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     */
022    package org.biojava3.core.sequence.views;
023    
024    import org.biojava3.core.sequence.template.Compound;
025    import org.biojava3.core.sequence.template.Sequence;
026    import org.biojava3.core.sequence.template.SequenceMixin;
027    import org.biojava3.core.sequence.template.SequenceProxyView;
028    
029    /**
030     * For a given sequence this class will return the base at the reversed
031     * position i.e. in a sequence of size 10, if you request base 2 you will get
032     * back the base at position 9. Sub-views can be made of this class which
033     * also respect the reversed calls.
034     *
035     * @author Andy Yates
036     * @param <C> Must be a subtype of @{link Compound}
037     */
038    public class ReversedSequenceView<C extends Compound> extends SequenceProxyView<C> {
039    
040        private final int sequenceSize;
041    
042        public ReversedSequenceView(Sequence<C> sequence) {
043            super(sequence);
044            this.sequenceSize = sequence.getLength();
045        }
046    
047        @Override
048        public String getSequenceAsString() {
049            return SequenceMixin.toString(this);
050        }
051    
052        protected int toIndex(int index) {
053            return (sequenceSize - index) + 1;
054        }
055    
056        @Override
057        public C getCompoundAt(int position) {
058            return super.getCompoundAt(toIndex(position));
059        }
060    }