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.io.mmtf;
022
023import java.util.List;
024import java.util.Map;
025
026import org.biojava.nbio.structure.Atom;
027import org.biojava.nbio.structure.Chain;
028
029/**
030 * Class to store the summary data for a given structure.
031 * @author Anthony Bradley
032 *
033 */
034public class MmtfSummaryDataBean {
035
036        private Map<String, Integer> chainIdToIndexMap;
037        private List<Chain> allChains;
038        private List<Atom> allAtoms;
039        private int numBonds;
040        
041        /**
042         * @return the list of chains (in all models) in the structure
043         */
044        public List<Chain> getAllChains() {
045                return allChains;
046        }
047        /**
048         * @param allChains the list of chains (in all models) in the structure
049         */
050        public void setAllChains(List<Chain> allChains) {
051                this.allChains = allChains;
052        }
053        /**
054         * @return the list of atoms (in all models) in the structure
055         */
056        public List<Atom> getAllAtoms() {
057                return allAtoms;
058        }
059        /**
060         * @param allAtoms the list of atoms (in all models) in the structure
061         */
062        public void setAllAtoms(List<Atom> allAtoms) {
063                this.allAtoms = allAtoms;
064        }
065        /**
066         * @return the number of covalent bonds in the structure
067         */
068        public int getNumBonds() {
069                return numBonds;
070        }
071        /**
072         * @param numBonds the number of covalent bonds in the structure
073         */
074        public void setNumBonds(int numBonds) {
075                this.numBonds = numBonds;
076        }
077        /**
078         * @return the map of chain ids (strings asymId) to the index of that chain in the allChains list. 
079         * This only applies for the first model in the structure.
080         */
081        public Map<String, Integer> getChainIdToIndexMap() {
082                return chainIdToIndexMap;
083        }
084        /**
085         * @param chainIdToIndexMap the map of chain ids (strings asymId) to the index of that chain in the allChains list. 
086         * This only applies for the first model in the structure.
087         */
088        public void setChainIdToIndexMap(Map<String, Integer> chainIdToIndexMap) {
089                this.chainIdToIndexMap = chainIdToIndexMap;
090        }
091}