/*
 *                    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.mmcif.model.ChemComp;

import java.io.Serializable;
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 extends Serializable {

        /** returns an identical copy of this Chain.
         * @return  an identical copy of this Chain
         */
        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
         */
        void addGroup(Group group);

        /** Get the 'private' asymId (internal chain IDs in mmCif) for this chain.
         *
         * @return the asymId
         * @see #setId(String)
         * @see #getName()
         */
        String getId() ;


        /**
         * Set the 'private' asymId (internal chain IDs in mmCif) for this chain.
         *
         * @param asymId the internal chain Id
         */
        void setId(String asymId) ;


        /**
         * Set the 'public' authId (chain ID in PDB file)
         *
         * @param authId the 'public' authId (chain ID in PDB file)
         * @see #getId()
         */
        void setName(String authId);

        /**
         * Get the 'public' authId (chain ID in PDB file)
         *
         * @return the authId for this chain.
         * @see #getId()
         */
        String getName();


        /**
         * 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)
         */
        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)
         */
        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()
         */
        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()
         */
        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)
         */
        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
         */
        Group getGroupByPDB(ResidueNumber resNum) throws StructureException;

        /**
         * Get all groups that are located between two PDB residue numbers.
         *
         * @param pdbresnumStart PDB residue number of start. If null, defaults to the chain start.
         * @param pdbresnumEnd PDB residue number of end. If null, defaults to the chain end.
         * @return Groups in between. or throws a StructureException if either start or end can not be found,
         * @throws StructureException
         */
        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. If null, defaults to the chain start.
         * @param pdbresnumEnd PDB residue number of end. If null, defaults to the chain 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
         *
         */
        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())
         */
        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()
         */
        int getSeqResLength();

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

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

        /**
         * Sets the 'private' asymId of this chain (Chain id in PDB file ).
         * @param asymId  a String specifying the name value
         * @see #getChainID()
         * @deprecated  use {@link #setId(String asymId)} instead
         */
        @Deprecated
        void setChainID(String asymId);



        /**
         * Gets the 'private' asymId of this chain.
         * @return a String representing the name value
         * @see #setChainID(String)
         * @deprecated  use getId() instead
         */
        @Deprecated
        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
         * @deprecated  use {@link #getId()} instead
         */
        String getInternalChainID();

        /**
         * Sets the internal chain ID that is used in mmCif files
         *
         * @param internalChainID
         * @since 3.0.5
         * @deprecated use {@link #setId()} instead
         */
        void setInternalChainID(String internalChainID);


        @Override
        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.
         */
        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 org.biojava.nbio.structure.io.PDBFileReader#LOAD_CHEM_COMP_PROPERTY} has been set.
         * @return amino acid sequence as string
         * @see #getSeqResSequence()
         */
        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()
         */
        String getSeqResSequence();

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

        /**
         * Sets the back-reference to its parent Structure.
         *
         * @param parent
         */
        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
        Structure getParent() ;


        /**
         * Returns the parent Structure of this chain.
         *
         * @return the parent Structure object
         * @see #setStructure(Structure)
         */
        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
         * @deprecated since biojava 5.0 this does not apply anymore. Chains contain either
         * polymeric groups or non-polymeric groups
         */
        @Deprecated
        List<Group> getAtomLigands();

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

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


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

        /**
         * Gets 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)
         */
        List<SeqMisMatch> getSeqMisMatches();

        /**
         * Returns the EntityType of this chain. Equivalent to getEntityInfo().getType()
         * @return
         * @see EntityType
         */
        EntityType getEntityType();

        /** Tests if a chain is consisting of water molecules only
         *
         * @return true if there are only solvent molecules in this chain.
         */
        public boolean isWaterOnly();

        /**  Returns true if the given chain is composed of non-polymeric (including water) groups only.
         *
         * @return true if only non-polymeric groups in this chain.
         */
        public boolean isPureNonPolymer();

        /**
         * Get the predominant {@link GroupType} for a given Chain, following these
         * rules: <li>if the ratio of number of residues of a certain
         * {@link GroupType} to total non-water residues is above the threshold
         * {@value #org.biojava.nbio.structure.StructureTools.RATIO_RESIDUES_TO_TOTAL}, then that {@link GroupType} is
         * returned</li> <li>if there is no {@link GroupType} that is above the
         * threshold then the {@link GroupType} with most members is chosen, logging
         * it</li>
         * <p>
         * See also {@link ChemComp#getPolymerType()} and
         * {@link ChemComp#getResidueType()} which follow the PDB chemical component
         * dictionary and provide a much more accurate description of groups and
         * their linking.
         * </p>
         *
         * @return
         */
        public GroupType getPredominantGroupType();

        /**
         * Tell whether given chain is a protein chain
         *
         * @return true if protein, false if nucleotide or ligand
         * @see #getPredominantGroupType()
         */
        public  boolean isProtein();

        /**
         * Tell whether given chain is DNA or RNA
         *
         * @return true if nucleic acid, false if protein or ligand
         * @see #getPredominantGroupType()
         */
        public  boolean isNucleicAcid();
}