestion | null {
if (key === null || key === undefined) return null
const found = this.suggested?.list.find((suggestion) => suggestion.key === key)
return found === undefined ? null : this.effective(found)
}
/** The suggestions as the map draws them, numbered as the rail and the list number them. */
private marks(): MarkedSuggestion[] {
return this.open().map((suggestion, i) => ({
suggestion,
number: i + 1,
lit: suggestion.key === this.lit || suggestion.key === this.current,
}))
}
/**
* Count the suggestions now rather than once the hand has let go: when the
* picture or the sequence's evidence arrives. Here, the count is in before
* this returns; kept where it was read, it is on its way.
*/
private countNow(): void {
window.clearTimeout(this.suggesting)
this.suggesting = 0
void this.recount().then(() => {
if (this.closed) return
this.paintSide()
this.schedule()
})
}
/** Whether there is anything to weigh suggestions against: the method's data here, or kept where it was read. */
private weighs(): boolean {
return this.method !== null || (this.methodKept !== null && this.props.suggest !== undefined)
}
/** Count the suggestions again once the hand has let go — after an edit, or an answer. */
private scheduleSuggestions(): void {
if (!this.weighs() || this.closed) return
window.clearTimeout(this.suggesting)
this.suggesting = window.setTimeout(() => {
this.suggesting = 0
if (this.closed) return
void this.recount().then(() => {
if (this.closed) return
this.paintSide()
this.schedule()
})
}, 30)
this.paintSuggestions()
}
/**
* The suggestions for the edit as it stands (§27.5): counted where the
* method's data is kept — off the stage's thread, so a hand on the map is
* never held up by them (§27.12) — or here where the picture brought it.
* Settles once they are in; a count overtaken by another edit is dropped
* for the one that follows it.
*/
private recount(): Promise<void> {
const grid = this.grid
if (grid === null || this.closed) return Promise.resolve()
const weights = this.learned.weights ?? INITIAL_WEIGHTS
if (this.method !== null) {
this.tookSuggestions(suggest({ ...this.method, grid, weights, ...(this.evidence === null ? {} : { evidence: this.evidence }) }))
return Promise.resolve()
}
const kept = this.methodKept
const ask = this.props.suggest
const layout = this.layout
if (kept === null || ask === undefined || layout === null) return Promise.resolve()
this.recountRequest?.cancel()
const edit = this.props.store.edit
const request = ask({ picture: kept, edit, layout, weights: [...weights], ...(this.evidence === null ? {} : { evidence: this.evidence }) })
this.recountRequest = request
this.paintSuggestions()
return request.promise.then(
(suggested) => {
if (this.closed || this.recountRequest !== request) return
this.recountRequest = null
if (this.props.store.edit === edit) this.tookSuggestions(suggested)
},
() => {
if (this.recountRequest === request) this.recountRequest = null
},
)
}
/** A count of the suggestions, taken: the one review is on and the one lit kept where they still are. */
private tookSuggestions(suggested: Suggested): void {
this.suggested = suggested
this.placeSuggestions()
const open = this.open()
if (this.current !== null && !open.some((suggestion) => suggestion.key === this.current)) this.current = null
if (this.mode === 'review' && this.current === null) {
// The next best, and framed (§27.6), as entering review and → and ←
// frame theirs. It used to become the one review was on without the map
// moving to it, so after a `Y` or an `N` the line under the toolbar
// named a suggestion the map was not showing, and the next answer was
// given looking at the last one's place.
this.current = open[0]?.key ?? null
const next = this.byKey(this.current)
if (next !== null) this.frameSuggestion(next)
}
if (this.lit !== null && this.byKey(this.lit) === null) this.lit = null
this.railSignature = ''
}
/** Light a suggestion — its marks, its label and its row at once — or none. */
private setLit(key: string | null): void {
if (key === this.lit) return
this.lit = key
for (const row of this.suggestionsCard.querySelectorAll<HTMLElement>('.edit-suggestion')) {
row.classList.toggle('is-lit', row.dataset.key === key)
}
this.schedule()
}
/** A suggestion pressed, on the rail or in the list: framed, and the one review is on. */
private pick(key: string): void {
const suggestion = this.byKey(key)
if (suggestion === null) return
if (this.mode === 'review') this.current = key
this.frameSuggestion(suggestion)
this.paintSide()
}
/** Frame what a suggestion concerns, with room round it to see the evidence. */
private frameSuggestion(suggestion: Suggestion): void {
const [a, b] = suggestion.extent
const room = Math.max(12, (b - a) * 0.4)
this.frameUnits(a - room, b + room)
}
/** Take a suggestion: its step made, with what it rested on kept in the history. */
private accept(suggestion: Suggestion, by: 'suggestion' | 'auto' = 'suggestion'): void {
if (by === 'suggestion') this.answer(suggestion, true)
if (this.current === suggestion.key) this.current = null
this.selection = null
this.props.store.apply(suggestion.step, by, `${suggestion.words} · ${percent(suggestion.confidence)} · ${suggestion.evidence.join(', ')}`)
}
/** Turn a suggestion down: gone from the map, struck through in the list, and learned from. */
private reject(suggestion: Suggestion): void {
this.answer(suggestion, false)
this.learned = { ...this.learned, rejected: [...this.learned.rejected, suggestion.key] }
this.props.store.keepLearned(this.learned)
if (this.current === suggestion.key) this.current = null
if (this.lit === suggestion.key) this.lit = null
this.scheduleSuggestions()
}
/** An answer, learned: one step of the confidence model towards it (§27.6). */
private answer(suggestion: Suggestion, accepted: boolean): void {
const weights = learn(this.learned.weights ?? INITIAL_WEIGHTS, suggestion.features, accepted)
this.learned = { ...this.learned, weights, answers: this.learned.answers + 1 }
this.props.store.keepLearned(this.learned)
}
/** A suggestion turned down, offered again. */
private restore(key: string): void {
this.learned = { ...this.learned, rejected: this.learned.rejected.filter((held) => held !== key) }
this.props.store.keepLearned(this.learned)
this.scheduleSuggestions()
}
/** Everything the answers taught, forgotten: the initial weights, nothing turned down. */
private forget(): void {
this.learned = { weights: null, answers: 0, rejected: [] }
this.props.store.keepLearned(this.learned)
this.scheduleSuggestions()
}
/**
* Auto mode's run (§27.6): the best suggestion at the threshold or above,
* applied as a step marked `auto`, the rest counted again, until none is left
* above it.
*/
private async runAuto(): Promise<void> {
if (this.autoRunning) return
this.autoRunning = true
try {
for (let k = 0; k < AUTO_MOST; k++) {
// Each taken as the finer rungs place it, where they do.
if (this.refining !== null) await this.refining
if (this.closed) return
const next = this.open().find((suggestion) => suggestion.confidence >= AUTO_THRESHOLD)
if (next === undefined) break
const before = this.props.store.applied
this.accept(next, 'auto')
window.clearTimeout(this.suggesting)
this.suggesting = 0
if (this.props.store.applied === before) break
await this.recount()
if (this.closed) return
}
} finally {
this.autoRunning = false
}
this.paintSide()
this.schedule()
}
/**
* The sidebar's cards, in their order (§27.3): what is selected, the
* sequences, the history, then the suggestions — first instead while review
* or auto mode is answering them — the export and the picture. Moved rather
* than built again, so a card keeps its scroll and whatever is typed in it.
*/
private arrangeSide(): void {
const answering = this.mode !== 'manual'
const cards = [
this.modesEl,
...(answering ? [this.suggestionsCard] : []),
this.selectionCard,
this.sequencesCard,
...(this.props.store.edit.original.genome === undefined ? [] : [this.genomeCard]),
this.historyCard,
...(answering ? [] : [this.suggestionsCard]),
this.exportCard.element,
this.pictureCard,
]
cards.forEach((card, i) => {
if (this.side.children[i] !== card) this.side.insertBefore(card, this.side.children[i] ?? null)
})
}
private setMode(mode: Mode): void {
if (mode !== 'manual' && this.suggested === null) return
this.mode = mode
this.arrangeSide()
this.stopPreview()
this.current = mode === 'review' ? (this.open()[0]?.key ?? null) : null
const current = this.byKey(this.current)
if (current !== null) this.frameSuggestion(current)
this.paintSide()
this.schedule()
}
/** Review's next suggestion, or the one before. */
private moveCurrent(delta: 1 | -1): void {
const open = this.open()
if (open.length === 0) return
const at = open.findIndex((suggestion) => suggestion.key === this.current)
const next = open[(Math.max(0, at) + delta + open.length) % open.length]
this.current = next.key
this.frameSuggestion(next)
this.paintSide()
}
/** Space held in review: the map, its bars and its lanes, as they would be with the suggestion taken. */
private startPreview(): void {
const current = this.byKey(this.current)
const layout = this.layout
if (current === null || layout === null || this.drag !== null) return
this.previewing = true
this.preview = { grid: LensGrid.of(EditedAssembly.of(this.props.store.tentative(current.step)), layout), units: null }
this.pictureDirty = true
this.paintReview()
this.schedule()
}
private stopPreview(): void {
if (!this.previewing) return
this.previewing = false
this.preview = null
this.pictureDirty = true
this.paintReview()
this.schedule()
}
/** The rail, painted again only when something it shows has changed. */
private paintRail(marks: readonly MarkedSuggestion[], toY: (unit: number) => number, ink: StageInk): void {
const [y0, y1] = this.sy.domain
const signature = `${y0.toFixed(3)}:${y1.toFixed(3)}:${this.lit}:${this.current}:${marks.map((m) => m.suggestion.key).join('|')}`
if (signature === this.railSignature) return
this.railSignature = signature
const items: RailItem[] = marks.map(({ suggestion, number }) => ({
key: suggestion.key,
number,
text: `${KIND_WORD[suggestion.kind]} ${percent(suggestion.confidence)}`,
title: suggestion.words,
extent: suggestion.extent,
lit: suggestion.key === this.lit,
current: suggestion.key === this.current,
}))
this.rail.paint(items, toY, ink)
}
/** The line under the toolbar that says where review is, and what its keys do. */
private paintReview(): void {
const bar = this.reviewBar
const current = this.byKey(this.current)
if (this.mode !== 'review') {
bar.classList.add('hidden')
bar.replaceChildren()
return
}
bar.classList.remove('hidden')
const open = this.open()
if (current === null) {
bar.replaceChildren(el('span', { class: 'edit-review-words', text: open.length === 0 ? 'review · nothing left to answer' : 'review' }))
return
}
const key = (text: string): HTMLElement => el('kbd', { class: 'kbd', text })
bar.replaceChildren(
el('span', { class: 'edit-review-where', text: `${open.findIndex((one) => one.key === current.key) + 1} of ${open.length}` }),
el('span', { class: 'edit-review-words', text: `${current.words} · ${percent(current.confidence)}` }),
el(
'span',
{ class: 'edit-review-keys' },
this.previewing ? el('span', { class: 'edit-review-state', text: 'as it would be' }) : '',
key('Y'),
' take it ',
key('N'),
' turn it down ',
key('←'),
key('→'),
' the others ',
key('space'),
' held: as it would be',
adjustableEnds(current).length > 0 ? ' · drag its ends to adjust it' : '',
),
)
}
/** The card of suggestions: the list, best first, each with its answer. */
private paintSuggestions(): void {
const card = this.suggestionsCard
const open = this.open()
const weighing = this.suggesting !== 0 || this.recountRequest !== null || this.autoRunning
// Their points being placed at the finer rungs (§27.5), after the count.
const placing = !weighing && this.refineRequest !== null
const head = el('h3', {
class: 'edit-card-head',
text:
this.suggested === null
? `suggestions${weighing ? ' · weighing…' : ''}`
: `suggestions · ${open.length}${weighing ? ' · weighing…' : placing ? ' · placing…' : ''}`,
})
if (!this.weighs() || this.suggested === null) {
card.replaceChildren(
head,
el('p', {
class: 'edit-empty',
text:
this.picture === null
? 'Weighed once the picture is read: the map’s own contact law, then every junction the reference makes, and every two ends that might meet.'
: // The first count, where the data is kept, is on its way.
this.weighs() && weighing
? 'Weighing the map’s own contact law, then every junction the reference makes, and every two ends that might meet…'
: 'The map gave the method nothing to weigh.',
}),
)
return
}
const children: HTMLElement[] = [head]
if (this.mode === 'auto') {
const ready = open.filter((suggestion) => suggestion.confidence >= AUTO_THRESHOLD).length
const run = this.act(
ready === 0 ? `none at ${percent(AUTO_THRESHOLD)} or more` : `apply ${ready} at ${percent(AUTO_THRESHOLD)} or more`,
'play',
'Apply them best first, counting again after each: every one a step marked auto, to undo like any other',
() => void this.runAuto(),
)
run.disabled = ready === 0 || this.autoRunning
children.push(el('div', { class: 'edit-acts' }, run))
}
if (open.length === 0) {
children.push(
el('p', {
class: 'edit-empty',
text:
this.declined().length > 0
? 'Nothing left to answer: what was turned down is below, to offer again. Drag along the diagonal to edit by hand.'
: 'Nothing to suggest: every junction the reference makes is one the map supports, and no two ends it leaves apart meet. Drag along the diagonal to edit by hand.',
}),
)
} else {
const list = el('ol', { class: 'edit-suggestions' })
open.forEach((suggestion, i) => list.append(this.suggestionRow(suggestion, i + 1)))
children.push(list)
}
const declined = this.declined()
if (declined.length > 0) {
const details = el('details', { class: 'edit-declined' })
details.append(el('summary', { text: `turned down · ${declined.length}` }))
const list = el('ul', { class: 'edit-declined-list' })
for (const suggestion of declined) {
const restore = el('button', {
class: 'btn btn-icon',
title: 'Offer it again',
attrs: { type: 'button', 'aria-label': `Offer ${suggestion.words} again` },
on: { click: () => this.restore(suggestion.key) },
})
restore.append(icon('undo-2', { size: 13 }))
list.append(el('li', {}, el('span', { class: 'edit-declined-words', text: suggestion.words }), restore))
}
details.append(list)
children.push(details)
}
if (this.learned.answers > 0) {
children.push(
el(
'p',
{ class: 'edit-note' },
`ranked by what ${this.learned.answers} ${this.learned.answers === 1 ? 'answer' : 'answers'} taught it · `,
el('button', { class: 'btn-link', text: 'forget', attrs: { type: 'button' }, title: 'Back to the initial weights, with nothing turned down', on: { click: () => this.forget() } }),
),
)
}
card.replaceChildren(...children)
}
private suggestionRow(suggestion: Suggestion, number: number): HTMLElement {
const lit = suggestion.key === this.lit
const current = suggestion.key === this.current
const row = el('li', {
class: `edit-suggestion${lit ? ' is-lit' : ''}${current ? ' is-current' : ''}`,
attrs: { 'data-key': suggestion.key },
on: { pointerenter: () => this.setLit(suggestion.key), pointerleave: () => this.setLit(null) },
})
const main = el('button', {
class: 'edit-suggestion-main',
title: 'Frame it on the map',
attrs: { type: 'button' },
on: { click: () => this.pick(suggestion.key), focus: () => this.setLit(suggestion.key) },
})
const kindIcon = { split: 'split', turn: 'flip-horizontal', move: 'move', join: 'merge' } as const
main.append(
el('span', { class: 'edit-suggestion-n', text: String(number) }),
icon(kindIcon[suggestion.kind], { size: 14 }),
el('span', { class: 'edit-suggestion-words', text: suggestion.words }),
el('span', { class: 'edit-suggestion-confidence', text: percent(suggestion.confidence) }),
)
// `adjusted` is the way back as well as the word (§27.6): its ends put
// back where the method found them, from the chip that says they moved.
const chipOf = (chip: string): HTMLElement => {
if (chip !== 'adjusted' || !this.adjustments.has(suggestion.key)) return el('span', { class: 'edit-chip', text: chip })
const back = el('button', {
class: 'edit-chip edit-chip-button',
title: 'Put its ends back where the method found them',
attrs: { type: 'button' },
on: {
click: () => {
this.adjustments.delete(suggestion.key)
this.railSignature = ''
this.paintSide()
this.schedule()
},
},
})
back.append(el('span', { text: 'adjusted' }), icon('undo-2', { size: 11 }))
return back
}
const chips = el('div', { class: 'edit-suggestion-chips' }, ...suggestion.evidence.map(chipOf))
const take = el('button', {
class: 'btn edit-suggestion-act',
title: 'Take it: its step, made (Y)',
attrs: { type: 'button', 'aria-label': `Take ${suggestion.words}` },
on: { click: () => this.accept(suggestion) },
})
take.append(icon('check', { size: 13 }), el('span', { text: 'take' }), el('kbd', { class: 'kbd', text: 'Y' }))
const down = el('button', {
class: 'btn edit-suggestion-act',
title: 'Turn it down: gone from the map, and learned from (N)',
attrs: { type: 'button', 'aria-label': `Turn down ${suggestion.words}` },
on: { click: () => this.reject(suggestion) },
})
down.append(icon('x', { size: 13 }), el('span', { text: 'turn down' }), el('kbd', { class: 'kbd', text: 'N' }))
row.append(main, el('div', { class: 'edit-suggestion-foot' }, chips, el('div', { class: 'edit-suggestion-acts' }, take, down)))
return row
}
private act(label: string, name: Parameters<typeof icon>[0], title: string, run: () => void, key?: string): HTMLButtonElement {
const button = el('button', {
class: 'btn edit-act',
title: key === undefined ? title : `${title} (${key})`,
attrs: { type: 'button' },
on: { click: run },
})
button.append(icon(name, { size: 14 }), el('span', { text: label }))
if (key !== undefined) button.append(el('kbd', { class: 'kbd', text: key }))
return button
}
private paintSelection(): void {
const card = this.selectionCard
const head = el('h3', { class: 'edit-card-head', text: 'selection' })
const selection = this.selection
if (selection === null) {
card.replaceChildren(
head,
el('p', {
class: 'edit-empty',
text: 'Press a piece, on the map or on a bar, and press it again for its whole sequence — or press the sequence’s name on a bar. Drag along the diagonal to select a stretch; drag off it to box two stretches, or press a corner for the stretch between its two ends.',
}),
)
return
}
if (selection.kind === 'stretch') {
const stretch = selection.stretch
const pieces = this.props.store.assembly.piecesIn(stretch.sequence, stretch.from, stretch.to).length
// One place earlier or later (§27.4): a sequence in the order, a piece among its sequence's.
const whole = isWholeSequence(this.props.store.assembly, stretch)
const earlier = this.act('earlier', 'chevron-up', whole ? 'One place earlier in the order — nothing is joined' : 'One place earlier among its sequence’s pieces', () => this.shiftSelection(-1), '↑')
const later = this.act('later', 'chevron-down', whole ? 'One place later in the order — nothing is joined' : 'One place later among its sequence’s pieces', () => this.shiftSelection(1), '↓')
earlier.disabled = shiftStep(this.props.store.assembly, stretch, -1) === null
later.disabled = shiftStep(this.props.store.assembly, stretch, 1) === null
card.replaceChildren(
head,
el('div', { class: 'edit-locus', text: formatLocus({ contig: stretch.sequence, start: stretch.from, end: stretch.to }) }),
el('div', {
class: 'edit-note',
text: `${fmt.bp(stretch.to - stretch.from)} · ${pieces} ${pieces === 1 ? 'piece' : 'pieces'}`,
}),
el(
'div',
{ class: 'edit-acts' },
earlier,
later,
this.act('turn', 'flip-horizontal', 'Turn the stretch round', () => this.turn(stretch), 'I'),
this.act('copy', 'copy', 'Copy the stretch in after itself', () => this.copy(stretch)),
this.act('own sequence', 'split', 'Make the stretch a sequence of its own', () => this.splitOut(stretch), 'S'),
this.act('set aside', 'trash-2', 'Take the stretch out of the assembly, with a reason', () => {
const rect = card.getBoundingClientRect()
this.asideMenu(stretch, rect.left + 16, rect.bottom - 8)
}, 'delete'),
),
el('p', {
class: 'edit-hint',
text: 'Drag its square, or its piece on a bar, to move it: let go between two sequences and it is a sequence of its own there, inside one and it goes in — ⇧ joins it to the end it is let go on, ⌥ copies it, I turns it on the way. Press it again for its whole sequence. A double click on a bar turns a piece.',
}),
)
return
}
const { rows, cols } = selection
const same = rows.sequence === cols.sequence && (rows.to <= cols.from || cols.to <= rows.from)
const rowText = formatLocus({ contig: rows.sequence, start: rows.from, end: rows.to })
const colText = formatLocus({ contig: cols.sequence, start: cols.from, end: cols.to })
const swap = this.act('swap them', 'arrow-left-right', 'Each stretch takes the other’s place', () => this.swap(rows, cols))
swap.disabled = !same
if (!same) swap.title = 'Two stretches of one sequence that do not overlap swap places'
card.replaceChildren(
head,
el('div', { class: 'edit-box-row' }, el('span', { class: 'edit-box-key', text: 'rows' }), el('span', { class: 'edit-locus', text: rowText })),
el('div', { class: 'edit-box-row' }, el('span', { class: 'edit-box-key', text: 'columns' }), el('span', { class: 'edit-locus', text: colText })),
el(
'div',
{ class: 'edit-acts' },
this.act('rows before columns', 'move', 'Move the rows’ stretch to just before the columns’', () => {
this.step({ op: 'move', sequence: rows.sequence, from: rows.from, to: rows.to, into: cols.sequence, at: rows.sequence === cols.sequence && cols.from > rows.to ? cols.from - (rows.to - rows.from) : cols.from, strand: 1 })
}),
this.act('columns after rows', 'move', 'Move the columns’ stretch to just after the rows’', () => {
this.step({ op: 'move', sequence: cols.sequence, from: cols.from, to: cols.to, into: rows.sequence, at: rows.sequence === cols.sequence && rows.to > cols.to ? rows.to - (cols.to - cols.from) : rows.to, strand: 1 })
}),
swap,
this.act('turn rows', 'flip-vertical', 'Turn the rows’ stretch round', () => this.turn(rows)),
this.act('turn columns', 'flip-horizontal', 'Turn the columns’ stretch round', () => this.turn(cols)),
),
)
}
private paintHistory(): void {
const store = this.props.store
const { history, cursor } = store.edit
const list = el('ol', { class: 'edit-history' })
const row = (count: number, text: string): HTMLElement => {
const item = el('li', {
class: `edit-history-row${count === cursor ? ' is-current' : ''}${count > cursor ? ' is-undone' : ''}`,
})
const button = el('button', {
class: 'edit-history-button',
attrs: { type: 'button', 'aria-current': count === cursor ? 'step' : 'false' },
title: count === cursor ? 'Where the edit stands' : count > cursor ? 'Redo up to here' : 'Go back to here',
on: { click: () => store.goTo(count) },
})
button.append(el('span', { class: 'edit-history-n', text: count === 0 ? '·' : String(count) }), el('span', { text }))
item.append(button)
return item
}
list.append(row(0, 'the file as it is'))
history.forEach((entry, i) => {
const item = row(i + 1, stepText(entry.step))
// A step a suggestion made says so, and what it rested on (§27.2).
if (entry.by !== 'reader') {
const by = el('span', { class: 'edit-history-by', text: entry.by === 'auto' ? 'auto' : 'suggested' })
if (entry.suggestion !== undefined) by.title = entry.suggestion
item.querySelector('.edit-history-button')?.append(by)
}
list.append(item)
})
const refusal = store.refusal === null ? null : el('p', { class: 'edit-note', text: store.refusal })
this.historyCard.replaceChildren(
el('h3', { class: 'edit-card-head', text: `history${history.length > 0 ? ` · ${cursor} of ${history.length}` : ''}` }),
...(refusal === null ? [] : [refusal]),
list,
)
}
/**
* A stretch set aside, put back (§27.4): a sequence of its own, last, as the
* file reads it — selected and framed, to be moved into place with ↑ ↓, its
* grip or a drag.
*/
private putBack(piece: Piece): void {
this.step({ op: 'restore', sequence: piece.sequence, start: piece.start, end: piece.end })
const units = this.grid === null || this.selection?.kind !== 'stretch' ? null : stretchUnits(this.grid, this.selection.stretch)
if (units !== null) this.frameUnits(units[0], units[1])
}
/** A sequence selected whole, as a press on its row or on its name on a bar does. */
private selectWhole(name: string): void {
const length = this.props.store.assembly.lengthOf(name)
if (length === null) return
this.selection = { kind: 'stretch', stretch: { sequence: name, from: 0, to: length } }
}
/** The grip of a sequence's row, focused again once the card is painted anew. */
private focusGrip(name: string): void {
for (const grip of this.sequencesCard.querySelectorAll<HTMLElement>('.edit-sequence-grip')) {
if (grip.dataset.sequence === name) grip.focus({ preventScroll: true })
}
}
/**
* A sequence's grip on the card (§27.4): dragged up or down the list, the
* sequence goes where it is let go — before the row under the pointer, or
* last — as one step, and nothing is joined. The card is not painted anew
* while it is held: the rows it measures stay the rows on screen.
*/
private wireGrip(grip: HTMLElement, name: string, list: HTMLElement): void {
grip.addEventListener('pointerdown', (event) => {
if (event.button !== 0) return
event.preventDefault()
grip.focus({ preventScroll: true })
grip.setPointerCapture(event.pointerId)
this.selectWhole(name)
this.paintSelection()
this.schedule()
const rows = [...list.querySelectorAll<HTMLElement>('.edit-sequence-row')]
const from = rows.findIndex((row) => row.contains(grip))
rows.forEach((row, i) => {
row.classList.toggle('is-lifted', i === from)
row.querySelector('.edit-sequence')?.classList.toggle('is-selected', i === from)
})
let target = from
const mark = (clientY: number): void => {
target = rows.findIndex((row) => {
const box = row.getBoundingClientRect()
return clientY < box.top + box.height / 2
})
if (target < 0) target = rows.length
const moves = target !== from && target !== from + 1
rows.forEach((row, i) => {
row.classList.toggle('is-drop-before', moves && i === target)
row.classList.toggle('is-drop-after', moves && target === rows.length && i === rows.length - 1)
})
}
const done = (commit: boolean): void => {
grip.removeEventListener('pointermove', onMove)
grip.removeEventListener('pointerup', onUp)
grip.removeEventListener('pointercancel', onCancel)
if (grip.hasPointerCapture(event.pointerId)) grip.releasePointerCapture(event.pointerId)
rows.forEach((row) => row.classList.remove('is-drop-before', 'is-drop-after', 'is-lifted'))
const assembly = this.props.store.assembly
const length = assembly.lengthOf(name)
if (!commit || length === null || target === from || target === from + 1) {
this.paintSide()
return
}
const before = assembly.sequences[target]?.name ?? null
this.step({ op: 'place', sequence: name, from: 0, to: length, before, strand: 1, whole: true })
this.focusGrip(name)
}
const onMove = (move: PointerEvent): void => mark(move.clientY)
const onUp = (): void => done(true)
const onCancel = (): void => done(false)
grip.addEventListener('pointermove', onMove)
grip.addEventListener('pointerup', onUp)
grip.addEventListener('pointercancel', onCancel)
})
}
private paintSequences(): void {
const assembly = this.props.store.assembly
const list = el('ul', { class: 'edit-sequences' })
for (const sequence of assembly.sequences) {
const length = assembly.lengthOf(sequence.name) ?? 0
const pieces = sequence.parts.filter((part) => !('gap' in part)).length
const selected =
this.selection?.kind === 'stretch' &&
this.selection.stretch.sequence === sequence.name &&
this.selection.stretch.from === 0 &&
this.selection.stretch.to === length
const button = el('button', {
class: `edit-sequence${selected ? ' is-selected' : ''}`,
attrs: { type: 'button' },
title: 'Select the whole sequence, and frame it',
on: {
click: () => {
this.selection = { kind: 'stretch', stretch: { sequence: sequence.name, from: 0, to: length } }
const grid = this.grid
const units = grid === null ? null : stretchUnits(grid, this.selection.stretch)
if (units !== null) this.frameUnits(units[0], units[1])
this.paintSide()
this.schedule()
},
// Its lines lit in the corner dot plot, as its name on a bar lights them (§27.3).
pointerenter: () => this.dotplot?.focusOn({ sequence: sequence.name, from: 0, to: length }),
pointerleave: () => this.dotplot?.focusOn(null),
},
})
const units = this.grid?.sequence(sequence.name)
if (units !== undefined && units !== null) button.dataset.cells = `${units.from} ${units.to}`
const circle = this.circularOf(sequence.name)
button.append(
el('span', { class: 'edit-sequence-name', text: sequence.name, ...(circle ? { title: 'circular' } : {}) }),
el('span', { class: 'edit-sequence-length', text: fmt.bp(length) }),
el('span', { class: 'edit-sequence-pieces', text: `${circle ? '○ ' : ''}${pieces === 1 ? '' : `${pieces} pieces`}` }),
)
if (this.renaming === sequence.name) {
list.append(el('li', { class: 'edit-sequence-row is-renaming' }, this.renameBox(sequence.name)))
continue
}
// A name of its own (§27.3): the pencil, or a double click on the row.
button.addEventListener('dblclick', (event) => {
event.preventDefault()
this.startRename(sequence.name)
})
const pencil = el('button', {
class: 'btn-icon edit-sequence-rename',
title: `Rename ${sequence.name}`,
attrs: { type: 'button', 'aria-label': `Rename ${sequence.name}` },
on: { click: () => this.startRename(sequence.name) },
})
pencil.append(icon('pencil', { size: 12 }))
// Its place in the order (§27.4): dragged by its grip, or ↑ ↓ on it.
const grip = el('button', {
class: 'edit-sequence-grip',
title: `Drag ${sequence.name} to another place in the order, or press ↑ ↓ — nothing is joined`,
attrs: { type: 'button', 'aria-label': `Move ${sequence.name} in the order`, 'data-sequence': sequence.name },
})
grip.append(icon('grip-vertical', { size: 13 }))
this.wireGrip(grip, sequence.name, list)
list.append(el('li', { class: 'edit-sequence-row' }, grip, button, pencil))
}
const aside =
assembly.aside.length === 0
? null
: el(
'div',
{ class: 'edit-aside' },
el('h4', { class: 'edit-card-sub', text: `set aside · ${assembly.aside.length}` }),
el(
'ul',
{ class: 'edit-aside-list' },
...assembly.aside.map((item) => {
const locus = formatLocus({ contig: item.piece.sequence, start: item.piece.start, end: item.piece.end })
// Back into the assembly, as a sequence of its own (§27.4).
const back = el('button', {
class: 'btn btn-quiet edit-aside-back',
title: 'Put it back: a sequence of its own, last, as the file reads it — one step, to undo like any other',
attrs: { type: 'button', 'aria-label': `Put back ${locus}` },
on: { click: () => this.putBack(item.piece) },
})
back.append(icon('undo-2', { size: 12 }), el('span', { text: 'put back' }))
return el(
'li',
{},
el('span', { class: 'edit-aside-locus', text: locus }),
// Sent to another genome of the metagenome, which (§27.10).
el('span', {
class: 'edit-aside-why',
text: item.genome === undefined ? item.why : `→ ${item.genome === '__unbinned__' ? 'no genome' : item.genome}`,
title: item.genome === undefined ? '' : `A contig of ${item.genome === '__unbinned__' ? 'no genome' : item.genome} now, by its contacts`,
}),
back,
)
}),
),
)
// Longest first, the order an assembly is conventionally written in: one
// step, undone as any is (§27.3).
const byLength = [...assembly.sequences].sort((a, b) => (assembly.lengthOf(b.name) ?? 0) - (assembly.lengthOf(a.name) ?? 0)).map((sequence) => sequence.name)
const sorted = byLength.every((name, i) => assembly.sequences[i].name === name)
const sort = el('button', {
class: 'btn btn-quiet edit-card-act',
title: sorted ? 'They are longest first already' : 'Put the sequences longest first — one step, to undo like any other',
attrs: { type: 'button' },
on: { click: () => this.step({ op: 'reorder', names: byLength }) },
})
sort.append(el('span', { text: 'longest first' }))
sort.disabled = sorted
this.sequencesCard.replaceChildren(
el('div', { class: 'edit-card-headrow' }, el('h3', { class: 'edit-card-head', text: `sequences · ${assembly.sequences.length}` }), sort),
...(this.sequencesNote === '' ? [] : [el('p', { class: 'edit-note edit-sequences-note', text: this.sequencesNote })]),
list,
...(aside === null ? [] : [aside]),
)
}
private startRename(name: string): void {
this.renaming = name
this.sequencesNote = ''
this.paintSequences()
// Focused as well as selected: `select` alone leaves the caret where the
// last repaint put it — on a row's grip, after a step a Tab has just taken.
const input = this.sequencesCard.querySelector<HTMLInputElement>('.edit-rename-input')
input?.focus()
input?.select()
}
/**
* The box a sequence is renamed in: Enter makes it a step, Escape or a click
* away leaves the name as it was. A name is one word, and one no other
* sequence of the edit has — a FASTA header and an AGP line are split on
* spaces, and two sequences of one name are one too many for either. And a
* name of the file's own is the sequence's that is that original whole, and
* nobody else's: the rename step's own rule, asked of it (`wholeOriginal`)
* rather than said again here, where it had come out as *nobody's* — a
* sequence renamed and wanting its own name back was refused it.
*/
private renameBox(name: string): HTMLElement {
const input = el('input', { class: 'input edit-rename-input', attrs: { type: 'text', value: name, 'aria-label': `New name for ${name}`, spellcheck: 'false', [TAB_WALKS]: '' } }) as HTMLInputElement
/** `false` where the name typed was refused, the note saying why. */
const done = (commit: boolean): boolean => {
if (this.renaming !== name) return true
this.renaming = null
const wanted = input.value.trim()
if (commit && wanted !== name) {
const taken = this.props.store.assembly.sequences.some((sequence) => sequence.name === wanted)
const original = this.props.store.edit.original
const renamed = this.props.store.assembly.sequence(name)
const theFiles = lengthsOf(original).has(wanted) && (renamed === null || wholeOriginal(renamed, original) !== wanted)
if (wanted === '' || /\s/.test(wanted)) this.sequencesNote = 'A name is one word: a FASTA header and an AGP line are split on spaces.'
else if (taken) this.sequencesNote = `${wanted} is the name of another sequence already.`
else if (theFiles) this.sequencesNote = `${wanted} is a name of the file’s own, for that sequence whole and no other.`
else {
this.sequencesNote = ''
this.step({ op: 'rename', sequence: name, name: wanted })
return true
}
this.paintSequences()
return false
}
this.paintSequences()
return true
}
input.addEventListener('keydown', (event) => {
const step = tabStep(event)
if (step !== null) {
// Enter that goes on to the next sequence's name, Shift+Tab to the one
// before (§26.8): a rename keeps a sequence's place in the list, so the
// next is found by where this one was. A refused name goes nowhere —
// the note says why, as it does after Enter.
event.preventDefault()
event.stopPropagation()
const names = this.props.store.assembly.sequences.map((sequence) => sequence.name)
const at = names.indexOf(name)
if (!done(true)) return
const next = this.props.store.assembly.sequences[at + step]?.name
if (at >= 0 && next !== undefined) this.startRename(next)
return
}
if (event.key === 'Enter') {
event.preventDefault()
done(true)
} else if (event.key === 'Escape') {
event.preventDefault()
event.stopPropagation()
done(false)
}
})
input.addEventListener('blur', () => done(false))
return input
}
/**
* On one genome of a metagenome (§27.10): what its contacts say about where
* its contigs belong — how much of their contacts stay with the genome, the
* contigs that meet another genome more, each with a way to send it there,
* and the contigs of other genomes that meet this one most, each with a way
* to bring it in.
*/
private paintGenome(): void {
const genome = this.props.store.edit.original.genome
if (genome === undefined) return
const links = this.links
const head = el('h3', { class: 'edit-card-head', text: `genome · ${genome}` })
if (this.linksRequest !== null) {
this.genomeCard.replaceChildren(
head,
el(
'p',
{ class: 'edit-note' },
`Reading every contact for where the contigs belong… ${this.linksDone === null ? '' : `${Math.round(this.linksDone * 100)}%`} `,
el('button', { class: 'btn-link', text: 'cancel', attrs: { type: 'button' }, on: { click: () => this.linksRequest?.cancel() } }),
),
)
return
}
if (links === null) {
this.genomeCard.replaceChildren(
head,
el('p', { class: 'edit-note', text: 'Which of its contigs meet another genome more, and which of other genomes’ meet this one: one pass over every contact of the file.' }),
...(this.props.genomeLinks === undefined
? []
: [el('button', { class: 'btn', text: 'read every contact', attrs: { type: 'button' }, on: { click: () => this.readLinks() } })]),
)
return
}
const assembly = this.props.store.assembly
const placed = new Set(assembly.sequences.flatMap((sequence) => sequence.parts.flatMap((part) => (isGap(part) ? [] : [part.sequence]))))
const inside = links.inside.filter((row) => placed.has(row.contig))
const own = inside.reduce((sum, row) => sum + row.own, 0)
const total = inside.reduce((sum, row) => sum + row.total, 0)
const label = (name: string): string => (name === '__unbinned__' ? 'no genome' : name)
const share = (part: number, whole: number): string => `${whole > 0 ? Math.round((100 * part) / whole) : 0}%`
// A contig that meets another genome more than this one, with enough contacts to say.
const strays = inside
.flatMap((row) => {
const other = row.partners.find((partner) => partner.genome !== genome)
return other !== undefined && other.contacts > row.own && row.total >= LEAST_LINKS ? [{ row, other }] : []
})
.sort((a, b) => b.other.contacts / b.row.total - a.other.contacts / a.row.total)
.slice(0, 8)
const candidates = links.outside
.filter((row) => !placed.has(row.contig) && row.contacts >= LEAST_LINKS && row.contacts / row.total >= BELONGS)
.slice(0, 8)
const stale = this.linksOf !== this.linksKey()
this.genomeCard.replaceChildren(
head,
el('p', {
class: 'edit-note',
text: `${share(own, total)} of its contigs’ contacts with other contigs are with its own${stale ? ' — read before the last contig came in' : ''}.`,
}),
el('h4', { class: 'edit-genome-sub', text: strays.length === 0 ? 'No contig of it meets another genome more' : 'Meet another genome more' }),
...(strays.length === 0
? []
: [
el(
'ul',
{ class: 'edit-genome-list' },
...strays.map(({ row, other }) =>
el(
'li',
{ class: 'edit-genome-row' },
el('span', { class: 'edit-genome-name', text: row.contig, title: row.contig }),
el('span', { class: 'edit-genome-share', text: `${share(row.own, row.total)} here · ${share(other.contacts, row.total)} ${label(other.genome)}` }),
el('button', {
class: 'btn edit-genome-act',
text: `send to ${label(other.genome)}`,
title: `Take ${row.contig} out of ${genome}, as a contig of ${label(other.genome)}: a step to undo like any other`,
attrs: { type: 'button' },
on: { click: () => this.send(row.contig, other.genome) },
}),
),
),
),
]),
el('h4', { class: 'edit-genome-sub', text: candidates.length === 0 ? 'No contig elsewhere meets this genome most' : 'Meet this genome most' }),
...(candidates.length === 0
? []
: [
el(
'ul',
{ class: 'edit-genome-list' },
...candidates.map((row) =>
el(
'li',
{ class: 'edit-genome-row' },
el('span', { class: 'edit-genome-name', text: row.contig, title: `${row.contig} · ${fmt.bp(row.length)} · of ${label(row.genome)}` }),
el('span', { class: 'edit-genome-share', text: `${label(row.genome)} · ${share(row.contacts, row.total)} of its contacts here` }),
el('button', {
class: 'btn edit-genome-act',
text: 'bring in',
title: `Bring ${row.contig} into ${genome}, whole, as a contig of its own: a step to undo like any other`,
attrs: { type: 'button' },
on: { click: () => this.props.store.bring({ name: row.contig, length: row.length, genome: row.genome }) },
}),
),
),
),
]),
...(stale && this.props.genomeLinks !== undefined
? [el('button', { class: 'btn-link', text: 'read again', attrs: { type: 'button' }, on: { click: () => this.readLinks() } })]
: []),
)
}
/** Send a contig of this genome to another (§27.10): every stretch of it the edit places, set aside as that genome's. */
private send(contig: string, genome: string): void {
const store = this.props.store
for (const landing of [...store.assembly.landings(contig)].sort((a, b) => b.offset - a.offset)) {
const length = landing.piece.end - landing.piece.start
store.apply({ op: 'aside', sequence: landing.sequence, from: landing.offset, to: landing.offset + length, why: 'contaminant', genome })
}
}
/** What the picture is of: the whole map, or one genome's contigs of a metagenome (§27.10). */
private pictureOf(): string {
const genome = this.props.store.edit.original.genome
return genome === undefined ? 'The whole map' : `${genome}’s contigs alone, the rest of the metagenome left out,`
}
private paintPicture(): void {
const picture = this.picture
const evidence = this.evidence
let sequence: string | null = null
if (this.readingEvidence) sequence = 'Reading the sequence for its telomeres and gaps…'
else if (evidence !== null) {
const facts = [...evidence.facts.values()]
const ends = facts.reduce((sum, fact) => sum + (fact.start === null ? 0 : 1) + (fact.end === null ? 0 : 1), 0)
const gaps = facts.reduce((sum, fact) => sum + fact.gaps.length, 0)
sequence =
`From ${evidence.from}: telomeric repeats at ${ends.toLocaleString('en-US')} of ${(2 * facts.length).toLocaleString('en-US')} ends` +
(evidence.gapsRead ? `, ${gaps.toLocaleString('en-US')} gap${gaps === 1 ? '' : 's'} of N` : '') +
' — a join that would bury a telomere counts against itself, and a break beside a gap is placed at it.'
}
this.pictureCard.replaceChildren(
el('h3', { class: 'edit-card-head', text: 'picture' }),
el('p', {
class: 'edit-note',
text:
picture === null
? `${this.pictureOf()}, read once for the stage.`
: `${this.pictureOf()} at ${fmt.bp(picture.binsize)} a cell, ${picture.n.toLocaleString('en-US')} cells a side, ${picture.balanced ? 'balanced' : 'raw counts'}; pieces move in whole cells, so a junction inside a cell is placed to the nearest edge.`,
}),
this.cellsChoice(),
// Zoomed past a cell: the window read again, finer (§27.9).
...(this.windowRead === null || this.windowRead.key !== this.windowKey()
? []
: [el('p', { class: 'edit-note edit-window-note', text: `Closer than a cell, the map on screen is read again at ${fmt.bp(this.windowRead.read.binsize)} a bin, through the edit.` })]),
...(sequence === null ? [] : [el('p', { class: 'edit-note edit-evidence-note', text: sequence })]),
)
}
// -------------------------------------------------------------------------
// Closing
// -------------------------------------------------------------------------
private teardown(): void {
if (this.closed) return
this.closed = true
this.request?.cancel()
this.request = null
this.linksRequest?.cancel()
this.linksRequest = null
this.recountRequest?.cancel()
this.recountRequest = null
this.refineRequest?.cancel()
this.refineRequest = null
this.dotplot?.destroy()
this.windowRequest?.cancel()
this.windowRequest = null
window.clearTimeout(this.windowTimer)
window.clearTimeout(this.suggesting)
if (this.frame !== 0) cancelAnimationFrame(this.frame)
window.removeEventListener('keydown', this.onKey, true)
window.removeEventListener('keyup', this.onKeyUp, true)
window.removeEventListener('blur', this.onBlur)
this.observer?.disconnect()
this.stopStore()
this.lanes?.destroy()
closeMenu()
// The picture is the stage's alone (§27.9): it goes with it.
this.picture = null
this.image = null
this.props.onClose()
}
}
|