@euphrasiologist/lwphylo 1.1.7 → 1.1.9

package/src/utils/readTree.js

@@ -1,74 +1,64 @@
 /**
- * Parse a Newick tree string into a doubly-linked
- * list of JS Objects.  Assigns node labels, branch
- * lengths and node IDs (numbering terminal before
- * internal nodes).
+ * Parse a Newick tree string into a doubly-linked list of JS Objects.
+ * Assigns labels, branch lengths, and node IDs (tips before internals if input emits them that way).
+ *
+ * Notes / limitations:
+ * - Quoted labels and NHX annotations are not fully supported.
+ * - Branch lengths in scientific notation are supported (parseFloat).
  */
 
-export default function (text) {
-    // remove whitespace
-    text = text.replace(/ \t/g, '');
+export default function readTree(text) {
+  // Remove all whitespace (space, tabs, newlines)
+  text = String(text).replace(/\s+/g, '');
 
-    var tokens = text.split(/(;|\(|\)|,)/),
-        root = { 'parent': null, 'children': [] },
-        curnode = root,
-        nodeId = 0;
+  const tokens = text.split(/(;|\(|\)|,)/);
+  const root = { parent: null, children: [] };
+  let curnode = root;
+  let nodeId = 0;
 
-    for (const token of tokens) {
-        if (token == "" || token == ';') {
-            continue
-        }
-        if (token == '(') {
-            // add a child to current node
-            let child = {
-                'parent': curnode,
-                'children': []
-            };
-            curnode.children.push(child);
-            curnode = child;  // climb up
-        }
-        else if (token == ',') {
-            // climb down, add another child to parent
-            curnode = curnode.parent;
-            let child = {
-                'parent': curnode,
-                'children': []
-            }
-            curnode.children.push(child);
-            curnode = child;  // climb up
-        }
-        else if (token == ')') {
-            // climb down twice
-            curnode = curnode.parent;
-            if (curnode === null) {
-                break;
-            }
-        }
-        else {
-            var nodeinfo = token.split(':');
+  for (const token of tokens) {
+    if (!token || token === ';') continue;
 
-            if (nodeinfo.length == 1) {
-                if (token.startsWith(':')) {
-                    curnode.label = "";
-                    curnode.branchLength = parseFloat(nodeinfo[0]);
-                } else {
-                    curnode.label = nodeinfo[0];
-                    curnode.branchLength = null;
-                }
-            }
-            else if (nodeinfo.length == 2) {
-                curnode.label = nodeinfo[0];
-                curnode.branchLength = parseFloat(nodeinfo[1]);
-            }
-            else {
-                // TODO: handle edge cases with >1 ":"
-                console.warn(token, "I don't know what to do with two colons!");
-            }
-            curnode.id = nodeId++;  // assign then increment
+    if (token === '(') {
+      const child = { parent: curnode, children: [] };
+      curnode.children.push(child);
+      curnode = child; // descend
+    } else if (token === ',') {
+      // back to parent, then create sibling
+      curnode = curnode.parent;
+      const child = { parent: curnode, children: [] };
+      curnode.children.push(child);
+      curnode = child;
+    } else if (token === ')') {
+      // ascend one level
+      curnode = curnode.parent;
+      if (curnode === null) break;
+    } else {
+      // label/branch-length chunk (e.g., "A:0.01" or "A")
+      const nodeinfo = token.split(':');
+      if (nodeinfo.length === 1) {
+        if (token.startsWith(':')) {
+          curnode.label = '';
+          curnode.branchLength = parseFloat(nodeinfo[0]);
+        } else {
+          curnode.label = nodeinfo[0];
+          curnode.branchLength = null;
         }
+      } else if (nodeinfo.length === 2) {
+        curnode.label = nodeinfo[0];
+        curnode.branchLength = parseFloat(nodeinfo[1]);
+      } else {
+        console.warn(token, "Unhandled token with multiple ':' characters");
+        curnode.label = nodeinfo[0] || '';
+        curnode.branchLength = parseFloat(nodeinfo[nodeinfo.length - 1]);
+      }
+      curnode.id = nodeId++; // assign then increment
     }
+  }
 
-    curnode.id = nodeId;
+  // Ensure root has an id if not assigned during parsing
+  if (root.id == null) root.id = nodeId;
 
-    return (root);
+  return root;
 }
+