/*
 *                  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 Sep 3, 2007
 *
 */
package org.biojava.nbio.structure;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.Serializable;
import java.lang.reflect.Method;
import java.util.Formatter;
import java.util.Locale;


/** A class to represent database cross references. This is just a simple bean that contains the infor from one
 * DBREF line
 *
 * @author Andreas Prlic
 * @since 4:56:14 PM
 * @version %I% %G%
 */
public class DBRef implements PDBRecord, Serializable{

        private final static Logger logger = LoggerFactory.getLogger(DBRef.class);

        private static final long serialVersionUID = -1050178577542224379L;

        private Structure parent;
        private String idCode;
        private String chainId;
        private int seqbegin;
        private char insertBegin;
        private int seqEnd;
        private char insertEnd;

        private String database;
        private String dbAccession;
        private String dbIdCode;

        private int dbSeqBegin;
        private char idbnsBegin;
        private int dbSeqEnd;
        private char idbnsEnd;

        private Long id;

        public DBRef() {
                insertBegin = ' ';
                insertEnd   = ' ';
                idbnsBegin  = ' ';
                idbnsEnd    = ' ';
        }

        /** Get the ID used by Hibernate.
         *
         * @return the ID used by Hibernate
         * @see #setId(Long)
         */
        public Long getId() {
                return id;
        }

        /** Set the ID used by Hibernate.
         *
         * @param id the id assigned by Hibernate
         * @see #getId()
         */
        public void setId(Long id) {
                this.id = id;
        }

        /** Set the structure object that this DBRef relates to.
         *
         * @param s a structure object
         * @see #getParent()
         */
        public void setParent(Structure s){
                parent = s;

        }

        /** Get the structure object that this DBRef relates to.
         *
         * @return s a structure object
         * @see #setParent(Structure)
         */
        public Structure getParent(){
                return parent;
        }

        /** Convert the DBRef object to a DBREF record as it is used in PDB files
         *
         * @return a PDB - DBREF formatted line
         */
        @Override
        public String toPDB(){

                 StringBuffer buf = new StringBuffer();
                 toPDB(buf);
                 return buf.toString();

        }

        /** Append the PDB representation of this DBRef to the provided StringBuffer
         *
         * @param buf the StringBuffer to write to.
         */
        @Override
        public void toPDB(StringBuffer buf){
                 Formatter formatter = new Formatter(new StringBuilder(),Locale.UK);
//        DBREF  3ETA A  990  1295  UNP    P06213   INSR_HUMAN    1017   1322
//        DBREF  3EH2 A    2   767  UNP    P53992   SC24C_HUMAN    329   1094
//        DBREF 3EH2 A    2   767     UNP   P53992  SC24C_HUMAN   329   1094
//        DBREF  3ETA A  990  1295  UNP    P06213   INSR_HUMAN    1017   1322
                formatter.format("DBREF  %4s %1s %4d%1s %4d%1s %-6s %-8s %-12s%6d%1c%6d%1c            ",
                                idCode, chainId,seqbegin,insertBegin,seqEnd,insertEnd,
                                database,dbAccession,dbIdCode,
                                dbSeqBegin,idbnsBegin,dbSeqEnd,idbnsEnd
                                );

                buf.append(formatter.toString());
                formatter.close();

        }
        /** String representation of a DBRef.
         * @return a String
         */
        @Override
        public String toString(){
                StringBuilder buf = new StringBuilder();

                try {

                        @SuppressWarnings("rawtypes")
                        Class c = Class.forName(DBRef.class.getName());
                        Method[] methods  = c.getMethods();

                        for (Method m : methods) {
                                String name = m.getName();

                                if (name.substring(0, 3).equals("get")) {
                                        if (name.equals("getClass")) {
                                                continue;
                                        }
                                        Object o = m.invoke(this);
                                        if (o != null) {
                                                buf.append(name.substring(3, name.length()));
                                                buf.append(": ").append(o).append(" ");
                                        }
                                }
                        }
                } catch (Exception e){
                        logger.error("Exception: ", e);
                }

                return buf.toString();
        }


        /** get the idCode for this entry
         *
         * @return the idCode
         * @see #setIdCode(String)
         */
        public String getIdCode() {
                return idCode;
        }

        /** Set the idCode for this entry.
         *
         * @param idCode the idCode for this entry
         * @see #getIdCode()
         */
        public void setIdCode(String idCode) {
                this.idCode = idCode;
        }

        /** The chain ID of the corresponding chain.
         *
         * @return chainId the ID of the corresponding chain.
         */
        public String getChainId() {
                return chainId;
        }


        /** The chain ID of the corresponding chain.
         *
         * @param chainId the ID of the corresponding chain
         * @see #getChainId()
         */
        public void setChainId(String chainId) {
                this.chainId = chainId;
        }


        /** The database of the db-ref.
         * uses the abbreviation as provided in the PDB files:
         *
         *<pre>   Database name                         database
                                                                         (code in columns 27 - 32)
        ----------------------------------------------------------
        GenBank                               GB
        Protein Data Bank                     PDB
        Protein Identification Resource       PIR
        SWISS-PROT                            SWS
        TREMBL                                TREMBL
        UNIPROT                               UNP
        </pre>
         * @return name of database of this DBRef
         * @see #setDatabase(String)
         */
        public String getDatabase() {
                return database;
        }

        /** Specifies the database value.
         *
         * @param database the database
         * @see #getDatabase()
         */
        public void setDatabase(String database) {
                this.database = database;
        }

        /** Sequence database accession code.
         * @return the dbAccession
         * @see #setDbAccession(String)
         * */
        public String getDbAccession() {
                return dbAccession;
        }

        /** Sequence database accession code.
         * @param dbAccession the dbAccession
         * @see #getDbAccession()
         * */
        public void setDbAccession(String dbAccession) {
                this.dbAccession = dbAccession;
        }


        /** Sequence database          identification code.
         *
         * @return the dbIdCode
         * @see #setDbIdCode(String)
         */
        public String getDbIdCode() {
                return dbIdCode;
        }

        /** Sequence database          identification code.
         *
         * @param dbIdCode identification code
         * @see #getDbIdCode()
         */
        public void setDbIdCode(String dbIdCode) {
                this.dbIdCode = dbIdCode;
        }

        /** Initial sequence number of the
        database seqment.
         * @return position
         * @see #setDbSeqBegin(int)
         */
        public int getDbSeqBegin() {
                return dbSeqBegin;
        }


        /** Initial sequence number of the
        database seqment.
         * @param dbSeqBegin a sequence position
         * @see #getDbSeqBegin()
         *
         */
        public void setDbSeqBegin(int dbSeqBegin) {
                this.dbSeqBegin = dbSeqBegin;
        }


        /** Ending sequence position  of the database segment.
         * @return dbSeqEnd
         * @see #setDbSeqEnd(int)
         */
        public int getDbSeqEnd() {
                return dbSeqEnd;
        }


        /** The begin of the sequence position in the database
         *
         * @param dbSeqEnd sequence position
         * @see #getDbSeqEnd()
         */
        public void setDbSeqEnd(int dbSeqEnd) {
                this.dbSeqEnd = dbSeqEnd;
        }

        /** Insertion code of initial residue of the segment, if PDB is the
        reference.
         * @return idbnsBegin isnertion code
         * @see #setIdbnsBegin(char)
         * */
        public char getIdbnsBegin() {
                return idbnsBegin;
        }

        /** Insertion code of initial residue of the segment, if PDB is the
        reference.
         * @param idbnsBegin insertion code
         * @see #getIdbnsBegin()
         * */
        public void setIdbnsBegin(char idbnsBegin) {
                this.idbnsBegin = idbnsBegin;
        }

        /** Insertion code of the ending
        residue of the segment, if PDB is
        the reference.
         * @return idbnsEnd insertion code
         * @see #setIdbnsEnd(char)
         */
        public char getIdbnsEnd() {
                return idbnsEnd;
        }


        /** Insertion code of the ending
        residue of the segment, if PDB is
        the reference.
         * @param idbnsEnd the insertion code
         * @see #setIdbnsEnd(char)
         */
        public void setIdbnsEnd(char idbnsEnd) {
                this.idbnsEnd = idbnsEnd;
        }

        /** Initial insertion code of the PDB sequence segment.
         *
         * @return insertBegin
         * @see #setInsertBegin(char)
         */

        public char getInsertBegin() {
                return insertBegin;
        }

        /** Initial insertion code of the PDB sequence segment.
         *
         * @param insertBegin
         * @see #getInsertBegin()
         */

        public void setInsertBegin(char insertBegin) {
                this.insertBegin = insertBegin;
        }

        /** Ending insertion code of the PDB sequence segment.
         *
         * @return insertEnd insertion code
         * @see #setInsertEnd(char)
         */
        public char getInsertEnd() {
                return insertEnd;
        }

        /** Ending insertion code of the PDB sequence segment.
         *
         * @param insertEnd insertEnd
         * @see #getInsertEnd()
         *
         */
        public void setInsertEnd(char insertEnd) {
                this.insertEnd = insertEnd;
        }

        /**   Initial sequence number of the PDB sequence segment.
         *
         * @return start seq. position
         * @see #setSeqBegin
         */
        public int getSeqBegin() {
                return seqbegin;
        }

        /**   Initial sequence number of the PDB sequence segment.
         *
         * @param seqbegin start seq. position
         * @see #getSeqBegin()
         */
        public void setSeqBegin(int seqbegin) {
                this.seqbegin = seqbegin;
        }

        /**Ending sequence number   of the PDB sequence segment.
         *
         * @return sequence end position
         * @see #getSeqEnd()
         */
        public int getSeqEnd() {
                return seqEnd;
        }

        /**Ending sequence number   of the PDB sequence segment.
         *
         * @param seqEnd sequence end position
         * @see #setSeqEnd(int)
         *
         */
        public void setSeqEnd(int seqEnd) {
                this.seqEnd = seqEnd;
        }

}