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 */
021package org.biojava.nbio.structure.secstruc;
022
023import org.biojava.nbio.structure.ResidueNumber;
024import org.biojava.nbio.structure.ResidueRangeAndLength;
025
026/**
027 * A secondary structure element (SSE) is an object representing a block of
028 * sequential residues that share the same secondary structure type.
029 *
030 * @author Aleix Lafita
031 * @since 4.1.1
032 *
033 */
034public class SecStrucElement {
035
036        private SecStrucType type;
037        private ResidueRangeAndLength range;
038        private int index;
039
040        /**
041         * Create a new SSE object. The start and end residue numbers cannot be the
042         * same.
043         *
044         * @param type
045         *            object describing the type of SS
046         * @param start
047         *            first residue of the SSE
048         * @param end
049         *            final residue of the SSE
050         * @param length
051         *            number of residues included in the SSE
052         * @param index
053         * @param chainID
054         *            the chain ID
055         */
056        public SecStrucElement(SecStrucType type, ResidueNumber start,
057                        ResidueNumber end, int length, int index, String chainID) {
058
059                this.type = type;
060                this.index = index;
061                range = new ResidueRangeAndLength(chainID, start, end, length);
062        }
063
064        /**
065         * Returns the {@link SecStrucType} of this element.
066         *
067         * @return
068         */
069        public SecStrucType getType() {
070                return type;
071        }
072
073        /**
074         * Returns the index of the SSE for its type. This is, the sequential
075         * position of this SSE relative to the other SSE of the same type.
076         *
077         * @return
078         */
079        public int getIndex() {
080                return index;
081        }
082
083        /**
084         * Return the length (number of residues) in the SSE.
085         *
086         * @return
087         */
088        public int getLength() {
089                return range.getLength();
090        }
091
092        /**
093         * Returns the ID of this element. The ID is the concatenation of the type
094         * letter and the numerical element identifier (e.g. H1, S1, ...).
095         *
096         * @return
097         */
098        public String getId() {
099                return type.toString() + index + "";
100        }
101
102        /**
103         * Returns the residue range of this SSE.
104         *
105         * @return
106         */
107        public ResidueRangeAndLength getRange() {
108                return range;
109        }
110
111        @Override
112        public String toString() {
113                return getId() + ": " + range.toString();
114        }
115
116}