EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.model.molecular;

import java.io.Serializable;

import javax.persistence.Embeddable;

import javax.persistence.Lob;

import javax.xml.bind.annotation.XmlAccessType;

import javax.xml.bind.annotation.XmlAccessorType;

import javax.xml.bind.annotation.XmlElement;

import javax.xml.bind.annotation.XmlRootElement;

import javax.xml.bind.annotation.XmlType;

import org.apache.log4j.Logger;

import org.codehaus.plexus.util.StringUtils;

/**

 * A sequence contains the genetic code of a DNA or RNA part. It is basically a string

 * based on 4 letters: ATGC (Adenin, Thymin, Guanin, Cytosin) for DNA and AUGC (Thymin replaced by Uracil)

 * for RNA.

 * <BR>

 * The direction of the string shall always be 5'-3' which is a convention.

 * <BR>

 * The sequence has a length which is stored as such if no further information is given. If the sequence

 * string is given the length is computed automatically.

 *

 * @author a.mueller

 * @created 2013-07-05

 */

@XmlAccessorType(XmlAccessType.FIELD)

@XmlType(name = "SequenceString", propOrder = {

	"string",

	"length"

})

@XmlRootElement(name = "SequenceString")

@Embeddable

public class SequenceString implements Cloneable, Serializable{

	private static final long serialVersionUID = 45735207807329055L;

	private static final Logger logger = Logger.getLogger(SequenceString.class);

	/**{@link #getString()}*/

	@XmlElement(name = "String")

    @Lob

	private String string;

	@XmlElement(name = "Length")

	private Integer length;

// ******************** FACTORY METHOD ******************/

	public static SequenceString NewInstance(){

		SequenceString result = new SequenceString();

		return result;

	}

	public static SequenceString NewInstance(String sequence){

		SequenceString result = new SequenceString();

		result.setString(sequence);

		return result;

	}

// ********************* CONSTRUCTOR ********************/

	private SequenceString(){};

// ********************* GETTER / SETTER ********************/

	/**

	 * The sequence as a string of base pairs in direction 5'->3'.

	 */

	public String getString(){

		return this.string;

	}

	/**

	 * Sets the sequence. Also {@link #getLength() length information} will be set automatically.

	 * @see #getString()

	 * @param sequence    sequence

	 */

	public void setString(String sequence){

		this.string = sequence;

		this.length = (sequence == null ? 0 : sequence.length());

	}

	/**

	 * The length of the sequence. Will be calculated if the {@link #getString() sequence}  is set.

	 * @return the length of the sequence.

	 */

	public Integer getLength(){

		return this.length;

	}

	/**

	 * Sets the {@link #getLength() length}, if the {@link #getString() sequence} is not set.

	 * If {@link #getString() sequence}  is available, length has no effect.

	 * @see #getLength()

	 * @param length    length

	 */

	public void setLength(Integer length){

		if (StringUtils.isBlank(string)){

			this.length = length;

		}

	}

	// ********************* CLONE ********************/

	/**

	 * Clones <i>this</i> sequence. This is a shortcut that enables to create

	 * a new instance that differs only slightly from <i>this</i> sequencing by

	 * modifying only some of the attributes.<BR><BR>

	 *

	 *

	 * @see eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()

	 * @see java.lang.Object#clone()

	 */

	@Override

	public Object clone()  {

		try{

		SequenceString result = (SequenceString)super.clone();

		//don't change sequence, length

		return result;

		}catch (CloneNotSupportedException e) {

			logger.warn("Object does not implement cloneable");

			e.printStackTrace();

			return null;

		}

	}

}