cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/ViralName.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.model.name;
  11
  12
  13 import java.util.Map;
  14
  15 import javax.persistence.Entity;
  16 import javax.persistence.Transient;
  17 import javax.xml.bind.annotation.XmlAccessType;
  18 import javax.xml.bind.annotation.XmlAccessorType;
  19 import javax.xml.bind.annotation.XmlElement;
  20 import javax.xml.bind.annotation.XmlRootElement;
  21 import javax.xml.bind.annotation.XmlType;
  22
  23 import org.apache.log4j.Logger;
  24 import org.hibernate.envers.Audited;
  25 import org.hibernate.search.annotations.Field;
  26 import org.hibernate.search.annotations.Indexed;
  27 import org.hibernate.validator.constraints.Length;
  28 import org.springframework.beans.factory.annotation.Configurable;
  29
  30 import eu.etaxonomy.cdm.common.CdmUtils;
  31 import eu.etaxonomy.cdm.model.common.CdmBase;
  32 import eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy;
  33 import eu.etaxonomy.cdm.validation.annotation.NullOrNotEmpty;
  34
  35 /**
  36  * The taxon name class for viral taxa. The scientific name will be stored
  37  * as a string (consisting eventually of several words even combined also with
  38  * non alphabetical characters) in the inherited {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#setTitleCache(String) titleCache} attribute.
  39  * Classification has no influence on the names of viral taxon names and no
  40  * viral taxon must be taxonomically included in another viral taxon with
  41  * higher rank. For examples see ICTVdb:
  42  * "http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/vn_indxA.htm"
  43  * <P>
  44  * This class corresponds to: NameViral according to the ABCD schema.
  45  *
  46  * @author m.doering
  47  * @version 1.0
  48  * @created 08-Nov-2007 13:07:02
  49  */
  50 @XmlAccessorType(XmlAccessType.FIELD)
  51 @XmlType(name = "", propOrder = {
  52     "acronym"
  53 })
  54 @XmlRootElement(name = "ViralName")
  55 @Entity
  56 @Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonNameBase")
  57 @Audited
  58 @Configurable
  59 public class ViralName extends TaxonNameBase<ViralName, INameCacheStrategy<ViralName>> implements Cloneable {
  60         private static final long serialVersionUID = 4516625507432071817L;
  61         private static final Logger logger = Logger.getLogger(ViralName.class);
  62
  63 //    @XmlTransient
  64 //    @Transient
  65 //      protected INameCacheStrategy<ViralName> cacheStrategy;
  66
  67         @XmlElement(name = "Acronym")
  68         @Field
  69     //TODO Val #3379
  70 //      @NullOrNotEmpty
  71         @Length(max = 255)
  72         private String acronym;
  73
  74         // ************* CONSTRUCTORS *************/
  75
  76         protected ViralName(){
  77                 super();
  78         }
  79
  80         /**
  81          * Class constructor: creates a new viral taxon name instance
  82          * only containing its {@link Rank rank}.
  83          *
  84          * @param       rank  the rank to be assigned to <i>this</i> viral taxon name
  85          * @see         TaxonNameBase#TaxonNameBase(Rank)
  86          */
  87         public ViralName(Rank rank) {
  88                 super(rank);
  89         }
  90
  91 //***********************
  92
  93         private static Map<String, java.lang.reflect.Field> allFields = null;
  94         @Override
  95     protected Map<String, java.lang.reflect.Field> getAllFields(){
  96         if (allFields == null){
  97                         allFields = CdmUtils.getAllFields(this.getClass(), CdmBase.class, false, false, false, true);
  98                 }
  99         return allFields;
 100     }
 101
 102 //*************************
 103
 104         //********* METHODS **************************************/
 105
 106         /**
 107          * Creates a new viral taxon name instance only containing its {@link Rank rank}.
 108          *
 109          * @param       rank  the rank to be assigned to <i>this</i> viral taxon name
 110          * @see         #ViralName(Rank)
 111          */
 112         public static ViralName NewInstance(Rank rank){
 113                 return new ViralName(rank);
 114         }
 115
 116         /**
 117          * Returns the accepted acronym (an assigned abbreviation) string for <i>this</i>
 118          * viral taxon name. For instance PCV stays for Peanut Clump Virus.
 119          *
 120          * @return  the string containing the accepted acronym of <i>this</i> viral taxon name
 121          */
 122         public String getAcronym(){
 123                 return this.acronym;
 124         }
 125         /**
 126          * @see  #getAcronym()
 127          */
 128         public void setAcronym(String acronym){
 129                 this.acronym = acronym;
 130         }
 131
 132         /**
 133          * Generates and returns the string with the scientific name of <i>this</i>
 134          * viral taxon name. This string may be stored in the inherited
 135          * {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache() titleCache} attribute.
 136          * This method overrides the generic and inherited
 137          * method from {@link TaxonNameBase TaxonNameBase} .
 138          *
 139          * @return  the string with the composed name of <i>this</i> viral taxon name with authorship (and maybe year)
 140          * @see         eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
 141          * @see         eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()
 142          * @see         TaxonNameBase#generateTitle()
 143          */
 144 //      @Override
 145 //      public String generateTitle(){
 146 //              logger.warn("not yet implemented");
 147 //              return this.toString();
 148 //      }
 149
 150         @Override
 151         public String generateFullTitle(){
 152                 logger.warn("not yet implemented");
 153                 return this.toString();
 154         }
 155
 156         /**
 157          * Returns the boolean value "true" if the components of <i>this</i> viral taxon name
 158          * follow the rules of the corresponding
 159          * {@link NomenclaturalCode International Code of Virus Classification and Nomenclature},
 160          * "false" otherwise.
 161          * This method overrides and implements the isCodeCompliant method from
 162          * the abstract {@link TaxonNameBase#isCodeCompliant() TaxonNameBase} class.
 163          *
 164          * @return  the boolean value expressing the compliance of <i>this</i> viral taxon name to its nomenclatural code
 165          * @see         TaxonNameBase#isCodeCompliant()
 166          */
 167         @Override
 168         @Transient
 169         public boolean isCodeCompliant() {
 170                 logger.warn("not yet implemented");
 171                 return false;
 172         }
 173
 174
 175         /**
 176          * Returns the {@link NomenclaturalCode nomenclatural code} that governs
 177          * the construction of <i>this</i> viral taxon name, that is the
 178          * International Code of Virus Classification and Nomenclature.
 179          * This method overrides the getNomeclaturalCode method from {@link TaxonNameBase TaxonNameBase}.
 180          *
 181          * @return  the nomenclatural code for viruses
 182          * @see         #isCodeCompliant()
 183          * @see         TaxonNameBase#getHasProblem()
 184          * @see         TaxonNameBase#getNomenclaturalCode()
 185          */
 186         @Override
 187         public NomenclaturalCode getNomenclaturalCode(){
 188                 return NomenclaturalCode.ICVCN;
 189         }
 190
 191
 192         /**
 193          * Returns the {@link eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy cache strategy} used to generate
 194          * several strings corresponding to <i>this</i> viral taxon name.
 195          *
 196          * @return  the cache strategy used for <i>this</i> viral taxon name
 197          * @see         eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
 198          * @see     eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
 199          */
 200 //      @Override
 201 //      @Transient
 202 //      public INameCacheStrategy getCacheStrategy() {
 203 //              return cacheStrategy;
 204 //      }
 205
 206
 207         /**
 208          * @see  #getCacheStrategy()
 209          */
 210 //      @Override
 211 //      public void setCacheStrategy(INameCacheStrategy cacheStrategy) {
 212 //              this.cacheStrategy = cacheStrategy;
 213 //      }
 214
 215
 216 //*********************** CLONE ********************************************************/
 217
 218         /**
 219          * Clones <i>this</i> viral name. This is a shortcut that enables to create
 220          * a new instance that differs only slightly from <i>this</i> viral name by
 221          * modifying only some of the attributes.
 222          *
 223          * @see eu.etaxonomy.cdm.model.name.TaxonNameBase#clone()
 224          * @see java.lang.Object#clone()
 225          */
 226         @Override
 227         public Object clone() {
 228                 ViralName result = (ViralName)super.clone();
 229                 //no changes to: acronym
 230                 return result;
 231         }
 232 }