X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Frio%2FTestRIO.java;h=5d2c34e23f0a46858f57d44c98d9eaf51e5d78fc;hb=aec065f948a075773794133f102ea19eb1d59f64;hp=81604468fde645431d4e427e7f011bcf2180db3c;hpb=3d6a64e0371ffedf725bf8467211ed860f298550;p=jalview.git

diff --git a/forester/java/src/org/forester/rio/TestRIO.java b/forester/java/src/org/forester/rio/TestRIO.java
index 8160446..5d2c34e 100644
--- a/forester/java/src/org/forester/rio/TestRIO.java
+++ b/forester/java/src/org/forester/rio/TestRIO.java
@@ -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.AGRESSIVE );
             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);";
@@ -134,7 +134,7 @@ 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.AGRESSIVE );
             //
             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 );