set printRootInfo so root labels are not lost.

[vamsas.git] / src / uk / ac / vamsas / objects / utils / trees / NewickFile.java

diff --git a/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
index 521c616..d6f5f57 100644 (file)
--- a/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
+++ b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
@@ -56,7 +56,7 @@ public class NewickFile {
   // File IO Flags\r
   boolean ReplaceUnderscores = true;\r
 \r
-  boolean printRootInfo = false;\r
+  boolean printRootInfo = true; // in case root has anything to preserve\r
 \r
   private Pattern[] NodeSafeName = new Pattern[] {\r
       Pattern.compile("[\\[,:'()]"), // test for requiring quotes\r
@@ -673,7 +673,7 @@ public class NewickFile {
   private String printRootField(SequenceNode root) {\r
     return (printRootInfo) ? (((root.getName() == null) ? "" : nodeName(root\r
         .getName()))\r
-        + ((HasBootstrap) ? ((root.getBootstrap() > -1) ? (" " + root\r
+        + ((HasBootstrap) ? ((root.getBootstrap() > -1) ? ((root.getName()!=null ? " " : "") + root\r
             .getBootstrap()) : "") : "") + ((RootHasDistance) ? (":" + root.dist)\r
         : ""))\r
         : "";\r