// 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;
+ "ms" );
System.out.println( "Mapping based on : " + gsdii.getTaxCompBase() );
log_writer.println( "Mapping based on : " + gsdii.getTaxCompBase() );
- if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
- final GSDIR gsdir = ( GSDIR ) gsdii;
- System.out.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() );
- log_writer.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() );
- }
try {
final PhylogenyWriter writer = new PhylogenyWriter();
if ( base_algorithm == ALGORITHM.GSDIR ) {
- writer.toPhyloXML( out_file,
- ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTrees(),
- 0,
- ForesterUtil.LINE_SEPARATOR );
+ writer.toPhyloXML( out_file, ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree(), 0 );
}
else {
writer.toPhyloXML( out_file, gene_tree, 0 );