/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on 28.04.2004
 * @author Andreas Prlic
 *
 */
package org.biojava.nbio.structure;

import org.biojava.nbio.structure.io.FileConvert;

import java.util.ArrayList;
import java.util.List;

import javax.vecmath.Point3d;


/**
 * Implementation of an Atom of a PDB file.
 * currently the coordinates of an atom are represented by a double[3] array.
 * @author Andreas Prlic
 * @since 1.4
 * @version %I% %G%
 */
public class AtomImpl implements Atom {

        private static final long serialVersionUID = -2258364127420562883L;

        /**
         * The inital capacity of the bonds list.
         * Most atoms have a maximum of 3 heavy atom neighbors.
         */
        public static final int BONDS_INITIAL_CAPACITY = 3;

        private String name;
        private Element element;        
        private Point3d coords;
        private int pdbserial;
        private short charge;

        private float occupancy ;
        private float tempfactor;

        private char altLoc ;
        private Group parent;

        private List<Bond> bonds;

        public AtomImpl () {
                name       = null;
                element    = Element.R;
                coords     = new Point3d();
                occupancy  = 0.0f;
                tempfactor = 0.0f;
                altLoc     = 0;
                parent     = null;
                bonds      = null; // let's save some memory and let's not initialise this until it's needed - JD 2016-03-02
                charge     = 0;
        }

        /**
         * {@inheritDoc}
         */
        @Override
        public void   setName(String s) { name = s ;}

        /**
         * {@inheritDoc}
         */
        @Override
        public String getName()         { return name ;}

        /**
         * {@inheritDoc}
         */
        @Override
        public void setPDBserial(int i) { pdbserial = i    ; }

        /**
         * {@inheritDoc}
         */
        @Override
        public int  getPDBserial()      { return pdbserial ; }

        /**
         * {@inheritDoc}
         */
        @Override
        public void     setCoords( double[] c ) { 
                coords = new Point3d(c); 
        }

        /**
         * {@inheritDoc}
         */
        @Override
        public double[] getCoords() { 
                double[] c = new double[3];
                coords.get(c);
                return c;               
        }
        
        /**
         * {@inheritDoc}
         */
        @Override
        public Point3d getCoordsAsPoint3d() {
                return coords;
        }

        @Override
        public void setX(double x) {
                coords.x = x ;
        }
        
        @Override
        public void setY(double y) {
                coords.y = y ;
        }
        
        @Override
        public void setZ(double z) {
                coords.z = z ;
        }

        /**
         * {@inheritDoc}
         */
        @Override
        public double getX() { return coords.x; }

        /**
         * {@inheritDoc}
         */
        @Override
        public double getY() { return coords.y; }

        /**
         * {@inheritDoc}
         */
        @Override
        public double getZ() { return coords.z; }

        /**
         * Set alternate Location.
         * @see #getAltLoc
         */
        @Override
        public void setAltLoc(Character c) {
                // after changing altLoc from Character to char, we do this to keep the interface the same as it used to be - JD 2016-01-27
                if (c==null)
                        altLoc = 0;
                else
                        altLoc = c ;
        }

        /**
         * Get alternate Location.
         * @return a Character object representing the alt loc value
         * @see #setAltLoc
         */
        @Override
        public Character getAltLoc() {
                // after changing altLoc from Character to char, we do this to keep the interface the same as it used to be - JD 2016-01-27
                if (altLoc==0 ) return null;
                return altLoc ;
        }

        @Override
        public String toString() {
                return name + " " + element + " " + pdbserial + " " + coords.x + " " + coords.y + " " + coords.z;
        }

        @Override
        public void   setOccupancy(float occu){
                occupancy = occu ;
        }

        @Override
        public float getOccupancy(){
                return occupancy;
        }

        @Override
        public void   setTempFactor(float temp) {
                tempfactor = temp ;
        }

        @Override
        public float getTempFactor() {
                return tempfactor;
        }

        /** returns and identical copy of this  object .
         * @return  and identical copy of this  object
         */
        @Override
        public Object clone() {
                AtomImpl n = new AtomImpl();
                n.setOccupancy(getOccupancy());
                n.setTempFactor(getTempFactor());
                n.altLoc = altLoc; // since char is a primitive we can do this (to avoid going through getter/setter that check for nulls)
                n.setCharge(getCharge());
                double[] coords = getCoords();
                n.setX(coords[0]);
                n.setY(coords[1]);
                n.setZ(coords[2]);
                n.setPDBserial(getPDBserial());
                n.setName(getName());
                n.setElement(getElement());
                // NOTE bonds can't be cloned here, they would need to be cloned at the
                //      chain or group level (depending if they are intra or inter group bonds) -- JD 2016-03-02

                return n ;
        }

        /**
         * {@inheritDoc}
         */
        @Override
        public void setGroup(Group parent){
                this.parent = parent;
        }

        /**
         * {@inheritDoc}
         */
        @Override
        public Group getGroup(){
                return parent;
        }

        /**
         * {@inheritDoc}
         */
        @Override
        public Element getElement() {
                return element;
        }

        /**
         * {@inheritDoc}
         */
        @Override
        public void setElement(Element e) {
                this.element = e;

        }

        @Override
        public String toPDB() {

                return FileConvert.toPDB(this);
        }

        @Override
        public void toPDB(StringBuffer buf) {
                FileConvert.toPDB(this,buf);

        }

        /**
         * {@inheritDoc}
         */
        @Override
        public List<Bond> getBonds() {
                return bonds;
        }

        /**
         * {@inheritDoc}
         */
        @Override
        public boolean hasBond(Atom other){
                if ( bonds == null)
                        return false;

                for (Bond b : bonds){
                        if ( b.getAtomA().equals(other) || b.getAtomB().equals(other))
                                return true;
                }
                return false;
        }

        /**
         * {@inheritDoc}
         */
        @Override
        public void setBonds(List<Bond> bonds) {
                this.bonds = bonds;
        }

        @Override
        public void addBond(Bond bond) {
                if (bonds==null) {
                        bonds = new ArrayList<Bond>(BONDS_INITIAL_CAPACITY);
                }
                bonds.add(bond);
        }

        @Override
        public short getCharge() {
                // Get the charge
                return charge;
        }

        @Override
        public void setCharge(short inputCharge) {
                // Set the charge
                charge = inputCharge;

        }
}