// 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
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.application;
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 );
}
if ( ( first < 0 ) || ( last < 0 ) ) {
ForesterUtil
- .fatalError( PRG_NAME,
- "attempt to set first or last evaluator topology to use to a number less than zero" );
+ .fatalError( PRG_NAME,
+ "attempt to set first or last evaluator topology to use to a number less than zero" );
}
if ( norm < 0 ) {
ForesterUtil.fatalError( PRG_NAME, "illegal value for normalizer [" + norm + "]" );
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 + "]: "
}
if ( ( last >= evaluators.length ) || ( last <= first ) ) {
ForesterUtil.fatalError( PRG_NAME, "illegal value for first or last evaluator topology to use [" + first
- + ", " + last + "]" );
+ + ", " + last + "]" );
}
double value = 1;
if ( norm > 0 ) {
- value = norm / ( 1 + last - first );
+ value = norm / ( ( 1 + last ) - first );
}
ForesterUtil.programMessage( PRG_NAME, "first topology to use: " + first );
String is_last = "";
is_last = " (corresponds to last topology in file)";
}
ForesterUtil.programMessage( PRG_NAME, "last topology to use : " + last + is_last );
- ForesterUtil.programMessage( PRG_NAME, "sum of topologies used as evaluators: " + ( last - first + 1 ) );
+ ForesterUtil.programMessage( PRG_NAME, "sum of topologies used as evaluators: " + ( ( last - first ) + 1 ) );
if ( norm > 0 ) {
ForesterUtil.programMessage( PRG_NAME, "normalizer: " + norm + " (" + ForesterUtil.round( value, 6 ) + ")" );
}
System.out.println( "Usage:" );
System.out.println();
System.out.println( PRG_NAME
- + " [options] <confidence type> <target tree file> <evaluators tree file> <outfile>" );
+ + " [options] <confidence type> <target tree file> <evaluators tree file> <outfile>" );
System.out.println();
System.out.println( "options:" );
System.out.println();
System.out.println( " -" + STRICT_OPTION
- + " : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match" );
+ + " : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match" );
System.out.println( " -" + NORMALIZE_OPTION
- + "=<d>: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]" );
+ + "=<d>: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]" );
System.out.println( " -" + FIRST_OPTION + "=<i>: first evaluator topology to use (0-based) [default: 0]" );
System.out.println( " -" + LAST_OPTION
- + "=<i>: last evaluator topology to use (0-based) [default: use all until final topology]" );
+ + "=<i>: last evaluator topology to use (0-based) [default: use all until final topology]" );
System.out.println();
}
final PhylogenyNode node = it.next();
if ( ext_nodes.contains( node ) ) {
throw new IllegalArgumentException( "external node [" + node.toString() + "] of " + msg
- + " is not unique" );
+ + " is not unique" );
}
ext_nodes.add( node );
}