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.features;
023
024import org.biojava.nbio.core.sequence.template.AbstractSequence;
025import org.biojava.nbio.core.sequence.template.Compound;
026
027import java.util.ArrayList;
028import java.util.List;
029
030/**
031 * DNA Sequences produced by modern sequencers usually have quality informaion
032 * attached to them. This feature allows to store the information directly in
033 * the DNASequence
034 *
035 * @since 3.0.3
036 * @author brandstaetter
037 */
038public class QualityFeature<S extends AbstractSequence<C>, C extends Compound> extends AbstractFeature<S, C> {
039
040        private List<Number> qualities = new ArrayList<Number>();
041
042        /**
043         * @param type
044         * @param source
045         */
046        public QualityFeature(String type, String source) {
047                super(type, source);
048        }
049
050        /**
051         * @return the qualities
052         */
053        public List<Number> getQualities() {
054                return qualities;
055        }
056
057        /**
058         * @param qualities the qualities to set
059         */
060        public void setQualities(List<Number> qualities) {
061                this.qualities = qualities;
062        }
063
064        /**
065         * @param bioindex the biological index (starts with 1)
066         * @return the quality value at the given biological index (starts with 1)
067         */
068        public Number getQualityAt(int bioindex) {
069                return qualities.get(bioindex - 1);
070        }
071
072        /**
073         * @param biostart biological start index (starts with 1)
074         * @param bioend biological end index (starts with 1)
075         * @return a sublist of the qualities between the given biological indices
076         */
077        public List<Number> getQualities(int biostart, int bioend) {
078                return qualities.subList(biostart - 1, bioend - 1);
079        }
080}