// 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.sequence;
public class BasicSequence implements Sequence {
private final char[] _mol_sequence;
- private final String _identifier;
+ private String _identifier;
private final TYPE _type;
private BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
_type = type;
}
+ public void setIdentifier( final String id ) {
+ _identifier = id;
+ }
+
@Override
public String getIdentifier() {
return _identifier;
@Override
public int getNumberOfGapResidues() {
int gaps = 0;
- for( int i = 0; i < _mol_sequence.length; ++i ) {
- if ( _mol_sequence[ i ] == GAP ) {
+ for( final char element : _mol_sequence ) {
+ if ( element == GAP ) {
++gaps;
}
}
public String getMolecularSequenceAsString() {
return new String( getMolecularSequence() );
}
+
+ @Override
+ public boolean isGapAt( final int position ) {
+ return getResidueAt( position ) == GAP;
+ }
}