/*
 *                    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 25.04.2004
 * @author Andreas Prlic
 *
 */
package org.biojava.nbio.structure;

import org.biojava.nbio.core.sequence.template.Sequence;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.PDBFileReader;

import java.util.List;

/**
 * <p>
 * Defines the interface for a Chain. A Chain corresponds to a Chain in a PDB file.
 * A chain consists out of a list of {@link Group} objects. A Group can either be
 * an {@link AminoAcid}, {@link HetatomImpl Hetatom} or {@link NucleotideImpl Nucleotide}.
 * </p>
 *
 * <p>
 * The BioJava API provides access to both the ATOM and SEQRES records in a PDB file.
 * During parsing of a PDB file it aligns the ATOM and SEQRES groups and joins them.
 * The SEQRES sequence can be accessed via  {@link #getSeqResGroups()} and the
 * ATOM groups via {@link #getAtomGroups()}. Groups that have been observed
 * (i.e. they are in the ATOM records) can be detected by {@link Group}.has3D()
 *  </p>
 *
 * @author Andreas Prlic
 * @version %I% %G%
 * @since 1.4
 */
public interface Chain {

	/** returns an identical copy of this Chain.
	 * @return  an identical copy of this Chain
	 */
	public Object clone();

	/** add a group to the list of ATOM record group of this chain.
	 * To add SEQRES records a more complex alignment between ATOM and SEQRES residues
	 * is required, please see SeqRes2AtomAligner for more details on that.
	 * @param group  a Group object
	 */
	public void addGroup(Group group);

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

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


	/**
	 * Return the Group at given position,
	 * from within Groups with observed density in the chain, i.e.
	 * those with coordinates in ATOM and HETATMS (including waters) records.
	 * @param position  an int
	 * @return a Group object
	 * @see #getAtomLength()
	 * @see #getAtomGroups()
	 * @see #getSeqResGroup(int)
	 */
	public Group getAtomGroup (int position);

	/**
	 * Return the Group at given position,
	 * from within groups in the SEQRES records of the chain, i.e.
	 * the aminoacids/nucleotides in the construct.
	 * @param position  an int
	 * @return a Group object
	 * @see #getSeqResLength()
	 * @see #getSeqResGroups()
	 * @see #getAtomGroup(int)
	 */
	public Group getSeqResGroup (int position);


	/**
	 * Return all Groups with observed density in the chain, i.e.
	 * those with coordinates in ATOM and HETATMS (including waters) records.
	 *
	 * @return a List object representing the Groups of this Chain.
	 * @see #setAtomGroups(List)
	 * @see #getAtomLength()
	 * @see #getSeqResGroups()
	 */
	public List<Group> getAtomGroups();

	/**
	 * Set all Groups with observed density in the chain, i.e.
	 * those with coordinates in ATOM and HETATMs (including waters) records.
	 * @param groups a List object representing the Groups of this Chain.
	 * @see #getAtomGroups()
	 */
	public void setAtomGroups(List<Group> groups);

	/**
	 * Return a List of all (observed) Groups of a special type, one of: {@link GroupType#AMINOACID},
	 * {@link GroupType#HETATM} or {@link GroupType#NUCLEOTIDE}.
	 * Note that if a standard aminoacid appears as a HETATM (because it is part of a ligand) then
	 * it is still considered as {@link GroupType#AMINOACID} and not as {@link GroupType#HETATM}.
	 * @param type  GroupType
	 * @return a List object
	 * @see #setAtomGroups(List)
	 */
	public List<Group> getAtomGroups (GroupType type);


	/**
	 * Get a group by its PDB residue numbering. If the PDB residue number is not known,
	 * throws a StructureException.
	 *
	 * @param resNum the PDB residue number of the group
	 * @return the matching group
	 * @throws StructureException
	 */
	public Group getGroupByPDB(ResidueNumber resNum) throws StructureException;

	/** Get all groups that are located between two PDB residue numbers.
	 *
	 * @param pdbresnumStart PDB residue number of start
	 * @param pdbresnumEnd PDB residue number of end
	 * @return Groups in between. or throws a StructureException if either start or end can not be found,
	 * @throws StructureException
	 */
	public Group[] getGroupsByPDB(ResidueNumber pdbresnumStart, ResidueNumber pdbresnumEnd) throws StructureException;


	/** Get all groups that are located between two PDB residue numbers. In contrast to getGroupsByPDB
	 * this method call ignores if the exact outer groups are not found. This is useful e.g. when requesting the range
	 * of groups as specified by the DBREF records - these frequently are rather inaccurate.
	 *
	 *
	 * @param pdbresnumStart PDB residue number of start
	 * @param pdbresnumEnd PDB residue number of end
	 * @param ignoreMissing ignore missing groups in this range.
	 * @return Groups in between. or throws a StructureException if either start or end can not be found,
	 * @throws StructureException
	 *
	 */
	public Group[] getGroupsByPDB(ResidueNumber pdbresnumStart, ResidueNumber pdbresnumEnd,boolean ignoreMissing) throws StructureException;


	/**
	 * Returns the number of Groups with observed density in the chain, i.e.
	 * those with coordinates in ATOM and HETATMs (including waters) records
	 *
	 * @return the length
	 * @see #getAtomGroup(int)
	 * @see #getAtomGroups()
	 * @see #getSeqResLength())
	 */
	public int getAtomLength();

	/**
	 * Returns the number of groups in the SEQRES records of the chain, i.e.
	 * the number of aminoacids/nucleotides in the construct
	 *
	 * @return the length
	 * @see #getSeqResGroup(int)
	 * @see #getSeqResGroups()
	 * @see #getAtomLength()
	 */
	public int getSeqResLength();

	/**
	 * Sets the Entity information
	 * @param entityInfo the EntityInfo
	 * @see #getEntityInfo()
	*/
	public void setEntityInfo(EntityInfo entityInfo);

	/**
	 * Returns the EntityInfo for this chain.
	 *
	 * @return the EntityInfo object
	 * @see #setEntityInfo(EntityInfo)
	 */
	public EntityInfo getEntityInfo();

	/**
	 * Sets the name of this chain (Chain id in PDB file ).
	 * @param name  a String specifying the name value
	 * @see #getChainID()
	 */
	public void setChainID(String name);



	/**
	 * Gets the name of this chain (Chain id in PDB file ).
	 * @return a String representing the name value
	 * @see #setChainID(String)
	 */
	public String getChainID();


	/**
	 * If available, returns the internal chain ID that is used in mmCIF files (asym_id), otherwise null
	 *
	 * @return String or null
	 * @since 3.0.5
	 */
	public String getInternalChainID();

	/**
	 * Sets the internal chain ID that is used in mmCif files
	 *
	 * @param internalChainID
	 * @since 3.0.5
	 */
	public void setInternalChainID(String internalChainID);


	@Override
	public String toString();


	/**
	 * Converts the SEQRES groups of a Chain to a Biojava Sequence object.
	 *
	 * @return the SEQRES groups of the Chain as a Sequence object.
	 */
	public Sequence<?> getBJSequence()  ;

	/**
	 * Returns the sequence of amino acids as it has been provided in the ATOM records.
	 * Non-standard residues will be present in the string only if the property
	 * {@value PDBFileReader#LOAD_CHEM_COMP_PROPERTY} has been set.
	 * @return amino acid sequence as string
	 * @see #getSeqResSequence()
	 */
	public String getAtomSequence();

	/**
	 * Returns the PDB SEQRES sequence as a one-letter sequence string.
	 * Non-standard residues are represented by an "X".
	 * @return one-letter PDB SEQRES sequence as string
	 * @see #getAtomSequence()
	 */
	public String getSeqResSequence();

	/**
	 * Sets the Swissprot id of this chain.
	 * @param sp_id  a String specifying the swissprot id value
	 * @see #getSwissprotId()
	 */
	public void setSwissprotId(String sp_id);

	/**
	 * Gets the Swissprot id of this chain.
	 * @return a String representing the swissprot id value
	 * @see #setSwissprotId(String sp_id)
	 */
	public String getSwissprotId() ;


	/**
	 * Returns a List of all SEQRES groups of a special type, one of: {@link GroupType#AMINOACID},
	 * {@link GroupType#HETATM} or {@link GroupType#NUCLEOTIDE}.
	 * @param type  a GroupType
	 * @return an List object
	 * @see #setSeqResGroups(List)
	 */
	public List<Group> getSeqResGroups (GroupType type);

	/**
	 * Returns a list of all groups in SEQRES records of the chain, i.e.
	 * the aminoacids/nucleotides in the construct.
	 * @return a List of all Group objects of this chain
	 * @see #setSeqResGroups(List)
	 * @see #getSeqResLength()
	 * @see #getAtomGroups()
	 */
	public List<Group> getSeqResGroups ();

	/**
	 * Sets the list of SeqResGroups for this chain.
	 *
	 * @param seqResGroups a List of Group objects that from the SEQRES groups of this chain.
	 * @see #getSeqResGroups()
	 */
	public void setSeqResGroups(List<Group> seqResGroups);

	/**
	 * Sets the back-reference to its parent Structure.
	 * @param parent the parent Structure object for this Chain
	 * @see #getStructure()
	 * @deprecated  use setStructure instead
	 *
	 */
	@Deprecated
	public void setParent(Structure parent) ;

	/** Sets the back-reference to its parent Structure.
	 *
	 * @param parent
	 */

	public void setStructure(Structure parent) ;

	/**
	 * Returns the parent Structure of this chain.
	 *
	 * @return the parent Structure object
	 * @see #setStructure(Structure)
	 * @deprecated use getStructure(Structure) instead.
	 */
	@Deprecated
	public Structure getParent() ;


	/**
	 * Returns the parent Structure of this chain.
	 *
	 * @return the parent Structure object
	 * @see #setStructure(Structure)
	 */
	public Structure getStructure() ;

	/**
	 * Gets all groups that are not polymer groups and that are not solvent groups.
	 * Will automatically fetch Chemical Component files from the PDB web site, even if
	 * {@link FileParsingParameters#setLoadChemCompInfo(boolean)} has not been set to true.
	 * Otherwise the Ligands could not correctly be identified.
	 * @return list of Groups that are ligands
	 */
	public List<Group> getAtomLigands();

	/**
	 * Convert this Chain to a String in PDB format
	 * @return
	 */
	public String toPDB();

	/**
	 * Convert this Chain to a String in mmCIF format
	 * @return
	 */
	public String toMMCIF();


	/** Set annotated sequence mismatches for this chain. This is based on the STRUCT_REF_SEQ_DIF mmCif category
	 *
	 * @param seqMisMatches
	 */
	public void setSeqMisMatches(List<SeqMisMatch> seqMisMatches);

	/** Get annotated sequence mismatches for this chain. This is based on the STRUCT_REF_SEQ_DIF mmCif category
	 *
	 * @returns a list of sequence mismatches (or null if none found)
	 */
	public List<SeqMisMatch> getSeqMisMatches();
}
