// 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
private Map<PhylogenyNode, STATE_TYPE> getStatesForCharacterForTraceback( final Phylogeny p,
final CharacterStateMatrix<STATE_TYPE> matrix,
final int character_index ) {
- final Map<PhylogenyNode, STATE_TYPE> states = new HashMap<PhylogenyNode, STATE_TYPE>( matrix
- .getNumberOfIdentifiers() );
+ final Map<PhylogenyNode, STATE_TYPE> states = new HashMap<PhylogenyNode, STATE_TYPE>( matrix.getNumberOfIdentifiers() );
for( int indentifier_index = 0; indentifier_index < matrix.getNumberOfIdentifiers(); ++indentifier_index ) {
final STATE_TYPE state = matrix.getState( indentifier_index, character_index );
if ( state == null ) {
.getName() );
getInternalStatesMatrixPriorToTraceback().setIdentifier( identifier_index,
ForesterUtil.isEmpty( node.getName() ) ? node
- .getId()
- + "" : node.getName() );
+ .getId() + "" : node.getName() );
++identifier_index;
}
for( int character_index = 0; character_index < external_node_states_matrix.getNumberOfCharacters(); ++character_index ) {
else if ( current_binary_state == ABSENT ) {//new
setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );//new
}//new
- // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS );
+ // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS );
}
}
}