From d628acddddd23599ecf4a0f9b6dd5bab3c574e22 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 16 Jan 2013 01:06:32 +0000 Subject: [PATCH] not needed --- .../java/src/org/forester/application/nhx_too.java | 112 -------------------- 1 file changed, 112 deletions(-) delete mode 100644 forester/java/src/org/forester/application/nhx_too.java 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 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] \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 allowed_options = new ArrayList(); - 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(); - } -} -- 1.7.10.2