// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
// 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
// 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.
// 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
// 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
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
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 PRG_NAME = "confadd";
final static private String PRG_VERSION = "1.01";
final static private String PRG_DATE = "2010.10.26";
final static private String WWW = "www.phylosoft.org/forester/";
public static void main( final String args[] ) {
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() );
Phylogeny[] evaluators = null;
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
try {
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 ) );
- 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() );
- 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 + "]: "
}
catch ( final IOException e ) {
ForesterUtil.fatalError( PRG_NAME, "failed to read evaluator topologies from [" + evaluators_file + "]: "
}
if ( ( last >= evaluators.length ) || ( last <= first ) ) {
ForesterUtil.fatalError( PRG_NAME, "illegal value for first or last evaluator topology to use [" + first
}
if ( ( last >= evaluators.length ) || ( last <= first ) ) {
ForesterUtil.fatalError( PRG_NAME, "illegal value for first or last evaluator topology to use [" + first
is_last = " (corresponds to last topology in file)";
}
ForesterUtil.programMessage( PRG_NAME, "last topology to use : " + last + is_last );
is_last = " (corresponds to last topology in file)";
}
ForesterUtil.programMessage( PRG_NAME, "last topology to use : " + last + is_last );
if ( norm > 0 ) {
ForesterUtil.programMessage( PRG_NAME, "normalizer: " + norm + " (" + ForesterUtil.round( value, 6 ) + ")" );
}
if ( norm > 0 ) {
ForesterUtil.programMessage( PRG_NAME, "normalizer: " + norm + " (" + ForesterUtil.round( value, 6 ) + ")" );
}
System.out.println( " -" + FIRST_OPTION + "=<i>: first evaluator topology to use (0-based) [default: 0]" );
System.out.println( " -" + LAST_OPTION
System.out.println( " -" + FIRST_OPTION + "=<i>: first evaluator topology to use (0-based) [default: 0]" );
System.out.println( " -" + LAST_OPTION
final PhylogenyNode node = it.next();
if ( ext_nodes.contains( node ) ) {
throw new IllegalArgumentException( "external node [" + node.toString() + "] of " + msg
final PhylogenyNode node = it.next();
if ( ext_nodes.contains( node ) ) {
throw new IllegalArgumentException( "external node [" + node.toString() + "] of " + msg