not needed

diff --git a/forester/java/src/org/forester/application/nhx_too.java b/forester/java/src/org/forester/application/nhx_too.java
deleted file mode 100644 (file)
index 1061c5c..0000000
--- a/forester/java/src/org/forester/application/nhx_too.java
+++ /dev/null
@@ -1,112 +0,0 @@
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// 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
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// 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
-//
-// Contact: phylosoft @ gmail . com
-// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
-
-package org.forester.application;
-
-import java.io.File;
-import java.io.IOException;
-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;
-import org.forester.util.ForesterUtil;
-
-public class nhx_too {
-
-    final static private String PRG_NAME                 = "nhx_too";
-    final static private String PRG_VERSION              = "0.1";
-    final static private String PRG_DATE                 = "2008.03.04";
-    final static private String INT_NODE_NAME_IS_SUPPORT = "is";
-
-    public static void main( final String args[] ) {
-        ForesterUtil.printProgramInformation( nhx_too.PRG_NAME, nhx_too.PRG_VERSION, nhx_too.PRG_DATE );
-        if ( ( args.length < 3 ) || ( args.length > 3 ) ) {
-            System.out.println();
-            System.out.println( nhx_too.PRG_NAME + ": wrong number of arguments" );
-            System.out.println();
-            System.out.println( "Usage: \"" + nhx_too.PRG_NAME + " [options] <infile> <outfile>\n" );
-            System.out.println( " Options: -" + nhx_too.INT_NODE_NAME_IS_SUPPORT
-                    + ": internal node names are support values (i.e. MrBayes output)" );
-            System.out.println();
-            System.exit( -1 );
-        }
-        CommandLineArguments cla = null;
-        try {
-            cla = new CommandLineArguments( args );
-        }
-        catch ( final Exception e ) {
-            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
-        }
-        final List<String> allowed_options = new ArrayList<String>();
-        allowed_options.add( nhx_too.INT_NODE_NAME_IS_SUPPORT );
-        final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
-        if ( dissallowed_options.length() > 0 ) {
-            ForesterUtil.fatalError( nhx_too.PRG_NAME, "Unknown option(s): " + dissallowed_options );
-        }
-        final File phylogeny_infile = cla.getFile( 0 );
-        final File phylogeny_outfile = cla.getFile( 1 );
-        boolean int_node_name_is_support = false;
-        if ( cla.isOptionSet( nhx_too.INT_NODE_NAME_IS_SUPPORT ) ) {
-            int_node_name_is_support = true;
-        }
-        Phylogeny p = null;
-        try {
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogeny_infile, true );
-            p = factory.create( phylogeny_infile, pp )[ 0 ];
-        }
-        catch ( final Exception e ) {
-            ForesterUtil.fatalError( nhx_too.PRG_NAME, "Could not read \"" + phylogeny_infile + "\" [" + e.getMessage()
-                    + "]" );
-        }
-        if ( int_node_name_is_support ) {
-            try {
-                PhylogenyMethods.transferInternalNodeNamesToConfidence( p );
-            }
-            catch ( final Exception e ) {
-                ForesterUtil.unexpectedFatalError( nhx_too.PRG_NAME,
-                                                   "Failure during moving of internal names to support values ["
-                                                           + e.getMessage() + "]" );
-            }
-        }
-        try {
-            final PhylogenyWriter w = new PhylogenyWriter();
-            w.toNewHampshireX( p, phylogeny_outfile );
-        }
-        catch ( final IOException e ) {
-            ForesterUtil.fatalError( nhx_too.PRG_NAME, "Failure to write output [" + e.getMessage() + "]" );
-        }
-        System.out.println();
-        System.out.println( "Done [wrote \"" + phylogeny_outfile + "\"]." );
-        System.out.println();
-    }
-}