Merge pull request #62 from clockor2/read-tree-bug-#58

fix: fix multi tree read newick bug
clockor2 · Apr 12, 2024 · f32f0ce · f32f0ce
2 parents ece3b15 + e8d04b2
commit f32f0ce
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/src/io/readers/newick.ts b/src/io/readers/newick.ts
@@ -19,6 +19,14 @@ export function readNewick(str: string): Tree {
   const stack: number[] = [];
   const nodes: Node[] = [];
 
+  // check for multiple trees
+  if (str.includes('\n')) {
+    str = str.slice(0, str.indexOf('\n'));
+    console.warn(
+      'Multiple trees in Newick string. Only reading the first tree. Use readTreesFromNewick() to read all trees.'
+    );
+  }
+
   for (let l = 0; l < str.length; ) {
     while (l < str.length && (str.charAt(l) < '!' || str.charAt(l) > '~')) ++l;
     if (l == str.length) break;

diff --git a/test/io/readers.spec.ts b/test/io/readers.spec.ts
@@ -18,11 +18,11 @@ import { beastAnnotation, nhxAnnotation } from '../../src/io/writers/newick';
 
 // test read local files
 describe('read', () => {
-    test('readTreesFromNewick', () => {
+    test('readNewick', () => {
 
         const inNewick = readFileSync('test/data/egTree.nwk', 'utf-8');
 
-        const tree = readTreesFromNewick(inNewick)[0];
+        const tree = readNewick(inNewick);
 
         // test the number of leaves
         expect(tree.leafList.length).toBe(274);