/*
 *                    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/
 *
 */
package org.biojava.nbio.core.sequence.io.embl;

import java.util.LinkedList;
import java.util.List;


/**
 * this class contains the parsed data of embl file
 *
 * @author Noor Aldeen Al Mbaidin
 * @since 5.0.0
 */

public class EmblRecord {

	private EmblId emblId;
	private List<EmblReference> emblReference;
	private List<String> accessionNumber = new LinkedList<>();
	private String projectIdentifier;
	private String orGanelle;
	private String createdDate;
	private String featureHeader;
	private String featureTable;
	private String lastUpdatedDate;
	private String sequenceDescription;
	private List<String> keyword = new LinkedList<>();
	private String organismSpecies;
	private String organismClassification;
	private String databaseCrossReference;
	private String assemblyHeader;
	private String assemblyInformation;
	private String constructedSequence;
	private String sequenceHeader;
	private String sequence;

	/**
	 * The ID (IDentification) line
	 * The tokens represent:
	 * 1. Primary accession number
	 * 2. Sequence version number
	 * 3. Topology: 'circular' or 'linear'
	 * 4. Molecule type
	 * 5. Data class
	 * 6. Taxonomic division
	 * 7. Sequence length
	 *
	 * @return
	 */
	public EmblId getEmblId() {
		return emblId;
	}

	public void setEmblId(EmblId emblId) {
		this.emblId = emblId;
	}

	/**
	 * The Reference (RN, RC, RP, RX, RG, RA, RT, RL) Lines
	 * These lines comprise the literature citations within the database.
	 * The citations provide access to the papers from which the data has been
	 * abstracted.
	 *
	 * @return
	 */
	public List<EmblReference> getEmblReference() {
		return emblReference;
	}

	public void setEmblReference(List<EmblReference> emblReference) {
		this.emblReference = emblReference;
	}

	/**
	 * The AC (Accession number) line lists the accession numbers associated with
	 * the entry.
	 *
	 * @return
	 */
	public List<String> getAccessionNumber() {
		return accessionNumber;
	}

	public void setAccessionNumber(List<String> accessionNumber) {
		this.accessionNumber = accessionNumber;
	}

	/**
	 * @return String
	 */
	public String getProjectIdentifier() {
		return projectIdentifier;
	}

	public void setProjectIdentifier(String projectIdentifier) {
		this.projectIdentifier = projectIdentifier;
	}

	/**
	 * The OG (OrGanelle) linetype indicates the sub-cellular location of non-nuclear
	 * sequences.
	 *
	 * @return
	 */
	public String getOrGanelle() {
		return orGanelle;
	}

	public void setOrGanelle(String orGanelle) {
		this.orGanelle = orGanelle;
	}

	/**
	 * The DT  line shows when an entry first appeared in the database
	 *
	 * @return
	 */
	public String getCreatedDate() {
		return createdDate;
	}

	public void setCreatedDate(String createdDate) {
		this.createdDate = createdDate;
	}

	/**
	 * The FH (Feature Header) lines are present only to improve readability of
	 * an entry when it is printed or displayed on a terminal screen.
	 *
	 * @return
	 */
	public String getFeatureHeader() {
		return featureHeader;
	}

	public void setFeatureHeader(String featureHeader) {
		this.featureHeader = featureHeader;
	}

	/**
	 * The FT (Feature Table) lines provide a mechanism for the annotation of the
	 * sequence data. Regions or sites in the sequence which are of interest are
	 * listed in the table.
	 *
	 * @return
	 */
	public String getFeatureTable() {
		return featureTable;
	}

	public void setFeatureTable(String featureTable) {
		this.featureTable = featureTable;
	}

	/**
	 * The DT (DaTe) line shows when an entry was last updated in the database.
	 *
	 * @return String
	 */
	public String getLastUpdatedDate() {
		return lastUpdatedDate;
	}

	public void setLastUpdatedDate(String lastUpdatedDate) {
		this.lastUpdatedDate = lastUpdatedDate;
	}

	/**
	 * The DE (Description) lines contain general descriptive information about the
	 * sequence stored. This may include the designations of genes for which the
	 * sequence codes, the region of the genome from which it is derived, or other
	 * information which helps to identify the sequence.
	 *
	 * @return
	 */
	public String getSequenceDescription() {
		return sequenceDescription;
	}

	public void setSequenceDescription(String sequenceDescription) {
		this.sequenceDescription = sequenceDescription;
	}

	/**
	 * The KW (KeyWord) lines provide information which can be used to generate
	 * cross-reference indexes of the sequence entries based on functional,
	 * structural, or other categories deemed important.
	 *
	 * @return
	 */
	public List<String> getKeyword() {
		return keyword;
	}

	public void setKeyword(List<String> keyword) {
		this.keyword = keyword;
	}

	/**
	 * The OS (Organism Species) line specifies the preferred scientific name of
	 * the organism which was the source of the stored sequence. In most
	 * cases this is done by giving the Latin genus and species designations,
	 * followed (in parentheses) by the preferred common name in English where known.
	 *
	 * @return String
	 */
	public String getOrganismSpecies() {
		return organismSpecies;
	}

	public void setOrganismSpecies(String organismSpecies) {
		this.organismSpecies = organismSpecies;
	}

	/**
	 * The OC (Organism Classification) lines contain the taxonomic classification
	 * Of the source organism
	 *
	 * @return
	 */
	public String getOrganismClassification() {
		return organismClassification;
	}

	public void setOrganismClassification(String organismClassification) {
		this.organismClassification = organismClassification;
	}

	/**
	 * The DR (Database Cross-reference) line cross-references other databases which
	 * contain information related to the entry in which the DR line appears.
	 *
	 * @return
	 */
	public String getDatabaseCrossReference() {
		return databaseCrossReference;
	}

	public void setDatabaseCrossReference(String databaseCrossReference) {
		this.databaseCrossReference = databaseCrossReference;
	}

	/**
	 * The AH (Assembly Header) line provides column headings for the assembly information.
	 *
	 * @return
	 */
	public String getAssemblyHeader() {
		return assemblyHeader;
	}

	public void setAssemblyHeader(String assemblyHeader) {
		this.assemblyHeader = assemblyHeader;
	}

	/**
	 * The AS (Assembly Information) lines provide information on the composition of
	 * a TPA or TSA sequence.
	 *
	 * @return String
	 */
	public String getAssemblyInformation() {
		return assemblyInformation;
	}

	public void setAssemblyInformation(String assemblyInformation) {
		this.assemblyInformation = assemblyInformation;
	}

	/**
	 * Con(structed) sequences in the CON data classes represent complete
	 * chromosomes, genomes and other long sequences constructed from segment entries.
	 *
	 * @return
	 */
	public String getConstructedSequence() {
		return constructedSequence;
	}

	public void setConstructedSequence(String constructedSequence) {
		this.constructedSequence = constructedSequence;
	}

	/**
	 * The SQ (SeQuence header) line marks the beginning of the sequence data and
	 * Gives a summary of its content.
	 *
	 * @return
	 */
	public String getSequenceHeader() {
		return sequenceHeader;
	}

	public void setSequenceHeader(String sequenceHeader) {
		this.sequenceHeader = sequenceHeader;
	}

	/**
	 * The Sequence Data Line
	 *
	 * @return
	 */
	public String getSequence() {
		return sequence;
	}

	public void setSequence(String sequence) {
		this.sequence = sequence;
	}

}
