| 1 |
9479da48
|
Andreas Müller
|
/**
|
| 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 |
f6765014
|
ben.clark
|
import javax.persistence.Entity;
|
| 14 |
|
|
import javax.persistence.FetchType;
|
| 15 |
228c04ef
|
Katja Luther
|
import javax.persistence.JoinColumn;
|
| 16 |
f6765014
|
ben.clark
|
import javax.persistence.ManyToOne;
|
| 17 |
b70a7f94
|
Andreas Kohlbecker
|
import javax.persistence.Transient;
|
| 18 |
dd2d8fac
|
a.babadshanjan
|
import javax.xml.bind.annotation.XmlAccessType;
|
| 19 |
|
|
import javax.xml.bind.annotation.XmlAccessorType;
|
| 20 |
|
|
import javax.xml.bind.annotation.XmlElement;
|
| 21 |
|
|
import javax.xml.bind.annotation.XmlIDREF;
|
| 22 |
a2312bea
|
a.babadshanjan
|
import javax.xml.bind.annotation.XmlRootElement;
|
| 23 |
dd2d8fac
|
a.babadshanjan
|
import javax.xml.bind.annotation.XmlSchemaType;
|
| 24 |
|
|
import javax.xml.bind.annotation.XmlType;
|
| 25 |
9479da48
|
Andreas Müller
|
|
| 26 |
f6765014
|
ben.clark
|
import org.apache.log4j.Logger;
|
| 27 |
|
|
import org.hibernate.annotations.Cascade;
|
| 28 |
|
|
import org.hibernate.annotations.CascadeType;
|
| 29 |
ee91bcd9
|
ben.clark
|
import org.hibernate.envers.Audited;
|
| 30 |
f6765014
|
ben.clark
|
|
| 31 |
483579cd
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
|
| 32 |
1d36aa54
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
| 33 |
f6765014
|
ben.clark
|
|
| 34 |
9479da48
|
Andreas Müller
|
/**
|
| 35 |
09887ea6
|
m.geoffroy
|
* The class representing a typification of one or several {@link TaxonNameBase taxon names} by a
|
| 36 |
483579cd
|
Andreas Müller
|
* {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or a figure}. All {@link TaxonNameBase taxon names}
|
| 37 |
d82717cb
|
m.geoffroy
|
* which have a {@link Rank rank} "species aggregate" or lower can only be typified
|
| 38 |
|
|
* by specimens. Moreover each typification by a specimen (or by a figure) has a
|
| 39 |
2d4607f2
|
a.babadshanjan
|
* {@link SpecimenTypeDesignationStatus status} like "holotype" or "isotype".
|
| 40 |
9e86cd74
|
m.geoffroy
|
* <P>
|
| 41 |
|
|
* This class corresponds to: <ul>
|
| 42 |
|
|
* <li> NomenclaturalType according to the TDWG ontology
|
| 43 |
|
|
* <li> Typification (partially) according to the TCS
|
| 44 |
|
|
* <li> NomenclaturalTypeDesignation according to the ABCD schema
|
| 45 |
|
|
* </ul>
|
| 46 |
79263e24
|
m.geoffroy
|
*
|
| 47 |
d82717cb
|
m.geoffroy
|
* @see TypeDesignationBase
|
| 48 |
7eba4302
|
m.geoffroy
|
* @see NameTypeDesignation
|
| 49 |
|
|
* @author m.doering
|
| 50 |
9479da48
|
Andreas Müller
|
* @version 1.0
|
| 51 |
7eba4302
|
m.geoffroy
|
* @created 08-Nov-2007 13:06:38
|
| 52 |
9479da48
|
Andreas Müller
|
*/
|
| 53 |
a2312bea
|
a.babadshanjan
|
@XmlRootElement(name = "SpecimenTypeDesignation")
|
| 54 |
dd2d8fac
|
a.babadshanjan
|
@XmlAccessorType(XmlAccessType.FIELD)
|
| 55 |
|
|
@XmlType(name = "SpecimenTypeDesignation", propOrder = {
|
| 56 |
2d4607f2
|
a.babadshanjan
|
"typeSpecimen"
|
| 57 |
dd2d8fac
|
a.babadshanjan
|
})
|
| 58 |
9479da48
|
Andreas Müller
|
@Entity
|
| 59 |
ee91bcd9
|
ben.clark
|
@Audited
|
| 60 |
a42e27ce
|
Andreas Müller
|
public class SpecimenTypeDesignation extends TypeDesignationBase<SpecimenTypeDesignationStatus> implements ITypeDesignation, Cloneable {
|
| 61 |
a3a73c60
|
Andreas Müller
|
private static final long serialVersionUID = 6481627446997275007L;
|
| 62 |
bb6bc58f
|
n.hoffmann
|
private static final Logger logger = Logger.getLogger(SpecimenTypeDesignation.class);
|
| 63 |
dd2d8fac
|
a.babadshanjan
|
|
| 64 |
|
|
@XmlElement(name = "TypeSpecimen")
|
| 65 |
ddae61ce
|
a.babadshanjan
|
@XmlIDREF
|
| 66 |
|
|
@XmlSchemaType(name = "IDREF")
|
| 67 |
ee91bcd9
|
ben.clark
|
@ManyToOne(fetch = FetchType.LAZY)
|
| 68 |
ac7f8217
|
Katja Luther
|
@JoinColumn(name="typeSpecimen_id")
|
| 69 |
903cecc9
|
Cherian Mathew
|
@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
|
| 70 |
483579cd
|
Andreas Müller
|
private DerivedUnit typeSpecimen;
|
| 71 |
dd2d8fac
|
a.babadshanjan
|
|
| 72 |
dce4c9cb
|
Andreas Müller
|
// /**
|
| 73 |
|
|
// * Creates a new specimen type designation instance
|
| 74 |
1d36aa54
|
Andreas Müller
|
// * (including its {@link reference.Reference reference source} and eventually
|
| 75 |
dce4c9cb
|
Andreas Müller
|
// * the taxon name string originally used by this reference when establishing
|
| 76 |
|
|
// * the former designation) and adds it to the corresponding
|
| 77 |
|
|
// * {@link HomotypicalGroup#getSpecimenTypeDesignations() specimen type designation set} of the
|
| 78 |
|
|
// * {@link HomotypicalGroup homotypical group}.
|
| 79 |
|
|
// *
|
| 80 |
|
|
// * @param specimen the derived unit (specimen or figure) used as type
|
| 81 |
|
|
// * @param status the type designation status
|
| 82 |
|
|
// * @param citation the reference source for the new designation
|
| 83 |
|
|
// * @param citationMicroReference the string with the details describing the exact localisation within the reference
|
| 84 |
|
|
// * @param originalNameString the taxon name string used originally in the reference source for the new designation
|
| 85 |
483579cd
|
Andreas Müller
|
// * @see #SpecimenTypeDesignation(DerivedUnit, TypeDesignationStatus, Reference, String, String)
|
| 86 |
dce4c9cb
|
Andreas Müller
|
// * @see HomotypicalGroup#addSpecimenTypeDesignation(SpecimenTypeDesignation, boolean)
|
| 87 |
483579cd
|
Andreas Müller
|
// * @see occurrence.DerivedUnit
|
| 88 |
dce4c9cb
|
Andreas Müller
|
// */
|
| 89 |
483579cd
|
Andreas Müller
|
// protected static SpecimenTypeDesignation NewInstance2(DerivedUnit specimen, TypeDesignationStatus status,
|
| 90 |
1d36aa54
|
Andreas Müller
|
// Reference citation, String citationMicroReference, String originalNameString){
|
| 91 |
dce4c9cb
|
Andreas Müller
|
// SpecimenTypeDesignation specTypeDesig = new SpecimenTypeDesignation(specimen, status, citation, citationMicroReference, originalNameString);
|
| 92 |
|
|
// return specTypeDesig;
|
| 93 |
|
|
// }
|
| 94 |
|
|
|
| 95 |
3c629d82
|
Andreas Müller
|
|
| 96 |
7eba4302
|
m.geoffroy
|
// ************* CONSTRUCTORS *************/
|
| 97 |
|
|
/**
|
| 98 |
|
|
* Class constructor: creates a new empty specimen type designation.
|
| 99 |
|
|
*
|
| 100 |
483579cd
|
Andreas Müller
|
* @see #SpecimenTypeDesignation(DerivedUnit, SpecimenTypeDesignationStatus,
|
| 101 |
1d36aa54
|
Andreas Müller
|
* Reference, String, String, boolean)
|
| 102 |
7eba4302
|
m.geoffroy
|
*/
|
| 103 |
3c629d82
|
Andreas Müller
|
protected SpecimenTypeDesignation(){
|
| 104 |
|
|
}
|
| 105 |
|
|
|
| 106 |
a641fad9
|
ben.clark
|
public static SpecimenTypeDesignation NewInstance() {
|
| 107 |
|
|
return new SpecimenTypeDesignation();
|
| 108 |
|
|
}
|
| 109 |
|
|
|
| 110 |
7eba4302
|
m.geoffroy
|
/**
|
| 111 |
|
|
* Class constructor: creates a new specimen type designation instance
|
| 112 |
1d36aa54
|
Andreas Müller
|
* (including its {@link eu.etaxonomy.cdm.model.reference.Reference reference source} and
|
| 113 |
c99ad027
|
n.hoffmann
|
* eventually the taxon name string originally used by this reference when
|
| 114 |
d82717cb
|
m.geoffroy
|
* establishing the former designation).
|
| 115 |
7eba4302
|
m.geoffroy
|
*
|
| 116 |
c99ad027
|
n.hoffmann
|
* @param specimen the derived unit (specimen or figure) used
|
| 117 |
|
|
* as type
|
| 118 |
7eba4302
|
m.geoffroy
|
* @param status the type designation status
|
| 119 |
|
|
* @param citation the reference source for the new designation
|
| 120 |
c99ad027
|
n.hoffmann
|
* @param citationMicroReference the string with the details describing
|
| 121 |
|
|
* the exact localisation within the reference
|
| 122 |
|
|
* @param originalNameString the taxon name string used originally in the
|
| 123 |
|
|
* reference source for the new designation
|
| 124 |
57883822
|
m.geoffroy
|
* @param isNotDesignated the boolean flag indicating whether there is no specimen type at all for
|
| 125 |
|
|
* <i>this</i> specimen type designation
|
| 126 |
7eba4302
|
m.geoffroy
|
* @see #SpecimenTypeDesignation()
|
| 127 |
1d36aa54
|
Andreas Müller
|
* @see TaxonNameBase#addSpecimenTypeDesignation(Specimen, SpecimenTypeDesignationStatus, Reference, String, String, boolean, boolean)
|
| 128 |
57883822
|
m.geoffroy
|
* @see TypeDesignationBase#isNotDesignated()
|
| 129 |
483579cd
|
Andreas Müller
|
* @see eu.etaxonomy.cdm.model.occurrence.DerivedUnit
|
| 130 |
7eba4302
|
m.geoffroy
|
*/
|
| 131 |
483579cd
|
Andreas Müller
|
protected SpecimenTypeDesignation(DerivedUnit specimen, SpecimenTypeDesignationStatus status, Reference citation, String citationMicroReference,
|
| 132 |
57883822
|
m.geoffroy
|
String originalNameString, boolean isNotDesignated) {
|
| 133 |
|
|
super(citation, citationMicroReference, originalNameString, isNotDesignated);
|
| 134 |
9479da48
|
Andreas Müller
|
this.setTypeSpecimen(specimen);
|
| 135 |
228c04ef
|
Katja Luther
|
|
| 136 |
9479da48
|
Andreas Müller
|
this.setTypeStatus(status);
|
| 137 |
|
|
}
|
| 138 |
|
|
|
| 139 |
7eba4302
|
m.geoffroy
|
//********* METHODS **************************************/
|
| 140 |
ad45fc6d
|
Andreas Müller
|
|
| 141 |
|
|
|
| 142 |
|
|
/* (non-Javadoc)
|
| 143 |
|
|
* @see eu.etaxonomy.cdm.model.name.TypeDesignationBase#removeType()
|
| 144 |
|
|
*/
|
| 145 |
|
|
@Override
|
| 146 |
|
|
public void removeType() {
|
| 147 |
|
|
this.setTypeSpecimen(null);
|
| 148 |
|
|
}
|
| 149 |
|
|
|
| 150 |
7eba4302
|
m.geoffroy
|
/**
|
| 151 |
483579cd
|
Andreas Müller
|
* Returns the {@link DerivedUnit.DerivedUnit derived unit} (specimen or figure) that is used
|
| 152 |
d82717cb
|
m.geoffroy
|
* in <i>this</i> specimen type designation to typify the {@link TaxonNameBase taxon name}.
|
| 153 |
7eba4302
|
m.geoffroy
|
*
|
| 154 |
|
|
* @see #getHomotypicalGroup()
|
| 155 |
|
|
*/
|
| 156 |
483579cd
|
Andreas Müller
|
public DerivedUnit getTypeSpecimen(){
|
| 157 |
9479da48
|
Andreas Müller
|
return this.typeSpecimen;
|
| 158 |
|
|
}
|
| 159 |
bb2f0f32
|
Andreas Müller
|
|
| 160 |
7eba4302
|
m.geoffroy
|
/**
|
| 161 |
|
|
* @see #getTypeSpecimen()
|
| 162 |
|
|
*/
|
| 163 |
483579cd
|
Andreas Müller
|
public void setTypeSpecimen(DerivedUnit typeSpecimen){
|
| 164 |
bb2f0f32
|
Andreas Müller
|
if (this.typeSpecimen == typeSpecimen){
|
| 165 |
|
|
return;
|
| 166 |
|
|
}
|
| 167 |
|
|
if (this.typeSpecimen != null){
|
| 168 |
|
|
this.typeSpecimen.removeSpecimenTypeDesignation(this);
|
| 169 |
|
|
}
|
| 170 |
|
|
if (typeSpecimen != null && ! typeSpecimen.getSpecimenTypeDesignations().contains(this)){
|
| 171 |
|
|
typeSpecimen.addSpecimenTypeDesignation(this);
|
| 172 |
|
|
}
|
| 173 |
f1d41e41
|
Andreas Müller
|
this.typeSpecimen = typeSpecimen;
|
| 174 |
9479da48
|
Andreas Müller
|
}
|
| 175 |
|
|
|
| 176 |
dce4c9cb
|
Andreas Müller
|
/* (non-Javadoc)
|
| 177 |
|
|
* @see eu.etaxonomy.cdm.model.name.ITypeDesignation#isLectoType()
|
| 178 |
3c629d82
|
Andreas Müller
|
*/
|
| 179 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 180 |
dce4c9cb
|
Andreas Müller
|
public boolean isLectoType() {
|
| 181 |
ece46ca8
|
Andreas Kohlbecker
|
if(getTypeStatus() == null){
|
| 182 |
|
|
return false;
|
| 183 |
|
|
}
|
| 184 |
2d4607f2
|
a.babadshanjan
|
return getTypeStatus().isLectotype();
|
| 185 |
3c629d82
|
Andreas Müller
|
}
|
| 186 |
|
|
|
| 187 |
a42e27ce
|
Andreas Müller
|
//*********************** CLONE ********************************************************/
|
| 188 |
|
|
|
| 189 |
|
|
/**
|
| 190 |
|
|
* Clones <i>this</i> type specimen. This is a shortcut that enables to create
|
| 191 |
|
|
* a new instance that differs only slightly from <i>this</i> type specimen by
|
| 192 |
|
|
* modifying only some of the attributes.
|
| 193 |
|
|
*
|
| 194 |
|
|
* @see eu.etaxonomy.cdm.model.name.TypeDesignationBase#clone()
|
| 195 |
|
|
* @see java.lang.Object#clone()
|
| 196 |
|
|
*/
|
| 197 |
|
|
@Override
|
| 198 |
|
|
public Object clone() {
|
| 199 |
|
|
SpecimenTypeDesignation result;
|
| 200 |
|
|
try {
|
| 201 |
|
|
result = (SpecimenTypeDesignation)super.clone();
|
| 202 |
|
|
//no changes to: typeSpecimen
|
| 203 |
|
|
return result;
|
| 204 |
|
|
} catch (CloneNotSupportedException e) {
|
| 205 |
|
|
logger.warn("Object does not implement cloneable");
|
| 206 |
|
|
e.printStackTrace();
|
| 207 |
|
|
return null;
|
| 208 |
|
|
}
|
| 209 |
|
|
}
|
| 210 |
ad45fc6d
|
Andreas Müller
|
|
| 211 |
a42e27ce
|
Andreas Müller
|
|
| 212 |
9479da48
|
Andreas Müller
|
}
|