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9479da48
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Andreas Müller
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/**
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* Copyright (C) 2007 EDIT
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1120db75
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Andreas Kohlbecker
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* European Distributed Institute of Taxonomy
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4 |
9479da48
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Andreas Müller
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* http://www.e-taxonomy.eu
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5 |
1120db75
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Andreas Kohlbecker
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*
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6 |
9479da48
|
Andreas Müller
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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.description;
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03abbcde
|
Andreas Müller
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import java.util.ArrayList;
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13 |
e27511ac
|
Andreas Müller
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import java.util.Arrays;
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14 |
03abbcde
|
Andreas Müller
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import java.util.List;
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15 |
9479da48
|
Andreas Müller
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16 |
03abbcde
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Andreas Müller
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import javax.persistence.Entity;
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17 |
f6765014
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ben.clark
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import javax.persistence.FetchType;
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18 |
a7f52c55
|
Andreas Müller
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import javax.persistence.OneToMany;
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19 |
1e2f5c73
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Andreas Müller
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import javax.persistence.Transient;
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20 |
519bff7b
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Andreas Müller
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import javax.validation.constraints.NotEmpty;
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21 |
01b7ddbf
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a.babadshanjan
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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.XmlElementWrapper;
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import javax.xml.bind.annotation.XmlRootElement;
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e9829ef9
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Andreas Müller
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import javax.xml.bind.annotation.XmlTransient;
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27 |
01b7ddbf
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a.babadshanjan
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import javax.xml.bind.annotation.XmlType;
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9479da48
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Andreas Müller
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23de68fc
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Andreas Müller
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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03abbcde
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Andreas Müller
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import org.hibernate.annotations.Cascade;
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import org.hibernate.annotations.CascadeType;
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ee91bcd9
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ben.clark
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import org.hibernate.envers.Audited;
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17a0cbe8
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ben.clark
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import org.hibernate.search.annotations.Indexed;
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51db8d4a
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ben.clark
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import org.hibernate.search.annotations.IndexedEmbedded;
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a1587c24
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ben.clark
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import eu.etaxonomy.cdm.validation.Level2;
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03abbcde
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Andreas Müller
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9479da48
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Andreas Müller
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/**
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50c72f11
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m.geoffroy
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* This class represents information pieces expressed in categorical type of
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f51e2565
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m.geoffroy
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* data (in opposition to {@link QuantitativeData quantitative data} on one side and to literal data on
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4daf2f37
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m.geoffroy
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* the other side). Only {@link TaxonDescription taxon descriptions} and
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* {@link SpecimenDescription specimen descriptions} may contain categorical data.<BR>
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f51e2565
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m.geoffroy
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* The "color of petals" {@link Feature feature} for instance can be described with
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* {@link State state terms} such as "blue" or "white". If the color of petals of a
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* particular tree is described as "mostly blue" and "exceptionally white" two
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* {@link StateData state data} instances must be assigned to an instance of the
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* present class: the first one with the state "blue" and the {@link Modifier modifier}
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3a9870fa
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m.geoffroy
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* "mostly" and the second one with the state "white" and the modifier "exceptionally".
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* Whenever more than one state data belongs to a categorical data they should be
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1120db75
|
Andreas Kohlbecker
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* interpreted as being related by the inclusive disjunction "or".
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50c72f11
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m.geoffroy
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* <P>
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* This class corresponds partially to CodedDescriptionType according to
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* the SDD schema.
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1120db75
|
Andreas Kohlbecker
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*
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9479da48
|
Andreas Müller
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* @author m.doering
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a88578ce
|
Andreas Müller
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* @since 08-Nov-2007 13:06:15
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9479da48
|
Andreas Müller
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*/
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01b7ddbf
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a.babadshanjan
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "CategoricalData", propOrder = {
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"orderRelevant",
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6f00d6f6
|
Andreas Müller
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"stateData",
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"unknownData"
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01b7ddbf
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a.babadshanjan
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})
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@XmlRootElement(name = "CategoricalData")
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9479da48
|
Andreas Müller
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@Entity
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ee91bcd9
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ben.clark
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@Audited
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17a0cbe8
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ben.clark
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@Indexed(index = "eu.etaxonomy.cdm.model.description.DescriptionElementBase")
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50e52e0f
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Andreas Müller
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public class CategoricalData extends DescriptionElementBase {
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93ad7e54
|
Andreas Müller
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1120db75
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Andreas Kohlbecker
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private static final long serialVersionUID = -6298361966947668998L;
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23de68fc
|
Andreas Müller
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private static final Logger logger = LogManager.getLogger(CategoricalData.class);
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1120db75
|
Andreas Kohlbecker
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//whether the sequence of ordered states is important
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@XmlElement(name = "OrderRelevant")
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private boolean orderRelevant;
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@XmlElementWrapper(name = "States")
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@XmlElement(name = "State")
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7d39593c
|
Andreas Müller
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@OneToMany(fetch = FetchType.LAZY, mappedBy="categoricalData", orphanRemoval=true)
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a7f52c55
|
Andreas Müller
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@Cascade({ CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
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0930d1c2
|
Andreas Kohlbecker
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@IndexedEmbedded(depth = 3)
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1120db75
|
Andreas Kohlbecker
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@NotEmpty(groups = Level2.class)
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07d5561c
|
Andreas Müller
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private List<StateData> stateData = new ArrayList<>();
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73ee5c85
|
Andreas Kohlbecker
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@XmlElement(name = "UnknownData")
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private final Boolean unknownData = false;
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1120db75
|
Andreas Kohlbecker
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//****************************** FACTORY METHOD *******************************/
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/**
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* Creates a new empty categorical data instance.
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*/
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public static CategoricalData NewInstance(){
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return new CategoricalData();
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}
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73ee5c85
|
Andreas Kohlbecker
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a774af50
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unknown
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/**
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* @param habitat
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* @return
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*/
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public static CategoricalData NewInstance(Feature feature) {
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return new CategoricalData( new ArrayList<>() , feature);
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}
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106 |
e27511ac
|
Andreas Müller
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/**
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* Creates a new empty categorical data instance.
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*/
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public static CategoricalData NewInstance(State state, Feature feature){
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return new CategoricalData( Arrays.asList( new State[]{state}) , feature);
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}
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112 |
1120db75
|
Andreas Kohlbecker
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//******************* CONSTRUCTOR *********************************************/
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/**
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* Class constructor: creates a new empty categorical data instance.
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*/
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protected CategoricalData() {
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super(null);
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}
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e27511ac
|
Andreas Müller
|
/**
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* Class constructor: creates a new empty categorical data instance.
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*/
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protected CategoricalData(List<State> states, Feature feature) {
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super(feature);
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for (State state : states){
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128 |
73ee5c85
|
Andreas Kohlbecker
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addStateData(state);
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129 |
e27511ac
|
Andreas Müller
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}
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130 |
73ee5c85
|
Andreas Kohlbecker
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131 |
e27511ac
|
Andreas Müller
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}
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1120db75
|
Andreas Kohlbecker
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// ****************** GETTER / SETTER *********************************************/
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/**
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* Returns the (ordered) list of {@link State states} describing the {@link Feature feature}
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* corresponding to <i>this</i> categorical data.
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*/
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f3dabfca
|
Andreas Müller
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public List<StateData> getStateData(){
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return this.stateData;
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142 |
1120db75
|
Andreas Kohlbecker
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}
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144 |
7d39593c
|
Andreas Müller
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@Deprecated
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145 |
73ee5c85
|
Andreas Kohlbecker
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protected void setStateData(List<StateData> stateData){
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146 |
f3dabfca
|
Andreas Müller
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this.stateData = stateData;
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147 |
1120db75
|
Andreas Kohlbecker
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}
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/**
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150 |
f3dabfca
|
Andreas Müller
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* Adds a {@link State state} to the list of {@link #getStateData() states}
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151 |
1120db75
|
Andreas Kohlbecker
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* describing the {@link Feature feature} corresponding to <i>this</i> categorical data.
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*
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* @param state the state to be added to <i>this</i> categorical data
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154 |
f3dabfca
|
Andreas Müller
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* @see #getStateData()
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155 |
1120db75
|
Andreas Kohlbecker
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*/
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156 |
b3bec3a9
|
Andreas M��ller
|
@SuppressWarnings("deprecation")
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157 |
f3dabfca
|
Andreas Müller
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public void addStateData(StateData stateData){
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this.stateData.add(stateData);
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159 |
7d39593c
|
Andreas Müller
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stateData.setCategoricalData(this);
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160 |
1120db75
|
Andreas Kohlbecker
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}
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/**
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* Convenience method which creates a state data from a given state with no modifiers
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* and adds it to the list of state data
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165 |
f3dabfca
|
Andreas Müller
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* @see #addStateData(StateData)
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166 |
1120db75
|
Andreas Kohlbecker
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* @param state
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*/
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168 |
2eb8c59a
|
Andreas Müller
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public StateData addStateData(State state){
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169 |
1120db75
|
Andreas Kohlbecker
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StateData stateData = StateData.NewInstance(state);
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170 |
7d39593c
|
Andreas Müller
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addStateData(stateData);
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171 |
2eb8c59a
|
Andreas Müller
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return stateData;
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172 |
1120db75
|
Andreas Kohlbecker
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}
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/**
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176 |
f3dabfca
|
Andreas Müller
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* Removes one element from the set of {@link #getStateData() states}
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177 |
1120db75
|
Andreas Kohlbecker
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* describing the {@link Feature feature} corresponding to <i>this</i> categorical data.
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*
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* @param state the state which should be removed
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180 |
f3dabfca
|
Andreas Müller
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* @see #getStateData()
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* @see #addStateData(State)
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182 |
1120db75
|
Andreas Kohlbecker
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*/
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183 |
b3bec3a9
|
Andreas M��ller
|
@SuppressWarnings("deprecation")
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184 |
f3dabfca
|
Andreas Müller
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public void removeStateData(StateData stateData){
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this.stateData.remove(stateData);
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186 |
b3bec3a9
|
Andreas M��ller
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stateData.setCategoricalData(null);
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187 |
1120db75
|
Andreas Kohlbecker
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}
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//rename to isStateSequenceIntentional ??
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/**
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* Returns the boolean value of the flag indicating whether the sequence of
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* {@link StateData state data} belonging to <i>this</i> categorical data is intentional
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* (true) and therefore relevant for interpretation or analysis or not (false).
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* The use of this flag depends mostly on the {@link Feature feature} of <i>this</i> categorical data.
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*
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* @return the boolean value of the orderRelevant flag
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*/
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public boolean getOrderRelevant(){
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return this.orderRelevant;
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}
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/**
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* @see #getOrderRelevant()
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*/
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public void setOrderRelevant(boolean orderRelevant){
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this.orderRelevant = orderRelevant;
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}
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// ********************* CONVENIENCE ******************************************/
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210 |
3cdfd4b6
|
Andreas Müller
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/**
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211 |
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* Convenience method to test the existence of a given state in the state data.
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* Note: the method ignores modifiers so state data having the state may still be
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* modified by its modifiers.
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*
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* @param state the given {@link State}
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* @return <code>true</code> if the state exists
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*/
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public boolean hasState(State state) {
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return getStatesOnly().contains(state);
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}
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222 |
1120db75
|
Andreas Kohlbecker
|
/**
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223 |
9b8a8049
|
Andreas Müller
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* Convenience method returning only the list of states. Leaving out modifiers and modifying text.
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224 |
1120db75
|
Andreas Kohlbecker
|
*/
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225 |
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@Transient
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226 |
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public List<State> getStatesOnly(){
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227 |
9b8a8049
|
Andreas Müller
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List<State> result = new ArrayList<>();
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228 |
f3dabfca
|
Andreas Müller
|
for (StateData stateData : getStateData()){
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229 |
1120db75
|
Andreas Kohlbecker
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State state = stateData.getState();
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230 |
9b8a8049
|
Andreas Müller
|
if (state != null){
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231 |
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result.add(state);
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232 |
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}
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233 |
1120db75
|
Andreas Kohlbecker
|
}
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234 |
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return result;
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235 |
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}
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236 |
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/**
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238 |
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* Convenience method which to set the list of states (no modifiers or modifying text allowed).
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239 |
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* All existing state data are removed.
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240 |
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* @return
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241 |
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*/
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242 |
f3dabfca
|
Andreas Müller
|
public List<StateData> setStateDataOnly(List<State> states){
|
243 |
6a65a580
|
Patrick Plitzner
|
List<StateData> stateDataList = new ArrayList<>(getStateData());
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244 |
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for (StateData stateData : stateDataList) {
|
245 |
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removeStateData(stateData);
|
246 |
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}
|
247 |
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for (State state : states) {
|
248 |
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addStateData(state);
|
249 |
1120db75
|
Andreas Kohlbecker
|
}
|
250 |
f3dabfca
|
Andreas Müller
|
return this.stateData;
|
251 |
1120db75
|
Andreas Kohlbecker
|
}
|
252 |
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|
253 |
e9829ef9
|
Andreas Müller
|
@Transient
|
254 |
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@XmlTransient
|
255 |
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@Override
|
256 |
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public boolean isCharacterData() {
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257 |
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return true;
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258 |
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}
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259 |
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260 |
50e52e0f
|
Andreas Müller
|
//********************************** toString **************************************/
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261 |
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262 |
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@Override
|
263 |
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public String toString() {
|
264 |
0f720e98
|
Andreas Müller
|
return (getFeature()!=null ? getFeature().getLabel(): "") +
|
265 |
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"[" + stateData +
|
266 |
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(orderRelevant? ", orderRelevant=" + orderRelevant:"") +
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267 |
|
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(unknownData? ", unknownData=" + unknownData:"")
|
268 |
e0d15cb3
|
Andreas Müller
|
+ "]";
|
269 |
50e52e0f
|
Andreas Müller
|
}
|
270 |
|
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|
271 |
a42e27ce
|
Andreas Müller
|
|
272 |
|
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//*********************************** CLONE *****************************************/
|
273 |
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|
274 |
1120db75
|
Andreas Kohlbecker
|
/**
|
275 |
|
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* Clones <i>this</i> categorical data. This is a shortcut that enables to create
|
276 |
|
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* a new instance that differs only slightly from <i>this</i> categorical data by
|
277 |
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* modifying only some of the attributes.
|
278 |
ee0b6690
|
Andreas Müller
|
* @throws CloneNotSupportedException
|
279 |
1120db75
|
Andreas Kohlbecker
|
*
|
280 |
|
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* @see eu.etaxonomy.cdm.model.description.DescriptionElementBase#clone()
|
281 |
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* @see java.lang.Object#clone()
|
282 |
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*/
|
283 |
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@Override
|
284 |
ee0b6690
|
Andreas Müller
|
public CategoricalData clone() {
|
285 |
1120db75
|
Andreas Kohlbecker
|
|
286 |
44900eab
|
Andreas Müller
|
CategoricalData result = (CategoricalData)super.clone();
|
287 |
|
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|
288 |
|
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//states
|
289 |
|
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result.stateData = new ArrayList<>();
|
290 |
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for (StateData stateData : getStateData()){
|
291 |
|
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StateData newState = stateData.clone();
|
292 |
|
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result.addStateData(newState);
|
293 |
1120db75
|
Andreas Kohlbecker
|
}
|
294 |
44900eab
|
Andreas Müller
|
|
295 |
|
|
//no changes to: orderRelevant
|
296 |
|
|
return result;
|
297 |
1120db75
|
Andreas Kohlbecker
|
}
|
298 |
ee0b6690
|
Andreas Müller
|
}
|