// 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.phylogeny.data;
}
}
+ @Override
public StringBuffer asSimpleText() {
final StringBuffer sb = new StringBuffer();
if ( isUnassigned() ) {
return sb;
}
+ @Override
public StringBuffer asText() {
final StringBuffer sb = new StringBuffer();
if ( isUnassigned() || isSpeciationOrDuplication() || isOther() || isRoot() || isTransfer() || isFusion() ) {
return sb;
}
+ @Override
public PhylogenyData copy() {
if ( isUnassigned() ) {
return new Event();
return ( _duplications > 0 ) && ( _gene_losses < 1 ) && ( _speciations < 1 );
}
+ @Override
public boolean isEqual( final PhylogenyData event ) {
if ( ( event == null ) || !( event instanceof Event ) ) {
return false;
_event_type = EventType.mixed;
}
+ @Override
public StringBuffer toNHX() {
final StringBuffer sb = new StringBuffer();
if ( !isUnassigned() && ( isSpeciationOrDuplication() || isDuplication() || isSpeciation() ) ) {
return sb;
}
+ @Override
public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
writer.write( ForesterUtil.LINE_SEPARATOR );
writer.write( indentation );