@euphrasiologist/lwphylo 1.1.11 → 1.1.13

package/dist/index.js

@@ -1,2 +1,2 @@
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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};
+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,l}function l(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),l=t-e[0],h=o-e[1],d=l*l+h*h;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]+l*f,y:e[1]+h*f,z:Math.min(f,a)}}return l.radius=function(t){return arguments.length?(n=Math.max(0,+t),o()):n},l.distortion=function(n){return arguments.length?(t=Math.max(0,+n),o()):t},l.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]],l},l.scales=function(n,t){return arguments.length?(r={xscale:n,yscale:t},l):r},l.setScales=l.scales,l.clampZ=function(n){return 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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=2*Math.PI;new Map(n.map(n=>[n.thisId,n]));const e=new Map;let r=null;for(const t of n)null==t.parentId&&(r=t.thisId),e.has(t.parentId)||e.set(t.parentId,[]),e.get(t.parentId).push(t);const i=[];for(const s of n){const n=s.thisId;if(n===r)continue;const c=e.get(n)||[];if(c.length<2)continue;const a=c.map(n=>(n.angle%t+t)%t).sort((n,t)=>n-t),o=a[0],l=a[a.length-1],h=l-o,d=t-h;let u,f,p;h<=d?(u=o,f=l,p=h):(u=l,f=o,p=d),p<1e-6||!isFinite(s.r)||s.r<=0||i.push({start:u,end:f,radius:s.r,thisId:n,parentId:s.parentId})}return i}(t.data),t}function a(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 o(n){const t=a(n),e=function(n){const t=a(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=a(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 l(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),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": "1.1.11",
+  "version": "1.1.13",
   "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

@@ -6,10 +6,13 @@ export default function describeArc(cx, cy, radius, startAngle, endAngle) {
 
   let a0 = norm(startAngle);
   let a1 = norm(endAngle);
-  let delta = a1 - a0; if (delta < 0) delta += TAU;
+
+  // delta in the *clockwise* direction (increasing angle after Y inversion)
+  let delta = a1 - a0;
+  if (delta < 0) delta += TAU;
 
   const largeArcFlag = delta > Math.PI ? 1 : 0;
-  const sweepFlag = 0; // CCW after Y inversion
+  const sweepFlag = 1; // CLOCKWISE sweep to match getArcs' start→end
 
   const start = polarToCartesian(cx, cy, radius, a0);
   const end   = polarToCartesian(cx, cy, radius, a1);

package/src/radial/getArcs.js

@@ -1,52 +1,65 @@
 /**
- * Build *per-edge* minor arcs for a radial tree.
- * For each non-root node (child), we draw a small arc at the *parent's* radius
- * from the parent's angle to the child's angle (minor arc ≤ π).
- *
- * Input: a "radialData" array with fields:
- *   thisId, parentId, angle (radians), r (radius at this node)
- *
- * Output: [{ parentId, childId, radius, start, end }]
- *   where start/end are angles (radians), radius is parent's r
+ * Build arc descriptors for each internal parent:
+ *  - One arc per internal node at radius = parent.r
+ *  - Start/end angles choose the *shortest* wrap-aware span covering the children
+ *  - Skips degenerate spans (delta ~ 0)
  */
-
-function normalize(theta) {
-  const t = theta % (2 * Math.PI);
-  return t < 0 ? t + 2 * Math.PI : t;
-}
-
-function minorArc(a, b) {
-  // returns [start, end] representing the minor arc from a -> b
-  a = normalize(a); b = normalize(b);
-  let diff = b - a;
-  if (diff <= -Math.PI) diff += 2 * Math.PI;
-  else if (diff > Math.PI) diff -= 2 * Math.PI;
-  return [a, a + diff]; // draw from a to a+diff
-}
-
 export default function getArcs(pd) {
+  const TAU = Math.PI * 2;
+  const norm = (t) => ((t % TAU) + TAU) % TAU;
+  const EPS = 1e-6;
+
+  // Quick lookups
   const byId = new Map(pd.map(d => [d.thisId, d]));
-  // Find root thisId
-  const root = pd.find(d => d.parentId == null)?.thisId;
+  const childrenByParent = new Map();
+  let root = null;
 
-  const arcs = [];
   for (const d of pd) {
-    if (d.thisId === root) continue;
-    const parent = byId.get(d.parentId);
-    if (!parent) continue;
+    if (d.parentId == null) root = d.thisId;
+    if (!childrenByParent.has(d.parentId)) childrenByParent.set(d.parentId, []);
+    childrenByParent.get(d.parentId).push(d);
+  }
 
-    // minor arc from parent.angle -> child.angle at radius parent.r
-    const [start, end] = minorArc(parent.angle, d.angle);
+  const arcs = [];
+
+  for (const parent of pd) {
+    const pid = parent.thisId;
+    if (pid === root) continue; // no arc above root
+    const kids = childrenByParent.get(pid) || [];
+    if (kids.length < 2) continue; // need at least two children
+
+    // Collect & sort child angles
+    const A = kids.map(k => norm(k.angle)).sort((a, b) => a - b);
+    const aMin = A[0], aMax = A[A.length - 1];
+
+    // Two candidate spans: direct (aMin -> aMax) and wrapped (aMax -> aMin across 2π)
+    const direct = aMax - aMin;
+    const wrapped = TAU - direct;
+
+    // Choose the shorter span. We'll draw **CCW** (sweepFlag = 0) in describeArc.
+    let start, end, span;
+    if (direct <= wrapped) {
+      start = aMin;
+      end = aMax;
+      span = direct;
+    } else {
+      // wrapped is shorter: go CCW from aMax up through 2π to aMin
+      start = aMax;
+      end = aMin;
+      span = wrapped;
+    }
+
+    if (span < EPS || !isFinite(parent.r) || parent.r <= 0) continue;
 
-    if (!isFinite(parent.r) || parent.r === 0 || start === end) continue;
     arcs.push({
-      parentId: parent.thisId,
-      childId: d.thisId,
-      radius: parent.r,
       start,
-      end
+      end,
+      radius: parent.r,
+      thisId: pid,
+      parentId: parent.parentId
     });
   }
+
   return arcs;
 }
 

package/src/radial/polarToCartesian.js

@@ -1,12 +1,7 @@
-/**
- * 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 (centerX, centerY, radius, angleInRadians) {
   return {
     x: centerX + radius * Math.cos(angleInRadians),
-    y: centerY - radius * Math.sin(angleInRadians) // <- was + ; now -
+    y: centerY - radius * Math.sin(angleInRadians)
   };
 }