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

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

diff --cc src/jalview/project/Jalview2XML.java
index ab4a3eb,801632f..4ad61d9
--- 1/src/jalview/project/Jalview2XML.java
--- 2/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@@ -2859,9 -2856,7 +2859,11 @@@ public class Jalview2XM
          }
          String name = (jarentry == null ? null : jarentry.getName());
          if (name != null && name.endsWith(".xml")
 -                && name.indexOf(" Dataset for ") < 0 // BH 2019.05.21
 +        // 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