// Copyright (C) 2010 Christian M Zmasek
// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
// 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
import java.io.IOException;
import java.io.Writer;
+import java.util.ArrayList;
import java.util.List;
import org.forester.sequence.Sequence;
return _type;
}
+ @Override
public void setIdentifier( final int row, final Object id ) {
_identifiers[ row ] = id;
}
+ @Override
public void setResidueAt( final int row, final int col, final char residue ) {
_data[ row ][ col ] = residue;
}
return sb.toString();
}
+ @Override
public void write( final Writer w ) throws IOException {
final int max = determineMaxIdLength() + 1;
for( int row = 0; row < _data.length; ++row ) {
}
return msa;
}
+
+ @Override
+ public List<Character> getColumnAt( final int col ) {
+ final List<Character> column = new ArrayList<Character>();
+ for( int row = 0; row < getNumberOfSequences(); ++row ) {
+ column.add( getResidueAt( row, col ) );
+ }
+ return column;
+ }
}