@euphrasiologist/lwphylo 1.1.14 → 1.1.15

package/dist/index.js

@@ -1,2 +1,2 @@
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e={};n.data.forEach(n=>{e[n.thisId]={...n}});let r={};const i=function(n){e[n]&&(r[n]=e[n],e[n].children&&e[n].children.forEach(n=>{i(n)}))};i(t);const s=[["data",Object.values(r)]],c=s[0][1].map(n=>n.thisId);var a=[];for(const t in n)"data"!==t&&a.push([t,n[t]]);var o=a.map(n=>[n[0],n[1].filter(n=>c.includes(n.thisId))]);return Object.fromEntries(s.concat(o))}export{e as describeArc,d as parentFisheye,n as phisheye,c as radialLayout,u as readTree,o as rectangleLayout,f as subTree,h as unrooted};
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n(t){if(!t.children||0===t.children.length)return t.ntips=1,1;let e=0;for(const r of t.children)e+=n(r);return t.ntips=e,e}(n),n.start=0,n.end=2,n.angle=0,n.ntips=function(n){var t=0;for(const e of function(n){const t=[n],e=[];for(;t.length;){const n=t.shift();e.push(n);for(const e of n.children)t.push(e)}return e}(n))0==e.children.length&&t++;return t}(n),n.x=0,n.y=0);let t=n.start;for(let e=0;e<n.children.length;e++){const r=n.children[e],i=(n.end-n.start)*(r.ntips/n.ntips);r.start=t,r.end=t+i,r.angle=r.start+(r.end-r.start)/2,t=r.end;const s=r.angle*Math.PI,c=r.branchLength??0;r.x=n.x+c*Math.sin(s),r.y=n.y+c*Math.cos(s),l(r)}return n}function h(n){var t={},e=i(l(n));return t.data=e,t.edges=function(n,t=!1){const e=[...n].sort((n,t)=>n.thisId-t.thisId),r=new Map(e.map(n=>[n.thisId,n])),i=[];for(const n of e){if(null==n.parentId)continue;const e=r.get(n.parentId);e&&(t?(i.push({x1:n.x,y1:n.y,id1:n.thisId,x2:e.x,y2:n.y,id2:void 0}),i.push({x1:e.x,y1:n.y,id1:void 0,x2:e.x,y2:e.y,id2:n.parentId})):i.push({x1:n.x,y1:n.y,id1:n.thisId,x2:e.x,y2:e.y,id2:n.parentId}))}return i}(e),t}function d(n,t){const e=function(n,t="thisId"){return new Map(n.map(n=>[n[t],n]))}(t),r=e.get(n.parentId);return r?{px:r.fisheye.x,py:r.fisheye.y}:null}function u(n){const t=(n=String(n).replace(/\s+/g,"")).split(/(;|\(|\)|,)/),e={parent:null,children:[]};let r=e,i=0;for(const n of t)if(n&&";"!==n)if("("===n){const n={parent:r,children:[]};r.children.push(n),r=n}else if(","===n){r=r.parent;const n={parent:r,children:[]};r.children.push(n),r=n}else if(")"===n){if(r=r.parent,null===r)break}else{const t=n.split(":");1===t.length?n.startsWith(":")?(r.label="",r.branchLength=parseFloat(t[0])):(r.label=t[0],r.branchLength=null):2===t.length?(r.label=t[0],r.branchLength=parseFloat(t[1])):(console.warn(n,"Unhandled token with multiple ':' characters"),r.label=t[0]||"",r.branchLength=parseFloat(t[t.length-1])),r.id=i++}return null==e.id&&(e.id=i),e}function f(n,t){let e={};n.data.forEach(n=>{e[n.thisId]={...n}});let r={};const i=function(n){e[n]&&(r[n]=e[n],e[n].children&&e[n].children.forEach(n=>{i(n)}))};i(t);const s=[["data",Object.values(r)]],c=s[0][1].map(n=>n.thisId);var a=[];for(const t in n)"data"!==t&&a.push([t,n[t]]);var o=a.map(n=>[n[0],n[1].filter(n=>c.includes(n.thisId))]);return Object.fromEntries(s.concat(o))}export{e as describeArc,d as parentFisheye,n as phisheye,c as radialLayout,u as readTree,o as rectangleLayout,f as subTree,h as unrooted};
 //# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@euphrasiologist/lwphylo",
-  "version": "1.1.14",
+  "version": "1.1.15",
   "description": "A lightweight, low level javascript library to plot phylogenies from Newick files.",
   "main": "dist/@euphrasiologist/lwphylo.js",
   "unpkg": "dist/@euphrasiologist/lwphylo.min.js",

package/src/radial/describeArc.js

@@ -1,25 +1,37 @@
-import polarToCartesian from "./polarToCartesian.js"
+import polarToCartesian from "./polarToCartesian.js";
 
+/**
+ * Draw the shortest arc between startAngle and endAngle (radians), CCW.
+ * If the CW path is shorter, swap start/end so the CCW path is still shortest.
+ * Works with Y-inverted screen coords (polarToCartesian already inverts Y).
+ */
 export default function describeArc(cx, cy, radius, startAngle, endAngle) {
   const TAU = Math.PI * 2;
   const norm = (t) => ((t % TAU) + TAU) % TAU;
-
   let a0 = norm(startAngle);
   let a1 = norm(endAngle);
 
-  // delta in the *clockwise* direction (increasing angle after Y inversion)
-  let delta = a1 - a0;
-  if (delta < 0) delta += TAU;
+  // CCW and CW spans
+  const ccw = (a1 - a0 + TAU) % TAU;
+  const cw = (a0 - a1 + TAU) % TAU;
+
+  // Ensure we always take the shorter span *in CCW* by swapping if needed
+  if (cw < ccw) {
+    const tmp = a0; a0 = a1; a1 = tmp;
+  }
+
+  const delta = (a1 - a0 + TAU) % TAU;          // now the shorter CCW span
+  if (delta < 1e-9) {
+    const p = polarToCartesian(cx, cy, radius, a0);
+    return `M ${p.x} ${p.y}`;                   // degenerate span → no arc
+  }
 
-  const largeArcFlag = delta > Math.PI ? 1 : 0;
-  const sweepFlag = 1; // CLOCKWISE sweep to match getArcs' start→end
+  const largeArcFlag = delta > Math.PI ? 1 : 0; // should be 0 for “shortest”, but keep for safety
+  const sweepFlag = 0;                          // CCW
 
-  const start = polarToCartesian(cx, cy, radius, a0);
-  const end   = polarToCartesian(cx, cy, radius, a1);
+  const p0 = polarToCartesian(cx, cy, radius, a0);
+  const p1 = polarToCartesian(cx, cy, radius, a1);
 
-  return [
-    "M", start.x, start.y,
-    "A", radius, radius, 0, largeArcFlag, sweepFlag, end.x, end.y
-  ].join(" ");
+  return `M ${p0.x} ${p0.y} A ${radius} ${radius} 0 ${largeArcFlag} ${sweepFlag} ${p1.x} ${p1.y}`;
 }
 

package/src/radial/polarToCartesian.js

@@ -1,37 +1,4 @@
-import polarToCartesian from "./polarToCartesian.js";
-
-/**
- * Draw the shortest arc between startAngle and endAngle on a circle.
- * - Angles are radians.
- * - Works with Y-inverted screen coords (our polarToCartesian already inverts Y).
- * - Automatically picks CW or CCW sweep to follow the *shorter* path.
- */
-export default function describeArc(cx, cy, radius, startAngle, endAngle) {
-  const TAU = Math.PI * 2;
-  const norm = (t) => ((t % TAU) + TAU) % TAU;
-
-  const a0 = norm(startAngle);
-  const a1 = norm(endAngle);
-
-  // CCW delta (a0 -> a1), and CW delta (a0 -> a1 going the other way)
-  const ccw = (a1 - a0 + TAU) % TAU;
-  const cw  = (a0 - a1 + TAU) % TAU;
-
-  // Choose the shorter sweep
-  const sweepFlag = cw < ccw ? 1 : 0;         // 1 = CW, 0 = CCW (SVG spec)
-  const delta = Math.min(ccw, cw);
-  const largeArcFlag = delta > Math.PI ? 1 : 0;
-
-  // If degenerate, just move to the point
-  if (delta < 1e-9) {
-    const p = polarToCartesian(cx, cy, radius, a0);
-    return `M ${p.x} ${p.y}`;
-  }
-
-  // Use the original angles; sweepFlag picks direction
-  const p0 = polarToCartesian(cx, cy, radius, a0);
-  const p1 = polarToCartesian(cx, cy, radius, a1);
-
-  return `M ${p0.x} ${p0.y} A ${radius} ${radius} 0 ${largeArcFlag} ${sweepFlag} ${p1.x} ${p1.y}`;
+// src/radial/polarToCartesian.js
+export default function (cx, cy, r, t) {
+  return { x: cx + r * Math.cos(t), y: cy - r * Math.sin(t) };
 }
-