inprogress

[jalview.git] / forester / java / src / org / forester / application / rio.java

diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java
index 3230c41..3ccacf5 100644 (file)
--- a/forester/java/src/org/forester/application/rio.java
+++ b/forester/java/src/org/forester/application/rio.java
@@ -55,8 +55,8 @@ import org.forester.util.ForesterUtil;
 public class rio {
 
     final static private String PRG_NAME              = "rio";
-    final static private String PRG_VERSION           = "4.000 beta 8";
-    final static private String PRG_DATE              = "2013.01.11";
+    final static private String PRG_VERSION           = "4.000 beta 9";
+    final static private String PRG_DATE              = "2013.01.14";
     final static private String E_MAIL                = "phyloxml@gmail.com";
     final static private String WWW                   = "https://sites.google.com/site/cmzmasek/home/software/forester";
     final static private String HELP_OPTION_1         = "help";
@@ -308,13 +308,13 @@ public class rio {
                     final NHXParser nhx = ( NHXParser ) p;
                     nhx.setReplaceUnderscores( false );
                     nhx.setIgnoreQuotes( true );
-                    nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+                    nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
                 }
                 else if ( p instanceof NexusPhylogeniesParser ) {
                     final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
                     nex.setReplaceUnderscores( false );
                     nex.setIgnoreQuotes( true );
-                    nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
+                    nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
                 }
                 else {
                     throw new RuntimeException( "unknown parser type: " + p );