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* The structure drawn on the GPU, through three.js (§25).
*
* The one place in this application a picture is not a `CanvasRenderingContext2D`,
* and the reason is stated in `package.json`'s comment on the dependency: a lit
* tube of thousands of beads under an orbiting camera, with sorted transparency
* and picking, is not the arithmetic the hand-written PDF and charts were the
* cheaper answer for. It draws the structure cell of a deck and nothing else.
*
* ## Thin, on purpose
*
* Everything with a number in it lives in `structure/scene.ts`, `camera.ts`
* and `colour.ts` and is tested in node; this module turns those numbers into
* buffers and back. It holds no camera state of its own — it is handed a
* {@link StructureView} and applies its camera to a three.js one on every
* frame — so the picture it draws and the picture the vector painter draws
* are projections of the same object, and the export can never show a
* different angle from the screen.
*
* ## What is rebuilt when
*
* Geometry is expensive and colours are not, so the two are kept apart. The
* tube, the bead instances and the stick instances are rebuilt only when the
* structure, the representation, a radius or the set of *shown* beads changes;
* a change of colouring, of what is lit, of what is hovered or of the camera
* touches a colour attribute or a matrix and nothing else. A colouring by a
* track sampled on every pan would otherwise rebuild a tube per frame.
*
* ## Picking
*
* Against the bead instances, always — including under a tube, where the
* beads are not drawn. The pick mesh sits on a layer the camera does not
* render and the raycaster does, so a pick is always a bead index and never a
* point on a surface with no locus.
*/
import {
AmbientLight,
BufferAttribute,
CatmullRomCurve3,
Color,
ConeGeometry,
CylinderGeometry,
DirectionalLight,
Fog,
FrontSide,
InstancedBufferAttribute,
InstancedMesh,
Matrix4,
Mesh,
MeshBasicMaterial,
MeshStandardMaterial,
Object3D,
OrthographicCamera,
PerspectiveCamera,
Plane,
Quaternion,
Raycaster,
Scene,
SphereGeometry,
TubeGeometry,
Vector2,
Vector3,
WebGLRenderer,
} from 'three'
import { basis, eyeOf, halfHeight } from './camera'
import { hexOf } from './colour'
import { MARKED_BEAD, drawStructureLabels } from './painter'
import type { StructureView } from './painter'
import { centroidOf } from './scene'
import type { Structure } from './scene'
import type { BeadColours } from './colour'
/** The attribute {@link ghostable} reads each bead's alpha from. */
const GHOST_ALPHA = 'ghostAlpha'
/** Below this an alpha is *gone*: the fragment is discarded and writes no depth. */
const GHOST_GONE = 0.004
/** What the renderer clears to and writes labels in, read off the page. */
export interface RenderPalette {
background: string
ink: string
halo: string
}
/** The layer the pick mesh lives on: raycast, never drawn. */
const PICK_LAYER = 1
/** Radial segments of a tube and a stick. Eight reads as round at any size a cell draws. */
const RADIAL = 8
/** Tube segments per bead along a run. */
const TUBE_PER_BEAD = 4
export class StructureRenderer {
readonly el: HTMLCanvasElement
private renderer: WebGLRenderer | null = null
private readonly scene = new Scene()
private perspective = new PerspectiveCamera(40, 1, 0.01, 100)
private orthographic = new OrthographicCamera(-1, 1, 1, -1, 0.01, 100)
private readonly root = new Object3D()
private readonly lights = new Object3D()
private beads: InstancedMesh | null = null
private picks: InstancedMesh | null = null
private halos: InstancedMesh | null = null
private sticks: InstancedMesh | null = null
private tubes: Mesh[] = []
/** The dashes across the gaps of every chain: ink, always drawn. */
private gapDashes: InstancedMesh | null = null
/** The hovered contact's chord: dashes of ink between its two beads. */
private chord: InstancedMesh | null = null
/** The loops as chords (§25.5): one cylinder of ink per pair. */
private chords: InstancedMesh | null = null
/** The map's contacts from the pinned bead, one coloured cylinder each. */
/** The reader's measurements, as dashed ink. */
private measures: InstancedMesh | null = null
private measuresFrom: ReadonlyArray<readonly [number, number]> | null = null
/** The genomic ruler's ticks: small ink beads. */
private ticks: InstancedMesh | null = null
private ticksFrom: ReadonlyArray<{ bead: number; label: string }> | null = null
private marks: InstancedMesh | null = null
private marksFrom: ReadonlyArray<{ bead: number; colour: string }> | null = null
/** Which bead each drawn mark sits on, so its ghosting can follow the bead's. */
private marksBeads: number[] = []
/** The same for the ruler's ticks. */
private ticksBeads: number[] = []
/** The compared model, in this one's frame: its own group, rebuilt when it changes. */
private readonly overlayRoot = new Object3D()
private overlayFrom: Structure | null = null
private overlayKey = ''
/** The model's reach in scene units, measured once per model. */
private reach: { of: Structure; radius: number } | null = null
/** The two clipping planes of the depth slab, kept and re-aimed each frame. */
private readonly slabPlanes = [new Plane(), new Plane()]
private chordsFrom: ReadonlyArray<readonly [number, number]> | null = null
/** The centre of rotation — a ball at the camera's target with the three axes through it. */
private readonly centre = new Object3D()
private centreBall: Mesh | null = null
/** The three arms out of the ball, shaft, head and stub apiece. */
private centreArms: Mesh[] = []
/** The centre left out of one frame: a *copy this* snapshot (§7.2). */
private withoutCentre = false
private readonly raycaster = new Raycaster()
private width = 1
private height = 1
private view: StructureView | null = null
private palette: RenderPalette
/** The model the geometry was built from, so a model that **moves** rebuilds it. */
private builtStructure: Structure | null = null
/** What the geometry was last built for, so a change elsewhere does not rebuild it. */
private built: string | null = null
/** Bead index per pick instance, since hidden beads are not instanced. */
private pickBeads: Int32Array = new Int32Array(0)
private shown: Uint8Array = new Uint8Array(0)
/** `true` after the GPU took the context away; the next frame rebuilds. */
lost = false
private readonly onLost = (event: Event): void => {
event.preventDefault()
this.lost = true
}
private readonly onRestored = (): void => {
this.lost = false
this.built = null
this.render()
}
constructor(palette: RenderPalette) {
this.palette = palette
this.el = document.createElement('canvas')
this.el.className = 'structure-canvas'
this.el.addEventListener('webglcontextlost', this.onLost)
this.el.addEventListener('webglcontextrestored', this.onRestored)
this.scene.add(this.root)
this.scene.add(this.lights)
this.scene.add(this.centre)
this.centre.visible = false
this.scene.add(this.overlayRoot)
const ambient = new AmbientLight(0xffffff, 0.9)
const key = new DirectionalLight(0xffffff, 1.6)
key.position.set(1, 1.2, 1.5)
const fill = new DirectionalLight(0xffffff, 0.5)
fill.position.set(-1, -0.4, -1)
this.lights.add(ambient, key, fill)
this.raycaster.layers.set(PICK_LAYER)
}
/** Whether this browser gave a WebGL context at all. */
get available(): boolean {
return this.contextOrNull() !== null
}
private contextOrNull(): WebGLRenderer | null {
if (this.renderer !== null) return this.renderer
try {
this.renderer = new WebGLRenderer({ canvas: this.el, antialias: true, alpha: false })
this.renderer.setPixelRatio(Math.min(2, window.devicePixelRatio || 1))
this.renderer.setSize(this.width, this.height, false)
return this.renderer
} catch {
return null
}
}
setPalette(palette: RenderPalette): void {
this.palette = palette
// The fog and the ink are the page's, so a change of theme is a recolour.
this.recolour()
this.render()
}
/** CSS pixels. */
setSize(width: number, height: number): void {
this.width = Math.max(1, Math.round(width))
this.height = Math.max(1, Math.round(height))
this.renderer?.setSize(this.width, this.height, false)
this.render()
}
/** Adopt a view and draw it. */
setView(view: StructureView): void {
const previous = this.view
this.view = view
const key = buildKey(view)
// **The model itself, as well as the key.** {@link buildKey} is counts and
// style: how many beads, how they are drawn, how wide. It says nothing
// about *where* the beads are, because until the mirrors (§25.5) nothing
// ever moved them — a model was built once from its file and stood still.
// A reflection and a turn into another model's frame both hand this a new
// `Structure` with the same counts and the same style, so the key matched,
// the geometry was never rebuilt, and the fibre on screen stayed exactly
// where it was while the chain **names** — drawn by the panel from the
// structure on every frame — flipped. The picture and its labels
// disagreed about which model was on screen.
if (key !== this.built || this.builtStructure !== view.structure) {
this.rebuild(view)
this.built = key
this.builtStructure = view.structure
} else if (previous === null || previous.colours !== view.colours || previous.lit !== view.lit) {
this.recolour()
}
this.rebuildOverlay(view)
this.mark()
this.render()
}
/**
* The bead under a point in the canvas, in CSS pixels from its top-left, or
* `-1`.
*/
pick(x: number, y: number): number {
const view = this.view
if (view === null || this.picks === null) return -1
const ndc = new Vector2((x / this.width) * 2 - 1, -(y / this.height) * 2 + 1)
const camera = this.applyCamera(view)
this.raycaster.setFromCamera(ndc, camera)
const hits = this.raycaster.intersectObject(this.picks, false)
const first = hits.find((hit) => hit.instanceId !== undefined)
if (first === undefined || first.instanceId === undefined) return -1
return this.pickBeads[first.instanceId] ?? -1
}
/**
* The picture at a size, as a 2D canvas: the GL frame plus the labels.
*
* Rendered at the requested size rather than screen-grabbed, so a 300 dpi
* export is a 300 dpi drawing (§7.2's rule, kept for the one raster here).
*
* `centre: false` leaves the centre of rotation out: it says where the
* model *turns*, which is a control, and *copy this* is the model alone.
*/
snapshot(width: number, height: number, options: { centre?: boolean } = {}): HTMLCanvasElement | null {
const renderer = this.contextOrNull()
const view = this.view
if (renderer === null || view === null) return null
const out = document.createElement('canvas')
out.width = Math.max(1, Math.round(width))
out.height = Math.max(1, Math.round(height))
const ctx = out.getContext('2d')
if (ctx === null) return null
const heldWidth = this.width
const heldHeight = this.height
const heldRatio = renderer.getPixelRatio()
try {
this.withoutCentre = options.centre === false
renderer.setPixelRatio(1)
this.width = out.width
this.height = out.height
renderer.setSize(out.width, out.height, false)
this.render()
ctx.drawImage(this.el, 0, 0)
} finally {
this.withoutCentre = false
this.width = heldWidth
this.height = heldHeight
renderer.setPixelRatio(heldRatio)
renderer.setSize(heldWidth, heldHeight, false)
this.render()
}
// The words on the model, in the cell's own CSS pixels scaled to this
// canvas: the same function the vector page writes them with
// (`structure/painter.ts`), so the PNG and the PDF name the same things.
ctx.save()
ctx.setTransform(out.width / heldWidth, 0, 0, out.height / heldHeight, 0, 0)
drawStructureLabels(ctx, { width: heldWidth, height: heldHeight }, view, this.palette)
ctx.restore()
return out
}
render(): void {
const renderer = this.contextOrNull()
const view = this.view
if (renderer === null || view === null || this.lost) return
const camera = this.applyCamera(view)
const background = new Color(hexOf(this.palette.background))
this.scene.background = background
// The depth slab: two planes facing each other along the line of sight,
// either side of the centre of rotation, at a fraction of the model's
// reach — everything nearer than the front one or farther than the back
// one is cut away, which is how the inside of a globule is looked at.
// Measured whether or not the slab clips, because it is also the depth the
// fog is read against — see below.
const half = this.slabHalf(view)
if (view.style.slab < 1) {
const { forward } = basis(view.camera)
const [tx, ty, tz] = view.camera.target
const f = new Vector3(forward[0], forward[1], forward[2])
const t = new Vector3(tx, ty, tz)
// Keep what is on the far side of the front plane (normal along
// forward) and the near side of the back plane (normal against it).
this.slabPlanes[0].setFromNormalAndCoplanarPoint(f, t.clone().addScaledVector(f, -half))
this.slabPlanes[1].setFromNormalAndCoplanarPoint(f.clone().negate(), t.clone().addScaledVector(f, half))
renderer.clippingPlanes = this.slabPlanes
} else if (renderer.clippingPlanes.length > 0) {
renderer.clippingPlanes = []
}
// **The depth cue and the slab are one instrument.** The fog starts at the
// centre of rotation — the plane the slab is centred on, which ⌘-click
// moves — and reaches the page exactly where the slab cuts, so what the
// fog is saying is *how close this is to being cut away*. It used to be
// set from the camera distance alone, which on a thin slab left every one
// of the few beads it kept already half dissolved: the fog was measuring
// the whole model while the slab was showing a slice of it.
//
// The slider weakens it by pushing that plane out: at 1 the far side of
// the slab is the page, at a half it is half way there.
const d = view.camera.distance
const f = view.style.fog
this.scene.fog = view.style.fogOn && f > 0 ? new Fog(background, d, d + half / f) : null
this.placeCentre(view)
renderer.render(this.scene, camera)
}
/**
* Half the slab's thickness, in scene units: how far either side of the
* centre of rotation the model is kept. The model's whole reach at slab 1,
* so the slider runs from a sheet to everything.
*
* **In the scene's units, not the file's.** It used to be
* `structure.scale * 2 * slab`, and `scale` is the factor back to the
* file's own units — nanometres, or whatever the solver worked in — while
* the coordinates it is stored beside are the *normalised* ones. On a model
* whose radius of gyration was a thousand nanometres the planes were put a
* thousand times too far apart, which is why the slab appeared to do
* nothing at any setting.
*/
private slabHalf(view: StructureView): number {
return Math.max(1e-3, this.reachOf(view.structure) * view.style.slab)
}
/**
* How far the farthest present bead is from the model's centre, in scene
* units. Measured once per model: it is a fact about the coordinates, and
* they do not change under the camera.
*/
private reachOf(structure: Structure): number {
if (this.reach !== null && this.reach.of === structure) return this.reach.radius
const all = centroidOf(structure, { [Symbol.iterator]: () => counting(structure.set.length) })
const radius = all === null ? 1 : Math.max(1e-3, all.radius)
this.reach = { of: structure, radius }
return radius
}
/**
* The bead under the pointer, or the nearest one within `radius` pixels.
*
* A bead is a few pixels across and a fibre is thinner; asking a reader to
* land a pointer exactly on one is asking them to aim at the picture rather
* than at the model. So the ray is cast first — which is exact, and respects
* what is in front of what — and only where it hits nothing does the search
* widen to the nearest bead whose centre falls within the radius, the
* nearest to the eye winning where several do.
*
* Screen space and one pass over the beads, rather than a fan of rays: a ray
* against an instanced mesh tests every instance, so eight of them is eight
* times the work for a worse answer.
*/
pickNear(x: number, y: number, radius: number): number {
const exact = this.pick(x, y)
if (exact >= 0) return exact
const view = this.view
if (view === null || radius <= 0) return -1
const camera = this.applyCamera(view)
const { structure } = view
const point = new Vector3()
// The planes are the ones the last frame was clipped by, which is what the
// reader is looking at.
const clipped = view.style.slab < 1
let best = -1
let bestAway = Infinity
let bestDepth = Infinity
for (let i = 0; i < structure.set.length; i++) {
if (this.shown[i] !== 1) continue
point.set(structure.x[i], structure.y[i], structure.z[i])
// What the slab has cut away cannot be aimed at: it is not on screen.
if (clipped && (this.slabPlanes[0].distanceToPoint(point) < 0 || this.slabPlanes[1].distanceToPoint(point) < 0)) {
continue
}
point.project(camera)
if (point.z < -1 || point.z > 1) continue
const px = (point.x * 0.5 + 0.5) * this.width
const py = (0.5 - point.y * 0.5) * this.height
const away = Math.hypot(px - x, py - y)
if (away > radius) continue
// Nearest to the eye first, and only then nearest to the pointer: a bead
// behind another is not the one being aimed at.
if (point.z < bestDepth - 1e-6 || (point.z < bestDepth + 1e-6 && away < bestAway)) {
best = i
bestAway = away
bestDepth = point.z
}
}
return best
}
/**
* The centre of rotation, when the style shows it (§25.5): a ball at the
* camera's target with three arms out of it, sized to the view so it reads
* the same at every zoom, drawn over the model since a centre inside a tube
* is still the centre. Rebuilt only when the size changes by more than a
* little.
*
* **Arms rather than lines through it, and a head on each.** The gizmo is on
* by default now, so it has to say what it is at a glance and to somebody
* who never read a word about it: a ball where the model turns, and one arm
* per axis pointing the way that axis *goes*. Six half-lines crossing in a
* dot said none of that — which way was +x, and which end was the centre,
* were both things a reader had to turn the model to find out. The dot is
* still drawn in ink and the arms in the axis colours every 3D tool uses
* (x red, y green, z blue), so the thing the reader already knows is the
* thing they see.
*
* The whole gizmo carries the model's **planted frame** (`axesFrame`): the
* identity is the model's own axes, and *replant* writes the view's there.
*/
private placeCentre(view: StructureView): void {
const show = view.style.axes && !this.withoutCentre
this.centre.visible = show
if (!show) return
const size = view.camera.distance * 0.12
if (this.centreBall === null || Math.abs(this.centre.scale.x - size) / size > 0.01) {
this.centre.clear()
this.centreBall?.geometry.dispose()
for (const arm of this.centreArms) arm.geometry.dispose()
this.centreArms = []
this.centreBall = new Mesh(
new SphereGeometry(0.075, 16, 12),
new MeshBasicMaterial({ color: hexOf(this.palette.ink), transparent: true, opacity: 0.8, depthTest: false }),
)
this.centreBall.renderOrder = 10
this.centre.add(this.centreBall)
// One arm per axis: a shaft from the ball and a head at its end, so the
// sign is read off the picture rather than inferred from it. The
// negative half is a thinner, shorter stub — enough to say the axis is
// a line and not a ray, and not enough to be mistaken for the head.
const axes: Array<{ dir: [number, number, number]; colour: number }> = [
{ dir: [1, 0, 0], colour: 0xd8453c },
{ dir: [0, 1, 0], colour: 0x2f9e44 },
{ dir: [0, 0, 1], colour: 0x3b7ddd },
]
for (const axis of axes) {
const material = new MeshBasicMaterial({ color: axis.colour, transparent: true, opacity: 0.95, depthTest: false })
const shaft = new Mesh(new CylinderGeometry(0.022, 0.022, 0.8, 10), material)
const head = new Mesh(new ConeGeometry(0.07, 0.22, 12), material)
const stub = new Mesh(new CylinderGeometry(0.012, 0.012, 0.45, 8), material)
// A cylinder stands up the y axis; turn it to the axis it draws.
const turn = new Quaternion().setFromUnitVectors(
new Vector3(0, 1, 0),
new Vector3(axis.dir[0], axis.dir[1], axis.dir[2]),
)
shaft.quaternion.copy(turn)
head.quaternion.copy(turn)
stub.quaternion.copy(turn)
shaft.position.set(axis.dir[0] * 0.4, axis.dir[1] * 0.4, axis.dir[2] * 0.4)
head.position.set(axis.dir[0] * 0.91, axis.dir[1] * 0.91, axis.dir[2] * 0.91)
stub.position.set(axis.dir[0] * -0.225, axis.dir[1] * -0.225, axis.dir[2] * -0.225)
for (const part of [shaft, head, stub]) {
part.renderOrder = 10
this.centre.add(part)
this.centreArms.push(part)
}
}
this.centre.scale.setScalar(size)
}
const [x, y, z] = view.camera.target
this.centre.position.set(x, y, z)
const [qx, qy, qz, qw] = view.style.axesFrame
this.centre.quaternion.set(qx, qy, qz, qw)
}
destroy(): void {
this.el.removeEventListener('webglcontextlost', this.onLost)
this.el.removeEventListener('webglcontextrestored', this.onRestored)
this.clear()
this.renderer?.dispose()
this.renderer = null
}
// -------------------------------------------------------------------------
// Building
// -------------------------------------------------------------------------
private clear(): void {
for (const mesh of [this.beads, this.picks, this.halos, this.sticks, ...this.tubes]) {
if (mesh === null) continue
this.root.remove(mesh)
mesh.geometry.dispose()
const material = mesh.material
if (Array.isArray(material)) material.forEach((m) => m.dispose())
else material.dispose()
}
for (const ink of [this.chords, this.chord, this.gapDashes, this.measures, this.ticks, this.marks]) {
if (ink === null) continue
this.root.remove(ink)
ink.geometry.dispose()
;(ink.material as MeshBasicMaterial).dispose()
}
this.chords = null
this.chordsFrom = null
this.gapDashes = null
this.measures = null
this.measuresFrom = null
this.ticks = null
this.ticksBeads = []
this.ticksFrom = null
this.marks = null
this.marksBeads = []
this.marksFrom = null
this.beads = null
this.picks = null
this.halos = null
this.sticks = null
this.tubes = []
this.chord = null
}
private rebuild(view: StructureView): void {
this.clear()
const { structure, style } = view
const n = structure.set.length
const shown = shownBeads(view)
this.shown = shown
let count = 0
for (let i = 0; i < n; i++) count += shown[i]
const beadRadius = structure.step * style.beadRadius
const stickRadius = structure.step * style.tubeRadius
const lit = true
// The pick instances, always: one sphere per shown bead at the bead radius
// or, under a tube, at the tube's, so a pick on the tube lands on the bead
// the surface belongs to.
const pickRadius = style.beads ? beadRadius : Math.max(stickRadius, beadRadius * 0.6)
this.pickBeads = new Int32Array(count)
this.picks = new InstancedMesh(new SphereGeometry(1, 8, 6), new MeshBasicMaterial(), Math.max(1, count))
this.picks.count = count
this.picks.layers.set(PICK_LAYER)
const matrix = new Matrix4()
let at = 0
for (let i = 0; i < n; i++) {
if (shown[i] === 0) continue
matrix.makeScale(pickRadius, pickRadius, pickRadius)
matrix.setPosition(structure.x[i], structure.y[i], structure.z[i])
this.picks.setMatrixAt(at, matrix)
this.pickBeads[at] = i
at++
}
this.picks.instanceMatrix.needsUpdate = true
// A raycast against an instanced mesh is gated by its bounding sphere,
// which three computes once and never again: left as it was, it is the
// sphere of a mesh that had no instances yet, and every ray misses. The
// same sphere is what frustum culling reads, which is why every object
// under the root is added with culling off (`frustumCulled = false`): a
// halo or a chord placed after its sphere was computed was culled as
// out of view and never drawn.
this.picks.computeBoundingSphere()
this.root.add(this.picks)
this.picks.frustumCulled = false
const drawBeads = style.beads
const drawSticks = style.sticks
const drawTube = style.tube
if (drawBeads) {
this.beads = new InstancedMesh(new SphereGeometry(1, 16, 12), surface(lit), Math.max(1, count))
this.beads.geometry.setAttribute(GHOST_ALPHA, ghostAttribute(count, true))
this.beads.count = count
at = 0
for (let i = 0; i < n; i++) {
if (shown[i] === 0) continue
const r = beadRadius
matrix.makeScale(r, r, r)
matrix.setPosition(structure.x[i], structure.y[i], structure.z[i])
this.beads.setMatrixAt(at, matrix)
at++
}
this.beads.instanceMatrix.needsUpdate = true
this.root.add(this.beads)
this.beads.frustumCulled = false
}
// The dashes across every gap, whatever else is drawn: ink, a little
// wider than a stick, so a chain that stops where a bead is missing reads
// as one chain with a hole in it rather than as two chains.
//
// **Ghosted with the chain they belong to.** They were flat ink at full
// opacity, so a ghosted chromosome kept its dashes at full strength: a
// model faded to almost nothing still had a cage of black dashes over it,
// which read as the one thing being *shown*. A gap is a fact about a
// chain, so it fades with the chain — which means remembering, per
// segment, which pair of beads it crosses.
const gaps = gapPairsOf(view, shown)
if (gaps.length > 0) {
const segments: Array<[Vector3, Vector3]> = []
const owners: number[] = []
const dash = stickRadius * 3
const gap = stickRadius * 2
for (let g = 0; g < gaps.length; g++) {
const [a, b] = gaps[g]
const from = new Vector3(structure.x[a], structure.y[a], structure.z[a])
const to = new Vector3(structure.x[b], structure.y[b], structure.z[b])
const length = from.distanceTo(to)
const dir = to.clone().sub(from).normalize()
for (let at = 0; at < length; at += dash + gap) {
const end = Math.min(length, at + dash)
segments.push([from.clone().addScaledVector(dir, at), from.clone().addScaledVector(dir, end)])
owners.push(g)
}
}
this.gapDashes = cylinders(segments, stickRadius * INK_SHARE, ghostable(inkMaterial(this.palette.ink, 1)))
this.gapDashes.geometry.setAttribute(GHOST_ALPHA, ghostAttribute(Math.max(1, segments.length), true))
this.gapDashes.userData['gaps'] = gaps
this.gapDashes.userData['owners'] = Int32Array.from(owners)
this.root.add(this.gapDashes)
}
if (drawSticks || drawTube) {
// Sticks between neighbours on a run, as instanced cylinders, each
// turned from the y axis onto its pair. A tube's runs of one bead have
// no tube and are given a stick's worth of nothing, which is what a lone
// bead is.
const pairs = pairsOf(view, shown)
if (drawSticks && pairs.length > 0) {
this.sticks = new InstancedMesh(
new CylinderGeometry(1, 1, 1, RADIAL, 1, true),
surface(lit),
pairs.length,
)
this.sticks.geometry.setAttribute(GHOST_ALPHA, ghostAttribute(pairs.length, true))
const q = new Quaternion()
const up = new Vector3(0, 1, 0)
const dir = new Vector3()
for (let p = 0; p < pairs.length; p++) {
const [a, b] = pairs[p]
dir.set(structure.x[b] - structure.x[a], structure.y[b] - structure.y[a], structure.z[b] - structure.z[a])
const length = dir.length()
q.setFromUnitVectors(up, dir.clone().normalize())
matrix.compose(
new Vector3((structure.x[a] + structure.x[b]) / 2, (structure.y[a] + structure.y[b]) / 2, (structure.z[a] + structure.z[b]) / 2),
q,
new Vector3(stickRadius, length, stickRadius),
)
this.sticks.setMatrixAt(p, matrix)
}
this.sticks.instanceMatrix.needsUpdate = true
this.sticks.userData['pairs'] = pairs
this.root.add(this.sticks)
this.sticks.frustumCulled = false
}
if (drawTube) {
for (const chain of structure.chains) {
if (view.haplotype >= 0 && chain.hap !== view.haplotype) continue
for (let r = 0; r < chain.runs.length; r += 2) {
const from = chain.runs[r]
const to = chain.runs[r + 1]
const run: number[] = []
for (let k = from; k < to; k++) if (shown[chain.beads[k]] === 1) run.push(chain.beads[k])
if (run.length < 2) continue
const points = run.map((i) => new Vector3(structure.x[i], structure.y[i], structure.z[i]))
const curve = new CatmullRomCurve3(points, false, 'catmullrom', 0.5)
const segments = Math.max(1, (run.length - 1) * TUBE_PER_BEAD)
const geometry = new TubeGeometry(curve, segments, stickRadius, RADIAL, false)
// Which bead each ring of vertices belongs to, by arc length along
// the polyline, so a colouring reads along the fibre.
const owner = new Int32Array(segments + 1)
const lengths = cumulative(points)
const total = lengths[lengths.length - 1]
for (let s = 0; s <= segments; s++) {
const along = (s / segments) * total
let k = 0
while (k + 1 < lengths.length - 1 && lengths[k + 1] <= along) k++
const span = lengths[k + 1] - lengths[k]
const t = span > 0 ? (along - lengths[k]) / span : 0
owner[s] = run[t < 0.5 ? k : k + 1]
}
geometry.setAttribute('color', new BufferAttribute(new Float32Array(geometry.attributes.position.count * 3), 3))
geometry.setAttribute(GHOST_ALPHA, ghostAttribute(geometry.attributes.position.count, false))
const mesh = new Mesh(geometry, surface(lit, true))
mesh.userData['owner'] = owner
mesh.userData['radial'] = RADIAL
this.tubes.push(mesh)
this.root.add(mesh)
}
}
}
}
// The halo behind a hovered or pinned bead: a copy of the sphere, a little
// larger, drawn back faces only, which reads as an outline round it.
// Translucent and depth-tested rather than back faces only: it sits **in
// front of** the bead or tube it marks, which it encloses, and **behind**
// any part of the model nearer the eye, as a ball at that place would.
// The outline it used to be read through a tube in front of it and was
// swallowed by one behind.
this.halos = new InstancedMesh(
new SphereGeometry(1, 16, 12),
new MeshBasicMaterial({
color: hexOf(this.palette.ink),
side: FrontSide,
transparent: true,
opacity: 0.55,
depthWrite: false,
}),
8,
)
this.halos.count = 0
this.root.add(this.halos)
this.halos.frustumCulled = false
// The chords are cylinders rather than GL lines, which are one pixel
// wide on every platform that matters: a line that says *these two touch*
// has to be seen at the size of the tube it crosses. Placed by `mark`.
this.chord = null
this.chords = null
this.chordsFrom = null
this.recolour()
}
/** Write every colour attribute from the view's colours, lit mask and palette. */
private recolour(): void {
const view = this.view
if (view === null) return
const { structure } = view
const n = structure.set.length
const rgb = view.colours.rgb
// **The colour is the bead's own, ghosted or not.** Fading is alpha
// (`ghostable`), not a mix towards the page: a ghosted bead keeps its hue,
// lets the model behind it through rather than painting over it, and at an
// opacity of zero is gone rather than page-coloured and still in the way.
const colourOf = (i: number, out: Color): void => {
out.setRGB(rgb[i * 3], rgb[i * 3 + 1], rgb[i * 3 + 2])
}
const alphaOf = (i: number): number => (view.lit !== null && view.lit[i] === 0 ? view.style.opacity : 1)
const colour = new Color()
if (this.beads !== null) {
const alpha = this.beads.geometry.getAttribute(GHOST_ALPHA) as BufferAttribute
for (let at = 0; at < this.pickBeads.length; at++) {
colourOf(this.pickBeads[at], colour)
this.beads.setColorAt(at, colour)
alpha.setX(at, alphaOf(this.pickBeads[at]))
}
if (this.beads.instanceColor !== null) this.beads.instanceColor.needsUpdate = true
alpha.needsUpdate = true
}
if (this.sticks !== null) {
const pairs = this.sticks.userData['pairs'] as Array<[number, number]>
const alpha = this.sticks.geometry.getAttribute(GHOST_ALPHA) as BufferAttribute
const other = new Color()
for (let p = 0; p < pairs.length; p++) {
colourOf(pairs[p][0], colour)
colourOf(pairs[p][1], other)
colour.lerp(other, 0.5)
this.sticks.setColorAt(p, colour)
// A stick spanning the edge of the window fades to the mean of its two
// ends, so the fibre thins into the ghost rather than stopping dead.
alpha.setX(p, (alphaOf(pairs[p][0]) + alphaOf(pairs[p][1])) / 2)
}
if (this.sticks.instanceColor !== null) this.sticks.instanceColor.needsUpdate = true
alpha.needsUpdate = true
}
if (this.gapDashes !== null) {
// The mean of the pair it crosses, as a stick takes: a gap that spans
// the edge of the window thins into the ghost rather than stopping dead.
const gaps = this.gapDashes.userData['gaps'] as Array<[number, number]> | undefined
const owners = this.gapDashes.userData['owners'] as Int32Array | undefined
const alpha = this.gapDashes.geometry.getAttribute(GHOST_ALPHA) as BufferAttribute | undefined
if (gaps !== undefined && owners !== undefined && alpha !== undefined) {
for (let s = 0; s < owners.length; s++) {
const [a, b] = gaps[owners[s]]
alpha.setX(s, (alphaOf(a) + alphaOf(b)) / 2)
}
alpha.needsUpdate = true
}
}
for (const tube of this.tubes) {
const owner = tube.userData['owner'] as Int32Array
const radial = tube.userData['radial'] as number
const attribute = tube.geometry.getAttribute('color') as BufferAttribute
const array = attribute.array as Float32Array
const alpha = tube.geometry.getAttribute(GHOST_ALPHA) as BufferAttribute
const alphas = alpha.array as Float32Array
for (let s = 0; s < owner.length; s++) {
colourOf(owner[s], colour)
const a = alphaOf(owner[s])
for (let ring = 0; ring <= radial; ring++) {
const v = s * (radial + 1) + ring
array[v * 3] = colour.r
array[v * 3 + 1] = colour.g
array[v * 3 + 2] = colour.b
alphas[v] = a
}
}
attribute.needsUpdate = true
alpha.needsUpdate = true
}
this.fadeMarks()
if (this.halos !== null) {
;(this.halos.material as MeshBasicMaterial).color.setHex(hexOf(this.palette.ink))
}
for (const ink of [this.chord, this.chords, this.gapDashes, this.measures, this.ticks]) {
if (ink !== null) (ink.material as MeshBasicMaterial).color.setHex(hexOf(this.palette.ink))
}
void n
}
/** Place the halos and the chord for what is hovered and pinned. */
private mark(): void {
const view = this.view
if (view === null || this.halos === null) return
const { structure, style } = view
const marked = [...new Set([...view.hovered, ...(view.pinned >= 0 ? [view.pinned] : [])])].filter(
(i) => i >= 0 && i < structure.set.length && this.shown[i] === 1,
)
const stickRadius = structure.step * style.tubeRadius
const radius =
(style.beads ? structure.step * style.beadRadius : Math.max(stickRadius, structure.step * style.beadRadius * 0.6)) *
1.45
const matrix = new Matrix4()
const count = Math.min(marked.length, 8)
for (let at = 0; at < count; at++) {
const i = marked[at]
matrix.makeScale(radius, radius, radius)
matrix.setPosition(structure.x[i], structure.y[i], structure.z[i])
this.halos.setMatrixAt(at, matrix)
}
this.halos.count = count
this.halos.instanceMatrix.needsUpdate = true
// The loops as chords, rebuilt only when the list is a new one: the panel
// hands the same array back frame after frame while nothing changed.
const wanted = style.chords ? view.chords : NO_CHORDS
if (this.chordsFrom !== wanted) {
this.chordsFrom = wanted
if (this.chords !== null) {
this.root.remove(this.chords)
this.chords.geometry.dispose()
this.chords = null
}
const kept = wanted.filter(([a, b]) => this.shown[a] === 1 && this.shown[b] === 1)
if (kept.length > 0) {
const segments = kept.map(
([a, b]) =>
[
new Vector3(structure.x[a], structure.y[a], structure.z[a]),
new Vector3(structure.x[b], structure.y[b], structure.z[b]),
] as [Vector3, Vector3],
)
this.chords = cylinders(segments, stickRadius * INK_SHARE, inkMaterial(this.palette.ink, 0.9))
this.root.add(this.chords)
}
}
// The reader's measurements: dashes of ink between the two beads.
if (this.measuresFrom !== view.measures) {
this.measuresFrom = view.measures
if (this.measures !== null) {
this.root.remove(this.measures)
this.measures.geometry.dispose()
this.measures = null
}
const segments: Array<[Vector3, Vector3]> = []
for (const [a, b] of view.measures) {
if (this.shown[a] !== 1 || this.shown[b] !== 1) continue
const from = new Vector3(structure.x[a], structure.y[a], structure.z[a])
const to = new Vector3(structure.x[b], structure.y[b], structure.z[b])
const length = from.distanceTo(to)
const dir = to.clone().sub(from).normalize()
const dash = stickRadius * 2.5
const gap = stickRadius * 1.5
for (let at = 0; at < length; at += dash + gap) {
segments.push([from.clone().addScaledVector(dir, at), from.clone().addScaledVector(dir, Math.min(length, at + dash))])
}
}
if (segments.length > 0) {
this.measures = cylinders(segments, stickRadius * 0.6, inkMaterial(this.palette.ink, 1))
this.root.add(this.measures)
}
}
// The ruler's ticks: a small bead of ink at each, over the model.
if (this.ticksFrom !== view.ruler) {
this.ticksFrom = view.ruler
if (this.ticks !== null) {
this.root.remove(this.ticks)
this.ticks.geometry.dispose()
this.ticks = null
}
const kept = view.ruler.filter((tick) => this.shown[tick.bead] === 1)
if (kept.length > 0) {
const r = Math.max(stickRadius * 1.6, structure.step * style.beadRadius * 0.8)
const mesh = new InstancedMesh(
new SphereGeometry(1, 10, 8),
ghostable(inkMaterial(this.palette.ink, 1)),
kept.length,
)
mesh.geometry.setAttribute(GHOST_ALPHA, ghostAttribute(kept.length, true))
const matrix = new Matrix4()
kept.forEach((tick, at) => {
matrix.makeScale(r, r, r)
matrix.setPosition(structure.x[tick.bead], structure.y[tick.bead], structure.z[tick.bead])
mesh.setMatrixAt(at, matrix)
})
mesh.instanceMatrix.needsUpdate = true
mesh.frustumCulled = false
this.ticks = mesh
this.ticksBeads = kept.map((tick) => tick.bead)
this.root.add(mesh)
}
}
// The reader's marked places: the bead again at twice the radius, in the
// mark's own colour. A place is a thing on the model, so it is drawn as a
// bigger bead rather than as one more line over it.
if (this.marksFrom !== view.marks) {
this.marksFrom = view.marks
if (this.marks !== null) {
this.root.remove(this.marks)
this.marks.geometry.dispose()
this.marks = null
}
const kept = view.marks.filter((mark) => this.shown[mark.bead] === 1)
if (kept.length > 0) {
const mesh = new InstancedMesh(
new SphereGeometry(1, 16, 12),
// **No `vertexColors`.** The colour of a marked bead comes from the
// instance, through `setColorAt`, and asking for vertex colours as
// well made every one of them *black*: `vertexColors` defines
// `USE_COLOR`, whose shader does `vColor.rgb *= color`, and `color`
// is an attribute a plain sphere has not got. A missing attribute
// reads as `(0, 0, 0)` — `defaultAttributeValues` would have said
// otherwise but exists only on `ShaderMaterial` — and the next line
// of the same chunk multiplies the instance colour into that zero.
// So a mark drawn in the colour the Manual annotations card gave it
// came out black, while the same mark in an exported PDF came out
// right, the 2D painter taking the colour as a colour.
//
// `ghostable`, though, because a mark **outside the window is
// ghosted** like the bead it sits on (§25.5). It was not, so a
// telomere — which rides this same channel — stayed a solid yellow
// ball in a model faded to a trace, and a genome's worth of them read
// as the brightest thing in a picture of one window. The 2D painter
// had it right from the start, so the screen and the exported PDF
// disagreed about the same model.
ghostable(new MeshStandardMaterial({ roughness: 0.55, metalness: 0 })),
kept.length,
)
const matrix = new Matrix4()
const colour = new Color()
kept.forEach((mark, at) => {
const r = structure.step * style.beadRadius * MARKED_BEAD
matrix.makeScale(r, r, r)
matrix.setPosition(structure.x[mark.bead], structure.y[mark.bead], structure.z[mark.bead])
mesh.setMatrixAt(at, matrix)
colour.set(mark.colour)
mesh.setColorAt(at, colour)
})
mesh.geometry.setAttribute(GHOST_ALPHA, ghostAttribute(kept.length, true))
mesh.instanceMatrix.needsUpdate = true
if (mesh.instanceColor !== null) mesh.instanceColor.needsUpdate = true
mesh.frustumCulled = false
this.marks = mesh
this.marksBeads = kept.map((mark) => mark.bead)
this.root.add(mesh)
}
}
// The hovered contact's chord: dashes of ink, wider than the loops', on
// top of everything else that is a line.
if (this.chord !== null) {
this.root.remove(this.chord)
this.chord.geometry.dispose()
this.chord = null
}
const chord = view.chord
if (chord !== null && this.shown[chord[0]] === 1 && this.shown[chord[1]] === 1) {
const [a, b] = chord
const from = new Vector3(structure.x[a], structure.y[a], structure.z[a])
const to = new Vector3(structure.x[b], structure.y[b], structure.z[b])
const length = from.distanceTo(to)
const dir = to.clone().sub(from).normalize()
const dash = stickRadius * 3
const gap = stickRadius * 2
const segments: Array<[Vector3, Vector3]> = []
for (let at = 0; at < length; at += dash + gap) {
segments.push([from.clone().addScaledVector(dir, at), from.clone().addScaledVector(dir, Math.min(length, at + dash))])
}
this.chord = cylinders(segments, stickRadius * 0.8, inkMaterial(this.palette.ink, 1))
this.root.add(this.chord)
}
// The marks and the ticks are built *here*, and `recolour` runs before
// `mark` — so a mesh made this frame would keep the opaque alpha it was
// filled with until the next time the window moved. That is a telomere
// drawn whole over a model faded to a trace, which is the thing this is
// for.
this.fadeMarks()
}
/**
* Fade every mark with the bead it sits on (§25.5).
*
* The reader's own marked places, the telomeres that ride the same channel,
* and the ruler's ticks. A place on the fibre is a fact about that bead, so
* a mark on a bead that is barely there is barely there — and a window of a
* genome used to be read against a constellation of solid yellow telomeres
* nowhere near it, the brightest thing in a picture of somewhere else.
*
* Called from both roads into the picture, because the two meshes are built
* in `mark` and the alphas are written in `recolour`, and neither runs after
* the other in every frame.
*/
private fadeMarks(): void {
const view = this.view
if (view === null) return
const alphaOf = (i: number): number => (view.lit !== null && view.lit[i] === 0 ? view.style.opacity : 1)
for (const drawn of [
{ mesh: this.marks, beads: this.marksBeads },
{ mesh: this.ticks, beads: this.ticksBeads },
]) {
const attribute = drawn.mesh?.geometry.getAttribute(GHOST_ALPHA) as BufferAttribute | undefined
if (attribute === undefined) continue
for (let at = 0; at < drawn.beads.length; at++) attribute.setX(at, alphaOf(drawn.beads[at]))
attribute.needsUpdate = true
}
}
/**
* The compared model (§25.5), in this model's frame: its runs as a thin
* tube in its own colours, rebuilt only when the model or the radius
* changes. Ghosting and the window do not apply to it — it is the other
* model, whole, beside this one — and it is drawn a little thinner so the
* two read apart where they cross.
*/
private rebuildOverlay(view: StructureView): void {
const overlay = view.overlay
const key = overlay === null ? '' : `${view.style.tubeRadius}|${view.style.tube}|${view.style.sticks}`
if (overlay?.structure === this.overlayFrom && key === this.overlayKey) {
if (overlay !== null) this.recolourOverlay(overlay.colours)
return
}
this.overlayFrom = overlay?.structure ?? null
this.overlayKey = key
for (const child of [...this.overlayRoot.children]) {
this.overlayRoot.remove(child)
const mesh = child as Mesh
mesh.geometry?.dispose()
const material = mesh.material
if (Array.isArray(material)) material.forEach((m) => m.dispose())
else material?.dispose()
}
if (overlay === null) return
const o = overlay.structure
const radius = view.structure.step * view.style.tubeRadius * 0.7
for (const chain of o.chains) {
for (let r = 0; r < chain.runs.length; r += 2) {
const run: number[] = []
for (let k = chain.runs[r]; k < chain.runs[r + 1]; k++) if (o.present[chain.beads[k]] === 1) run.push(chain.beads[k])
if (run.length < 2) continue
const points = run.map((i) => new Vector3(o.x[i], o.y[i], o.z[i]))
const curve = new CatmullRomCurve3(points, false, 'catmullrom', 0.5)
const segments = Math.max(1, (run.length - 1) * TUBE_PER_BEAD)
const geometry = new TubeGeometry(curve, segments, radius, RADIAL, false)
const owner = new Int32Array(segments + 1)
const lengths = cumulative(points)
const total = lengths[lengths.length - 1]
for (let sgm = 0; sgm <= segments; sgm++) {
const along = (sgm / segments) * total
let k = 0
while (k + 1 < lengths.length - 1 && lengths[k + 1] <= along) k++
const span = lengths[k + 1] - lengths[k]
const t = span > 0 ? (along - lengths[k]) / span : 0
owner[sgm] = run[t < 0.5 ? k : k + 1]
}
geometry.setAttribute('color', new BufferAttribute(new Float32Array(geometry.attributes.position.count * 3), 3))
const mesh = new Mesh(geometry, surface(true, true))
mesh.userData['owner'] = owner
mesh.userData['radial'] = RADIAL
mesh.frustumCulled = false
this.overlayRoot.add(mesh)
}
}
this.recolourOverlay(overlay.colours)
}
private recolourOverlay(colours: BeadColours): void {
const rgb = colours.rgb
for (const child of this.overlayRoot.children) {
const mesh = child as Mesh
const owner = mesh.userData['owner'] as Int32Array | undefined
const radial = mesh.userData['radial'] as number | undefined
const attribute = mesh.geometry.getAttribute('color') as BufferAttribute | undefined
if (owner === undefined || radial === undefined || attribute === undefined) continue
const array = attribute.array as Float32Array
const perRing = radial + 1
for (let v = 0; v < attribute.count; v++) {
const ring = Math.min(owner.length - 1, Math.floor(v / perRing))
const i = owner[ring]
array[v * 3] = rgb[i * 3]
array[v * 3 + 1] = rgb[i * 3 + 1]
array[v * 3 + 2] = rgb[i * 3 + 2]
}
attribute.needsUpdate = true
}
}
/** The three.js camera for a view, positioned from the pure one. */
private applyCamera(view: StructureView): PerspectiveCamera | OrthographicCamera {
const camera = view.camera
const aspect = this.width / this.height
const eye = eyeOf(camera)
const { up } = basis(camera)
const near = Math.max(0.005, camera.distance * 0.02)
const far = camera.distance * 30 + 10
if (camera.projection === 'orthographic') {
const half = halfHeight(camera)
const cam = this.orthographic
cam.left = -half * aspect
cam.right = half * aspect
cam.top = half
cam.bottom = -half
cam.near = near
cam.far = far
cam.position.set(eye[0], eye[1], eye[2])
cam.up.set(up[0], up[1], up[2])
cam.lookAt(camera.target[0], camera.target[1], camera.target[2])
cam.updateProjectionMatrix()
this.lights.position.copy(cam.position)
this.lights.quaternion.copy(cam.quaternion)
return cam
}
const cam = this.perspective
cam.fov = camera.fov
cam.aspect = aspect
cam.near = near
cam.far = far
cam.position.set(eye[0], eye[1], eye[2])
cam.up.set(up[0], up[1], up[2])
cam.lookAt(camera.target[0], camera.target[1], camera.target[2])
cam.updateProjectionMatrix()
// The lights ride with the eye, so the lit side of the model is the side
// the reader is looking at whatever the orbit.
this.lights.position.copy(cam.position)
this.lights.quaternion.copy(cam.quaternion)
return cam
}
}
/** The material a bead, a stick or a tube is drawn in: shaded, or flat. */
function surface(lit: boolean, vertexColors = false): MeshStandardMaterial | MeshBasicMaterial {
return ghostable(
lit
? new MeshStandardMaterial({ roughness: 0.6, metalness: 0.05, vertexColors })
: new MeshBasicMaterial({ vertexColors }),
)
}
/**
* Let a material draw each bead at its own alpha, from a {@link GHOST_ALPHA}
* attribute.
*
* **Ghosting used to be a colour, and a colour is not transparency.** A ghosted
* bead was its own colour mixed towards the page, which on a white page reads
* as *pale* — the thing behind it is still hidden, because the geometry is
* still opaque and still writes depth, and at an opacity of zero the bead does
* not disappear, it becomes a white bead that punches a hole in whatever it is
* in front of. The 2D painter never had this problem (`painter.ts` sets
* `globalAlpha` and always has), so the same model exported to PDF and drawn on
* screen disagreed about what ghosting meant. This is the screen catching up:
* the alpha is real, `0` is gone and `1` is as drawn, exactly as §25.5 says.
*
* One attribute serves both kinds of geometry because GLSL does not care which
* it came from: on an `InstancedMesh` an `InstancedBufferAttribute` of this name
* is one value per instance, and on a plain `Mesh` a `BufferAttribute` of it is
* one per vertex, and `attribute float` reads either.
*
* A fragment under {@link GHOST_GONE} is **discarded** rather than blended.
* That is what makes zero mean *gone*: a discarded fragment writes no depth, so
* a bead the reader has faded all the way out stops hiding the model behind it
* instead of standing there invisibly in the way.
*
* `defaultAttributeValues` is the safety net for a geometry that has no such
* attribute at all — the overlay's tubes, anything added later. Without it a
* missing attribute reads as zero and every fragment would discard, which is a
* model that silently does not draw.
*/
function ghostable<T extends MeshStandardMaterial | MeshBasicMaterial>(material: T): T {
material.transparent = true
// `defaultAttributeValues` is a real property of every three material and is
// missing from its types, so it is reached through a narrow cast rather than
// left out — without it a geometry with no such attribute reads zero and
// discards every fragment, which is a model that silently does not draw.
const defaults = material as unknown as { defaultAttributeValues?: Record<string, number[]> }
defaults.defaultAttributeValues = { ...defaults.defaultAttributeValues, [GHOST_ALPHA]: [1] }
material.onBeforeCompile = (shader) => {
shader.vertexShader = `attribute float ${GHOST_ALPHA};\nvarying float vGhostAlpha;\n${shader.vertexShader}`.replace(
'#include <begin_vertex>',
`#include <begin_vertex>\n\tvGhostAlpha = ${GHOST_ALPHA};`,
)
shader.fragmentShader = `varying float vGhostAlpha;\n${shader.fragmentShader}`.replace(
'#include <dithering_fragment>',
`#include <dithering_fragment>\n\tif ( vGhostAlpha < ${GHOST_GONE.toFixed(4)} ) discard;\n\tgl_FragColor.a *= vGhostAlpha;`,
)
}
// Without a key of its own three would hand this material a program compiled
// for an unpatched one of the same kind, and the attribute would never exist.
material.customProgramCacheKey = () => GHOST_ALPHA
return material
}
/** One value per instance or per vertex, filled opaque, for {@link ghostable}. */
function ghostAttribute(count: number, instanced: boolean): BufferAttribute | InstancedBufferAttribute {
const values = new Float32Array(Math.max(1, count)).fill(1)
return instanced ? new InstancedBufferAttribute(values, 1) : new BufferAttribute(values, 1)
}
/** Which beads are drawn at all under this view. */
function shownBeads(view: StructureView): Uint8Array {
const { structure, style } = view
const n = structure.set.length
const shown = new Uint8Array(n)
for (let i = 0; i < n; i++) {
if (structure.present[i] === 0) continue
if (view.haplotype >= 0 && structure.model.hap[i] !== view.haplotype) continue
if (view.lit !== null && view.lit[i] === 0 && style.others === 'hide') continue
shown[i] = 1
}
return shown
}
/** The bead pairs a stick joins: neighbours on a run. */
function pairsOf(view: StructureView, shown: Uint8Array): Array<[number, number]> {
const { structure } = view
const pairs: Array<[number, number]> = []
for (const chain of structure.chains) {
if (view.haplotype >= 0 && chain.hap !== view.haplotype) continue
for (let r = 0; r < chain.runs.length; r += 2) {
for (let k = chain.runs[r] + 1; k < chain.runs[r + 1]; k++) {
const a = chain.beads[k - 1]
const b = chain.beads[k]
if (shown[a] === 1 && shown[b] === 1) pairs.push([a, b])
}
}
}
return pairs
}
/** The two beads either side of each gap in a chain: the last of one run, the first of the next. */
function gapPairsOf(view: StructureView, shown: Uint8Array): Array<[number, number]> {
const { structure } = view
const pairs: Array<[number, number]> = []
for (const chain of structure.chains) {
if (view.haplotype >= 0 && chain.hap !== view.haplotype) continue
for (let r = 2; r < chain.runs.length; r += 2) {
const a = chain.beads[chain.runs[r - 1] - 1]
const b = chain.beads[chain.runs[r]]
if (shown[a] === 1 && shown[b] === 1) pairs.push([a, b])
}
}
return pairs
}
const NO_CHORDS: ReadonlyArray<readonly [number, number]> = []
/**
* A black line along or across the fibre — a gap's dashes, a loop's chord — as
* a share of the tube's own radius.
*
* Half. These lines are *about* the model rather than part of it, and one as
* thick as the fibre it crosses reads as a piece of fibre; at half it reads as
* a line drawn over one, which is what it is.
*/
const INK_SHARE = 0.5
/** A flat material of the page's ink, for every line the model carries. */
/** `0, 1, … n − 1`, for a helper that wants an iterable of every bead. */
function* counting(n: number): Generator<number, void, void> {
for (let i = 0; i < n; i++) yield i
}
function inkMaterial(ink: string, opacity: number): MeshBasicMaterial {
return opacity >= 1
? new MeshBasicMaterial({ color: hexOf(ink) })
: new MeshBasicMaterial({ color: hexOf(ink), transparent: true, opacity })
}
/**
* One instanced mesh of cylinders, one per segment, each turned from the y
* axis onto its two ends. Never culled: a segment placed after the sphere
* was computed was culled as out of view and never drawn.
*/
function cylinders(
segments: ReadonlyArray<readonly [Vector3, Vector3]>,
radius: number,
material: MeshBasicMaterial,
): InstancedMesh {
const mesh = new InstancedMesh(new CylinderGeometry(1, 1, 1, 8, 1, true), material, Math.max(1, segments.length))
mesh.count = segments.length
const matrix = new Matrix4()
const q = new Quaternion()
const up = new Vector3(0, 1, 0)
segments.forEach(([from, to], at) => {
const dir = to.clone().sub(from)
const length = dir.length()
q.setFromUnitVectors(up, length > 0 ? dir.normalize() : up)
matrix.compose(from.clone().add(to).multiplyScalar(0.5), q, new Vector3(radius, Math.max(length, 1e-6), radius))
mesh.setMatrixAt(at, matrix)
})
mesh.instanceMatrix.needsUpdate = true
mesh.frustumCulled = false
return mesh
}
/** Cumulative polyline length at each point, from zero. */
function cumulative(points: Vector3[]): number[] {
const out = [0]
for (let k = 1; k < points.length; k++) out.push(out[k - 1] + points[k].distanceTo(points[k - 1]))
return out
}
/** What the geometry depends on, so a change elsewhere leaves it alone. */
function buildKey(view: StructureView): string {
const { structure, style } = view
let litKey = ''
if (view.lit !== null && style.others === 'hide') {
// Under `hide` the lit mask changes which beads exist, so it is part of
// the key; under `ghost` and `show` it is a colour and is not.
let hash = 0
for (let i = 0; i < view.lit.length; i++) hash = (hash * 31 + view.lit[i]) | 0
litKey = String(hash)
}
return [
structure.set.length,
structure.placed,
style.beads,
style.sticks,
style.tube,
style.beadRadius,
style.tubeRadius,
view.haplotype,
style.others,
litKey,
].join('|')
}
|