@euphrasiologist/lwphylo 1.1.9 → 1.1.11

package/dist/index.js

@@ -1,2 +1,2 @@
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c=[["data",Object.values(r)]],a=c[0][1].map(n=>n.thisId);var s=[];for(const t in n)"data"!==t&&s.push([t,n[t]]);var o=s.map(n=>[n[0],n[1].filter(n=>a.includes(n.thisId))]);return Object.fromEntries(c.concat(o))}export{r as describeArc,p as parentFisheye,n as phisheye,h as radialLayout,I as readTree,u as rectangleLayout,g as subTree,f as unrooted};
+const n={circular:()=>{let n=200,t=2,e=[0,0],r={},i=0,s=0,c=n*n,a=10;function o(){const e=Math.exp(t);return i=e/(e-1)*n,s=t/n,c=n*n,h}function h(n){!function(){if(!r||"function"!=typeof r.xscale||"function"!=typeof r.yscale)throw new Error("phisheye.circular: call .scales(xscale, yscale) before using the fisheye.")}();const t=r.xscale(n.x),o=r.yscale(n.y),h=t-e[0],l=o-e[1],d=h*h+l*l;if(0===d||d>=c)return{x:t,y:o,z:d>=c?1:a};const u=Math.sqrt(d),f=i*(1-Math.exp(-u*s))/u*.75+.25;return{x:e[0]+h*f,y:e[1]+l*f,z:Math.min(f,a)}}return h.radius=function(t){return arguments.length?(n=Math.max(0,+t),o()):n},h.distortion=function(n){return arguments.length?(t=Math.max(0,+n),o()):t},h.focus=function(n){if(!arguments.length)return e.slice();if(!Array.isArray(n)||2!==n.length)throw new Error("focus expects [x, y] in pixels.");return e=[+n[0],+n[1]],h},h.scales=function(n,t){return arguments.length?(r={xscale:n,yscale:t},h):r},h.setScales=h.scales,h.clampZ=function(n){return 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e<=-Math.PI?e+=2*Math.PI:e>Math.PI&&(e-=2*Math.PI),[n,n+e]}function o(n){const t={};return t.data=s(n),t.radii=function(n){const t=s(n),e=new Map(t.map(n=>[n.thisId,n])),r=t.find(n=>null==n.parentId)?.thisId,i=[];for(const n of t){if(n.thisId===r)continue;const t=e.get(n.parentId);if(!t)continue;const s=n.angle,c=t.r,a=n.r;i.push({parentId:t.thisId,childId:n.thisId,x0:c*Math.cos(s),y0:c*Math.sin(s),x1:a*Math.cos(s),y1:a*Math.sin(s),isTip:!!n.isTip})}return i}(n),t.arcs=function(n){const t=new Map(n.map(n=>[n.thisId,n])),e=n.find(n=>null==n.parentId)?.thisId,r=[];for(const i of n){if(i.thisId===e)continue;const n=t.get(i.parentId);if(!n)continue;const[s,c]=a(n.angle,i.angle);isFinite(n.r)&&0!==n.r&&s!==c&&r.push({parentId:n.thisId,childId:i.thisId,radius:n.r,start:s,end:c})}return r}(t.data),t}function h(n){const t=i(n),e=new Map(t.map((n,t)=>[n.thisId,t])),r=[];!function n(t){t.children&&0!==t.children.length?t.children.forEach(n):r.push(t.id)}(n);const s=new Map(r.map((n,t)=>[n,t+1]));return function n(r){const i=e.get(r.id);if(!r.children||0===r.children.length){const n=s.get(r.id);return t[i].y0=n,t[i].y1=n,n}const c=function(n){let t=0,e=0;for(let r of n)null!=r&&(r=+r)>=r&&(++t,e+=r);if(t)return e/t}(r.children.map(n));return t[i].y0=c,t[i].y1=c,c}(n),function n(r,i){const s=e.get(r.id),c=i??0,a=c+(t[s].branchLength??0);t[s].x0=c,t[s].x1=a,r.children&&r.children.length&&r.children.forEach(t=>n(t,a))}(n,0),t.map(n=>{const{y:t,x:e,angle:r,...i}=n;return i})}function l(n){const t=h(n),e=function(n){const t=h(n),e=new Map;for(const n of t){if(null==n.parentId)continue;const t=e.get(n.parentId);t?t.push(n):e.set(n.parentId,[n])}const r=[];for(const[n,t]of e.entries()){if(!t.length)continue;const e=t.map(n=>n.y0),i=Math.min(...e),s=Math.max(...e),c=t[0].x0;r.push({parentId:n,x0:c,x1:c,y0:i,y1:s,heights:s-i})}return r}(n),r=function(n){const t=h(n),e=new Map(t.map(n=>[n.thisId,n])),r=[];for(const n of t){if(null==n.parentId)continue;const t=e.get(n.parentId);if(!t)continue;const i=n.x0,s=n.y0,c=t.y0,a=Math.min(s,c),o=Math.max(s,c);r.push({parentId:n.parentId,childId:n.thisId,x:i,y0:a,y1:o})}return r}(n);new Map(t.map(n=>[n.thisId,n]));const i=t.filter(n=>null!=n.parentId).map(n=>({parentId:n.parentId,childId:n.thisId,thisId:n.thisId,thisLabel:n.thisLabel,isTip:n.isTip,x0:n.x0,x1:n.x1,y0:n.y0,y1:n.y0}));return{data:t,vertical_lines:e,child_vertical_lines:r,horizontal_lines:i}}function d(n){null===n.parent&&(function 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),d(r)}return n}function u(n){var t={},e=i(d(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 f(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 p(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 I(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,f as parentFisheye,n as phisheye,o as radialLayout,p as readTree,l as rectangleLayout,I as subTree,u as unrooted};
 //# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@euphrasiologist/lwphylo",
-  "version": "1.1.9",
+  "version": "1.1.11",
   "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

@@ -1,28 +1,18 @@
-import polarToCartesian from "./polarToCartesian.js";
-
-/**
- * Describe an SVG arc path between two angles (radians).
- * Always draws the MINOR arc (≤ π). Angles are normalized to [0, 2π).
- */
-function normalize(theta) {
-  const t = theta % (2 * Math.PI);
-  return t < 0 ? t + 2 * Math.PI : t;
-}
+import polarToCartesian from "./polarToCartesian.js"
 
 export default function describeArc(cx, cy, radius, startAngle, endAngle) {
-  let a0 = normalize(startAngle);
-  let a1 = normalize(endAngle);
+  const TAU = Math.PI * 2;
+  const norm = (t) => ((t % TAU) + TAU) % TAU;
 
-  // Choose the minor arc direction
-  let diff = a1 - a0;
-  if (diff <= -Math.PI) diff += 2 * Math.PI;
-  else if (diff > Math.PI) diff -= 2 * Math.PI;
+  let a0 = norm(startAngle);
+  let a1 = norm(endAngle);
+  let delta = a1 - a0; if (delta < 0) delta += TAU;
 
-  const largeArcFlag = Math.abs(diff) > Math.PI ? 1 : 0; // for completeness (will be 0 with minor arc)
-  const sweepFlag = diff >= 0 ? 1 : 0;
+  const largeArcFlag = delta > Math.PI ? 1 : 0;
+  const sweepFlag = 0; // CCW after Y inversion
 
   const start = polarToCartesian(cx, cy, radius, a0);
-  const end = polarToCartesian(cx, cy, radius, a0 + diff);
+  const end   = polarToCartesian(cx, cy, radius, a1);
 
   return [
     "M", start.x, start.y,

package/src/radial/polarToCartesian.js

@@ -1,9 +1,12 @@
 /**
- * Convert polar to Cartesian: angle in radians, 0 at +x, CCW positive.
+ * Convert polar coordinates (radians) to cartesian (screen space).
+ * NOTE: Invert Y so angles increase counter-clockwise on screen,
+ * matching how you plot points with yScaleRadial (range [h,0]).
  */
-export default function polarToCartesian(cx, cy, r, angle) {
+export default function (centerX, centerY, radius, angleInRadians) {
   return {
-    x: cx + r * Math.cos(angle),
-    y: cy + r * Math.sin(angle)
+    x: centerX + radius * Math.cos(angleInRadians),
+    y: centerY - radius * Math.sin(angleInRadians) // <- was + ; now -
   };
 }
+

package/src/rectangle/rectangleLayout.js

@@ -1,28 +1,36 @@
-import getHorizontal from "./getHorizontal.js";
-import getVertical from "./getVertical.js";
-import getChildVerticals from "./getChildVerticals.js";
+import getHorizontal from "./getHorizontal.js"
+import getVertical from "./getVertical.js"
+import getChildVerticals from "./getChildVerticals.js"
 
 /**
  * Rectangle layout wrapper.
  * Returns:
  *  - data: per-node rows (x0,x1,y0=y1,...)
- *  - vertical_lines: single spanning vertical per parent (fast baseline draw)
- *  - child_vertical_lines: one vertical per edge (child->parent) for highlighting
- *  - horizontal_lines: child horizontals from parent.x -> child.x at child.y
+ *  - vertical_lines: single spanning vertical per parent (baseline draw)
+ *  - child_vertical_lines: one vertical per edge (for highlighting)
+ *  - horizontal_lines: per-edge child horizontals (x0->x1 at y), with labels & tip flags
  */
 export default function rectangleLayout(node) {
-  const data = getHorizontal(node); // per-node horizontally resolved
-  const vertical_lines = getVertical(node); // single spanning vertical per parent
-  const child_vertical_lines = getChildVerticals(node); // one vertical per child edge
+  const data = getHorizontal(node);              // per-node
+  const vertical_lines = getVertical(node);      // parent spans
+  const child_vertical_lines = getChildVerticals(node); // per-edge verticals
 
+  // IMPORTANT: include y0 & y1, and carry isTip/labels for the renderer
+  const byId = new Map(data.map(d => [d.thisId, d]));
   const horizontal_lines = data
     .filter(d => d.parentId != null)
     .map(d => ({
       parentId: d.parentId,
       childId: d.thisId,
-      x0: d.x0, x1: d.x1,
-      y: d.y0
+      thisId: d.thisId,
+      thisLabel: d.thisLabel,
+      isTip: d.isTip,
+      x0: d.x0,
+      x1: d.x1,
+      y0: d.y0,
+      y1: d.y0
     }));
 
   return { data, vertical_lines, child_vertical_lines, horizontal_lines };
 }
+