-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// 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
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// 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
package org.forester.application;
import java.io.File;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
private final static String BASE = "b_";
public static void main( final String args[] ) {
- if ( ( args.length != 2 ) ) {
- System.exit( -1 );
- }
+ File in = null;
+ File out = null;
try {
CommandLineArguments cla = null;
cla = new CommandLineArguments( args );
- final File in = cla.getFile( 0 );
- final File out = cla.getFile( 1 );
+ in = cla.getFile( 0 );
+ out = cla.getFile( 1 );
if ( out.exists() ) {
System.out.println( out + " already exists" );
System.exit( -1 );
processNode( node, i );
i++;
}
- // final PhylogenyWriter writer = new PhylogenyWriter();
- // writer.toPhyloXML( out, phylogeny_0, 0 );
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( out, phylogeny_0, 0 );
}
catch ( final Exception e ) {
System.out.println( e.getLocalizedMessage() );
// }
// }
private static void processNode( final PhylogenyNode node, final int i ) {
+ //if ( node.isExternal() ) {
+ // final String c = "" + node.getNodeData().getBinaryCharacters().getPresentCount();
+ // final String s = node.getNodeData().getTaxonomy().getScientificName();
+ // System.out.println( s + "\t" + c );
+ //}
+ // if ( !node.isExternal() ) {
+ // if ( !node.getNodeData().isHasTaxonomy() ) {
+ // if ( !ForesterUtil.isEmpty( node.getName() ) ) {
+ // if ( ( node.getName().indexOf( "_" ) < 0 ) && ( node.getName().indexOf( "&" ) < 0 )
+ // && ( node.getName().indexOf( " " ) < 0 ) ) {
+ // Taxonomy t = new Taxonomy();
+ // t.setScientificName( node.getName() );
+ // node.getNodeData().addTaxonomy( t );
+ // node.setName( "" );
+ // }
+ // }
+ // }
+ // }
if ( node.isExternal() ) {
- String c = "" + node.getNodeData().getBinaryCharacters().getPresentCount();
- String s = node.getNodeData().getTaxonomy().getScientificName();
- System.out.println( s + "\t" + c );
+ if ( node.getNodeData().isHasTaxonomy() ) {
+ // final Taxonomy t = node.getNodeData().getTaxonomy();
+ // t.setIdentifier( null );
+ //if ( !ForesterUtil.isEmpty( t.getTaxonomyCode() ) && t.getTaxonomyCode().length() == 5 ) {
+ // if ( node.getName().equalsIgnoreCase( t.getTaxonomyCode() ) ) {
+ // node.setName( "" );
+ // }
+ //}
+ node.setName( "" );
+ }
+ else {
+ System.out.println( "node " + node + " has not tax" );
+ }
}
}
-}
+}
\ No newline at end of file