/*
 *                    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 Jun 17, 2010
 * Author: ap3
 *
 */

package org.biojava.nbio.structure;

import java.io.Serializable;
import java.io.StringWriter;

/** 
 * Everything that is needed to uniquely describe a residue position
 *
 * @author Andreas Prlic
 *
 */
public class ResidueNumber implements Serializable, Comparable<ResidueNumber>
{

        private static final long serialVersionUID = 1773011704758536083L;
        private String chainName;
        private Character insCode;
        private Integer seqNum;

        public ResidueNumber() {
        }

        public ResidueNumber(ResidueNumber o) {
                this.chainName = o.chainName;
                this.insCode = o.insCode;
                this.seqNum = o.seqNum;
        }

        public ResidueNumber(String chainName, Integer residueNumber, Character insCode) {
                this.chainName = chainName;
                this.seqNum = residueNumber;
                this.insCode = insCode;
        }

        public String getChainName()
        {
                return chainName;
        }
        public void setChainName(String chainName)
        {
                this.chainName = chainName;
        }
        public Character getInsCode()
        {
                return insCode;
        }
        public void setInsCode(Character insCode)
        {
                this.insCode = insCode;
        }
        public Integer getSeqNum()
        {
                return seqNum;
        }
        public void setSeqNum(Integer seqNum)
        {
                this.seqNum = seqNum;
        }





        @Override
        public boolean equals(Object obj) {
                if (this == obj)
                        return true;
                if (obj == null)
                        return false;
                if (getClass() != obj.getClass())
                        return false;
                ResidueNumber other = (ResidueNumber) obj;
                if (chainName == null) {
                        if (other.chainName != null)
                                return false;
                } else if (!chainName.equals(other.chainName))
                        return false;
                if (insCode == null) {
                        if (other.insCode != null)
                                return false;
                } else if (!insCode.equals(other.insCode))
                        return false;
                if (seqNum == null) {
                        if (other.seqNum != null)
                                return false;
                } else if (!seqNum.equals(other.seqNum))
                        return false;

                return true;
        }
        
        /**
         * Check if the seqNum and insertion code are equivalent,
         * ignoring the chain
         * @param obj
         * @return
         */
        public boolean equalsPositional(Object obj) {
                if (this == obj)
                        return true;
                if (obj == null)
                        return false;
                if (getClass() != obj.getClass())
                        return false;
                ResidueNumber other = (ResidueNumber) obj;
                if (insCode == null) {
                        if (other.insCode != null)
                                return false;
                } else if (!insCode.equals(other.insCode))
                        return false;
                if (seqNum == null) {
                        if (other.seqNum != null)
                                return false;
                } else if (!seqNum.equals(other.seqNum))
                        return false;

                return true;

        }

        @Override
        public int hashCode() {
                final int prime = 31;
                int result = 1;
                result = prime * result + ((chainName == null) ? 0 : chainName.hashCode());
                result = prime * result + ((insCode == null) ? 0 : insCode.hashCode());
                result = prime * result + ((seqNum == null) ? 0 : seqNum.hashCode());
                return result;
        }

        /**
         * @return The residue number and insertion code as a string, eg "74A"
         * @see java.lang.Object#toString()
         */
        @Override
        public String toString() {

                StringWriter writer = new StringWriter();
                //         if ( chainName != null){
                //                 writer.append(chainName);
                //                 writer.append(":");
                //         }
                writer.append(String.valueOf(seqNum));
                if (  insCode != null && ( insCode != ' '))
                        writer.append(insCode);

                return writer.toString();
        }

        /**
         * @return The chain, number, and insertion code as a string, eg "B  74A" or "A    1 "
         */
        public String toPDB() {
                String insCodeS ;
                if ( insCode != null)
                        insCodeS = insCode+"";
                else insCodeS = " ";
                return String.format("%s%4d%-2s", chainName, seqNum, insCodeS);
        }


        /** Convert a string representation of a residue number to a residue number object.
         * The string representation can be a integer followed by a character.
         *
         * @param pdb_code
         * @return a ResidueNumber object, or null if the input was null
         */
        public static ResidueNumber fromString(String pdb_code) {
                if(pdb_code == null)
                        return null;

                ResidueNumber residueNumber = new ResidueNumber();
                Integer resNum = null;
                String icode = null;

                try {
                        resNum = Integer.parseInt(pdb_code);
                } catch ( NumberFormatException e){
                        // there is an insertion code..

                        // Split at any position that's either:
                        // preceded by a digit and followed by a non-digit, or
                        // preceded by a non-digit and followed by a digit.
                        String[] spl = pdb_code.split("(?<=\\d)(?=\\D)|(?<=\\D)(?=\\d)");
                        if ( spl.length == 2){
                                resNum = Integer.parseInt(spl[0]);
                                icode = spl[1];
                        }

                }

                residueNumber.setSeqNum(resNum);
                if ( icode == null)
                        residueNumber.setInsCode(null);
                else if ( icode.length() > 0)
                        residueNumber.setInsCode(icode.charAt(0));
                return residueNumber;
        }


        /**
         * Compare residue numbers by chain, sequence number, and insertion code
         */
        @Override
        public int compareTo(ResidueNumber other) {

                // chain id
                if (chainName != null && other.chainName != null) {
                        if (!chainName.equals(other.chainName)) return chainName.compareTo(other.chainName);
                }
                if (chainName != null && other.chainName == null) {
                        return 1;
                } else if (chainName == null && other.chainName != null) {
                        return -1;
                }

                return compareToPositional(other);
        }

        /**
         * Compare residue numbers by sequence number and insertion code,
         * ignoring the chain
         * @param other
         * @return
         */
        public int compareToPositional(ResidueNumber other) {
                // sequence number
                if (seqNum != null && other.seqNum != null) {
                        if (!seqNum.equals(other.seqNum)) return seqNum.compareTo(other.seqNum);
                }
                if (seqNum != null && other.seqNum == null) {
                        return 1;
                } else if (seqNum == null && other.seqNum != null) {
                        return -1;
                }

                // insertion code
                if (insCode != null && other.insCode != null) {
                        if (!insCode.equals(other.insCode)) return insCode.compareTo(other.insCode);
                }
                if (insCode != null && other.insCode == null) {
                        return 1;
                } else if (insCode == null && other.insCode != null) {
                        return -1;
                }

                return 0;
        }

        public String printFull() {
                final String chain = chainName==null? "" : chainName;
                return chain + "_" + toString();
        }

}