// 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.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
if ( dss_comp != null ) {
sb.append( ForesterUtil.getLineSeparator() );
sb.append( "\t" + ForesterUtil.normalizeString( "values for support means:", max_length, true, ' ' )
if ( dss_comp != null ) {
sb.append( ForesterUtil.getLineSeparator() );
sb.append( "\t" + ForesterUtil.normalizeString( "values for support means:", max_length, true, ' ' )
sb.append( ForesterUtil.round( dss_comp.arithmeticMean(), support_statistics.PLACES ) + "\t" );
sb.append( ForesterUtil.round( dss_comp.sampleStandardDeviation(), support_statistics.PLACES ) + "\t" );
sb.append( ForesterUtil.round( dss_comp.getMin(), support_statistics.PLACES ) + "\t" );
sb.append( ForesterUtil.round( dss_comp.arithmeticMean(), support_statistics.PLACES ) + "\t" );
sb.append( ForesterUtil.round( dss_comp.sampleStandardDeviation(), support_statistics.PLACES ) + "\t" );
sb.append( ForesterUtil.round( dss_comp.getMin(), support_statistics.PLACES ) + "\t" );
for( int i = 0; i < phylogenies_infiles.length; i++ ) {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
for( int i = 0; i < phylogenies_infiles.length; i++ ) {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser pp = ForesterUtil
- .createParserDependingOnFileType( phylogenies_infiles[ i ], true );
+ final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogenies_infiles[ i ], true );
phylogenies[ i ] = factory.create( phylogenies_infiles[ i ], pp )[ 0 ];
}
catch ( final IOException e ) {
phylogenies[ i ] = factory.create( phylogenies_infiles[ i ], pp )[ 0 ];
}
catch ( final IOException e ) {