chrono-phylo-tree
Version:
A React-based phylogenetic tree visualization library
1,118 lines (1,117 loc) • 51.2 kB
JavaScript
var Mt = Object.defineProperty;
var Lt = (r, n, o) => n in r ? Mt(r, n, { enumerable: !0, configurable: !0, writable: !0, value: o }) : r[n] = o;
var ct = (r, n, o) => Lt(r, typeof n != "symbol" ? n + "" : n, o);
import { jsxs as X, Fragment as wt, jsx as y } from "react/jsx-runtime";
import { useState as P, useEffect as Et } from "react";
const Tt = (r, ...n) => r.sort(
(o, a) => {
for (const d of n) {
const [c, l] = [o, a].map((_) => d(_));
if (c !== l) return c - l;
}
return 0;
}
);
class gt {
constructor({
id: n,
name: o = "",
apparition: a = 0,
duration: d = 0,
ancestor: c,
descendants: l = [],
description: _,
image: m
}) {
ct(this, "id");
ct(this, "name", "");
ct(this, "apparition", 0);
ct(this, "duration", 0);
ct(this, "ancestor");
ct(this, "descendants", []);
ct(this, "description");
ct(this, "display", !0);
ct(this, "image");
if (d <= 0)
throw new Error("The duration of the species must be greater than 0");
this.id = n, this.name = o, this.apparition = a, this.duration = d, this.ancestor = c, this.descendants = l, this.description = _ === "" ? void 0 : _, this.image = m === "" ? void 0 : m;
}
onPosition(n = !0) {
return n && this.firstAncestor().stepsUntil(this) % 2 === 0;
}
copy() {
const n = this.firstAncestor(), o = n.allDescendants(!1).indexOf(this);
return gt.fromJSON(n.toJSON()).allDescendants(!1)[o];
}
unlinkAncestor() {
if (!this.ancestor)
return;
this.ancestor.descendants = this.ancestor.descendants.filter((o) => o !== this);
const n = this.ancestor;
return this.ancestor = void 0, [n.firstAncestor(), this];
}
unlinkDescendant(n) {
if (this.descendants.includes(n))
return this.descendants = this.descendants.filter((o) => o !== n), n.ancestor = void 0, [this.firstAncestor(), n];
}
linkAncestor(n) {
if (!(this.ancestor === n && n.descendants.includes(this))) {
if (n.apparition > this.apparition)
throw new Error(`The ancestor's apparition (${n.apparition}) must be before or equal the descendant's apparition (${this.apparition})`);
if (n.extinction() < this.apparition)
throw new Error(`The ancestor's extinction (${n.extinction()}) must be after or equal the descendant's apparition (${this.apparition})`);
this.ancestor !== n && this.unlinkAncestor(), this.ancestor = n, n.descendants.push(this);
}
}
linkDescendant(n) {
if (!(n.ancestor === this && this.descendants.includes(n))) {
if (n.apparition < this.apparition)
throw new Error(`The descendant's apparition (${n.apparition}) must be after or equal the ancestor's apparition (${this.apparition})`);
if (n.extinction() > this.extinction())
throw new Error(`The descendant's extinction (${n.extinction()}) must be before or equal the ancestor's extinction (${this.extinction()})`);
this.descendants.includes(n) || (n.ancestor && n.unlinkAncestor(), this.descendants.push(n), n.ancestor = this);
}
}
linkDescendants(n) {
for (const o of n)
try {
this.linkDescendant(o);
} catch (a) {
console.error(`Error linking descendant ${o.name} to ancestor ${this.name}:`, a);
}
}
addDescendant({
id: n,
name: o = "",
afterApparition: a = 0,
duration: d = 0,
description: c,
image: l,
copy: _ = !1
}) {
if (a < 0 || a > this.duration)
throw new Error(`The apparition of the descendant must be between the apparition (${this.apparition}) and the extinction (${this.extinction()}) of the ancestor`);
const m = _ ? this.copy() : this, s = new gt({
id: n,
name: o,
apparition: m.apparition + Math.max(a, 0),
duration: Math.max(d, 0),
description: c,
image: l
});
return s.linkAncestor(m), _ ? m : s;
}
removeDescendant(n) {
this.descendants = this.descendants.filter((o) => o !== n);
}
addAncestor({
id: n,
name: o = "",
previousApparition: a = 0,
duration: d = 0,
description: c,
image: l,
display: _ = !0,
copy: m = !1
}) {
if (a < 0)
throw new Error(`The apparition of the ancestor must be before or equal the apparition (${this.apparition}) of the descendant`);
if (d < a)
throw new Error(`The extiction of the ancestor must be after or equal the apparition (${this.apparition}) of the descendant`);
const s = m ? this.copy() : this, p = new gt({
id: n,
name: o,
apparition: s.apparition - Math.max(a, 0),
duration: d,
description: c,
image: l
});
return p.display = _, s.linkAncestor(p), m ? s : p;
}
extinction() {
return this.apparition + this.duration;
}
absoluteExtinction() {
return this.descendants.length > 0 ? Math.max(...this.allDescendants(!1).map((n) => n.extinction())) : this.extinction();
}
absoluteDuration() {
return this.absoluteExtinction() - this.apparition;
}
firstAncestor(n = !1) {
return this.ancestor ? this.ancestor.display || n ? this.ancestor.firstAncestor() : this : this;
}
cousinsExtinction() {
return this.firstAncestor().absoluteExtinction();
}
allDescendants(n = !0) {
const o = n ? Tt(this.descendants, (s) => -s.apparition, (s) => -s.absoluteExtinction()) : this.descendants;
if (o.length === 0)
return [this];
const a = o.filter((s) => s.apparition >= this.extinction()), d = o.filter((s) => a.indexOf(s) === -1), l = (this.onPosition(n) ? Math.ceil : Math.floor)(a.length / 2), _ = a.slice(0, l), m = a.slice(l);
return _.flatMap((s) => s.allDescendants(n)).concat([this]).concat(m.flatMap((s) => s.allDescendants(n))).concat(d.flatMap((s) => s.allDescendants(n)));
}
stepsChain(n, o = !1) {
var a;
return this.allDescendants(!1).includes(n) ? [this].concat(((a = this.descendants.find((d) => d.allDescendants(!1).includes(n))) == null ? void 0 : a.stepsChain(n)) ?? []).filter((d) => d.display || o) : [];
}
stepsUntil(n, o = !1) {
if (this.allDescendants(!1).includes(n))
return this.stepsChain(n, o).length - 1;
}
stepsUntilLastDescendant(n = !1) {
return this.descendants.length === 0 ? 0 : Math.max(...this.allDescendants(!1).filter((o) => o.descendants.length === 0).map((o) => this.stepsUntil(o, n) ?? 0));
}
toJSON() {
return {
name: this.name,
apparition: this.ancestor ? void 0 : this.apparition,
afterApparition: this.ancestor ? this.apparition - this.ancestor.apparition : void 0,
description: this.description,
duration: this.duration,
descendants: this.descendants.length > 0 ? this.descendants.map((n) => n.toJSON()) : void 0,
image: this.image
};
}
async saveJSON(n) {
try {
const o = JSON.stringify(this.toJSON(), null, 2), a = new Blob([o], { type: "application/json" }), d = URL.createObjectURL(a), c = document.createElement("a");
c.href = d, c.download = n ?? `${this.name}.json`, c.click(), URL.revokeObjectURL(d);
} catch (o) {
console.error("Error saving file:", o);
}
}
static fromJSON({
id: n,
name: o,
duration: a,
description: d,
image: c,
descendants: l,
..._
}, m) {
const s = _.afterApparition ?? 0, p = m ? m.apparition : _.apparition ?? 0, w = new gt({
id: n,
name: o,
apparition: p + s,
duration: a,
ancestor: m,
description: d,
image: c
});
if (l)
for (const A of l)
w.descendants.push(gt.fromJSON(A, w));
return w;
}
}
const Xt = ({
speciesList: r,
width: n = 1e3,
height: o = 50,
padding: a = 0,
stroke: d = "grey",
format: c = (w) => w.toString(),
chronoScale: l = !0,
showImages: _ = !0,
presentTime: m,
handleMouseMove: s,
children: p
}) => {
const w = r.map((F) => F.copy()), A = Math.min(...w.map((F) => F.apparition)), L = Math.max(...w.map((F) => F.apparition - A)), C = new gt({
name: "",
apparition: A,
duration: L
});
return C.display = !1, C.linkDescendants(w), /* @__PURE__ */ y(
It,
{
commonAncestor: C,
width: n,
height: o,
padding: a,
stroke: d,
format: c,
chronoScale: l,
showImages: _,
presentTime: m,
handleMouseMove: s,
children: (F, T, B, V) => p == null ? void 0 : p(F, T, B, V)
}
);
}, It = ({
commonAncestor: r,
width: n = 1e3,
height: o = 50,
padding: a = 0,
stroke: d = "grey",
format: c = (w) => w.toString(),
chronoScale: l = !0,
showImages: _ = !0,
presentTime: m,
handleMouseMove: s,
children: p
}) => {
const [w, A] = P(!1), [L, C] = P(void 0), [F, T] = P(void 0), [B, V] = P(r.allDescendants().reduce((t, e) => t.set(e, !0), /* @__PURE__ */ new Map()));
Et(() => {
V(r.allDescendants().reduce((t, e) => t.set(e, !0), /* @__PURE__ */ new Map()));
}, [r]);
const Z = (t) => {
C(w ? void 0 : t), A(!w);
}, rt = (t) => {
const e = new Map(B);
e.set(t, !B.get(t)), V(e);
}, et = (t) => {
T(t);
}, K = m !== void 0 && l, g = (t) => _ ? t.map((e) => e.image ? 2 : 1).reduce((e, i) => e + i) : t.length;
return /* @__PURE__ */ X(wt, { children: [
/* @__PURE__ */ y(
"svg",
{
width: n * (K ? (Math.min(m, r.absoluteExtinction()) - r.apparition) / r.absoluteDuration() : 1),
height: o * g(K ? r.allDescendants().filter((t) => t.apparition < m) : r.allDescendants()),
onMouseMove: (t) => {
s == null || s(t.clientX, t.clientY);
},
children: /* @__PURE__ */ y(
At,
{
commonAncestor: r,
species: r,
y: -1,
scaleX: n / (l ? r.absoluteDuration() : Math.max(0, r.stepsUntilLastDescendant()) + 1),
scaleY: o,
padding: a,
stroke: d,
format: c,
chronoScale: l,
showImages: _,
presentTime: m,
toggleShowMenu: Z,
hoverShowMenu: et,
showDesc: B,
changeShowDesc: rt
}
)
}
),
p == null ? void 0 : p(L, w, Z, F)
] });
}, At = ({
commonAncestor: r,
species: n,
y: o,
scaleX: a,
scaleY: d,
padding: c = 0,
stroke: l = "grey",
format: _ = (F) => F.toString(),
chronoScale: m = !0,
showImages: s = !0,
presentTime: p = void 0,
toggleShowMenu: w,
hoverShowMenu: A,
showDesc: L,
changeShowDesc: C
}) => {
const F = p !== void 0 && m, T = r.allDescendants().filter((g) => F ? g.apparition < p : !0), B = T.indexOf(n), V = (m ? n.apparition - r.apparition : r.stepsUntil(n) ?? 0) * a, Z = V + (m ? Math.min(L.get(n) ? n.duration : n.absoluteDuration(), F ? p - n.apparition : n.absoluteDuration()) : 1) * a, rt = s && B > 0 ? [...Array(B).keys()].map((g) => T[g]).map((g) => (g.image ? 2 : 1) * d).reduce((g, t) => g + t) : B * d, et = n.descendants.filter((g) => F ? g.apparition < p : !0), K = et.length > 0 ? V + (Math.min(...et.map((g) => g.apparition)) - n.apparition) * a : Z;
return /* @__PURE__ */ X("g", { children: [
o >= 0 && /* @__PURE__ */ y(
"line",
{
x1: V,
y1: o,
x2: V,
y2: rt,
stroke: l
}
),
n.display && /* @__PURE__ */ y(
jt,
{
commonAncestor: r,
species: n,
height: d,
x1: V,
x2: Z,
x0: K,
y: rt,
stroke: l,
changeShowDesc: () => C(n),
showDesc: L.get(n),
padding: c,
format: _,
chronoScale: m,
showImages: s,
presentTime: p,
toggleShowMenu: w,
hoverShowMenu: A
}
),
n.descendants.map((g, t) => /* @__PURE__ */ y("g", { className: L.get(n) && et.includes(g) ? "block" : "hidden", children: /* @__PURE__ */ y(
At,
{
commonAncestor: r,
species: g,
y: g.display ? rt : -1,
scaleX: a,
scaleY: d,
padding: c,
stroke: l,
format: _,
chronoScale: m,
showImages: s,
presentTime: p,
toggleShowMenu: w,
showDesc: L,
changeShowDesc: C,
hoverShowMenu: A
}
) }, T.length + t))
] }, B);
}, jt = ({
commonAncestor: r,
species: n,
height: o,
x1: a,
x2: d,
x0: c,
y: l,
stroke: _,
showDesc: m = !0,
changeShowDesc: s = () => {
},
padding: p = 0,
format: w = (Z) => Z.toString(),
chronoScale: A = !0,
showImages: L = !0,
presentTime: C,
toggleShowMenu: F,
hoverShowMenu: T,
className: B,
buttonClassName: V
}) => {
const Z = C !== void 0, rt = r.allDescendants().filter((i) => Z ? i.apparition < C : !0), et = (i) => rt.indexOf(i), K = n.ancestor && et(n) > et(n.ancestor) ? -3 : 1, g = n.descendants.filter((i) => Z ? i.apparition < C : !0), t = g.filter((i) => i.apparition === n.extinction()).length === 0, e = w(Math.min(m ? n.extinction() : n.absoluteExtinction(), Z ? C : n.absoluteExtinction()));
return /* @__PURE__ */ X("g", { children: [
/* @__PURE__ */ y(
"line",
{
x1: a,
y1: l,
x2: d,
y2: l,
stroke: _
}
),
/* @__PURE__ */ y(
"foreignObject",
{
x: a + p,
y: l + p * K,
width: (A ? c ?? d : d) - a - 2 * p,
height: o + (L && n.image ? o : 0),
children: /* @__PURE__ */ X("div", { className: `flex flex-row justify-between w-full ${B ?? ""}`, children: [
/* @__PURE__ */ y("div", { children: A ? w(n.apparition) : "" }),
/* @__PURE__ */ X(
"button",
{
className: `p-0.625 justify-center flex flex-col items-center ${V ?? ""}`,
onClick: () => F(n),
onMouseEnter: () => T(n),
onMouseLeave: () => T(void 0),
children: [
n.name,
n.image && L && /* @__PURE__ */ y(
"img",
{
src: n.image,
alt: n.name,
style: { height: o }
}
)
]
}
),
g.length > 0 ? /* @__PURE__ */ y("button", { onClick: s, className: "h-1", style: { maxWidth: 4 }, children: (t || !m) && (!c || c === d) ? e : "" }) : /* @__PURE__ */ y("div", { children: A ? e : "" })
] })
}
),
A && c && c < d && /* @__PURE__ */ y(
"foreignObject",
{
x: c + p,
y: l + p * K,
width: d - c - 2 * p,
height: o,
children: /* @__PURE__ */ y("div", { className: "flex flex-row justify-end w-full", children: (t || !m) && A ? e : "" })
}
)
] });
}, Ft = (r, n, o) => r < n ? n : r > o ? o : r;
function Nt(r) {
return r && r.__esModule && Object.prototype.hasOwnProperty.call(r, "default") ? r.default : r;
}
var vt = { exports: {} };
/* @license
Papa Parse
v5.5.2
https://github.com/mholt/PapaParse
License: MIT
*/
var Pt = vt.exports, St;
function Ut() {
return St || (St = 1, function(r, n) {
((o, a) => {
r.exports = a();
})(Pt, function o() {
var a = typeof self < "u" ? self : typeof window < "u" ? window : a !== void 0 ? a : {}, d, c = !a.document && !!a.postMessage, l = a.IS_PAPA_WORKER || !1, _ = {}, m = 0, s = {};
function p(t) {
this._handle = null, this._finished = !1, this._completed = !1, this._halted = !1, this._input = null, this._baseIndex = 0, this._partialLine = "", this._rowCount = 0, this._start = 0, this._nextChunk = null, this.isFirstChunk = !0, this._completeResults = { data: [], errors: [], meta: {} }, (function(e) {
var i = et(e);
i.chunkSize = parseInt(i.chunkSize), e.step || e.chunk || (i.chunkSize = null), this._handle = new F(i), (this._handle.streamer = this)._config = i;
}).call(this, t), this.parseChunk = function(e, i) {
var h = parseInt(this._config.skipFirstNLines) || 0;
if (this.isFirstChunk && 0 < h) {
let E = this._config.newline;
E || (u = this._config.quoteChar || '"', E = this._handle.guessLineEndings(e, u)), e = [...e.split(E).slice(h)].join(E);
}
this.isFirstChunk && g(this._config.beforeFirstChunk) && (u = this._config.beforeFirstChunk(e)) !== void 0 && (e = u), this.isFirstChunk = !1, this._halted = !1;
var h = this._partialLine + e, u = (this._partialLine = "", this._handle.parse(h, this._baseIndex, !this._finished));
if (!this._handle.paused() && !this._handle.aborted()) {
if (e = u.meta.cursor, h = (this._finished || (this._partialLine = h.substring(e - this._baseIndex), this._baseIndex = e), u && u.data && (this._rowCount += u.data.length), this._finished || this._config.preview && this._rowCount >= this._config.preview), l) a.postMessage({ results: u, workerId: s.WORKER_ID, finished: h });
else if (g(this._config.chunk) && !i) {
if (this._config.chunk(u, this._handle), this._handle.paused() || this._handle.aborted()) return void (this._halted = !0);
this._completeResults = u = void 0;
}
return this._config.step || this._config.chunk || (this._completeResults.data = this._completeResults.data.concat(u.data), this._completeResults.errors = this._completeResults.errors.concat(u.errors), this._completeResults.meta = u.meta), this._completed || !h || !g(this._config.complete) || u && u.meta.aborted || (this._config.complete(this._completeResults, this._input), this._completed = !0), h || u && u.meta.paused || this._nextChunk(), u;
}
this._halted = !0;
}, this._sendError = function(e) {
g(this._config.error) ? this._config.error(e) : l && this._config.error && a.postMessage({ workerId: s.WORKER_ID, error: e, finished: !1 });
};
}
function w(t) {
var e;
(t = t || {}).chunkSize || (t.chunkSize = s.RemoteChunkSize), p.call(this, t), this._nextChunk = c ? function() {
this._readChunk(), this._chunkLoaded();
} : function() {
this._readChunk();
}, this.stream = function(i) {
this._input = i, this._nextChunk();
}, this._readChunk = function() {
if (this._finished) this._chunkLoaded();
else {
if (e = new XMLHttpRequest(), this._config.withCredentials && (e.withCredentials = this._config.withCredentials), c || (e.onload = K(this._chunkLoaded, this), e.onerror = K(this._chunkError, this)), e.open(this._config.downloadRequestBody ? "POST" : "GET", this._input, !c), this._config.downloadRequestHeaders) {
var i, h = this._config.downloadRequestHeaders;
for (i in h) e.setRequestHeader(i, h[i]);
}
var u;
this._config.chunkSize && (u = this._start + this._config.chunkSize - 1, e.setRequestHeader("Range", "bytes=" + this._start + "-" + u));
try {
e.send(this._config.downloadRequestBody);
} catch (E) {
this._chunkError(E.message);
}
c && e.status === 0 && this._chunkError();
}
}, this._chunkLoaded = function() {
e.readyState === 4 && (e.status < 200 || 400 <= e.status ? this._chunkError() : (this._start += this._config.chunkSize || e.responseText.length, this._finished = !this._config.chunkSize || this._start >= ((i) => (i = i.getResponseHeader("Content-Range")) !== null ? parseInt(i.substring(i.lastIndexOf("/") + 1)) : -1)(e), this.parseChunk(e.responseText)));
}, this._chunkError = function(i) {
i = e.statusText || i, this._sendError(new Error(i));
};
}
function A(t) {
(t = t || {}).chunkSize || (t.chunkSize = s.LocalChunkSize), p.call(this, t);
var e, i, h = typeof FileReader < "u";
this.stream = function(u) {
this._input = u, i = u.slice || u.webkitSlice || u.mozSlice, h ? ((e = new FileReader()).onload = K(this._chunkLoaded, this), e.onerror = K(this._chunkError, this)) : e = new FileReaderSync(), this._nextChunk();
}, this._nextChunk = function() {
this._finished || this._config.preview && !(this._rowCount < this._config.preview) || this._readChunk();
}, this._readChunk = function() {
var u = this._input, E = (this._config.chunkSize && (E = Math.min(this._start + this._config.chunkSize, this._input.size), u = i.call(u, this._start, E)), e.readAsText(u, this._config.encoding));
h || this._chunkLoaded({ target: { result: E } });
}, this._chunkLoaded = function(u) {
this._start += this._config.chunkSize, this._finished = !this._config.chunkSize || this._start >= this._input.size, this.parseChunk(u.target.result);
}, this._chunkError = function() {
this._sendError(e.error);
};
}
function L(t) {
var e;
p.call(this, t = t || {}), this.stream = function(i) {
return e = i, this._nextChunk();
}, this._nextChunk = function() {
var i, h;
if (!this._finished) return i = this._config.chunkSize, e = i ? (h = e.substring(0, i), e.substring(i)) : (h = e, ""), this._finished = !e, this.parseChunk(h);
};
}
function C(t) {
p.call(this, t = t || {});
var e = [], i = !0, h = !1;
this.pause = function() {
p.prototype.pause.apply(this, arguments), this._input.pause();
}, this.resume = function() {
p.prototype.resume.apply(this, arguments), this._input.resume();
}, this.stream = function(u) {
this._input = u, this._input.on("data", this._streamData), this._input.on("end", this._streamEnd), this._input.on("error", this._streamError);
}, this._checkIsFinished = function() {
h && e.length === 1 && (this._finished = !0);
}, this._nextChunk = function() {
this._checkIsFinished(), e.length ? this.parseChunk(e.shift()) : i = !0;
}, this._streamData = K(function(u) {
try {
e.push(typeof u == "string" ? u : u.toString(this._config.encoding)), i && (i = !1, this._checkIsFinished(), this.parseChunk(e.shift()));
} catch (E) {
this._streamError(E);
}
}, this), this._streamError = K(function(u) {
this._streamCleanUp(), this._sendError(u);
}, this), this._streamEnd = K(function() {
this._streamCleanUp(), h = !0, this._streamData("");
}, this), this._streamCleanUp = K(function() {
this._input.removeListener("data", this._streamData), this._input.removeListener("end", this._streamEnd), this._input.removeListener("error", this._streamError);
}, this);
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