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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.molecular;
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import java.io.Serializable;
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import javax.persistence.Embeddable;
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import javax.persistence.Lob;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.XmlElement;
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import javax.xml.bind.annotation.XmlRootElement;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.log4j.Logger;
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import org.codehaus.plexus.util.StringUtils;
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/**
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* A sequence contains the genetic code of a DNA or RNA part. It is basically a string
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* based on 4 letters: ATGC (Adenin, Thymin, Guanin, Cytosin) for DNA and AUGC (Thymin replaced by Uracil)
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* for RNA.
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* <BR>
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* The direction of the string shall always be 5'-3' which is a convention.
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* <BR>
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* The sequence has a length which is stored as such if no further information is given. If the sequence
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* string is given the length is computed automatically.
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*
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* @author a.mueller
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* @created 2013-07-05
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "SequenceString", propOrder = {
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"string",
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"length"
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})
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@XmlRootElement(name = "SequenceString")
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@Embeddable
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public class SequenceString implements Cloneable, Serializable{
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private static final long serialVersionUID = 45735207807329055L;
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private static final Logger logger = Logger.getLogger(SequenceString.class);
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/**{@link #getString()}*/
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@XmlElement(name = "String")
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@Lob
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private String string;
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@XmlElement(name = "Length")
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private Integer length;
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// ******************** FACTORY METHOD ******************/
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public static SequenceString NewInstance(){
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SequenceString result = new SequenceString();
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return result;
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}
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public static SequenceString NewInstance(String sequence){
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SequenceString result = new SequenceString();
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result.setString(sequence);
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return result;
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}
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// ********************* CONSTRUCTOR ********************/
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private SequenceString(){};
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// ********************* GETTER / SETTER ********************/
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/**
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* The sequence as a string of base pairs in direction 5'->3'.
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*/
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public String getString(){
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return this.string;
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}
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/**
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* Sets the sequence. Also {@link #getLength() length information} will be set automatically.
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* @see #getString()
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* @param sequence sequence
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*/
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public void setString(String sequence){
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this.string = sequence;
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this.length = (sequence == null ? 0 : sequence.length());
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}
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/**
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* The length of the sequence. Will be calculated if the {@link #getString() sequence} is set.
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* @return the length of the sequence.
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*/
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public Integer getLength(){
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return this.length;
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}
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/**
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* Sets the {@link #getLength() length}, if the {@link #getString() sequence} is not set.
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* If {@link #getString() sequence} is available, length has no effect.
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* @see #getLength()
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* @param length length
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*/
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public void setLength(Integer length){
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if (StringUtils.isBlank(string)){
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this.length = length;
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}
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}
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// ********************* CLONE ********************/
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/**
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* Clones <i>this</i> sequence. This is a shortcut that enables to create
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* a new instance that differs only slightly from <i>this</i> sequencing by
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* modifying only some of the attributes.<BR><BR>
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*
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*
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* @see eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()
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* @see java.lang.Object#clone()
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*/
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@Override
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public Object clone() {
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try{
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SequenceString result = (SequenceString)super.clone();
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//don't change sequence, length
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return result;
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}catch (CloneNotSupportedException e) {
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logger.warn("Object does not implement cloneable");
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e.printStackTrace();
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return null;
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}
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}
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}
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