From 6b0f584c112df7148426f1f1ca4294431f4c4c67 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 27 Jan 2026 21:45:13 +0000
Subject: [PATCH 1/2] Initial plan


From c58eec2c58efb1dd78d461ee8b33a6880ed3584b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 27 Jan 2026 21:47:49 +0000
Subject: [PATCH 2/2] Remove unused newick.js file and update documentation

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
---
 WEB_UI_ANALYSIS.md                            |   1 -
 .../src/main/webapp/scripts/newick.js         | 102 ------------------
 2 files changed, 103 deletions(-)
 delete mode 100644 treebase-web/src/main/webapp/scripts/newick.js

diff --git a/WEB_UI_ANALYSIS.md b/WEB_UI_ANALYSIS.md
index 538cadb3b..c50708791 100644
--- a/WEB_UI_ANALYSIS.md
+++ b/WEB_UI_ANALYSIS.md
@@ -417,7 +417,6 @@ styles/
 | `menuExpandable.js` | 6.1KB | Expandable menu navigation | Medium - Pure JS possible |
 | `ajaxProgress.js` | 1KB | Progress indicators | Medium - Uses DWR |
 | `d3.phylogram.js` | 12KB | D3-based tree rendering | Low - Uses D3 v7 |
-| `newick.js` | 3.2KB | Newick format parsing | Low - Pure JavaScript |
 | `sha1.js` | 4.4KB | SHA1 hashing | Low - Pure JavaScript |
 | `googleAnalytics.js` | 3.4KB | Analytics integration | Low - Standard GA |
 | `multiFileUpload.js` | 1KB | File upload handling | Medium |
diff --git a/treebase-web/src/main/webapp/scripts/newick.js b/treebase-web/src/main/webapp/scripts/newick.js
deleted file mode 100644
index 43715e668..000000000
--- a/treebase-web/src/main/webapp/scripts/newick.js
+++ /dev/null
@@ -1,102 +0,0 @@
-/**
- * Newick format parser in JavaScript.
- *
- * Copyright (c) Jason Davies 2010.
- *  
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *  
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *  
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- *
- * Example tree (from http://en.wikipedia.org/wiki/Newick_format):
- *
- * +--0.1--A
- * F-----0.2-----B            +-------0.3----C
- * +------------------0.5-----E
- *                            +---------0.4------D
- *
- * Newick format:
- * (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;
- *
- * Converted to JSON:
- * {
- *   name: "F",
- *   branchset: [
- *     {name: "A", length: 0.1},
- *     {name: "B", length: 0.2},
- *     {
- *       name: "E",
- *       length: 0.5,
- *       branchset: [
- *         {name: "C", length: 0.3},
- *         {name: "D", length: 0.4}
- *       ]
- *     }
- *   ]
- * }
- *
- * Converted to JSON, but with no names or lengths:
- * {
- *   branchset: [
- *     {}, {}, {
- *       branchset: [{}, {}]
- *     }
- *   ]
- * }
- */
-(function(exports) {
-  exports.parse = function(s) {
-    var ancestors = [];
-    var tree = {};
-    var tokens = s.split(/\s*(;|\(|\)|,|:)\s*/);
-    for (var i=0; i<tokens.length; i++) {
-      var token = tokens[i];
-      switch (token) {
-        case '(': // new branchset
-          var subtree = {};
-          tree.branchset = [subtree];
-          ancestors.push(tree);
-          tree = subtree;
-          break;
-        case ',': // another branch
-          var subtree = {};
-          ancestors[ancestors.length-1].branchset.push(subtree);
-          tree = subtree;
-          break;
-        case ')': // optional name next
-          tree = ancestors.pop();
-          break;
-        case ':': // optional length next
-          break;
-        default:
-          var x = tokens[i-1];
-          if (x == ')' || x == '(' || x == ',') {
-            tree.name = token;
-          } else if (x == ':') {
-            tree.length = parseFloat(token);
-          }
-      }
-    }
-    return tree;
-  };
-})(
-    // exports will be set in any commonjs platform; use it if it's available
-    typeof exports !== "undefined" ?
-    exports :
-    // otherwise construct a name space.  outside the anonymous function,
-    // "this" will always be "window" in a browser, even in strict mode.
-    this.Newick = {}
-);