root/trunk/cdmlib/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Sequence.java

/**
* 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.util.HashSet;
import java.util.Set;

import javax.persistence.Basic;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.ManyToOne;
import javax.persistence.OneToMany;
import javax.persistence.Transient;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlElementWrapper;
import javax.xml.bind.annotation.XmlIDREF;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlSchemaType;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;

import org.apache.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import org.hibernate.annotations.Index;
import org.hibernate.annotations.Table;
import org.hibernate.annotations.Type;
import org.hibernate.envers.Audited;
import org.joda.time.DateTime;
import org.springframework.beans.factory.annotation.Configurable;

import eu.etaxonomy.cdm.jaxb.DateTimeAdapter;
import eu.etaxonomy.cdm.model.common.IReferencedEntity;
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
import eu.etaxonomy.cdm.model.media.IMediaDocumented;
import eu.etaxonomy.cdm.model.media.Media;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;

/**
 * @author m.doering
 * @version 1.0
 * @created 08-Nov-2007 13:06:51
 */
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "Sequence", propOrder = {
    "sequence",
    "length",
    "dateSequenced",
    "barcode",
    "citationMicroReference",
    "publishedIn",
    "locus",
    "citations",
    "genBankAccession",
    "chromatograms"
})
@XmlRootElement(name = "Sequence")
@Entity
@Audited
@Configurable
@Table(appliesTo="Sequence", indexes = { @Index(name = "sequenceTitleCacheIndex", columnNames = { "titleCache" }) })
public class Sequence extends IdentifiableEntity<IIdentifiableEntityCacheStrategy<Sequence>> implements IReferencedEntity, IMediaDocumented{
        private static final long serialVersionUID = 8298983152731241775L;
        private static final Logger logger = Logger.getLogger(Sequence.class);
        
        //the sequence as a string of base pairs. 5'->3'
        @XmlElement(name = "Sequence")
        private String sequence;
        
        //should be calculated in case sequence is set
        @XmlElement(name = "Length")
        private Integer length;
        
        //should be calculated in case sequence is set
        @XmlElement (name = "DateSequenced", type= String.class)
        @XmlJavaTypeAdapter(DateTimeAdapter.class)
        @Type(type="dateTimeUserType")
        @Basic(fetch = FetchType.LAZY)
        private DateTime dateSequenced;
        
        //should be calculated in case sequence is set
        @XmlAttribute(name = "isBarcode")
        private boolean barcode;
        
        //the sequence as a string of base pairs. 5'->3'
        @XmlElement(name = "CitationMicroReference")
        private String citationMicroReference;
        
        @XmlElement(name = "PublishedIn")
    @XmlIDREF
    @XmlSchemaType(name = "IDREF")
    @ManyToOne(fetch = FetchType.LAZY)
    @Cascade(CascadeType.SAVE_UPDATE)
        private Reference publishedIn;
        
        @XmlElementWrapper(name = "Citations")
        @XmlElement(name = "Citation")
    @XmlIDREF
    @XmlSchemaType(name = "IDREF")
    @OneToMany(fetch = FetchType.LAZY)
        private Set<Reference> citations = new HashSet<Reference>();
        
        @XmlElementWrapper(name = "GenBankAccessions")
        @XmlElement(name = "GenBankAccession")
    @OneToMany(fetch = FetchType.LAZY)
        private Set<GenBankAccession> genBankAccession = new HashSet<GenBankAccession>();
        
        @XmlElement(name = "Locus")
    @XmlIDREF
    @XmlSchemaType(name = "IDREF")
    @ManyToOne(fetch = FetchType.LAZY)
    @Cascade(CascadeType.SAVE_UPDATE)
        private Locus locus;
        
        @XmlElementWrapper(name = "Chromatograms")
        @XmlElement(name = "Chromatogram")
    @XmlIDREF
    @XmlSchemaType(name = "IDREF")
    @OneToMany(fetch = FetchType.LAZY)
        private Set<Media> chromatograms = new HashSet<Media>();
        
        protected Sequence() {
                super(); // FIXME I think this is explicit - do we really need to call this?
                this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<Sequence>();
        }
        
        public Locus getLocus(){
                logger.debug("getLocus");
                return this.locus;
        }

        public void setLocus(Locus locus){
                this.locus = locus;
        }

        public Reference getPublishedIn(){
                return this.publishedIn;
        }
        
        public void setPublishedIn(Reference publishedIn){
                this.publishedIn = publishedIn;
        }

        public Set<Reference> getCitations() {
                return citations;
        }
        protected void setCitations(Set<Reference> citations) {
                this.citations = citations;
        }
        public void addCitation(Reference citation) {
                this.citations.add(citation);
        }
        public void removeCitation(Reference citation) {
                this.citations.remove(citation);
        }

        public Set<GenBankAccession> getGenBankAccession() {
                return genBankAccession;
        }

        public void addGenBankAccession(GenBankAccession genBankAccession) {
                this.genBankAccession.add(genBankAccession);
        }
        
        public void removeGenBankAccession(GenBankAccession genBankAccession) {
                this.genBankAccession.remove(genBankAccession);
        }
        
        public Set<Media> getChromatograms() {
                return chromatograms;
        }

        public void addChromatogram(Media chromatogram) {
                this.chromatograms.add(chromatogram);
        }
        
        public void removeChromatogram(Media chromatogram) {
                this.chromatograms.remove(chromatogram);
        }
        
        @Transient
        public Set<Media> getMedia() {
                return getChromatograms();
        }

        public String getSequence(){
                return this.sequence;
        }

        /**
         * 
         * @param sequence    sequence
         */
        public void setSequence(String sequence){
                this.sequence = sequence;
        }

        public Integer getLength(){
                return this.length;
        }

        /**
         * 
         * @param length    length
         */
        public void setLength(Integer length){
                this.length = length;
        }

        public DateTime getDateSequenced(){
                return this.dateSequenced;
        }

        /**
         * 
         * @param dateSequenced    dateSequenced
         */
        public void setDateSequenced(DateTime dateSequenced){
                this.dateSequenced = dateSequenced;
        }

        public boolean isBarcode(){
                return this.barcode;
        }

        /**
         * 
         * @param isBarcode    isBarcode
         */
        public void setBarcode(boolean barcode){
                this.barcode = barcode;
        }

        public String getCitationMicroReference(){
                return this.citationMicroReference;
        }

        /**
         * 
         * @param citationMicroReference    citationMicroReference
         */
        public void setCitationMicroReference(String citationMicroReference){
                this.citationMicroReference = citationMicroReference;
        }

        public Reference getCitation(){
                return publishedIn;
        }
        
        //*********************** 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> sequence 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{
                Sequence result = (Sequence)super.clone();
                
                result.citations = new HashSet<Reference>();
                for (Reference ref: this.citations){
                        result.citations.add((Reference) ref.clone());
                
                }
                
                result.genBankAccession = new HashSet<GenBankAccession>();
                for (GenBankAccession genBankAcc: this.genBankAccession){
                        result.genBankAccession.add((GenBankAccession)genBankAcc.clone());
                }
                
                result.chromatograms = new HashSet<Media>();
                
                for (Media chromatogram: this.chromatograms){
                        result.chromatograms.add((Media)chromatogram.clone());
                }
                
                return result;
                }catch (CloneNotSupportedException e) {
                        logger.warn("Object does not implement cloneable");
                        e.printStackTrace();
                        return null;
                }
        }
}