Jalview-JS/JAL-3253-applet newick Regex coding error fix JAL-3271

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 5a98605..7596db4 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -165,7 +165,7 @@ public class NewickFile extends FileParse
         return null;
       }
       return codePerl == null ? Platform.newRegex(code, code2)
-              : Platform.newRegexPerl(code2);
+              : Platform.newRegexPerl(codePerl);
     }
     return REGEX[id];
   }

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index ab4a3eb..4ad61d9 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -2862,6 +2862,8 @@ public class Jalview2XML
         // The question here is what to do with the two
         // .xml files in the jvp file. They are identical?
         // && name.indexOf(" Dataset for ") < 0 // BH 2019.05.21
+        // we need to talk about how to avoid the full duplication of
+        // reading these.
         )
         {
           JAXBContext jc = JAXBContext