// 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.PhylogenyMethods;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
final static private String PRG_NAME = "count_support";
final static private String PRG_VERSION = "1.0";
final static private String PRG_DATE = "2008.03.04";
final static private String PRG_NAME = "count_support";
final static private String PRG_VERSION = "1.0";
final static private String PRG_DATE = "2008.03.04";
private final static boolean WRITE_EVALUATORS_AS_NHX = false;
public static void main( final String args[] ) {
private final static boolean WRITE_EVALUATORS_AS_NHX = false;
public static void main( final String args[] ) {
- ForesterUtil
- .printProgramInformation( count_support.PRG_NAME, count_support.PRG_VERSION, count_support.PRG_DATE );
+ ForesterUtil.printProgramInformation( PRG_NAME,
+ null,
+ PRG_VERSION,
+ PRG_DATE,
+ E_MAIL,
+ WWW,
+ ForesterUtil.getForesterLibraryInformation() );
if ( ( args.length < 3 ) || ( args.length > 7 ) ) {
System.out.println();
System.out.println( count_support.PRG_NAME + ": wrong number of arguments" );
if ( ( args.length < 3 ) || ( args.length > 7 ) ) {
System.out.println();
System.out.println( count_support.PRG_NAME + ": wrong number of arguments" );
p = factory.create( phylogeny_infile, pp )[ 0 ];
}
catch ( final Exception e ) {
p = factory.create( phylogeny_infile, pp )[ 0 ];
}
catch ( final Exception e ) {
- ForesterUtil.fatalError( count_support.PRG_NAME, "Could not read \"" + phylogeny_infile + "\" ["
- + e.getMessage() + "]" );
+ ForesterUtil.fatalError( count_support.PRG_NAME,
+ "Could not read \"" + phylogeny_infile + "\" [" + e.getMessage() + "]" );
ev = factory.create( evaluators_infile, pp );
}
catch ( final Exception e ) {
ev = factory.create( evaluators_infile, pp );
}
catch ( final Exception e ) {
- ForesterUtil.fatalError( count_support.PRG_NAME, "Could not read \"" + evaluators_infile + "\" ["
- + e.getMessage() + "]" );
+ ForesterUtil.fatalError( count_support.PRG_NAME,
+ "Could not read \"" + evaluators_infile + "\" [" + e.getMessage() + "]" );
else {
System.out.println( "Writing " + ev.length + " evaluator phylogenies to :" + evaluators_outfile );
if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
else {
System.out.println( "Writing " + ev.length + " evaluator phylogenies to :" + evaluators_outfile );
if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
- w.toNewHampshireX( Arrays.asList( ev ), evaluators_outfile, ";"
- + ForesterUtil.getLineSeparator() );
+ w.toNewHampshireX( Arrays.asList( ev ),
+ evaluators_outfile,
+ ";" + ForesterUtil.getLineSeparator() );
}
else {
w.toNewHampshire( Arrays.asList( ev ), true, branch_lengths_in_ev_out, evaluators_outfile, ";"
}
else {
w.toNewHampshire( Arrays.asList( ev ), true, branch_lengths_in_ev_out, evaluators_outfile, ";"