// 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
// 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
import java.util.List;
import java.util.Set;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
final static private String PRG_NAME = "confadd";
final static private String PRG_VERSION = "1.01";
final static private String PRG_DATE = "2010.10.26";
- final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String E_MAIL = "phylosoft@gmail.com";
final static private String WWW = "www.phylosoft.org/forester/";
public static void main( final String args[] ) {
- ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ ForesterUtil.printProgramInformation( PRG_NAME, null, PRG_VERSION, PRG_DATE, E_MAIL, WWW, ForesterUtil.getForesterLibraryInformation() );
+
CommandLineArguments cla = null;
try {
cla = new CommandLineArguments( args );
Phylogeny[] evaluators = null;
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
try {
- targets = factory.create( target_file, ForesterUtil.createParserDependingOnFileType( target_file, true ) );
+ targets = factory.create( target_file, ParserUtils.createParserDependingOnFileType( target_file, true ) );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "failed to read target phylogenies from [" + target_file + "]: "
- + e.getLocalizedMessage() );
+ ForesterUtil.fatalError( PRG_NAME,
+ "failed to read target phylogenies from [" + target_file + "]: "
+ + e.getLocalizedMessage() );
}
int counter = 0;
for( final Phylogeny target : targets ) {
ForesterUtil.programMessage( PRG_NAME, "read in a total of " + targets.length + " targets" );
}
try {
- evaluators = factory.create( evaluators_file, ForesterUtil
- .createParserDependingOnFileType( evaluators_file, true ) );
+ evaluators = factory.create( evaluators_file,
+ ParserUtils.createParserDependingOnFileType( evaluators_file, true ) );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( PRG_NAME, "failed to read evaluator topologies from [" + evaluators_file + "]: "