/*
 *                  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 chainName 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;
	}

}
