From 84820486d5d9864e40a9639d4be7c11232ccacbb Mon Sep 17 00:00:00 2001
From: Remco Bouckaert <higgs.ml@gmail.com>
Date: Fri, 28 Jun 2024 11:02:33 +1200
Subject: [PATCH] deal with spaces in quoted attribute values #30

---
 src/beast/base/parser/NexusParser.java | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/src/beast/base/parser/NexusParser.java b/src/beast/base/parser/NexusParser.java
index f96fbee8..7c10b6a3 100644
--- a/src/beast/base/parser/NexusParser.java
+++ b/src/beast/base/parser/NexusParser.java
@@ -1,6 +1,7 @@
 package beast.base.parser;
 
 
+
 import java.io.*;
 import java.util.*;
 import java.util.regex.Matcher;
@@ -1385,6 +1386,24 @@ protected String getAttValue(final String attribute, final String str) {
         if (att.startsWith("\"") && att.endsWith("\"")) {
             final int start = matcher.start(1);
             att = str.substring(start + 1, str.indexOf('"', start + 1));
+        } else if (att.startsWith("\"")) { // but does not end with quote!
+
+        	// we are looking for the end quote
+        	int i = str.indexOf(attribute);
+        	i += attribute.length();
+        	// find start quote
+        	i = str.indexOf('"', i);
+        	if (i < 0) {
+        		return att;
+        	}
+        	i++;
+        	// find end quote
+        	int j = str.indexOf('"', i);
+        	if (j < 0) {
+        		return att;
+        	}
+        	// remove spaces
+        	att = str.substring(i, j).replaceAll("\\s", "");
         }
         return att;
     }