X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Frio%2FTestRIO.java;h=fa704b7a3b352f82243eacab2bc11ba4df7b4d4d;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=99f3d4801b67a60112d6335bbaa61041c00de6ce;hpb=789f3450d14e1f922072f4288833afab71993667;p=jalview.git

diff --git a/forester/java/src/org/forester/rio/TestRIO.java b/forester/java/src/org/forester/rio/TestRIO.java
index 99f3d48..fa704b7 100644
--- a/forester/java/src/org/forester/rio/TestRIO.java
+++ b/forester/java/src/org/forester/rio/TestRIO.java
@@ -18,7 +18,7 @@ import org.forester.util.ForesterUtil;
 public final class TestRIO {
 
     private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
-                                                          + "test_data" + ForesterUtil.getFileSeparator();
+            + "test_data" + ForesterUtil.getFileSeparator();
 
     public static void main( final String[] args ) {
         if ( !testRIO_GSDIR() ) {
@@ -48,7 +48,7 @@ public final class TestRIO {
             final NHXParser nhx = new NHXParser();
             nhx.setReplaceUnderscores( false );
             nhx.setIgnoreQuotes( true );
-            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
             //
             final String gene_trees_00_str = "(MOUSE,RAT);(MOUSE,RAT);(MOUSE,RAT);(RAT,MOUSE);";
             final Phylogeny[] gene_trees_00 = factory.create( gene_trees_00_str, nhx );
@@ -737,7 +737,7 @@ public final class TestRIO {
             final NHXParser nhx = new NHXParser();
             nhx.setReplaceUnderscores( false );
             nhx.setIgnoreQuotes( true );
-            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
             final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"
                     + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));"
                     + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);";