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The protein structure modules of BioJava.
There is a newer version: 7.2.2
/*
 *                    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.structure;

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

/**
 * PDB-specific
 * @author Jules Jacobsen
 * @since 1.7
 */
public class JournalArticle implements Serializable{

	private static final long serialVersionUID = 5062668226159515468L;
	private List authorList = new ArrayList();
	private List editorList = new ArrayList();
	private String title = "";
	private String ref = "";
	private String journalName = "";
	private String volume;
	private String startPage;
	private int publicationDate;
	private String publisher = "";
	private String refn = "";
	private String pmid = "";
	private String doi = "";
	private boolean published = false;

	/**
	 * Get the list of Authors of the JournalArticle
	 *
	 * @return the List of authors
	 */
	public List getAuthorList() {
		return authorList;
	}

	public void setAuthorList(List authorList) {
		this.authorList = authorList;
	}

	/**
	 * Get the list of editors of the JournalArticle
	 *
	 * @return the List of editors
	 */
	public List getEditorList() {
		return editorList;
	}

	public void setEditorList(List editorList) {
		this.editorList = editorList;
	}

	/**
	 * Get the value of DOI field.
	 * For example: 10.1016/S0969-2126(02)00720-7
	 *
	 * @return the value of doi
	 */
	public String getDoi() {
		return doi;
	}

	/**
	 * Set the value of doi
	 *
	 * @param doi new value of doi
	 */
	public void setDoi(String doi) {
		this.doi = doi;
	}

	/**
	 * Sets the publication state of a JournalArticle - TO BE PUBLISHED == false
	 * @param state
	 */
	public void setIsPublished(Boolean state) {
		this.published = state;
	}
	/**
	 * Get the value of PMID field.
	 * For example: 12005435
	 *
	 * @return the value of pmid
	 */
	public String getPmid() {
		return pmid;
	}

	/**
	 * Set the value of pmid
	 *
	 * @param pmid new value of pmid
	 */
	public void setPmid(String pmid) {
		this.pmid = pmid;
	}

	/**
	 * Get the value of REF field.
	 * For example: TO BE PUBLISHED
	 *
	 * @return the value of ref
	 */
	public String getRef() {
		return ref;
	}

	/**
	 * Set the value of the ref.
	 *
	 * @param ref new value of ref
	 */
	public void setRef(String ref) {
		this.ref = ref;
	}

	/**
	 * Get the value of REFN field.
	 * For example: ISSN 0969-2126
	 *
	 * @return the value of ref
	 */
	public String getRefn() {
		return refn;
	}

	/**
	 * Set the value of the refn
	 *
	 * @param refn new value of refn
	 */
	public void setRefn(String refn) {
		this.refn = refn;
	}

	/**
	 * Get the value of title
	 *
	 * @return the value of title
	 */
	public String getTitle() {
		return title;
	}

	/**
	 * Set the value of title
	 *
	 * @param title new value of title
	 */
	public void setTitle(String title) {
		this.title = title;
	}

	public String getJournalName() {
		return journalName;
	}

	public void setJournalName(String journalName) {
		this.journalName = journalName;
	}

	public int getPublicationDate() {
		return publicationDate;
	}

	public void setPublicationDate(int publicationDate) {
		this.publicationDate = publicationDate;
	}

	public boolean isPublished() {
		return published;
	}

	public void setPublished(boolean published) {
		this.published = published;
	}

	public String getPublisher() {
		return publisher;
	}

	public void setPublisher(String publisher) {
		this.publisher = publisher;
	}

	public String getStartPage() {
		return startPage;
	}

	public void setStartPage(String startPage) {
		this.startPage = startPage;
	}

	public String getVolume() {
		return volume;
	}

	public void setVolume(String volume) {
		this.volume = volume;
	}

	@Override
	public String toString() {
//        JRNL        AUTH   M.HAMMEL,G.SFYROERA,D.RICKLIN,P.MAGOTTI,
//        JRNL        AUTH 2 J.D.LAMBRIS,B.V.GEISBRECHT
//        JRNL        TITL   A STRUCTURAL BASIS FOR COMPLEMENT INHIBITION BY
//        JRNL        TITL 2 STAPHYLOCOCCUS AUREUS.
//        JRNL        REF    NAT.IMMUNOL.                  V.   8   430 2007
//        JRNL        REFN                   ISSN 1529-2908
//        JRNL        PMID   17351618
//        JRNL        DOI    10.1038/NI1450
		String eol = System.getProperty("line.separator");

		StringBuilder jrnlString = new StringBuilder();

		StringBuilder authString = new StringBuilder("JRNL        AUTH   ");
		StringBuilder titlString = new StringBuilder("JRNL        TITL   ");
		StringBuilder editString = new StringBuilder("JRNL        EDIT   ");
		StringBuilder refString = new StringBuilder("JRNL        REF    ");
		StringBuilder publString = new StringBuilder("JRNL        PUBL   ");
		StringBuilder refnString = new StringBuilder("JRNL        REFN                   ");
		StringBuilder pmidString = new StringBuilder("JRNL        PMID   ");
		StringBuilder doiString = new StringBuilder("JRNL        DOI    ");

		for (Author author : authorList) {
			authString.append(author).append(",");
		}
		jrnlString.append(authString).append(eol);
		titlString.append(title);
		jrnlString.append(titlString).append(eol);
		if (!editorList.isEmpty()) {
			for (Author editor : editorList) {
				editString.append(editor).append(",");
			}
			jrnlString.append(editString).append(eol);
		}
		refString.append(ref);
		jrnlString.append(refString).append(eol);
		if (!publisher.equals("")) {
			publString.append(publisher);
			jrnlString.append(publString).append(eol);
		}
		if (!refn.equals("")) {
			refnString.append(refn);
			jrnlString.append(refnString).append(eol);
		}
		if (!pmid.equals("")) {
			pmidString.append(pmid);
			jrnlString.append(pmidString).append(eol);
		}
		if (!doi.equals("")) {
			doiString.append(doi);
			jrnlString.append(doiString).append(eol);
		}

		return jrnlString.toString();
	}
}