/*
 *                    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 12.03.2004
 * @author Andreas Prlic
 *
 */
package org.biojava.bio.structure;


import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;

import org.biojava.bio.Annotation;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.symbol.IllegalSymbolException;

/**
 * A Chain in a PDB file. It contains several groups which can be of
 * one of the types defined in the {@link GroupType} constants.
 *
 * @author Andreas Prlic
 * @author Jules Jacobsen
 * @since 1.4
 */
public class ChainImpl implements Chain {

	/** The default chain identifier is an empty space.
	 *
	 */
	public static String DEFAULT_CHAIN_ID = "A";

	String swissprot_id ;
	String name ; // like in PDBfile
	List <Group> groups;
	Annotation annotation ;

	List<Group> seqResGroups;
	private Long id;
	Compound mol;
	Structure parent;
	Map<String, Integer> pdbResnumMap;

	/**
	 *  Constructs a ChainImpl object.
	 */
	public ChainImpl() {
		super();

		name = DEFAULT_CHAIN_ID;
		groups = new ArrayList<Group>() ;
		annotation = Annotation.EMPTY_ANNOTATION;
		seqResGroups = new ArrayList<Group>();
		pdbResnumMap = new HashMap<String,Integer>();

	}

	/** {@inheritDoc}
	 *
	 */
	public Long getId() {
		return id;
	}

	/** {@inheritDoc}
	 *
	 */
	public void setId(Long id) {
		this.id = id;
	}

	/** {@inheritDoc}
	 *
	 */
	public void setParent(Structure parent) {
		this.parent = parent;
	}

	/** Returns the parent Structure of this chain.
	 *
	 * @return the parent Structure object
	 */

	public Structure getParent() {


		return parent;
	}


	/** Returns an identical copy of this Chain .
	 * @return an identical copy of this Chain
	 */
	public Object clone() {
		// go through all groups and add to new Chain.
		Chain n = new ChainImpl();
		// copy chain data:

		n.setName( getName());
		n.setSwissprotId ( getSwissprotId());
		for (int i=0;i<groups.size();i++){
			Group g = (Group)groups.get(i);
			n.addGroup((Group)g.clone());
		}
		n.setHeader(this.getHeader());

		return n ;
	}

	/** {@inheritDoc}
	 *
	 */
	public void setAnnotation(Annotation anno){
		annotation = anno;
	}

	/** {@inheritDoc}
	 *
	 */
	public Annotation getAnnotation(){
		return annotation;
	}

	/** {@inheritDoc}
	 *
	 */
	public void setHeader(Compound mol) {
		this.mol = mol;
	}

	/** {@inheritDoc}
	 *
	 */
	public Compound getHeader() {
		return this.mol;
	}

	/** set the Swissprot id of this chains .
	 * @param sp_id  a String specifying the swissprot id value
	 * @see #getSwissprotId
	 */

	public void setSwissprotId(String sp_id){
		swissprot_id = sp_id ;
	}

	/** get the Swissprot id of this chains .
	 * @return a String representing the swissprot id value
	 * @see #setSwissprotId
	 */
	public String getSwissprotId() {
		return swissprot_id ;
	}

	/** {@inheritDoc}
	 *
	 */
	public void addGroup(Group group) {

		group.setParent(this);

		groups.add(group);

		// store the position internally for quick access of this group
		String pdbResnum = group.getPDBCode();
		if ( pdbResnum != null) {
			Integer pos = new Integer(groups.size()-1);
			// ARGH sometimes numbering in PDB files is confusing.
			// e.g. PDB: 1sfe
			/*
			 * ATOM    620  N   GLY    93     -24.320  -6.591   4.210  1.00 46.82           N
			 * ATOM    621  CA  GLY    93     -24.960  -6.849   5.497  1.00 47.35           C
			 * ATOM    622  C   GLY    93     -26.076  -5.873   5.804  1.00 47.24           C
			 * ATOM    623  O   GLY    93     -26.382  -4.986   5.006  1.00 47.56           O
             and ...
			 * HETATM 1348  O   HOH    92     -21.853 -16.886  19.138  1.00 66.92           O
			 * HETATM 1349  O   HOH    93     -26.126   1.226  29.069  1.00 71.69           O
			 * HETATM 1350  O   HOH    94     -22.250 -18.060  -6.401  1.00 61.97           O
			 */

			// this check is to give in this case the entry priority that is an AminoAcid / comes first...
			if (  pdbResnumMap.containsKey(pdbResnum)) {
				if ( group instanceof AminoAcid)
					pdbResnumMap.put(pdbResnum,pos);
			} else
				pdbResnumMap.put(pdbResnum,pos);
		}

	}

	/** return the group at position .
	 *
	 *
	 * @param position  an int
	 * @return a Group object
	 * @deprecated use getAtomGroup or getSeqResGroup instead
	 */
	public Group getGroup(int position) {

		return (Group)groups.get(position);
	}



	/** return the group at position .
	 *
	 *
	 * @param position  an int
	 * @return a Group object
	 */
	public Group getAtomGroup(int position) {

		return (Group)groups.get(position);
	}

	/** Return a list of all groups of one of the types defined in hte {@link GroupType} constants.
	 *
	 *
	 * @param type  a String
	 * @return an List object containing the groups of type...
	 * @deprecated use getAtomGroups instead
	 */
	public List<Group> getGroups( String type) {
		return getAtomGroups(type);
	}

	/**  Get the Groups of a certain type, that are listed int the ATOM records of the PDB file.
	 *
	 *  @param type the type of the groups to return. Can be one of the 3 types defined in the {@link GroupType} constants
	 *  @return a list of group objects
	 */
	public List<Group> getAtomGroups(String type){
		List<Group> tmp = new ArrayList<Group>() ;
		for (int i=0;i<groups.size();i++){
			Group g = (Group)groups.get(i);
			if (g.getType().equals(type)){
				tmp.add(g);
			}
		}

		return tmp ;
	}

	/** return all groups of this chain .
	 * @return a List object representing the Groups of this Chain.
	 * @deprecated use getAtomGroups instead
	 */
	public List<Group> getGroups(){
		return groups ;
	}


	/** {@inheritDoc}
	 *
	 */
	public List<Group> getAtomGroups(){
		return groups ;
	}

	/** {@inheritDoc}
	 *
	 */
	public void setAtomGroups(List<Group> groups){
		for (Group g:groups){
			g.setParent(this);
		}
		this.groups = groups;
	}

	/** {@inheritDoc}
	 *
	 */
	public Group[] getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd, boolean ignoreMissing)
	throws StructureException {

		if (! ignoreMissing )
			return getGroupsByPDB(pdbresnumStart, pdbresnumEnd);

		List<Group> retlst = new ArrayList<Group>();

		int startPos = Integer.MIN_VALUE;
		int endPos   = Integer.MAX_VALUE;
		boolean doIntCheck = true;
		try {
			startPos = Integer.parseInt(pdbresnumStart);
			endPos   = Integer.parseInt(pdbresnumEnd);

		} catch (Exception e){
			// has insertion code, in this case this will not work...
			doIntCheck = false;
		}


		boolean adding = false;
		boolean foundStart = false;

		for (Group g: groups){

			if ( g.getPDBCode().equals(pdbresnumStart)) {
				adding = true;
				foundStart = true;
			}

			if ( ! (foundStart && adding) ) {
				if ( doIntCheck){
					try {
						int pos = Integer.parseInt(g.getPDBCode());

						if ( pos >= startPos) {
							foundStart = true;
							adding = true;
						}
					} catch (Exception e){
						// insertion code catch. will not work with them...
					}
				}
			}

			if ( adding)
				retlst.add(g);

			if ( g.getPDBCode().equals(pdbresnumEnd)) {
				if ( ! adding)
					throw new StructureException("did not find start PDB residue number " + pdbresnumStart + " in chain " + name);
				adding = false;
				break;
			}
			if (doIntCheck && adding){

				try {
					int pos = Integer.parseInt(g.getPDBCode());
					if (pos >= endPos) {
						adding = false;
						break;
					}
				} catch (Exception e){
					// insertion code problem
				}
			}
		}

		if ( ! foundStart){
			throw new StructureException("did not find start PDB residue number " + pdbresnumStart + " in chain " + name);
		}


		//not checking if the end has been found in this case...

		return (Group[]) retlst.toArray(new Group[retlst.size()] );
	}


	public Group getGroupByPDB(String pdbresnum) throws StructureException {
		if ( pdbResnumMap.containsKey(pdbresnum)) {
			Integer pos = (Integer) pdbResnumMap.get(pdbresnum);
			return (Group) groups.get(pos.intValue());
		} else {
			throw new StructureException("unknown PDB residue number " + pdbresnum + " in chain " + name);
		}

	}

	/**
	 * {@inheritDoc}
	 *
	 */
	public Group[] getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd)
	throws StructureException {

		List<Group> retlst = new ArrayList<Group>();

		Iterator<Group> iter = groups.iterator();
		boolean adding = false;
		boolean foundStart = false;

		while ( iter.hasNext()){
			Group g = (Group) iter.next();
			if ( g.getPDBCode().equals(pdbresnumStart)) {
				adding = true;
				foundStart = true;
			}

			if ( adding)
				retlst.add(g);

			if ( g.getPDBCode().equals(pdbresnumEnd)) {
				if ( ! adding)
					throw new StructureException("did not find start PDB residue number " + pdbresnumStart + " in chain " + name);
				adding = false;
				break;
			}
		}

		if ( ! foundStart){
			throw new StructureException("did not find start PDB residue number " + pdbresnumStart + " in chain " + name);
		}
		if ( adding) {
			throw new StructureException("did not find end PDB residue number " + pdbresnumEnd + " in chain " + name);
		}

		return (Group[]) retlst.toArray(new Group[retlst.size()] );
	}



	/**
	 * @deprecated use getAtomLength instead
	 */
	public int getLength() {
		return getAtomLength();
	}

	/** {@inheritDoc}
	 *
	 */
	public int getLengthAminos() {

		List<Group> g = getAtomGroups(GroupType.AMINOACID);
		return g.size() ;
	}

	public int getSeqResLength() {
		//new method returns the length of the sequence defined in the SEQRES records
		return seqResGroups.size();
	}

	/** get and set the name of this chain (Chain id in PDB file ).
	 * @param nam a String specifying the name value
	 * @see #getName
	 *
	 */

	public void   setName(String nam) { name = nam;   }

	/** get and set the name of this chain (Chain id in PDB file ).
	 * @return a String representing the name value
	 * @see #setName
	 */
	public String getName()           {	return name;  }


	/** String representation.
	 * @return String representation of the Chain
	 *  */
	public String toString(){
		String newline = System.getProperty("line.separator");
		StringBuffer str = new StringBuffer();
		str.append("Chain >"+getName()+"<"+newline) ;
		if ( mol != null ){
			if ( mol.getMolName() != null){
				str.append(mol.getMolName()+newline);
			}
		}
		str.append("total SEQRES length: " + getSeqResGroups().size() +
				" total ATOM length:" + getAtomLength() + " residues " + newline);

		// loop over the residues

		for ( int i = 0 ; i < seqResGroups.size();i++){
			Group gr = (Group) seqResGroups.get(i);
			str.append(gr.toString() + newline) ;
		}
		return str.toString() ;

	}

	/** Convert the SEQRES groups of a Chain to a Biojava Sequence object.
     *
     * @return the SEQRES groups of the Chain as a Sequence object.
     * @throws IllegalSymbolException
     */
    public Sequence getBJSequence() throws IllegalSymbolException {

    	//List<Group> groups = c.getSeqResGroups();
    	String seq = getSeqResSequence();

    	String name = "";
    	if ( this.getParent() != null )
    		name = getParent().getPDBCode();
    	name += "." + getName();

    	return ProteinTools.createProteinSequence(seq, name );

    }



	/** get amino acid sequence of the chain. for backwards compatibility this returns
	 * the Atom sequence of the chain.
	 * @return a String representing the sequence.
	 * @deprecated use getAtomSequence instead
	 * @see #getAtomSequence()
	 * @see #getSeqResSequence()
	 */
	public String getSequence(){
		return getAtomSequence();
	}


	/** {@inheritDoc}
	 *
	 */
	public String getAtomSequence(){

		List<Group> aminos = getAtomGroups("amino");
		StringBuffer sequence = new StringBuffer() ;
		for ( int i=0 ; i< aminos.size(); i++){
			AminoAcid a = (AminoAcid)aminos.get(i);
			sequence.append( a.getAminoType());
		}

		return sequence.toString();

	}

	/** {@inheritDoc}
	 *
	 */
	public String getSeqResSequence(){

		StringBuffer str = new StringBuffer();
		for (Group group : seqResGroups) {
			if (group instanceof AminoAcid) {
				AminoAcid aa = (AminoAcid)group;
				str.append(aa.getAminoType()) ;
			}

		}
		return str.toString();

	}


	/** {@inheritDoc}
	 *
	 */
	public Group getSeqResGroup(int position) {

		return seqResGroups.get(position);
	}

	/** {@inheritDoc}
	 *
	 */
	public List<Group> getSeqResGroups(String type) {
		return seqResGroups;
	}

	/** {@inheritDoc}
	 *
	 */
	public List<Group> getSeqResGroups() {
		return seqResGroups;
	}

	/** {@inheritDoc}
	 *
	 */
	public void setSeqResGroups(List<Group> groups){
		for (Group g: groups){
			g.setParent(this);
		}
		this.seqResGroups = groups;
	}


	/** {@inheritDoc}
	 *
	 */
	public int getAtomLength() {

		return groups.size();
	}

}