// 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
_type = type;
}
+ @Override
public Object getIdentifier() {
return _identifier;
}
+ @Override
public int getLength() {
return _mol_sequence.length;
}
+ @Override
public char[] getMolecularSequence() {
return _mol_sequence;
}
+ @Override
public char getResidueAt( final int position ) {
return _mol_sequence[ position ];
}
+ @Override
public TYPE getType() {
return _type;
}
@Override
+ public int getNumberOfGapResidues() {
+ int gaps = 0;
+ for( int i = 0; i < _mol_sequence.length; ++i ) {
+ if ( _mol_sequence[ i ] == GAP ) {
+ ++gaps;
+ }
+ }
+ return gaps;
+ }
+
+ @Override
public String toString() {
final StringBuffer sb = new StringBuffer();
sb.append( _identifier.toString() );