001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 * Created on 01-21-2010
021 */
022package org.biojava.nbio.core.sequence.views;
023
024import org.biojava.nbio.core.sequence.template.ComplementCompound;
025import org.biojava.nbio.core.sequence.template.Sequence;
026import org.biojava.nbio.core.sequence.template.SequenceMixin;
027import org.biojava.nbio.core.sequence.template.SequenceProxyView;
028
029/**
030 * For a given sequence this class will create a view over the top of it
031 * and for every request the code will return the complement of the underlying
032 * base e.g. base A will become base T
033 *
034 * @author Andy Yates
035 * @param <C> Must be a subtype of @{link ComplementCompound} since
036 * only those support complements
037 */
038public class ComplementSequenceView<C extends ComplementCompound> extends SequenceProxyView<C> {
039
040        public ComplementSequenceView(Sequence<C> sequence) {
041                super(sequence);
042        }
043
044        @Override
045        public String getSequenceAsString() {
046                return SequenceMixin.toString(this);
047        }
048
049        @SuppressWarnings("unchecked")
050        @Override
051        public C getCompoundAt(int position) {
052                return (C) super.getCompoundAt(position).getComplement();
053        }
054
055        @SuppressWarnings("unchecked")
056        @Override
057        public int getIndexOf(C compound) {
058                return super.getIndexOf((C) compound.getComplement());
059        }
060
061        @SuppressWarnings("unchecked")
062        @Override
063        public int getLastIndexOf(C compound) {
064                return super.getLastIndexOf((C) compound.getComplement());
065        }
066}