/*
 *
 * 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/
 *
 */

package org.biojava.nbio.structure;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;

/**
 * Holds the data of sites presented in PDB files. <br/>
 * Example from the PDB flatfile:
 * <pre>
	SITE     1 AC1  3 GLY A  65  CYS A  67  HOH A 180
	SITE     1 AC2 10 HIS C  37  ALA C  39  THR C 152  LEU C 153
	SITE     2 AC2 10 HIS D  37  ALA D  39  THR D 152  LEU D 153
	SITE     3 AC2 10 SER D 154  GOL D 172
	</pre>
 * @author Amr AL-Hossary
 * @author Jules Jacobsen
 */
public class Site implements PDBRecord, Serializable, Comparable<Site> {

	private static final long serialVersionUID = -4577047072916341237L;
	private static final String lineEnd = System.getProperty("line.separator");

	private String siteID = "";
	private List<Group> groups = new ArrayList<Group>();
	//variables for REMARK 800
	private String evCode = "";
	private String description = "";

	public Site() {
	}

	public Site(String siteID, List<Group> groups) {
		this.siteID = siteID;
		this.groups = groups;
	}


	@Override
	public String toString() {
		StringBuilder stringBuilder = new StringBuilder("SITE ");
		stringBuilder.append(siteID).append(" ").append(groups.size()).append(" ");
		for (Group group : groups) {
			// 012345678910
			//'ARG H 221A '
			String groupString = String.format("%s %s",
						group.getPDBName(),
						group.getResidueNumber().toPDB());
			stringBuilder.append(groupString);
		}
		stringBuilder.append(lineEnd);
		return stringBuilder.toString();
	}


	@Override
	public String toPDB() {
		StringBuffer buffer = new StringBuffer();
		toPDB(buffer);
		return buffer.toString();
	}


	@Override
	public void toPDB(StringBuffer buf) {
		if (groups == null || groups.size() < 1) {
			return;
		}

		//SITE     1 CAT  3 HIS H  57  ASP H 102  SER H 195
		//SITE     1 AC1  6 ARG H 221A LYS H 224  HOH H 403  HOH H 460
		//SITE     2 AC1  6 HOH H 464  HOH H 497
		//         ^  ^   ^
		//     cont# id  group size
		//max 4 groups per line

		//counters for tracking where we are
		int seqNum = 0;
		int groupsWritten = 0;
		int groupNum = 0;
		//new StringBuilder for adding the groups to
		StringBuilder stringBuilder = new StringBuilder();

		while (groupsWritten < groups.size()) {
			StringBuilder groupsString = new StringBuilder();
			for (int i = 0; i < 4 && groupsWritten < groups.size(); i++) {
				Group group = groups.get(groupNum);
				// Make sure the pdbName is formatted as 3 width string.
				String groupString = String.format(Locale.UK, "%3s %s",
						group.getPDBName(), group.getResidueNumber().toPDB());
				groupsWritten++;
				groupNum++;
				if (i == 3 || groupsWritten == groups.size()) {
					// groupString = groupString.trim();
					groupString.replaceFirst("\\s+$", ""); // remove only trailing whitespace.
				}
				groupsString.append(groupString);
			}
			stringBuilder.append(String.format(Locale.UK, "SITE   %3d %3s %2d %-62s", seqNum + 1, siteID, groups.size(), groupsString.toString()));
			//iterate the line counter, add the end of line character
			seqNum++;
			stringBuilder.append(lineEnd);
		}

		buf.append(stringBuilder);
	}

	/**
	 * Appends the REMARK 800 section pertaining to the site onto the end of the
	 * StringBuffer provided.
	 *
	 * For example in pdb 1a4w:
	 * REMARK 800 SITE_IDENTIFIER: CAT
	 * REMARK 800 EVIDENCE_CODE: UNKNOWN
	 * REMARK 800 SITE_DESCRIPTION: ACTIVE SITE
	 *
	 * @param stringBuffer
	 */
	public void remark800toPDB(StringBuffer stringBuffer) {
		//REMARK 800 SITE_IDENTIFIER: CAT
		//REMARK 800 EVIDENCE_CODE: UNKNOWN
		//REMARK 800 SITE_DESCRIPTION: ACTIVE SITE

		stringBuffer.append(String.format(Locale.UK, "REMARK 800 SITE_IDENTIFIER: %-52s%s", siteID, lineEnd));
		stringBuffer.append(String.format(Locale.UK, "REMARK 800 EVIDENCE_CODE: %-54s%s", evCode, lineEnd));
		stringBuffer.append(String.format(Locale.UK, "REMARK 800 SITE_DESCRIPTION: %-51s%s", description, lineEnd));

	}

	/**
	 * Provides REMARK 800 section pertaining to the site as a string.
	 *
	 * For example in pdb 1a4w:
	 * REMARK 800 SITE_IDENTIFIER: CAT
	 * REMARK 800 EVIDENCE_CODE: UNKNOWN
	 * REMARK 800 SITE_DESCRIPTION: ACTIVE SITE
	 *
	 *
	 */
	public String remark800toPDB() {
		StringBuffer stringBuffer = new StringBuffer();
		remark800toPDB(stringBuffer);
		return stringBuffer.toString();
	}

	/**
	 * @param siteID the siteID to set
	 * e.g. CAT, AC1, AC2...
	 */
	public void setSiteID(String siteID) {
		this.siteID = siteID;
	}

	/**
	 * @return the siteID
	 * e.g. CAT, AC1, AC2...
	 */
	public String getSiteID() {
		return siteID;
	}

	/**
	 * @return the groups
	 */
	public List<Group> getGroups() {
		return groups;
	}

	/**
	 * @param residues the groups to set
	 */
	public void setGroups(List<Group> residues) {
		this.groups = residues;
	}


	/**
	 * gets the REMARK 800 description of the site
	 * @return description
	 */
	public String getDescription() {
		return description;
	}

	/**
	 * sets the REMARK 800 description of the site
	 */
	public void setDescription(String description) {
		this.description = description;
	}

	/**
	 * gets the REMARK 800 EVIDENCE CODE for the site.
	 * @return evidence code
	 */
	public String getEvCode() {
		return evCode;
	}

	/**
	 * sets the REMARK 800 EVIDENCE CODE for the site.
	 */
	public void setEvCode(String evCode) {
		this.evCode = evCode;
	}

	@Override
	public boolean equals(Object obj) {
		if (obj == null) {
			return false;
		}
		if (getClass() != obj.getClass()) {
			return false;
		}
		final Site other = (Site) obj;
		if ((this.siteID == null) ? (other.siteID != null) : !this.siteID.equals(other.siteID)) {
			return false;
		}
		if (this.groups != other.groups && (this.groups == null || !this.groups.equals(other.groups))) {
			return false;
		}
		if ((this.evCode == null) ? (other.evCode != null) : !this.evCode.equals(other.evCode)) {
			return false;
		}
		if ((this.description == null) ? (other.description != null) : !this.description.equals(other.description)) {
			return false;
		}
		return true;
	}

	@Override
	public int hashCode() {
		int hash = 5;
		hash = 37 * hash + (this.siteID != null ? this.siteID.hashCode() : 0);
		hash = 37 * hash + (this.groups != null ? this.groups.hashCode() : 0);
		hash = 37 * hash + (this.evCode != null ? this.evCode.hashCode() : 0);
		hash = 37 * hash + (this.description != null ? this.description.hashCode() : 0);
		return hash;
	}



	@Override
	public int compareTo(Site other) {
		return this.toString().compareTo(other.toString());
	}
}
