@euphrasiologist/lwphylo 1.1.9 → 1.1.10

package/dist/index.js

@@ -1,2 +1,2 @@
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+const t={circular:()=>{let t=200,n=2,e=[0,0],r={},i=0,s=0,a=t*t,c=10;function o(){const e=Math.exp(n);return i=e/(e-1)*t,s=n/t,a=t*t,h}function h(t){!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 n=r.xscale(t.x),o=r.yscale(t.y),h=n-e[0],l=o-e[1],u=h*h+l*l;if(0===u||u>=a)return{x:n,y:o,z:u>=a?1:c};const d=Math.sqrt(u),f=i*(1-Math.exp(-d*s))/d*.75+.25;return{x:e[0]+h*f,y:e[1]+l*f,z:Math.min(f,c)}}return h.radius=function(n){return arguments.length?(t=Math.max(0,+n),o()):t},h.distortion=function(t){return arguments.length?(n=Math.max(0,+t),o()):n},h.focus=function(t){if(!arguments.length)return e.slice();if(!Array.isArray(t)||2!==t.length)throw new Error("focus expects [x, y] in pixels.");return e=[+t[0],+t[1]],h},h.scales=function(t,n){return arguments.length?(r={xscale:t,yscale:n},h):r},h.setScales=h.scales,h.clampZ=function(t){return 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n){if(null==t.parentId)continue;const n=e.get(t.parentId);n?n.push(t):e.set(t.parentId,[t])}const r=[];for(const[t,n]of e.entries()){if(!n.length)continue;const e=n.map(t=>t.y0),i=Math.min(...e),s=Math.max(...e),a=n[0].x0;r.push({parentId:t,x0:a,x1:a,y0:i,y1:s,heights:s-i})}return r}(t),r=function(t){const n=l(t),e=new Map(n.map(t=>[t.thisId,t])),r=[];for(const t of n){if(null==t.parentId)continue;const n=e.get(t.parentId);if(!n)continue;const i=t.x0,s=t.y0,a=n.y0,c=Math.min(s,a),o=Math.max(s,a);r.push({parentId:t.parentId,childId:t.thisId,x:i,y0:c,y1:o})}return r}(t);new Map(n.map(t=>[t.thisId,t]));const i=n.filter(t=>null!=t.parentId).map(t=>({parentId:t.parentId,childId:t.thisId,thisId:t.thisId,thisLabel:t.thisLabel,isTip:t.isTip,x0:t.x0,x1:t.x1,y0:t.y0,y1:t.y0}));return{data:n,vertical_lines:e,child_vertical_lines:r,horizontal_lines:i}}function d(t){null===t.parent&&(function t(n){if(!n.children||0===n.children.length)return n.ntips=1,1;let e=0;for(const r of n.children)e+=t(r);return n.ntips=e,e}(t),t.start=0,t.end=2,t.angle=0,t.ntips=function(t){var n=0;for(const e of function(t){const n=[t],e=[];for(;n.length;){const t=n.shift();e.push(t);for(const e of t.children)n.push(e)}return e}(t))0==e.children.length&&n++;return n}(t),t.x=0,t.y=0);let n=t.start;for(let e=0;e<t.children.length;e++){const r=t.children[e],i=(t.end-t.start)*(r.ntips/t.ntips);r.start=n,r.end=n+i,r.angle=r.start+(r.end-r.start)/2,n=r.end;const s=r.angle*Math.PI,a=r.branchLength??0;r.x=t.x+a*Math.sin(s),r.y=t.y+a*Math.cos(s),d(r)}return t}function f(t){var n={},e=s(d(t));return n.data=e,n.edges=function(t,n=!1){const e=[...t].sort((t,n)=>t.thisId-n.thisId),r=new Map(e.map(t=>[t.thisId,t])),i=[];for(const t of e){if(null==t.parentId)continue;const e=r.get(t.parentId);e&&(n?(i.push({x1:t.x,y1:t.y,id1:t.thisId,x2:e.x,y2:t.y,id2:void 0}),i.push({x1:e.x,y1:t.y,id1:void 0,x2:e.x,y2:e.y,id2:t.parentId})):i.push({x1:t.x,y1:t.y,id1:t.thisId,x2:e.x,y2:e.y,id2:t.parentId}))}return i}(e),n}function p(t,n){const e=function(t,n="thisId"){return new Map(t.map(t=>[t[n],t]))}(n),r=e.get(t.parentId);return r?{px:r.fisheye.x,py:r.fisheye.y}:null}function I(t){const n=(t=String(t).replace(/\s+/g,"")).split(/(;|\(|\)|,)/),e={parent:null,children:[]};let r=e,i=0;for(const t of n)if(t&&";"!==t)if("("===t){const t={parent:r,children:[]};r.children.push(t),r=t}else if(","===t){r=r.parent;const t={parent:r,children:[]};r.children.push(t),r=t}else if(")"===t){if(r=r.parent,null===r)break}else{const n=t.split(":");1===n.length?t.startsWith(":")?(r.label="",r.branchLength=parseFloat(n[0])):(r.label=n[0],r.branchLength=null):2===n.length?(r.label=n[0],r.branchLength=parseFloat(n[1])):(console.warn(t,"Unhandled token with multiple ':' characters"),r.label=n[0]||"",r.branchLength=parseFloat(n[n.length-1])),r.id=i++}return null==e.id&&(e.id=i),e}function g(t,n){let e={};t.data.forEach(t=>{e[t.thisId]={...t}});let r={};const i=function(t){e[t]&&(r[t]=e[t],e[t].children&&e[t].children.forEach(t=>{i(t)}))};i(n);const s=[["data",Object.values(r)]],a=s[0][1].map(t=>t.thisId);var c=[];for(const n in t)"data"!==n&&c.push([n,t[n]]);var o=c.map(t=>[t[0],t[1].filter(t=>a.includes(t.thisId))]);return Object.fromEntries(s.concat(o))}export{r as describeArc,p as parentFisheye,t as phisheye,h as radialLayout,I as readTree,u as rectangleLayout,g as subTree,f as unrooted};
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@euphrasiologist/lwphylo",
-  "version": "1.1.9",
+  "version": "1.1.10",
   "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/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 };
 }
+