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.molecular;
|
11
|
|
12
|
|
13
|
import java.util.HashSet;
|
14
|
import java.util.Set;
|
15
|
|
16
|
import javax.persistence.Entity;
|
17
|
import javax.persistence.FetchType;
|
18
|
import javax.persistence.ManyToMany;
|
19
|
import javax.validation.constraints.NotNull;
|
20
|
import javax.xml.bind.annotation.XmlAccessType;
|
21
|
import javax.xml.bind.annotation.XmlAccessorType;
|
22
|
import javax.xml.bind.annotation.XmlElement;
|
23
|
import javax.xml.bind.annotation.XmlElementWrapper;
|
24
|
import javax.xml.bind.annotation.XmlIDREF;
|
25
|
import javax.xml.bind.annotation.XmlRootElement;
|
26
|
import javax.xml.bind.annotation.XmlSchemaType;
|
27
|
import javax.xml.bind.annotation.XmlType;
|
28
|
|
29
|
import org.apache.log4j.Logger;
|
30
|
import org.hibernate.envers.Audited;
|
31
|
|
32
|
import eu.etaxonomy.cdm.model.media.Media;
|
33
|
|
34
|
/**
|
35
|
* "A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the
|
36
|
* inferred evolutionary relationships among various biological species or other entities
|
37
|
* based upon similarities and differences in their physical and/or genetic characteristics.
|
38
|
* The taxa joined together in the tree are implied to have descended from a common ancestor."
|
39
|
* (Wikipedia).
|
40
|
* <BR> In the CDM we currently store phylogenetic trees only as media. This may change in future.
|
41
|
*
|
42
|
* @author m.doering
|
43
|
* @created 08-Nov-2007
|
44
|
*/
|
45
|
@XmlAccessorType(XmlAccessType.FIELD)
|
46
|
@XmlType(name = "PhylogeneticTree", propOrder = {
|
47
|
"usedSequences"
|
48
|
})
|
49
|
@XmlRootElement(name = "PhylogeneticTree")
|
50
|
@Entity
|
51
|
//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
|
52
|
//@Indexed(index = "eu.etaxonomy.cdm.model.media.Media")
|
53
|
@Audited
|
54
|
public class PhylogeneticTree extends Media implements Cloneable{
|
55
|
private static final long serialVersionUID = -7020182117362324067L;
|
56
|
private static final Logger logger = Logger.getLogger(PhylogeneticTree.class);
|
57
|
|
58
|
|
59
|
@XmlElementWrapper(name = "UsedSequences")
|
60
|
@XmlElement(name = "UsedSequence")
|
61
|
@XmlIDREF
|
62
|
@XmlSchemaType(name = "IDREF")
|
63
|
@ManyToMany(fetch = FetchType.LAZY)
|
64
|
@NotNull
|
65
|
private Set<Sequence> usedSequences = new HashSet<Sequence>();
|
66
|
|
67
|
//********************** Factory Method **********************************/
|
68
|
|
69
|
/**
|
70
|
* Factory method
|
71
|
* @return
|
72
|
*/
|
73
|
public static PhylogeneticTree NewInstance(){
|
74
|
return new PhylogeneticTree();
|
75
|
}
|
76
|
|
77
|
|
78
|
//***************** Constructor ****************************/
|
79
|
|
80
|
private PhylogeneticTree(){
|
81
|
super();
|
82
|
}
|
83
|
|
84
|
|
85
|
|
86
|
// ********************** GETTER / SETTER **************************/
|
87
|
|
88
|
public Set<Sequence> getUsedSequences() {
|
89
|
if(usedSequences == null) {
|
90
|
this.usedSequences = new HashSet<Sequence>();
|
91
|
}
|
92
|
return usedSequences;
|
93
|
}
|
94
|
|
95
|
public void addUsedSequences(Sequence usedSequence) {
|
96
|
this.usedSequences.add(usedSequence);
|
97
|
}
|
98
|
|
99
|
public void removeUsedSequences(Sequence usedSequence) {
|
100
|
this.usedSequences.remove(usedSequence);
|
101
|
|
102
|
}
|
103
|
|
104
|
//*********** CLONE **********************************/
|
105
|
|
106
|
/**
|
107
|
* Clones <i>this</i> phylogenetic tree. This is a shortcut that enables to
|
108
|
* create a new instance that differs only slightly from <i>this</i> phylogenetic tree
|
109
|
* by modifying only some of the attributes.<BR>
|
110
|
* This method overrides the clone method from {@link Media Media}.
|
111
|
*
|
112
|
* @see eu.etaxonomy.cdm.model.media.Media#clone()
|
113
|
* @see java.lang.Object#clone()
|
114
|
*/
|
115
|
@Override
|
116
|
|
117
|
public Object clone(){
|
118
|
PhylogeneticTree result;
|
119
|
try{
|
120
|
result= (PhylogeneticTree) super.clone();
|
121
|
result.usedSequences = new HashSet<Sequence>();
|
122
|
for (Sequence seq: this.usedSequences){
|
123
|
result.addUsedSequences((Sequence)seq.clone());
|
124
|
}
|
125
|
|
126
|
return result;
|
127
|
}catch (CloneNotSupportedException e) {
|
128
|
logger.warn("Object does not implement cloneable");
|
129
|
e.printStackTrace();
|
130
|
return null;
|
131
|
}
|
132
|
}
|
133
|
}
|