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 801632f..4ad61d9 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -800,6 +800,9 @@ public class Jalview2XML
           String fileName, JarOutputStream jout)
   {
 
+    // BH: Question: What is this Dataset for, as it seems to
+    // duplicate the actual XML file data.
+
     for (String dssids : dsses.keySet())
     {
       AlignFrame _af = dsses.get(dssids);
@@ -2856,7 +2859,11 @@ public class Jalview2XML
         }
         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