X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fnhx_too.java;h=1d212f0fb41060ce6f0dce787f08bcab2d3aeb4b;hb=e0914db6b0fa3516bc77186eec4d36dd9a753a24;hp=e7b8b96d071a7bf6897f238cbd874ed93fedcce7;hpb=493e40b0c936b65da342134da37e8b856b9b80af;p=jalview.git

diff --git a/forester/java/src/org/forester/application/nhx_too.java b/forester/java/src/org/forester/application/nhx_too.java
index e7b8b96..1d212f0 100644
--- a/forester/java/src/org/forester/application/nhx_too.java
+++ b/forester/java/src/org/forester/application/nhx_too.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,7 +15,7 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -31,8 +31,10 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.util.CommandLineArguments;
@@ -79,7 +81,7 @@ public class nhx_too {
         Phylogeny p = null;
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogeny_infile, true );
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogeny_infile, true );
             p = factory.create( phylogeny_infile, pp )[ 0 ];
         }
         catch ( final Exception e ) {
@@ -88,7 +90,7 @@ public class nhx_too {
         }
         if ( int_node_name_is_support ) {
             try {
-                ForesterUtil.transferInternalNodeNamesToConfidence( p );
+                PhylogenyMethods.transferInternalNodeNamesToConfidence( p );
             }
             catch ( final Exception e ) {
                 ForesterUtil.unexpectedFatalError( nhx_too.PRG_NAME,