// 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
public DistanceMatrix[] parse( final Object source ) throws IOException {
reset();
- final List<BasicTable<String>> tables = BasicTableParser.parse( source, VALUE_SEPARATOR, false, COMMENT, true );
+ final List<BasicTable<String>> tables = BasicTableParser.parse( source,
+ VALUE_SEPARATOR,
+ false,
+ false,
+ COMMENT,
+ true );
final DistanceMatrix[] distance_matrices = new DistanceMatrix[ tables.size() ];
int i = 0;
for( final BasicTable<String> table : tables ) {
throw new IOException( "illegal format for distance [" + table_value + "] at [" + ( col - 1 ) + ", " + row
+ "]" );
}
- distance_matrix.setValue( col - 1 + col_offset, row, d );
+ distance_matrix.setValue( ( col - 1 ) + col_offset, row, d );
}
private DistanceMatrix transform( final BasicTable<String> table ) throws IllegalArgumentException, IOException {
if ( table.getNumberOfColumns() == table.getNumberOfRows() ) {
first_line_is_size = true;
}
- else if ( table.getNumberOfColumns() != table.getNumberOfRows() + 1 ) {
+ else if ( table.getNumberOfColumns() != ( table.getNumberOfRows() + 1 ) ) {
throw new IllegalArgumentException( "attempt to create distance matrix with illegal dimensions [columns: "
+ table.getNumberOfColumns() + ", rows: " + table.getNumberOfRows() + "]" );
}
if ( first_line_is_size ) {
start_row = 1;
}
- for( int row = 0; row < table.getNumberOfRows() - start_row; row++ ) {
+ for( int row = 0; row < ( table.getNumberOfRows() - start_row ); row++ ) {
distance_matrix.setIdentifier( row, table.getValue( 0, row + start_row ) );
switch ( getInputMatrixType() ) {
case LOWER_TRIANGLE: