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* Segments and gene models: the lanes that draw *things on the sequence* rather
* than a value over it.
*
* One renderer over one layout: `drawModels` draws a segment and a gene model
* alike, each by its own structure rather than by the lane's kind (§8.16), and
* the hard part is the layout they share. Features overlap, and a lane 16
* pixels thick has room for two rows of them, so the layout is a greedy row
* packing — the same thing every genome browser does, and for the same reason:
* a peak drawn on top of another peak is one peak.
*
* Where the file carries strands and the lane has the rows for it, that packing
* runs **once per strand** into a band of its own — unstranded, then forward,
* then reverse, outward from the map (§8.16). Two features on the same bases and
* opposite strands are the case it is for: packed together they are two boxes
* one above the other and which is which is a colour you have to look up, and
* banded they are two boxes in the two places the strands live.
*
* The zoomed-out case is handled by *changing what is drawn*, not by drawing
* less of it. Past the point where there are more features than pixels, packing
* is meaningless — every row is full at every position — so the lane collapses
* to a single row of density. Nothing is dropped: the picture stops claiming to
* resolve individual features at the moment it stops being able to, which is the
* same bargain the matrix raster makes when it pools (`poolDisplay`).
*/
import { contigIndexOf } from '../genome/naming'
import { featureRange } from '../annotations/featureset'
import { strandBands, type BarScale, type FeatureDisplay } from '../annotations/fields'
import type { AnnotationKind, AnnotationPayload, FeatureSet } from '../annotations/types'
import { junctionCeiling } from '../annotations/junctions'
import {
BAR_GAP,
BAR_MIN_WIDTH,
barChartCaption,
barExtentOf,
barChartRows,
barColours,
dominantOf,
peakOf,
} from './barchart'
import { drawIdeogram, ideogramCaption } from './ideogram'
import { drawJunctions, junctionAt, junctionCaption, junctionLimits, type JunctionArc } from './junctions'
import { cutMiddle } from './laneLabel'
import { VARIANT_MIN_WIDTH } from './variants'
/**
* How far past its own feature a name below may run: this many times its width,
* or {@link OVERHANG_PX}, whichever is more.
*
* Four, because a gene four pixels wide has a name worth ten times that and is
* exactly the case the overhang exists for, while a name a dozen times wider
* than its peak is a label for the peaks either side of it.
*/
const OVERHANG_TIMES = 4
/**
* The overhang a name gets whatever its feature's width, in pixels.
*
* Enough for a short gene symbol — `YDR001C` — so the bound never costs the
* zoom where individual genes are the point, which is the zoom the below-the-
* feature placement was built for.
*/
const OVERHANG_PX = 80
import {
canvasToAcross,
laneGrowsInward,
laneCurve,
laneIsHorizontal,
laneLine,
laneMove,
laneRect,
laneText,
OUTLINE_WIDTH,
valueAcross,
type LaneFrame,
} from './lane'
import { stretchOf, strandOf, unitAt, type LocusAxis } from './locus'
/** Where one feature ended up. `along` is in canvas pixels. */
export interface FeaturePlacement {
/** Index into the {@link FeatureSet}. */
index: number
along0: number
along1: number
row: number
/**
* Placed on a stretch read backwards — a reversed piece of an edited
* sequence (§27.2): its blocks run the other way along the axis, and the
* strand it is drawn with is its own turned round ({@link placedStrand}).
*/
reversed?: boolean
}
/**
* The strand a placed feature has **on the axis**: its own, turned round where
* the stretch it is placed on is read backwards. What the arrow points by, the
* band it is packed in and the colour a strand key gives it.
*/
export function placedStrand(set: FeatureSet, placement: FeaturePlacement): number {
const own = sign(set.strand[placement.index])
return placement.reversed === true ? -own : own
}
export interface FeatureLayout {
placements: FeaturePlacement[]
/**
* How many rows the lane is divided into. At least 1.
*
* What the packing *used* on an unbanded lane, and what it was *given* on a
* banded one — see {@link layoutFeatures}. The difference matters because
* this is the divisor for the row height: a band that fits into fewer rows
* than it was allotted still has to sit where the allotment put it.
*/
rows: number
/** `true` when there were more features than pixels and rows were collapsed. */
dense: boolean
/** How many features the window actually holds, drawn or not. */
total: number
/**
* The arcs a junction lane drew, where one did (§8.23).
*
* Written by the renderer rather than the layout, because an arc's height is
* a fact about the paint — the lane's limits — and not about the packing. Kept
* here because the layout is what both surfaces hold on to for the hit test,
* so {@link featureAt} can answer with the curve under the pointer rather
* than with the box of an intron that nests three others.
*/
arcs?: JunctionArc[]
}
/** Gap between two features in the same row, in pixels, so they read as two. */
const ROW_GAP = 2
/** Never pack into more rows than this, however thick the lane is. */
const MAX_ROWS = 8
/**
* Beyond this many features the lane stops resolving individuals.
*
* Deliberately a *cap on work*, not only on appearance: past a hundred thousand
* candidates in one window the layout itself is the cost, and no arrangement of
* them is a picture anyone reads.
*/
const LAYOUT_CAP = 100_000
/**
* Place every feature the window shows into a row.
*
* Candidates come per contig from the sorted index, so the whole visible set is
* already in ascending order along the axis — which is exactly what a greedy
* packing needs, and why this makes one pass rather than sorting.
*
* The rows are **banded by strand** when the file uses more than one and the
* lane is at least that many rows tall (§8.16): each band gets a contiguous
* slice of the rows and is packed inside it. The bands come from the file rather
* than from the window (`strandBands`), so panning never re-lays out the lane;
* a lane too short to give every band a row falls back to the one packing over
* all of them, which is what a 16-pixel lane beside a map gets.
*/
export function layoutFeatures(
frame: LaneFrame,
axis: LocusAxis,
set: FeatureSet,
maxRows: number,
/**
* The narrowest one feature will be *drawn* — {@link FeaturePaint.minWidth}.
*
* It belongs here as well as in the paint because it changes the answer to
* "can these be told apart", which is the question the collapse below asks. A
* variant is one base, which is a hairline at every zoom a chromosome is
* browsed at, so it is drawn at a floor of three pixels — and the moment
* records are closer together than that floor plus the gap between them, the
* marks *merge*. Merged, a stretch of mixed substitutions draws as one solid
* bar in whichever ink was laid down last, which reads as a single
* three-kilobase variant: a claim the file does not make. Collapsing to
* density instead says the true thing, which is that there are many here.
*
* Zero — every caller but the variant lane — leaves the rule exactly as it
* was: a peak that is one pixel wide *is* one pixel of genome.
*/
leastWidth = 0,
/**
* Whether the rows may be banded by strand (§8.16).
*
* `true` for every lane whose glyph is a *box*, which is every lane but one.
* A barChart lane says `false`, and the reason is that banding spends the
* thing a chart is made of: the rows divide the lane's **height**, and a
* barChart's height is its value axis. Splitting a sixty-pixel lane into
* three strand bands buys a fact the card already states and costs two thirds
* of every reading on the lane — which is the one trade §8.16's argument for
* banding, "a colour you have to look up against a place you can see", does
* not survive when the place is also the measurement.
*/
banded = true,
): FeatureLayout {
const placements: FeaturePlacement[] = []
const span = Math.abs(frame.alongTo - frame.alongFrom)
let total = 0
for (const window of axis.windows(frame.domain)) {
// Alias-aware, because a deck draws one feature set beside every panel and
// each asks by the name *its* own file writes (§5.9). The set carries the
// spelling of the map it was loaded against, which is one of them at most.
const contig = contigIndexOf(set.contigs, window.contig)
if (contig < 0) continue
// The window's **own** stretch, not the first one on the axis with this
// name: a circular sequence panned across its junction is the same contig
// twice, and `segmentOf` would place the far half a sequence out (§8.15).
const segment = window.segment
if (!(segment.bpPerUnit > 0)) continue
// The piece this stretch is, on an edited axis: a feature across a cut is
// drawn to the cut and no further, since the rest of it is somewhere else
// on the axis — or, set aside, nowhere (§27.2). The whole contig otherwise.
const [lowBp, highBp] = stretchOf(segment)
const reversed = strandOf(segment) === -1
const [from, to] = featureRange(set, contig, window.start, window.end)
for (let i = from; i < to; i++) {
if (set.end[i] <= window.start || set.start[i] >= window.end) continue
// Counted before the cap is consulted, not after it. The loop used to
// stop dead at `LAYOUT_CAP`, which stopped the *count* with it — so the
// caption a collapsed lane writes ("17,400 features here") reported the
// cap rather than the window, and under-reported by however much a dense
// file exceeded it. The count is the one thing the picture can still
// carry once it has stopped resolving individuals; it must be the truth.
total++
if (placements.length >= LAYOUT_CAP) continue
const u0 = unitAt(segment, Math.max(set.start[i], lowBp))
const u1 = unitAt(segment, Math.min(set.end[i], highBp))
const along0 = frame.toPixel(u0)
const along1 = frame.toPixel(u1)
placements.push({
index: i,
along0: Math.min(along0, along1),
along1: Math.max(along0, along1),
row: 0,
...(reversed ? { reversed: true } : {}),
})
}
}
// More features than the lane can draw apart: no packing exists that separates
// them, so say so and draw one row. The count is kept, because "17,400
// features here" is the information the picture can still carry.
//
// The width one feature needs is its drawn floor plus the gap that makes two
// read as two — which for everything but a variant lane is the two pixels it
// has always been.
//
// **Asked of the fullest row the lane will use, not of the whole lane.** The
// test used to be `span / 2` over every feature in the window, whatever the
// lane was about to do with them — so a stranded gene set, which this lane
// spreads over a band per strand, was measured as though all of it went in
// one row. The same 230 yeast genes over the same window then drew as named
// boxes on a 680-pixel lane and as a solid grey density block on a
// 455-pixel one, because 230 falls either side of `span / 2` across that
// range: opening a side panel made the gene track appear to have been lost
// (§8.14, §8.16).
//
// Not `maxRows` either, which is the room the lane *has* rather than the rows
// it will fill: the packing moves a feature to a second row only when it
// **overlaps** one already there, so four rows do nothing for four hundred
// peaks that merely sit two to a pixel — they all land in row zero and merge
// into a bar, which is the case this rule exists for.
//
// The bands are a fact about the file (`strandBands`), so this answer does not
// move as a reader narrows a column, which is the whole complaint.
const bands = banded ? strandBands(set) : [0]
const spread = bands.length > 1 && frame.thickness / bands.length >= MIN_BAND_ROW ? bands : [0]
const needed = Math.max(2, leastWidth + ROW_GAP)
const fullest =
spread.length === 1
? placements.length
: Math.max(
...spread.map(
(strand) =>
placements.filter((placement) => placedStrand(set, placement) === strand).length,
),
)
const dense = fullest > span / needed
// Widened **into the placement**, here, once — so the box that is drawn, the
// box that is clicked and the box the packing keeps a row clear for are one
// number (§8.4). It was applied in the paint alone, which left a variant
// three pixels wide on screen and a fraction of a pixel wide to the pointer:
// two thirds of every mark was dead to hover and to click, and the spec said
// "three pixels to be seen and to be hit" while only the first was true.
//
// After the density decision and not before: a collapsed lane bins by
// position, and widening there would spread one variant's count over three
// pixels and inflate the profile.
if (leastWidth > 0 && !dense) {
for (const placement of placements) {
placement.along1 = Math.max(placement.along1, placement.along0 + leastWidth)
}
}
if (dense) {
return { placements, rows: 1, dense, total }
}
// Banded by strand where the file has more than one and the lane has the room
// for each: unstranded at the near edge, then forward, then reverse (§8.16). A
// band is a *sub-range of the rows*, so the packing below is the same greedy
// pass it always was — run once per band, over its own rows.
//
// Asked of the lane's **thickness** rather than of `maxRows`, and the
// difference is the whole of whether this works where it is most wanted.
// `maxRows` is calibrated on the height a row needs to carry a *name under a
// feature* — twenty-odd pixels — so a segments lane at its default sixteen
// gets one row and would never band at all, which is exactly the lane a
// stranded BED lands in. A band needs only {@link MIN_BAND_ROW}: a glyph and
// the gap under it. Where both fit, the bands win and the labels go back
// inside the features, which is what a lane that short does anyway.
if (spread.length > 1) {
const rows = Math.max(maxRows, bands.length)
const shares = shareRows(rows, bands.length)
let offset = 0
for (let band = 0; band < bands.length; band++) {
packRows(
placements.filter((placement) => placedStrand(set, placement) === bands[band]),
offset,
shares[band],
)
offset += shares[band]
}
// The *allocated* height, not the used one: a band that packed into one of
// its two rows still sits where the allocation put it, and reporting the
// smaller number would scale every row up and slide the bands over each
// other.
return { placements, rows: offset, dense: false, total }
}
if (maxRows <= 1) {
return { placements, rows: 1, dense, total }
}
const used = packRows(placements, 0, maxRows)
return { placements, rows: Math.max(1, used), dense: false, total }
}
/**
* The shortest a strand band may be, in pixels.
*
* A three-pixel glyph — the floor {@link glyphSizes} keeps for a block — plus the gap
* that makes two rows read as two, plus a pixel either side of the glyph. Below
* it the two strands are two hairlines and the packing has bought nothing;
* above it they are two rows of small boxes, which is what a sixteen-pixel
* segments lane should be when its file has both strands in it.
*/
const MIN_BAND_ROW = 8
/** `+1`, `-1` or `0`, so a strand column with other values in it still bands. */
function sign(strand: number): number {
return strand > 0 ? 1 : strand < 0 ? -1 : 0
}
/**
* Greedy row packing over `rows` rows starting at `from`. Returns how many were
* used.
*
* Candidates arrive in ascending order along the axis — the sorted index gives
* them that way, and a band is a filter over them, which preserves it — so this
* is one pass rather than a sort.
*/
function packRows(placements: FeaturePlacement[], from: number, rows: number): number {
const rowEnds: number[] = []
for (const placement of placements) {
let row = rowEnds.findIndex((end) => end + ROW_GAP <= placement.along0)
if (row < 0) {
if (rowEnds.length < rows) {
row = rowEnds.length
rowEnds.push(placement.along1)
} else {
// Every row is occupied here. Overlapping the row that frees up soonest
// loses the least, and it beats dropping the feature — an annotation
// that silently omits rows is one nobody can trust.
row = smallestIndex(rowEnds)
rowEnds[row] = Math.max(rowEnds[row], placement.along1)
}
} else {
rowEnds[row] = placement.along1
}
placement.row = from + row
}
return rowEnds.length
}
/**
* How the lane's rows are split between the strand bands.
*
* Evenly, with the remainder going to the earliest bands, and **not** in
* proportion to how many features each band holds in this window. Proportional
* would pack better and would move every glyph in the lane each time a pan
* changed the balance; an even split is the same split at every position in the
* genome, which is what makes the three bands readable as three bands.
*/
function shareRows(rows: number, bands: number): number[] {
const each = Math.floor(rows / bands)
const spare = rows - each * bands
return Array.from({ length: bands }, (_, i) => each + (i < spare ? 1 : 0))
}
function smallestIndex(values: number[]): number {
let best = 0
for (let i = 1; i < values.length; i++) if (values[i] < values[best]) best = i
return best
}
/** How many rows a lane of this thickness can hold at a legible row height. */
export function rowsThatFit(thickness: number, rowHeight = 11): number {
return Math.max(1, Math.min(MAX_ROWS, Math.floor(thickness / rowHeight)))
}
export interface FeaturePaint {
colour: string
guideColour: string
haloColour: string
font: string
opacity: number
/** Write feature names where they fit. */
labels: boolean
/**
* Edge each block in {@link guideColour}, the plot's ink: the `outline`
* preference, which is the rule along the top of a coverage track (§8.16).
*
* Required rather than defaulted, as it is on a track's paint, so that a new
* surface has to decide — one that forgot would draw its boxes unedged under
* tracks that are outlined, and one picture would say two things.
*/
outline: boolean
/**
* Put the name *under* the feature rather than inside it.
*
* What a genome browser does, and what a lane beside a contact map has no
* room for — which is the whole of the difference between the two callers. A
* name below is legible on a feature far narrower than the name, so a gene
* track stops being a row of anonymous boxes at any zoom where the genes are
* the point; a name inside is only ever legible on the wide ones.
*/
labelsBelow?: boolean
/**
* How tall the band under a feature is, or absent for this module's own.
*
* Passed in because it is measured in the same units as {@link font}: the app
* scales every canvas font together, and a band that stayed eleven pixels
* while the name in it grew would clip the name it exists to hold.
*/
labelBand?: number
/**
* A colour per feature, where one feature's ink is not the lane's.
*
* Resolved by `render/featureInk.ts` from the field the lane's style names
* (§8.16) — by strand, which is where every feature lane starts; by a called
* variant's substituted base, which is §8.14's older rule and still its
* default; by a column of the file; or not at all. Absent draws the whole set
* in {@link colour}, in one path, exactly as this always did — which is what
* `one colour` in the picker resolves to.
*
* The index is into the {@link FeatureSet}, not into the layout, because that
* is what a placement carries and what the label pass already uses.
*/
colourOf?: (index: number, reversed?: boolean) => string
/**
* Point a stranded feature the way it runs.
*
* `true` unless said otherwise, because a stranded file is the common case
* and the direction is the fact two colours cannot state: an ink says *which*
* strand, a point says *which way*, and a reader following an operon is
* reading the second. It reaches only the features that have a strand and the
* room for a head — see {@link ARROW_MIN_WIDTH} — so a peak set with no strand
* column comes out in the plain rectangles it always did, whatever this says.
*/
arrows?: boolean
/**
* How the rows are spent (`FeatureStyle.display`), which decides how thick a
* glyph is drawn in the row it is given. `expanded` when absent.
*/
display?: FeatureDisplay
/**
* What a barChart's bars are measured against (§8.17).
*
* Absent is `file` — one ceiling for every chart on the lane, which is the
* only setting under which two glyphs can be compared. `FeatureStyle.bars` in
* `annotations/fields.ts` says why the other reading exists.
*/
barScale?: BarScale
/**
* A value axis the reader has fixed, which overrides {@link barScale}.
*
* Absent is the file's own ceiling — the two readings §8.17 describes, both
* relative. Present, a bar's height is where its value falls between these two
* numbers, which is the only reading under which the same chart in two files
* draws the same way. See `render/barchart.ts`'s `barLimitsOf`.
*
* A junction lane reads it the same way (§8.23): an arc's height is its count
* between these two, and one under the floor is not drawn. It was called
* `barLimits` while a barChart was the only glyph with an axis.
*/
axisLimits?: { min: number; max: number }
}
/** Height a below-the-feature name needs, in canvas pixels. */
export const LABEL_BAND = 11
/**
* Every feature lane but a barChart: a glyph per feature, drawn by the feature's
* **own** structure rather than by the lane's kind (§8.16).
*
* A feature with no parts — a peak, a plain BED row, a variant — is one block.
* One with exons is a transcript: its exons are blocks on a hairline that
* stands for the introns between them, the coding span is drawn thick and the
* untranslated ends and every exon of a non-coding transcript thin, and one with
* a coding span and no exon table is a single exon split the same way. It used
* to be the kind that decided, which is how a BED12 or a bigBed of transcripts —
* a `segments` lane — came out as one plain box per gene: the exons and the
* coding span were read, carried and never drawn.
*
* **A stranded feature ends in a point**, on the block where it ends — the
* last exon in the direction it is transcribed — cut *out of* the block rather
* than drawn past it, so the glyph occupies exactly the bases the feature does
* and the box drawn, the box clicked and the box the packing kept a row clear
* for are one span (§8.4). No chevrons inside it: they were a second way of
* saying the same thing, laid over the one thing the glyph exists to show.
*
* Blocks have their corners rounded a little, and they take most of their row:
* a lane made taller draws its features thicker, up to {@link MAX_THICK}. With
* the outline on, each is edged in the plot's ink — the hairline along the top of
* a coverage track — down to {@link OUTLINE_MIN}.
* Variants stay square — a mark on a base is a mark, not a box to be shaped —
* and so does anything too narrow for a corner to be a corner.
*/
function drawModels(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
set: FeatureSet,
layout: FeatureLayout,
paint: FeaturePaint,
round: boolean,
): void {
if (layout.dense) {
drawDensity(ctx, frame, layout, paint)
return
}
const rowHeight = frame.thickness / layout.rows
const band = labelBandOf(paint, rowHeight)
// The glyph is centred in what is left of the row once the name has its band,
// rather than in the row: centring in the row and then writing under it puts
// the name over the next feature down.
const room = rowHeight - band
const sizes = glyphSizes(room, paint.display ?? 'expanded')
const pointed = paint.arrows !== false
ctx.save()
ctx.globalAlpha = paint.opacity
// One group of placements per ink, and both passes inside it: a transcript's
// introns and its exons are one glyph and must come out in one colour,
// whatever column the reader is colouring by (§8.16).
for (const [ink, placements] of groupByInk(layout, paint)) {
ctx.fillStyle = ink
// The introns first, so the blocks sit on them.
ctx.beginPath()
for (const placement of placements) {
const centre = placement.row * rowHeight + room / 2
intronPath(ctx, frame, set, placement, centre, sizes.line)
}
ctx.fill()
// The blocks that are edged, five numbers each, kept from the fill rather
// than walked again: the rule is then exactly the boundary of the ink under it.
const edged: number[] = []
ctx.beginPath()
for (const placement of placements) {
const centre = placement.row * rowHeight + room / 2
forEachBlock(set, placement, (along0, along1, coding, point) => {
const height = coding ? sizes.thick : sizes.thin
const top = centre - height / 2
const tip = pointed ? point : 0
blockPath(ctx, frame, along0, along1, top, height, tip, round)
if (paint.outline && Math.abs(along1 - along0) >= OUTLINE_MIN && height >= OUTLINE_MIN) {
edged.push(along0, along1, top, height, tip)
}
})
}
ctx.fill()
if (edged.length > 0) {
ctx.beginPath()
for (let i = 0; i < edged.length; i += 5) {
blockPath(ctx, frame, edged[i], edged[i + 1], edged[i + 2], edged[i + 3], edged[i + 4], round)
}
ctx.strokeStyle = paint.guideColour
ctx.lineWidth = OUTLINE_WIDTH
ctx.lineJoin = 'round'
ctx.stroke()
}
}
if (paint.labels) labelFeatures(ctx, frame, set, layout, paint, rowHeight)
ctx.restore()
}
/**
* How tall a feature's parts are drawn, given the room its row leaves for them.
*
* `thick` is a plain block and a coding span; `thin` an untranslated end and a
* non-coding exon, about three fifths of it, which is the ratio at which the two
* read as two weights of one shape rather than as two shapes; `line` the intron.
* Expanded and collapsed rows give the glyph all but a pixel either side of it,
* up to {@link MAX_THICK}: the cap is what keeps a lane dragged to two hundred
* pixels from drawing its genes as slabs, and it sits well above the nine and
* thirteen pixels a gene used to stop at whatever the lane was given. Squished
* rows are thin by design, and their glyphs are capped low for the same reason.
*/
export function glyphSizes(
room: number,
display: FeatureDisplay,
): { thick: number; thin: number; line: number } {
if (display === 'squished') {
const thick = clamp(room * 0.7, 2, SQUISHED_THICK)
return { thick, thin: Math.max(1.5, thick * 0.6), line: 1 }
}
const thick = clamp(room - 2, 3, MAX_THICK)
return { thick, thin: Math.max(2, thick * 0.6), line: thick >= 16 ? 1.5 : 1 }
}
/** The tallest a block is drawn, in pixels, however much room its row has. */
export const MAX_THICK = 22
/** …and the tallest in a squished row. */
const SQUISHED_THICK = 7
function clamp(value: number, low: number, high: number): number {
return value < low ? low : value > high ? high : value
}
/**
* Everything {@link layoutFeatures} needs that depends on what the lane *is*.
*
* One function rather than three conditionals repeated on each surface, and the
* reason is the reason `annotations/types.ts` gives for its kind predicates: the
* map lanes and the 1D browser lay out the same file with the same code, and
* every per-kind number spelled at both is a chance for them to drift into two
* pictures of one lane. It was already two — the row height and the variant
* floor — and a barChart adds a third and a fourth.
*
* `scale` is the app's font scaling, passed in rather than imported because
* this module is free of the DOM and of the settings that decide it.
*/
export function featureLayoutFor(
kind: AnnotationKind,
thickness: number,
scale: (length: number) => number,
display: FeatureDisplay = 'expanded',
): { rows: number; least: number; banded: boolean } {
// A single base is a hairline at every zoom a chromosome is browsed at
// (§8.14).
const least = kind === 'variants' ? scale(VARIANT_MIN_WIDTH) : 0
// One row, never banded, whatever the display mode says. A karyotype's bands
// tile one shape (§8.22) and a junction's arc has its strand in which way it
// grows (§8.23): rows would cut the one and halve the other.
if (kind === 'ideogram' || kind === 'junctions') return { rows: 1, least, banded: false }
if (kind === 'barchart') {
// A chart's rows divide its value axis, so how many of them fit is a
// question about the *measurement* and not about the label under it — and
// no display mode reaches it (§8.17).
return { rows: barChartRows(thickness, rowsThatFit(thickness, scale(22))), least, banded: false }
}
// One row across the whole lane, strands and all: the point and the colour
// say which way each feature runs, and banding would halve the one row.
if (display === 'collapsed') return { rows: 1, least, banded: false }
if (display === 'squished') {
return {
rows: Math.max(1, Math.min(MAX_SQUISHED_ROWS, Math.floor(thickness / SQUISHED_ROW))),
least,
banded: true,
}
}
// Taller rows than a bare glyph needs, because each one carries a name under
// its features; `labelBandOf` refuses the band on a row too short for both,
// so a lane dragged down to sixteen pixels still falls back to names inside
// the wide features.
return { rows: rowsThatFit(thickness, scale(kind === 'gtf' ? 26 : 22)), least, banded: true }
}
/** A squished row, in pixels: a thin glyph and the gap under it, and no name. */
const SQUISHED_ROW = 8
/** …and how many of them a lane may hold, which is well past {@link MAX_ROWS}. */
const MAX_SQUISHED_ROWS = 32
/**
* The renderer a feature lane of this kind is drawn by.
*
* The same one-place argument {@link featureLayoutFor} makes, for the half of
* the decision that follows the layout: a two-armed `if` at two call sites is
* how a third arm reaches one surface and not the other, and the way that fails
* is a lane that draws charts beside the map and boxes in the browser.
*/
export function drawFeatures(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
set: FeatureSet,
layout: FeatureLayout,
paint: FeaturePaint,
kind: AnnotationKind,
): void {
if (kind === 'barchart') drawBarCharts(ctx, frame, set, layout, paint)
else if (kind === 'ideogram') drawIdeogram(ctx, frame, set, layout, paint)
else if (kind === 'junctions') drawJunctions(ctx, frame, set, layout, paint)
else drawModels(ctx, frame, set, layout, paint, kind !== 'variants')
}
/**
* The value axis a feature lane's glyphs stand on before a reader moves it, or
* `null` for a kind whose glyphs have none.
*
* Zero to a barChart's tallest bar (§8.17) and zero to a junction lane's
* largest count (§8.23): what each draws against under `auto`, and so where a
* ceiling drag, a ⌘-scroll and the typed field all start from. One function
* for both, because the three gestures ask it on two surfaces and a kind
* answered at some of those six places and not the others is a lane whose
* ceiling moves by one gesture and not by another.
*/
export function glyphExtentOf(
kind: AnnotationKind,
set: FeatureSet | undefined,
/**
* What the lane last drew, where the caller has it: a junction lane's `auto`
* is fitted to the junctions in view (`render/junctions.ts`), so a gesture
* that starts from the axis on screen starts from that — and from the file's
* largest count where nothing has been drawn yet.
*/
layout?: FeatureLayout,
): { min: number; max: number } | null {
if (set === undefined) return null
if (kind === 'barchart') return barExtentOf(set.bars)
if (kind === 'junctions') {
if (layout !== undefined && layout.placements.length > 0) return junctionLimits(set, undefined, layout)
const top = junctionCeiling(set)
return top > 0 ? { min: 0, max: top } : null
}
return null
}
/** {@link glyphExtentOf} for a row, whose set may not have arrived yet. */
export function glyphExtentOfRow(
row: { kind: AnnotationKind; payload?: AnnotationPayload },
layout?: FeatureLayout,
): { min: number; max: number } | null {
return glyphExtentOf(row.kind, row.payload?.kind === 'features' ? row.payload.data : undefined, layout)
}
/**
* The line under a feature lane's name, or `null` for none (§8.16, §8.17,
* §8.22, §8.23).
*
* One function for both surfaces, for {@link featureLayoutFor}'s reason: the
* map's lanes and the 1D browser wrote the same two branches, and a kind added
* to one of them and not the other is a lane with two captions.
*/
export function featureCaption(
kind: AnnotationKind,
set: FeatureSet,
layout: FeatureLayout,
barScale: BarScale,
axisLimits: { min: number; max: number } | undefined,
int: (value: number) => string,
num: (value: number) => string,
): string | null {
// Bands tile rather than overlap, so a genome's worth of them is still the
// karyotype: the caption names the ones under the window whatever the count.
if (kind === 'ideogram') return ideogramCaption(set, layout)
// …and arcs are drawn at every zoom, the strongest when there are too many.
if (kind === 'junctions') return junctionCaption(set, layout, axisLimits, int)
if (layout.dense) return `${int(layout.total)} ${kind === 'variants' ? 'variants' : 'features'} in view`
// What the top of a bar means, which is the one thing a chart without an
// axis cannot say for itself (§8.17).
return set.bars === undefined ? null : barChartCaption(set.bars, num, barScale, axisLimits)
}
/**
* A barChart: one chart per feature, drawn inside the bases the feature covers
* (§8.17).
*
* The second renderer over {@link layoutFeatures}' layout, and it is a second one
* rather than a flag on {@link drawModels} because nothing in it is a box:
* where that function asks *what colour is this feature and which way does it
* point*, this asks *what are its values and is there room to show them*.
*
* ## The two pictures, and the line between them
*
* With room, a feature is `expCount` bars standing on a common baseline, each
* the height of its own value against the file's ceiling. Without it, it is one
* box in the colour of the category that dominates the row and the height of
* that category's value — so the glyph gives up *which categories* long before
* it gives up *which one* and *how much*, and a lane zoomed out to a chromosome
* still reads as a map of where each tissue wins.
*
* The line is {@link BAR_MIN_WIDTH} per category and no fudge factor, because
* under a pixel a bar is not thin, it is gone: the canvas rounds it away or
* blends it into its neighbour, and a chart quietly missing half its categories
* is a different chart drawn with the same confidence.
*
* ## Why the bars are painted by category rather than by feature
*
* One path per *category*, filled once — so a lane of four hundred glyphs over
* fifty-four tissues is fifty-four fills rather than twenty-one thousand. The
* same argument {@link groupByInk} makes for boxes, and it matters more here
* because the number of pieces is the product of two counts rather than one.
*
* ## What is deliberately not drawn
*
* An axis. A chart sixteen pixels tall has no room for one, there are as many
* of them on the lane as there are features, and the ceiling is the same number
* for every one of them — so it is stated once, under the lane's label and in
* the card, where it can be read (§8.17). What *is* drawn is the baseline, once
* per glyph, because without it a row of short bars and a row of tall bars
* hanging from above are the same picture.
*/
export function drawBarCharts(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
set: FeatureSet,
layout: FeatureLayout,
paint: FeaturePaint,
): void {
const bars = set.bars
// A file that reached this lane with no categories on it — every row
// disagreeing about `expCount`, or a stored session restored against a set
// that was re-read as a BED. Boxes are the honest picture of it and are
// already written; drawing an empty chart would be an assertion that the
// values are all zero.
if (bars === undefined) {
drawModels(ctx, frame, set, layout, paint, true)
return
}
if (layout.dense) {
drawDensity(ctx, frame, layout, paint)
return
}
const rowHeight = frame.thickness / layout.rows
const band = labelBandOf(paint, rowHeight)
const chartHeight = Math.max(3, rowHeight - band - 2)
const width = bars.labels.length
const colours = barColours(bars)
const fixed = paint.axisLimits
// A fixed axis is not a *ceiling*, it is two ends, so it cannot be folded into
// the division below — and it overrides the per-feature reading rather than
// composing with it: "each chart against its own top" and "every chart against
// these two numbers" are contradictory answers to one question, and the one
// the reader typed wins.
const perFeature = fixed === undefined && paint.barScale === 'feature'
// A file of zeroes would divide every bar by nothing. One is the ceiling that
// draws all of them flat on the baseline, which is what that file says.
const fileCeiling = bars.max > 0 ? bars.max : 1
const inward = laneGrowsInward(frame.orientation)
/** What this feature's bars are divided by — see {@link FeaturePaint.barScale}. */
const ceilingOf = (index: number): number => {
if (!perFeature) return fileCeiling
const peak = peakOf(bars, index)
return Number.isFinite(peak) && peak > 0 ? peak : fileCeiling
}
/**
* How tall a bar stands, as a fraction of the chart.
*
* Clamped at both ends under a fixed axis, which is what a fixed axis means: a
* value above the ceiling draws full height rather than out of the lane and
* into the one above it, and one below the floor draws nothing rather than
* downwards through the baseline.
*/
const heightOf = (value: number, index: number): number => {
if (fixed === undefined) return value / ceilingOf(index)
return Math.max(0, Math.min(1, (value - fixed.min) / (fixed.max - fixed.min)))
}
const charted: FeaturePlacement[] = []
const collapsed: FeaturePlacement[] = []
for (const placement of layout.placements) {
const room = placement.along1 - placement.along0 >= width * BAR_MIN_WIDTH
;(room ? charted : collapsed).push(placement)
}
ctx.save()
ctx.globalAlpha = paint.opacity
// The baselines first, under everything, so a bar of zero still has a mark
// saying the feature is there.
ctx.fillStyle = paint.guideColour
ctx.globalAlpha = paint.opacity * 0.45
ctx.beginPath()
for (const placement of layout.placements) {
const base = baseOf(placement.row, rowHeight, band, chartHeight, inward)
const [x, y, w, h] = laneRect(frame, placement.along0, placement.along1, base, base)
ctx.rect(x, y, w, h)
}
ctx.fill()
ctx.globalAlpha = paint.opacity
for (let category = 0; category < width; category++) {
ctx.fillStyle = colours[category]
ctx.beginPath()
let drawn = false
for (const placement of charted) {
const value = bars.values[placement.index * width + category]
if (!Number.isFinite(value)) continue
// Nothing to draw is nothing drawn, and the test is the **height** rather
// than the value: under the file's own ceiling those are the same question
// (a positive value is a positive bar), and under a fixed axis they are
// not — a value below the floor is a real number with no ink, and a
// zero-height rectangle in the path is a bar the lane claims to have drawn.
const height = heightOf(value, placement.index)
if (!(height > 0)) continue
const span = placement.along1 - placement.along0
const slot = span / width
// The gap is dropped rather than shrinking the bars below the floor: two
// bars touching are still two heights, where two bars half a pixel wide
// are one smear.
const thickness = slot - BAR_GAP >= BAR_MIN_WIDTH ? slot - BAR_GAP : slot
const along0 = placement.along0 + category * slot
const [across0, across1] = barAcross(
placement.row,
rowHeight,
band,
chartHeight,
inward,
height,
)
const [x, y, w, h] = laneRect(frame, along0, along0 + thickness, across0, across1)
ctx.rect(x, y, w, h)
drawn = true
}
if (drawn) ctx.fill()
}
// The collapsed glyphs, gathered under the category each is dominated by, so
// the fills are bounded by the number of categories here too.
const byCategory = new Map<number, FeaturePlacement[]>()
for (const placement of collapsed) {
const at = dominantOf(bars, placement.index)
const held = byCategory.get(at)
if (held === undefined) byCategory.set(at, [placement])
else held.push(placement)
}
for (const [category, placements] of byCategory) {
// No dominant category is no answer, and takes the lane's own colour —
// never a category's, which would name one.
ctx.fillStyle = category < 0 ? paint.colour : colours[category]
ctx.beginPath()
for (const placement of placements) {
const value = peakOf(bars, placement.index)
// A floor of a twelfth, so a feature whose tallest category is near zero
// is still a mark rather than a gap in the lane. Against the *file's*
// ceiling whatever the switch says, because per feature this is the
// feature's own peak divided by itself — every collapsed glyph full
// height, which is a lane saying nothing. A fixed axis is honoured here
// too: it is the one reading that is about the numbers rather than about
// the picture, so a collapsed row has to obey it or a lane zoomed out
// would quietly change what its heights meant.
const against =
fixed === undefined
? value / fileCeiling
: Math.max(0, Math.min(1, (value - fixed.min) / (fixed.max - fixed.min)))
const height = Number.isFinite(value) ? Math.max(against, 1 / 12) : 1
const [across0, across1] = barAcross(
placement.row,
rowHeight,
band,
chartHeight,
inward,
height,
)
const [x, y, w, h] = laneRect(frame, placement.along0, placement.along1, across0, across1)
ctx.rect(x, y, w, h)
}
ctx.fill()
}
if (paint.labels) labelFeatures(ctx, frame, set, layout, paint, rowHeight)
ctx.restore()
}
/**
* Where one row's charts stand, in lane across-coordinates.
*
* The baseline follows {@link laneGrowsInward}, which is the one place this
* application decides which way a value grows: up the page on a horizontal lane
* and right across a vertical one, whichever edge of the map the lane is on. So
* a barChart on a bottom stack stands on its outer edge and grows towards the
* matrix, and the one on the top stack stands on its inner edge and grows away
* — which is what every profile lane beside them already does.
*/
function baseOf(
row: number,
rowHeight: number,
band: number,
chartHeight: number,
inward: boolean,
): number {
const top = row * rowHeight + (rowHeight - band - chartHeight) / 2
return inward ? top + chartHeight : top
}
/** The across-span of one bar at `height` of the chart, as a `[from, to]` pair. */
function barAcross(
row: number,
rowHeight: number,
band: number,
chartHeight: number,
inward: boolean,
height: number,
): [number, number] {
const clamped = height < 0 ? 0 : height > 1 ? 1 : height
const base = baseOf(row, rowHeight, band, chartHeight, inward)
return inward ? [base - clamped * chartHeight, base] : [base, base + clamped * chartHeight]
}
/**
* The narrowest a block can be and still be worth pointing, in pixels.
*
* A head is cut out of the block, so on a narrow one it eats the part that says
* *where*: at four pixels a pentagon and a rectangle are the same three pixels
* of ink with a different corner, and the reader has lost a pixel of extent to
* learn nothing. Six is where a head reads as a head.
*/
export const ARROW_MIN_WIDTH = 6
/** …and the shortest head worth cutting, once the two caps below are applied. */
const ARROW_MIN_HEAD = 2
/** The roundest a block's corner is, in pixels, however big the block. */
const MAX_RADIUS = 3
/**
* The smallest block that is edged when the outline is on, in pixels along the
* lane and across it.
*
* Under four a block is a tick, and a hairline round a tick is most of its ink:
* the colour that says which strand or which class would be lost to the plot's
* ink, on exactly the features too small to say it any other way.
*/
export const OUTLINE_MIN = 4
/**
* Walk one placed feature's blocks, in axis order: where each one runs, whether
* it is coding (drawn thick) or not, and which way it points, `0` for none.
*
* The point is on the block the feature *ends* in, in the direction it runs:
* the last one for a forward feature and the first for a reverse one, since the
* blocks come in axis order (`FeatureBuilder.finish` sorts a transcript's exons,
* which a GTF lists 5′ to 3′ and so backwards on the minus strand).
*/
function forEachBlock(
set: FeatureSet,
placement: FeaturePlacement,
visit: (along0: number, along1: number, coding: boolean, point: number) => void,
): void {
const index = placement.index
// The file's own strand picks *which* block is the tip, in base-pair order;
// the placed one says which way along the axis it points — the other way on
// a reversed piece, where the tip block is also mirrored to the other end.
const strand = sign(set.strand[index])
const pointing = placedStrand(set, placement)
const first = set.exonAt[index]
const last = set.exonAt[index + 1]
const cdsFrom = set.cdsStart[index]
const cdsTo = set.cdsEnd[index]
const coding = cdsTo > cdsFrom
if (first === last && !coding) {
// No parts: the feature is its own single block, at the placement's own
// extent — which carries a variant's floor, so the mark drawn is the mark
// the pointer finds (§8.14).
visit(placement.along0, placement.along1, true, pointing)
return
}
const start = set.start[index]
const scale = (placement.along1 - placement.along0) / Math.max(1, set.end[index] - start)
const at = (bp: number): number =>
placement.reversed === true
? placement.along1 - (bp - start) * scale
: placement.along0 + (bp - start) * scale
// Each exon, split where the coding span begins and ends: an exon can hold an
// untranslated end, the coding span, or — in a gene of one exon — both ends
// and the span between them.
const parts: Array<[number, number, boolean]> = []
const exons = first === last ? 1 : last - first
for (let k = 0; k < exons; k++) {
const from = first === last ? start : set.exonStart[first + k]
const to = first === last ? set.end[index] : set.exonEnd[first + k]
if (!coding) {
parts.push([from, to, false])
continue
}
if (from < cdsFrom) parts.push([from, Math.min(to, cdsFrom), false])
const inFrom = Math.max(from, cdsFrom)
const inTo = Math.min(to, cdsTo)
if (inTo > inFrom) parts.push([inFrom, inTo, true])
if (to > cdsTo) parts.push([Math.max(from, cdsTo), to, false])
}
const tip = strand > 0 ? parts.length - 1 : strand < 0 ? 0 : -1
for (let i = 0; i < parts.length; i++) {
const [from, to, isCoding] = parts[i]
if (!(to > from)) continue
const a = at(from)
const b = at(to)
visit(Math.min(a, b), Math.max(a, b), isCoding, i === tip ? pointing : 0)
}
}
/**
* The hairline a transcript's introns are, from the end of its first exon to
* the start of its last — under the blocks, so only the gaps between them show.
* Nothing for a feature of one block.
*/
function intronPath(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
set: FeatureSet,
placement: FeaturePlacement,
centre: number,
line: number,
): void {
const index = placement.index
const first = set.exonAt[index]
const last = set.exonAt[index + 1]
if (last - first < 2) return
const start = set.start[index]
const scale = (placement.along1 - placement.along0) / Math.max(1, set.end[index] - start)
const at = (bp: number): number =>
placement.reversed === true
? placement.along1 - (bp - start) * scale
: placement.along0 + (bp - start) * scale
const a = at(set.exonEnd[first])
const b = at(set.exonStart[last - 1])
const from = Math.min(a, b)
const to = Math.max(a, b)
if (!(to > from)) return
const [x, y, width, height] = laneRect(frame, from, to, centre - line / 2, centre + line / 2)
ctx.rect(x, y, width, height)
}
/**
* One block's outline: a box with its corners rounded, pointed at one end where
* `point` says so — `+1` at the far end along the axis, `-1` at the near one.
*
* Through `laneMove`/`laneLine`/`laneCurve`, so a right-hand lane's quarter turn
* stays `render/lane.ts`'s business (§8.8). The head is capped twice — by the
* block's height, so it is a point rather than a spear, and by a third of its
* width, so a short block keeps most of its body — and it is not cut at all
* below {@link ARROW_MIN_WIDTH}. Every outline is traced the same way round,
* whichever end is pointed, so blocks that overlap in one path add up rather
* than cancel into a hole.
*/
function blockPath(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
along0: number,
along1: number,
top: number,
height: number,
point: number,
round: boolean,
): void {
const width = along1 - along0
const head = point === 0 ? 0 : Math.min(height * 0.55, width * 0.35)
const pointed = point !== 0 && head >= ARROW_MIN_HEAD && width >= ARROW_MIN_WIDTH
const corner = round ? Math.min(MAX_RADIUS, height * 0.22, (width - (pointed ? head : 0)) / 2) : 0
// Under a pixel a corner is not a corner, and a one-pixel feature stays the
// crisp rectangle `laneRect` floors it to.
const r = corner >= 1 ? corner : 0
if (!pointed && r === 0) {
const [x, y, boxWidth, boxHeight] = laneRect(frame, along0, along1, top, top + height)
ctx.rect(x, y, boxWidth, boxHeight)
return
}
const bottom = top + height
const middle = top + height / 2
const near = pointed && point < 0 ? along0 + head : along0 + r
const far = pointed && point > 0 ? along1 - head : along1 - r
laneMove(ctx, frame, near, top)
laneLine(ctx, frame, far, top)
if (pointed && point > 0) {
laneLine(ctx, frame, along1, middle)
laneLine(ctx, frame, far, bottom)
} else if (r > 0) {
laneCurve(ctx, frame, along1, top, along1, top + r)
laneLine(ctx, frame, along1, bottom - r)
laneCurve(ctx, frame, along1, bottom, far, bottom)
} else {
laneLine(ctx, frame, along1, bottom)
}
laneLine(ctx, frame, near, bottom)
if (pointed && point < 0) {
laneLine(ctx, frame, along0, middle)
} else if (r > 0) {
laneCurve(ctx, frame, along0, bottom, along0, bottom - r)
laneLine(ctx, frame, along0, top + r)
laneCurve(ctx, frame, along0, top, near, top)
} else {
laneLine(ctx, frame, along0, top)
}
ctx.closePath()
}
/**
* The placements, gathered under the ink each is drawn in.
*
* Grouped by ink rather than one fill per feature: a lane of ten thousand boxes
* in one colour is one path, and a lane coloured by a twelve-category column is
* twelve — which is the difference between twelve state changes and ten
* thousand of them. The common case, no `colourOf`, is the single group it
* always was.
*
* It does reorder the painting, and where two features in one row overlap the
* one on top is now the one whose *ink* was laid down last rather than the one
* later in the set — so it can differ from the feature `featureAt` names. That
* happens only where the packing had to overlap two features in one row, where
* the hit test's answer is a real record at the place that was clicked either
* way, and the card names which.
*/
function groupByInk(
layout: FeatureLayout,
paint: FeaturePaint,
): Map<string, FeaturePlacement[]> {
const byInk = new Map<string, FeaturePlacement[]>()
for (const placement of layout.placements) {
const ink =
paint.colourOf === undefined ? paint.colour : paint.colourOf(placement.index, placement.reversed === true)
const held = byInk.get(ink)
if (held === undefined) byInk.set(ink, [placement])
else held.push(placement)
}
return byInk
}
/**
* How much of each row is given to a name written under the feature.
*
* Zero unless names go below *and* the row is tall enough to hold both — a row
* that gave half of eleven pixels to text would have three left for the gene,
* which is a line rather than a glyph.
*/
export function labelBandOf(paint: FeaturePaint, rowHeight: number): number {
const band = paint.labelBand ?? LABEL_BAND
// Room for the band *and* a glyph above it, in the band's own units — a row
// that gave half of its height to text would have a line left for the gene.
return paint.labelsBelow === true && paint.labels && rowHeight >= band + 9 ? band : 0
}
/**
* The zoomed-out picture: how many features cover each pixel.
*
* Boxes are the wrong answer once there are more features than pixels — every
* pixel is covered, so the lane is a solid bar and says only "there are genes
* here", which for a gene-dense genome is not news. A count profile says
* *how many*, which is the question that still has an answer at this zoom, and
* it costs one pass over placements that have already been computed.
*
* Scaled to the busiest pixel in view rather than to a fixed ceiling: the lane
* is a picture of relative density across what is on screen, and it rescales as
* the view moves for the same reason a track's autoscale does.
*/
function drawDensity(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
layout: FeatureLayout,
paint: FeaturePaint,
): void {
const from = Math.floor(Math.min(frame.alongFrom, frame.alongTo))
const slots = Math.max(1, Math.ceil(Math.abs(frame.alongTo - frame.alongFrom)) + 1)
const counts = new Float32Array(slots)
let peak = 0
for (const placement of layout.placements) {
const first = Math.max(0, Math.floor(placement.along0 - from))
const last = Math.min(slots - 1, Math.ceil(placement.along1 - from) - 1)
for (let slot = first; slot <= last; slot++) {
counts[slot]++
if (counts[slot] > peak) peak = counts[slot]
}
}
if (peak <= 0) return
const base = valueAcross(frame, 0)
ctx.save()
ctx.globalAlpha = paint.opacity
ctx.fillStyle = paint.colour
ctx.beginPath()
for (let slot = 0; slot < slots; slot++) {
if (counts[slot] === 0) continue
// A floor of one twelfth, so a pixel with a single feature under a busy
// neighbour is still visible rather than rounded away to nothing.
const height = Math.max(counts[slot] / peak, 1 / 12)
const [x, y, width, boxHeight] = laneRect(
frame,
from + slot,
from + slot + 1,
base,
valueAcross(frame, height),
)
ctx.rect(x, y, width, boxHeight)
}
ctx.fill()
ctx.restore()
}
/**
* Names: inside the feature beside a map, under it in a browser.
*
* Two placements because the two callers have two different amounts of room. A
* lane 46 pixels thick under a contact map has no *under*, so a name goes
* inside and only onto the features wide enough to hold one. A browser lane has
* a band to itself, so the name goes below and may run past a feature far
* narrower than it — which is what makes a gene track legible at the zoom where
* the genes, rather than their density, are the point.
*
* **Two bounds on that overhang, both of them corrections.**
*
* A name may be a few times wider than its feature and no more
* ({@link OVERHANG_TIMES}, {@link OVERHANG_PX}). Unbounded, a 46-character MACS
* name — its caller's run id plus a counter — was written under a peak three
* pixels wide and spanned a dozen unlabelled neighbours, so one peak in twenty
* carried a name and each name read as the label for the group it lay across.
* Past the bound the name is cut in the middle rather than dropped, because
* `LM331_…peak_1116` still says which set the peak is from and a reader who
* wants the rest hovers it.
*
* And the text is kept **inside the lane**, which is where the false gene names
* came from: a name centred on a feature at the edge of the window was cut by
* the lane's own clip, so `MSW1` was drawn as `SW1`, `HEH2` as `HE` and `MUS81`
* as `US81` — every one of them a plausible yeast symbol that a reader would
* search for or cite. A browser must never print a gene name that is not in the
* file (§8.16); the codebase's own rule for a group bar says the same thing
* ("half a group's name is a different group's name"), and there the name is
* dropped. Here it is nudged inward, which keeps it.
*/
function labelFeatures(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
set: FeatureSet,
layout: FeatureLayout,
paint: FeaturePaint,
rowHeight: number,
): void {
if (rowHeight < 9) return
const band = labelBandOf(paint, rowHeight)
ctx.save()
ctx.font = paint.font
ctx.fillStyle = paint.guideColour
ctx.textAlign = 'center'
ctx.textBaseline = 'middle'
// Where a name below is allowed to run past its own feature: a gene 4 px wide
// still has a name, and a browser that only labelled the wide ones would go
// blank at exactly the zoom where the names are the point. Bounded by the
// last name written *in the same row*, so two of them never overlap — which
// is the only thing that makes an overhanging label readable at all.
const lastRight = new Float64Array(layout.rows).fill(Number.NEGATIVE_INFINITY)
// The lane's own ends, in reading order. A name may not be written past them:
// whatever falls outside is cut by the clip, and a cut name is another name.
const edgeLo = Math.min(frame.alongFrom, frame.alongTo) + 1
const edgeHi = Math.max(frame.alongFrom, frame.alongTo) - 1
for (const placement of layout.placements) {
const name = set.name[placement.index]
if (name === '') continue
const width = placement.along1 - placement.along0
const middle = (placement.along0 + placement.along1) / 2
if (band === 0) {
const text = ctx.measureText(name).width
// Inside the feature: only where it genuinely fits, because a name that
// overflows its box is a name attached to whatever is next to it — and
// only where the box itself is whole, since a name centred in a box the
// window cut in half is centred on a place the feature does not have.
if (width < 18 || text + 6 > width) continue
if (middle - text / 2 < edgeLo || middle + text / 2 > edgeHi) continue
laneText(ctx, frame, name, middle, placement.row * rowHeight + rowHeight / 2, {
halo: paint.haloColour,
})
continue
}
// As wide as the name, or as wide as the overhang allows — whichever is
// smaller, and below a readable minimum nothing at all.
const allowed = Math.max(width * OVERHANG_TIMES, OVERHANG_PX)
const measure = (part: string): number => ctx.measureText(part).width
const fitted = measure(name) <= allowed ? name : cutMiddle(measure, name, allowed)
const text = measure(fitted)
if (text <= 0) continue
// Nudged inside the lane, and only then tested against its neighbour: a
// feature half off the left edge keeps its name by moving it right, which
// is what JBrowse does, and a feature so far out that nothing of it is
// visible has already been dropped by the layout.
const centre = Math.min(Math.max(middle, edgeLo + text / 2), edgeHi - text / 2)
const from = centre - text / 2
if (from < lastRight[placement.row] + 4) continue
lastRight[placement.row] = centre + text / 2
laneText(ctx, frame, fitted, centre, placement.row * rowHeight + rowHeight - band / 2 - 1, {
halo: paint.haloColour,
})
}
ctx.restore()
}
/**
* The feature under a canvas point, or `null`.
*
* Takes the *last* match rather than the first, so the feature drawn on top is
* the one the tooltip names. Within a row the placements are in axis order and
* later ones paint over earlier ones, which is only visible where the packing
* had to overlap them — but that is exactly where getting it wrong is confusing.
*/
export function featureAt(
frame: LaneFrame,
layout: FeatureLayout,
x: number,
y: number,
): FeaturePlacement | null {
// A lane of arcs is hit on its curves: three nested junctions share one span,
// and a box test would name the last of them wherever the pointer was.
if (layout.arcs !== undefined) return junctionAt(frame, layout, x, y)
// The exact inverse of what `laneRect` did when the boxes were drawn — through
// the same module, so the two cannot answer differently about an edge where
// `across` runs backwards against the canvas.
const along = laneIsHorizontal(frame.orientation) ? x : y
const across = canvasToAcross(frame, laneIsHorizontal(frame.orientation) ? y : x)
if (across < 0 || across > frame.thickness) return null
const rowHeight = frame.thickness / layout.rows
const row = Math.min(layout.rows - 1, Math.max(0, Math.floor(across / rowHeight)))
let found: FeaturePlacement | null = null
for (const placement of layout.placements) {
if (!layout.dense && placement.row !== row) continue
// A one-pixel feature is a two-pixel target: the drawn box is floored to a
// pixel, and a hit area narrower than what is on screen is unhittable.
if (along < placement.along0 - 1 || along > placement.along1 + 1) continue
found = placement
}
return found
}
/** Where a value lands across the lane; re-exported so callers need one import. */
export { valueAcross }
|