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* A structure as a scene: the beads, the chains they string, and the bridge
* between a place on the genome and a bead in space (§25).
*
* Pure, and deliberately so. Everything a renderer, a painter, a panel and an
* analysis task want to know about a model that is a *number* lives here, with
* no DOM, no canvas and no three.js: which bead holds a locus, where a chain
* breaks, how far two beads are apart in the file's own units, where the
* centroid is. The three.js adapter and the vector painter are thin over this,
* so the picture on screen and the picture on paper cannot disagree about a
* coordinate, and every one of these answers is tested in node.
*
* ## The row is the source of truth
*
* A scene is built *from* a `FeatureSet` carrying a `model` (`annotations/g3d.ts`)
* and never copies its loci: the set's `contig`, `start` and `end` arrays are
* what every locus question is answered from, and the set is what the lane
* beside the map, the search box and the analysis tasks already read. What the
* scene adds is the geometry those arrays do not have — chains, gaps, a
* normalised copy of the coordinates — and an index from a locus to its beads.
*
* ## Two coordinate systems, one factor between them
*
* The file's coordinates are kept in the model as written, in whatever units
* the solver used. The scene holds a **normalised** copy — centroid at the
* origin, radius of gyration one — because that is the only frame in which a
* default camera, a bead radius and a fog distance mean the same thing for a
* model in nanometres and one in solver units. `scale` is the factor back, so a
* distance printed to the reader is in the units the file had; nothing here
* claims a nanometre (§25's refusal).
*
* ## Chains and gaps
*
* A chain is one contig of one haplotype, in genomic order. Two beads are
* neighbours on it when their starts are exactly one spacing apart; a wider
* jump is a **gap** — a bin the solver left out — and the tube breaks there
* rather than bridging it, because a line through the gap would be a path
* this app invented. A bead the file placed at `NaN` is *not present* and
* breaks its chain the same way.
*/
import { featureRange } from '../annotations/featureset'
import type { FeatureSet, StructureModel } from '../annotations/types'
/** One contig of one haplotype, as the beads string it. */
export interface Chain {
/** Index into {@link Structure.contigs}. */
contig: number
/** Index into the model's haplotype list. */
hap: number
/** The bead indices (rows of the set) in genomic order. */
beads: Int32Array
/**
* The runs of consecutive, present beads: `[from, to)` pairs into
* {@link beads}, flattened. A tube is drawn per run and never across the
* boundary between two.
*/
runs: Int32Array
}
export interface Structure {
/** The row's own set — every locus is read from here. */
readonly set: FeatureSet
readonly model: StructureModel
/** The set's contig names, in its order. */
readonly contigs: readonly string[]
readonly haplotypes: readonly string[]
/** The bead spacing, in base pairs. */
readonly width: number
readonly chains: readonly Chain[]
/** Bead index → index into {@link chains}. */
readonly chainOf: Int32Array
/** Bead index → its position along its chain, `0..beads.length-1`. */
readonly along: Int32Array
/** Normalised coordinates: centroid at the origin, radius of gyration one. */
readonly x: Float32Array
readonly y: Float32Array
readonly z: Float32Array
/** `1` where the file placed the bead, `0` where it is `NaN`. */
readonly present: Uint8Array
/** File units per normalised unit — the radius of gyration, in the file's units. */
readonly scale: number
/**
* The typical distance between neighbouring beads, normalised: the median
* over every run, floored at a fraction of the model's size. Bead and tube
* radii are fractions of this, so a radius setting reads the same on every
* model — and stays visible on a dense one.
*/
readonly step: number
/** How many beads the file placed. */
readonly placed: number
}
/** A bead's locus, for a readout or an echo back onto the map. */
export interface BeadLocus {
contig: string
start: number
end: number
haplotype: string
/** Index into the model's haplotype list. */
hap: number
}
/**
* Build the scene for a set, or `null` for a set that carries no model.
*
* One pass over the set for the chains, one for the centroid, one for the
* radius of gyration and one to normalise — four passes over a few thousand
* beads, once per row, which is nothing beside the sort the parser already did.
*/
export function buildStructure(set: FeatureSet): Structure | null {
const model = set.model
if (model === undefined) return null
const n = set.length
const present = new Uint8Array(n)
let placed = 0
for (let i = 0; i < n; i++) {
if (Number.isFinite(model.x[i]) && Number.isFinite(model.y[i]) && Number.isFinite(model.z[i])) {
present[i] = 1
placed++
}
}
// The centroid and the radius of gyration over the placed beads only: a bead
// the file did not place has no say in where the model is.
let cx = 0
let cy = 0
let cz = 0
for (let i = 0; i < n; i++) {
if (present[i] === 0) continue
cx += model.x[i]
cy += model.y[i]
cz += model.z[i]
}
if (placed > 0) {
cx /= placed
cy /= placed
cz /= placed
}
let sum = 0
for (let i = 0; i < n; i++) {
if (present[i] === 0) continue
const dx = model.x[i] - cx
const dy = model.y[i] - cy
const dz = model.z[i] - cz
sum += dx * dx + dy * dy + dz * dz
}
// A model of one bead, or of beads all at one point, has no size to
// normalise by; one file unit per normalised unit keeps the arithmetic
// finite and the picture a dot, which is what such a file is.
const gyration = placed > 0 ? Math.sqrt(sum / placed) : 0
const scale = gyration > 0 ? gyration : 1
const x = new Float32Array(n)
const y = new Float32Array(n)
const z = new Float32Array(n)
for (let i = 0; i < n; i++) {
if (present[i] === 0) {
x[i] = Number.NaN
y[i] = Number.NaN
z[i] = Number.NaN
continue
}
x[i] = (model.x[i] - cx) / scale
y[i] = (model.y[i] - cy) / scale
z[i] = (model.z[i] - cz) / scale
}
const chains = chainsOf(set, model, present)
const chainOf = new Int32Array(n).fill(-1)
const along = new Int32Array(n).fill(-1)
chains.forEach((chain, at) => {
for (let k = 0; k < chain.beads.length; k++) {
chainOf[chain.beads[k]] = at
along[chain.beads[k]] = k
}
})
return {
set,
model,
contigs: set.contigs,
haplotypes: model.haplotypes,
width: model.width,
chains,
chainOf,
along,
x,
y,
z,
present,
scale,
step: stepOf(chains, x, y, z),
placed,
}
}
/**
* The chains, one per `(contig, haplotype)` that has a bead, in contig order
* and then haplotype order.
*
* Read off the set's per-contig runs rather than by grouping every row: the
* sort has already put each contig's beads together and its two homologues at
* every locus side by side, so a chain is a filter over one run.
*/
function chainsOf(set: FeatureSet, model: StructureModel, present: Uint8Array): Chain[] {
const chains: Chain[] = []
for (let c = 0; c < set.contigs.length; c++) {
const from = set.contigAt[c]
const to = set.contigAt[c + 1]
if (to <= from) continue
for (let hap = 0; hap < model.haplotypes.length; hap++) {
const beads: number[] = []
for (let i = from; i < to; i++) if (model.hap[i] === hap) beads.push(i)
if (beads.length === 0) continue
const indices = Int32Array.from(beads)
chains.push({ contig: c, hap, beads: indices, runs: runsOf(set, model.width, indices, present) })
}
}
return chains
}
/**
* The runs of consecutive present beads along one chain, as `[from, to)`
* pairs into the chain's bead list.
*
* A run ends where the next bead is missing, or where it is more than one
* spacing on — the two ways a solver leaves a hole. A run of one bead is still
* a run: it draws as a bead and no tube.
*/
function runsOf(set: FeatureSet, width: number, beads: Int32Array, present: Uint8Array): Int32Array {
const runs: number[] = []
let from = -1
for (let k = 0; k < beads.length; k++) {
const bead = beads[k]
if (present[bead] === 0) {
if (from >= 0) runs.push(from, k)
from = -1
continue
}
if (from < 0) {
from = k
continue
}
const previous = beads[k - 1]
const adjacent = set.start[bead] - set.start[previous] <= width
if (!adjacent) {
runs.push(from, k)
from = k
}
}
if (from >= 0) runs.push(from, beads.length)
return Int32Array.from(runs)
}
/** The median distance between neighbouring beads, over every run. */
function stepOf(chains: readonly Chain[], x: Float32Array, y: Float32Array, z: Float32Array): number {
const steps: number[] = []
for (const chain of chains) {
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]
steps.push(Math.hypot(x[b] - x[a], y[b] - y[a], z[b] - z[a]))
}
}
}
if (steps.length === 0) return 1
steps.sort((a, b) => a - b)
const median = steps[steps.length >> 1]
// Floored at a fraction of the model's own size (the coordinates are
// normalised to a radius of gyration of 1): a genome of thousands of 5 kb
// beads steps a hundredth of its extent, and a tube that thin is a hairline
// on any screen. The floor is what keeps a bead a bead on a dense model,
// and it is below the step of any model a reader can tell beads apart on.
return Math.max(median > 0 ? median : 1, STEP_FLOOR)
}
/** The least a step is taken to be, in units of the radius of gyration. */
const STEP_FLOOR = 0.035
// ---------------------------------------------------------------------------
// The bridge: (contig, bp) ↔ bead
// ---------------------------------------------------------------------------
/**
* The beads holding `bp` on `contig` — one per haplotype, in haplotype order.
*
* Every homologue, because the map beside the model has one axis and one
* `chr7`, and a locus on it is a locus on both chains. Where no bead's interval
* holds the base — a gap the solver left, or a position past the last bead —
* the nearest bead of each haplotype is answered *if it is within one spacing*,
* and nothing otherwise: a bead lit for a locus it is not at would be the one
* claim a model beside a map must never make. The same refusal
* `PanelDeck.echoHover` makes off the end of a shorter block.
*
* A binary search over the contig's run, which the sort makes possible: rows
* are ordered by start, and every bead is one spacing wide, so the candidates
* are the beads whose start is the last one at or before `bp` and, for the
* nearest-bead rule, the one after it.
*/
export function beadsAt(structure: Structure, contig: string, bp: number): number[] {
const set = structure.set
const c = contigIndex(structure, contig)
if (c < 0 || !Number.isFinite(bp)) return []
const from = set.contigAt[c]
const to = set.contigAt[c + 1]
if (to <= from) return []
// Every bead starting before or at `bp`, and every bead starting after: the
// boundary between them is where the answer is, on both sides of it.
const first = lowerBound(set.start, from, to, Math.floor(bp) + 1) // first start > bp
const perHap = new Map<number, { bead: number; away: number }>()
const consider = (bead: number): void => {
const start = set.start[bead]
const end = set.end[bead]
const away = bp < start ? start - bp : bp >= end ? bp - end + 1 : 0
if (away > structure.width) return
const hap = structure.model.hap[bead]
const held = perHap.get(hap)
if (held === undefined || away < held.away) perHap.set(hap, { bead, away })
}
// The beads at the last start at or before `bp` (all haplotypes share it), and
// the beads at the first start after it.
for (let i = first - 1; i >= from && set.start[i] === set.start[first - 1]; i--) consider(i)
for (let i = first; i < to && set.start[i] === set.start[first]; i++) consider(i)
// Exact hits win over near misses on every haplotype: a homologue whose bead
// holds the base must not be answered with its neighbour because the other
// homologue has a gap there.
const exact = [...perHap.values()].some((held) => held.away === 0)
return [...perHap.entries()]
.filter(([, held]) => !exact || held.away === 0)
.sort((a, b) => a[0] - b[0])
.map(([, held]) => held.bead)
}
/**
* Every bead overlapping `[from, to)` on `contig`, in set order — both
* haplotypes interleaved, as the set holds them.
*
* The same backed-off binary search `featureRange` makes, with the back-off
* being one spacing since every bead is that wide.
*/
export function beadsIn(structure: Structure, contig: string, from: number, to: number): number[] {
const set = structure.set
const c = contigIndex(structure, contig)
if (c < 0) return []
const [lo, hi] = featureRange(set, c, from, to)
const out: number[] = []
for (let i = lo; i < hi; i++) {
if (set.end[i] > from && set.start[i] < to) out.push(i)
}
return out
}
/** Where a bead is on the genome, and on which homologue. */
export function lociOf(structure: Structure, bead: number): BeadLocus {
const set = structure.set
const hap = structure.model.hap[bead]
return {
contig: set.contigs[set.contig[bead]],
start: set.start[bead],
end: set.end[bead],
haplotype: structure.haplotypes[hap] ?? '',
hap,
}
}
/**
* The distance between two beads **in the file's own units**, or `NaN` where
* either is not placed.
*/
export function distanceBetween(structure: Structure, a: number, b: number): number {
if (structure.present[a] === 0 || structure.present[b] === 0) return Number.NaN
return (
Math.hypot(
structure.x[b] - structure.x[a],
structure.y[b] - structure.y[a],
structure.z[b] - structure.z[a],
) * structure.scale
)
}
/** Every bead of a contig, both haplotypes, in set order; `[]` for a name the model lacks. */
export function beadsOf(structure: Structure, contig: string): number[] {
const c = contigIndex(structure, contig)
if (c < 0) return []
const out: number[] = []
for (let i = structure.set.contigAt[c]; i < structure.set.contigAt[c + 1]; i++) out.push(i)
return out
}
/** The contig names the model has, in the set's order. */
export function contigsOf(structure: Structure): string[] {
return [...structure.contigs]
}
function contigIndex(structure: Structure, contig: string): number {
return structure.contigs.indexOf(contig)
}
/** First index in `[from, to)` whose value is `>= target`, else `to`. */
function lowerBound(values: Int32Array, from: number, to: number, target: number): number {
let low = from
let high = to
while (low < high) {
const mid = (low + high) >> 1
if (values[mid] >= target) high = mid
else low = mid + 1
}
return low
}
/**
* The centroid of a set of beads, normalised, for framing a camera on them.
*
* `null` where none of them is placed.
*/
export function centroidOf(
structure: Structure,
beads: Iterable<number>,
): { x: number; y: number; z: number; radius: number } | null {
let count = 0
let cx = 0
let cy = 0
let cz = 0
const held: number[] = []
for (const bead of beads) {
if (structure.present[bead] === 0) continue
held.push(bead)
cx += structure.x[bead]
cy += structure.y[bead]
cz += structure.z[bead]
count++
}
if (count === 0) return null
cx /= count
cy /= count
cz /= count
let radius = 0
for (const bead of held) {
const d = Math.hypot(structure.x[bead] - cx, structure.y[bead] - cy, structure.z[bead] - cz)
if (d > radius) radius = d
}
return { x: cx, y: cy, z: cz, radius }
}
/**
* The beads that sit at a **telomere**: the two ends of every chain.
*
* Both ends, every chain, with nothing asked of the session. An earlier rule
* asked — the start only from a first bead at base zero, the far end only
* against a length the file itself declared, and neither for a sequence ticked
* circular — on the argument that the end of a *chain* is not the end of a
* *chromosome*. It is a true argument and it made the mark useless: on a whole
* yeast genome it painted five beads out of the thirty-two a reader was
* looking for, because a model's own lengths are a lower bound and a lower
* bound cannot establish an end. The mark is a **chain end**, drawn wherever a
* chain ends, and that is what it now claims.
*
* Beads the file left unplaced are skipped, so a chain that begins with a gap
* is measured from the first bead that is actually somewhere. A chain of one
* bead gets one mark rather than two: it is one place, and drawing it twice
* would say there were two.
*/
export function telomereBeads(structure: Structure): number[] {
const out: number[] = []
for (const chain of structure.chains) {
let first = -1
let last = -1
for (const bead of chain.beads) {
if (structure.present[bead] !== 1) continue
if (first < 0) first = bead
last = bead
}
if (first < 0) continue
out.push(first)
if (last !== first) out.push(last)
}
return out
}
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