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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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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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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.Set;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.ManyToOne;
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import javax.persistence.OneToMany;
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import javax.persistence.Transient;
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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.XmlIDREF;
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import javax.xml.bind.annotation.XmlRootElement;
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import javax.xml.bind.annotation.XmlSchemaType;
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import javax.xml.bind.annotation.XmlTransient;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.log4j.Logger;
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import org.hibernate.annotations.Cascade;
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import org.hibernate.annotations.CascadeType;
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import org.hibernate.envers.Audited;
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import org.hibernate.search.annotations.Indexed;
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import org.hibernate.validator.constraints.NotEmpty;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.validation.Level2;
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/**
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* This class represents information pieces expressed in numerical data
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* (in opposition to {@link CategoricalData categorical data} on one side and to literal data on
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* the other side). Only {@link TaxonDescription taxon descriptions} and
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* {@link SpecimenDescription specimen descriptions} may contain quantitative data.<BR>
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* The "length of leaves" {@link Feature feature} for instance can be measured in inches.
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* If the length of leaves of a particular tree is described as
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* "typically between 3 and 5 inches" and "at the utmost 8 inches" then three
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* {@link StatisticalMeasurementValue statistical measurement value} instances
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* must be assigned to an instance of the present class
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* (with the {@link MeasurementUnit measurement unit} set to "inch"):<ul>
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* <li> the first one with the value "3" and the {@link StatisticalMeasure statistical measure}
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* "typical lower boundary",
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* <li> the second one with the value "5" and the statistical measure
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* "typical upper boundary"
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* <li> the third one with the value "8" and the statistical measure "maximum"
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* </ul>
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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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*
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* @author m.doering
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* @version 1.0
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* @created 08-Nov-2007 13:06:46
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "QuantitativeData", propOrder = {
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"unit",
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"statisticalValues",
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"unknownData"
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})
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@XmlRootElement(name = "QuantitativeData")
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@Entity
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@Indexed(index = "eu.etaxonomy.cdm.model.description.DescriptionElementBase")
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@Audited
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public class QuantitativeData extends DescriptionElementBase implements Cloneable {
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private static final long serialVersionUID = -2755806455420051488L;
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private static final Logger logger = Logger.getLogger(QuantitativeData.class);
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@XmlElement(name = "MeasurementUnit")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.LAZY)
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private MeasurementUnit unit;
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@XmlElementWrapper(name = "StatisticalValues")
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@XmlElement(name = "StatisticalValue")
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@OneToMany(fetch = FetchType.LAZY, mappedBy="quantitativeData", orphanRemoval=true)
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@Cascade({ CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
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@NotEmpty(groups = Level2.class)
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private Set<StatisticalMeasurementValue> statisticalValues = new HashSet<StatisticalMeasurementValue>();
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//see #4471
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// @Column(precision = 20, scale = 10)
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// private BigDecimal minimum;
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//
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// @Column(precision = 20, scale = 10)
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// private BigDecimal maximum;
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//
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// @Column(precision = 20, scale = 10)
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// private BigDecimal average;
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//
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// @Column(precision = 16, scale = 8)
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// private BigDecimal variance;
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//
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// @Column(precision = 16, scale = 8)
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// private BigDecimal standardDeviation;
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//
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// @Column(precision = 20, scale = 10)
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// private BigDecimal singleValue;
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//
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// private Integer sampleSize;
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@XmlElement(name = "UnknownData")
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private Boolean unknownData = false;
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// ******************************** FACTORY METHOD *******************************/
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/**
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* Creates a new empty quantitative data instance.
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*/
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public static QuantitativeData NewInstance(){
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return new QuantitativeData();
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}
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// ******************************** FACTORY METHOD *******************************/
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/**
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* Creates a new empty quantitative data instance.
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*/
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public static QuantitativeData NewInstance(Feature feature){
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return new QuantitativeData(feature);
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}
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// ******************************** CONSTRUCTOR *******************************/
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/**
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* Class constructor: creates a new empty quantitative data instance.
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*/
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protected QuantitativeData(){
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super(null);
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}
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/**
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* Class constructor: creates a new empty quantitative data instance.
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*/
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protected QuantitativeData(Feature feature){
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super(feature);
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}
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// ******************************** GETTER /SETTER *******************************/
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/**
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* Returns the set of {@link StatisticalMeasurementValue statistical measurement values} describing
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* the {@link Feature feature} corresponding to <i>this</i> quantitative data.
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*/
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public Set<StatisticalMeasurementValue> getStatisticalValues() {
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return statisticalValues;
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}
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@Deprecated //for internal use only
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protected void setStatisticalValues(Set<StatisticalMeasurementValue> statisticalValues) {
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this.statisticalValues = statisticalValues;
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}
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/**
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* Adds a {@link StatisticalMeasurementValue statistical measurement value} to the set of
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* {@link #getStatisticalValues() statistical measurement values} describing
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* the {@link Feature feature} corresponding to <i>this</i> quantitative data.
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*
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* @param statisticalValue the statistical measurement value to be added to
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* <i>this</i> quantitative data
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* @see #getStatisticalValues()
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*/
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@SuppressWarnings("deprecation")
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public void addStatisticalValue(StatisticalMeasurementValue statisticalValue) {
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this.statisticalValues.add(statisticalValue);
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statisticalValue.setQuantitativeData(this);
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}
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/**
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* Removes one element from the set of {@link #getStatisticalValues() statistical measurement values}
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* describing the {@link Feature feature} corresponding to <i>this</i> quantitative data.
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*
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* @param statisticalValue the statistical measurement value which should be removed
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* @see #getStatisticalValues()
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* @see #addStatisticalValue(StatisticalMeasurementValue)
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*/
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@SuppressWarnings("deprecation")
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public void removeStatisticalValue(StatisticalMeasurementValue statisticalValue) {
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this.statisticalValues.remove(statisticalValue);
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statisticalValue.setQuantitativeData(null);
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}
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/**
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* Returns the {@link MeasurementUnit measurement unit} used in <i>this</i>
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* quantitative data.
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*/
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public MeasurementUnit getUnit(){
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return this.unit;
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}
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/**
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* @see #getUnit()
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*/
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public void setUnit(MeasurementUnit unit){
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this.unit = unit;
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}
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// ******************************** TRANSIENT METHODS *******************************/
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/**
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* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
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* with the corresponding {@link StatisticalMeasure statistical measure} "minimum" and
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* belonging to <i>this</i> quantitative data. Returns <code>null</code> if no such
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* statistical measurement value instance exists.
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*/
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@Transient
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public Float getMin(){
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return getSpecificStatisticalValue(StatisticalMeasure.MIN());
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}
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/**
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* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
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* with the corresponding {@link StatisticalMeasure statistical measure} "maximum" and
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* belonging to <i>this</i> quantitative data. Returns <code>null</code> if no such
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* statistical measurement value instance exists.
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*/
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@Transient
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public Float getMax(){
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return getSpecificStatisticalValue(StatisticalMeasure.MAX());
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}
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/**
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* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
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* with the corresponding {@link StatisticalMeasure statistical measure}
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* "typical lower boundary" and belonging to <i>this</i> quantitative data.
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* Returns <code>null</code> if no such statistical measurement value instance exists.
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*/
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@Transient
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public Float getTypicalLowerBoundary(){
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return getSpecificStatisticalValue(StatisticalMeasure.TYPICAL_LOWER_BOUNDARY());
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}
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/**
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* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
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* with the corresponding {@link StatisticalMeasure statistical measure}
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* "average" and belonging to <i>this</i> quantitative data.
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* Returns <code>null</code> if no such statistical measurement value instance exists.
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*/
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@Transient
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public Float getAverage(){
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return getSpecificStatisticalValue(StatisticalMeasure.AVERAGE());
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}
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/**
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* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
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* with the corresponding {@link StatisticalMeasure statistical measure}
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* "standard deviation" and belonging to <i>this</i> quantitative data.
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* Returns <code>null</code> if no such statistical measurement value instance exists.
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*/
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@Transient
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public Float getStandardDeviation(){
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return getSpecificStatisticalValue(StatisticalMeasure.STANDARD_DEVIATION());
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}
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/**
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* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
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* with the corresponding {@link StatisticalMeasure statistical measure}
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* "sample size" and belonging to <i>this</i> quantitative data.
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* Returns <code>null</code> if no such statistical measurement value instance exists.
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*/
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@Transient
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public Float getSampleSize(){
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return getSpecificStatisticalValue(StatisticalMeasure.SAMPLE_SIZE());
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}
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/**
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* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
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* with the corresponding {@link StatisticalMeasure statistical measure}
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* "typical upper boundary" and belonging to <i>this</i> quantitative data.
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* Returns <code>null</code> if no such statistical measurement value instance exists.
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*/
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@Transient
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public Float getTypicalUpperBoundary(){
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return getSpecificStatisticalValue(StatisticalMeasure.TYPICAL_UPPER_BOUNDARY());
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}
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/**
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* Returns the statistical value of type <code>type</code>.
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* If no such value exists <code>null</code> is returned. If multiple such
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* values exist an arbitrary one is returned.
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* @param type
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* @return the value
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*/
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public Float getSpecificStatisticalValue(StatisticalMeasure type){
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Float result = null;
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for (StatisticalMeasurementValue value : statisticalValues){
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if (type.equals(value.getType())){
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result = value.getValue();
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break;
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}
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}
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return result;
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}
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/**
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* Sets the statistical value for the minimum.
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* If such value exists the old value is replaced by the new value.
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* The new value is returned.
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* @param type
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* @param value
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* @return the newValue
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*/
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@Transient
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public StatisticalMeasurementValue setMinimum(Float value, Set<DefinedTerm> modifiers){
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return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.MIN());
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}
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/**
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* Sets the statistical value for the maximum.
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* If such value exists the old value is replaced by the new value.
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* The new value is returned.
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* @param type
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* @param value
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* @return the newValue
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*/
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@Transient
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public StatisticalMeasurementValue setMaximum(Float value, Set<DefinedTerm> modifiers){
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return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.MAX());
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}
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/**
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* Sets the statistical value for the average.
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* If such value exists the old value is replaced by the new value.
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* The new value is returned.
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* @param type
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* @param value
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* @return the newValue
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*/
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@Transient
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public StatisticalMeasurementValue setAverage(Float value, Set<DefinedTerm> modifiers){
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return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.AVERAGE());
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}
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/**
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* Sets the statistical value for the standard deviation.
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* If such value exists the old value is replaced by the new value.
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* The new value is returned.
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* @param type
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* @param value
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* @return the newValue
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*/
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@Transient
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public StatisticalMeasurementValue setStandardDeviation(Float value, Set<DefinedTerm> modifiers){
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return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.STANDARD_DEVIATION());
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}
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/**
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* Sets the statistical value for the sample size.
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* If such value exists the old value is replaced by the new value.
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* The new value is returned.
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* @param type
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* @param value
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* @return the newValue
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*/
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@Transient
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public StatisticalMeasurementValue setSampleSize(Float value, Set<DefinedTerm> modifiers){
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return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.SAMPLE_SIZE());
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}
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/**
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* Sets the statistical value for the typical lower boundary.
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* If such value exists the old value is replaced by the new value.
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* The new value is returned.
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* @param type
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* @param value
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* @return the newValue
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*/
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@Transient
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public StatisticalMeasurementValue setTypicalLowerBoundary(Float value, Set<DefinedTerm> modifiers){
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return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.TYPICAL_LOWER_BOUNDARY());
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}
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/**
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* Sets the statistical value for the typical upper boundary.
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* If such value exists the old value is replaced by the new value.
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* The new value is returned.
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* @param type
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* @param value
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* @return the newValue
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*/
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@Transient
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public StatisticalMeasurementValue setTypicalUpperBoundary(Float value, Set<DefinedTerm> modifiers){
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return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.TYPICAL_UPPER_BOUNDARY());
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}
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/**
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* Sets the statistical value of type <code>type</code>.
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* If such value exists the old value is replaced by the new value.
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* The new value is returned.
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* @param type
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* @param value
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* @return the newValue
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*/
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public StatisticalMeasurementValue setSpecificStatisticalValue(Float value, Set<DefinedTerm> modifiers, StatisticalMeasure type){
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StatisticalMeasurementValue result = null;
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StatisticalMeasurementValue existingSmValue = null;
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for (StatisticalMeasurementValue existingValue : statisticalValues){
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if (type.equals(existingValue.getType())){
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existingSmValue = existingValue;
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break;
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}
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}
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if (value == null && existingSmValue == null){
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return null;
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}else if (value == null && existingSmValue != null){
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this.removeStatisticalValue(existingSmValue);
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return null;
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}else if (value != null && existingSmValue == null){
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result = StatisticalMeasurementValue.NewInstance(type, value);
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if (modifiers != null){
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for (DefinedTerm modifier : modifiers){
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result.addModifier(modifier);
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}
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}
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this.addStatisticalValue(result);
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} else if (value != null && existingSmValue != null){
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result = existingSmValue;
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result.setValue(value);
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//remove existing modifiers
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Iterator<DefinedTerm> it = result.getModifiers().iterator();
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while (it.hasNext()){
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it.remove();
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}
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//add new modifiers
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449
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if (modifiers != null){
|
450
|
for (DefinedTerm modifier : modifiers){
|
451
|
result.addModifier(modifier);
|
452
|
}
|
453
|
}
|
454
|
}
|
455
|
return result;
|
456
|
}
|
457
|
|
458
|
// public StatisticalMeasurementValue setSpecificStatisticalValue_old(Float value, Set<DefinedTerm> modifiers, StatisticalMeasure type){
|
459
|
// StatisticalMeasurementValue result = null;
|
460
|
// if (value != null){
|
461
|
// StatisticalMeasurementValue newValue = StatisticalMeasurementValue.NewInstance();
|
462
|
// newValue.setValue(value);
|
463
|
// if (modifiers != null){
|
464
|
// newValue.getModifiers().addAll(modifiers);
|
465
|
// }
|
466
|
// newValue.setType(type);
|
467
|
// result = newValue;
|
468
|
// }
|
469
|
// for (StatisticalMeasurementValue existingValue : statisticalValues){
|
470
|
// if (type.equals(existingValue.getType())){
|
471
|
// result = existingValue;
|
472
|
// statisticalValues.remove(existingValue);
|
473
|
// break;
|
474
|
// }
|
475
|
// }
|
476
|
// if (result != null){
|
477
|
// statisticalValues.add(result);
|
478
|
// }
|
479
|
// return result;
|
480
|
// }
|
481
|
|
482
|
public Boolean getUnknownData() {
|
483
|
return unknownData;
|
484
|
}
|
485
|
|
486
|
public void setUnknownData(Boolean unknownData) {
|
487
|
this.unknownData = unknownData;
|
488
|
}
|
489
|
|
490
|
//
|
491
|
// public BigDecimal getMinimum() {
|
492
|
// return minimum;
|
493
|
// }
|
494
|
//
|
495
|
// public void setMinimum(BigDecimal minimum) {
|
496
|
// this.minimum = minimum;
|
497
|
// }
|
498
|
//
|
499
|
// public BigDecimal getMaximum() {
|
500
|
// return maximum;
|
501
|
// }
|
502
|
//
|
503
|
// public void setMaximum(BigDecimal maximum) {
|
504
|
// this.maximum = maximum;
|
505
|
// }
|
506
|
//
|
507
|
// public BigDecimal getVariance() {
|
508
|
// return variance;
|
509
|
// }
|
510
|
//
|
511
|
// public void setVariance(BigDecimal variance) {
|
512
|
// this.variance = variance;
|
513
|
// }
|
514
|
//
|
515
|
// public BigDecimal getSingleValue() {
|
516
|
// return singleValue;
|
517
|
// }
|
518
|
//
|
519
|
// public void setSingleValue(BigDecimal singleValue) {
|
520
|
// this.singleValue = singleValue;
|
521
|
// }
|
522
|
|
523
|
//
|
524
|
// public void setAverage(BigDecimal average) {
|
525
|
// this.average = average;
|
526
|
// }
|
527
|
//
|
528
|
// public void setStandardDeviation(BigDecimal standardDeviation) {
|
529
|
// this.standardDeviation = standardDeviation;
|
530
|
// }
|
531
|
//
|
532
|
// public void setSampleSize(Integer sampleSize) {
|
533
|
// this.sampleSize = sampleSize;
|
534
|
// }
|
535
|
|
536
|
|
537
|
@Transient
|
538
|
@XmlTransient
|
539
|
@Override
|
540
|
public boolean isCharacterData() {
|
541
|
return true;
|
542
|
}
|
543
|
|
544
|
|
545
|
//*********************************** CLONE *****************************************/
|
546
|
|
547
|
/**
|
548
|
* Clones <i>this</i> quantitative data. This is a shortcut that enables to create
|
549
|
* a new instance that differs only slightly from <i>this</i> quantitative data by
|
550
|
* modifying only some of the attributes.
|
551
|
*
|
552
|
* @see eu.etaxonomy.cdm.model.description.DescriptionElementBase#clone()
|
553
|
* @see java.lang.Object#clone()
|
554
|
*/
|
555
|
@Override
|
556
|
public Object clone() {
|
557
|
|
558
|
try {
|
559
|
QuantitativeData result = (QuantitativeData)super.clone();
|
560
|
|
561
|
//states
|
562
|
result.statisticalValues = new HashSet<StatisticalMeasurementValue>();
|
563
|
for (StatisticalMeasurementValue data : getStatisticalValues()){
|
564
|
//TODO do we need to clone here?
|
565
|
StatisticalMeasurementValue newData = (StatisticalMeasurementValue)data.clone();
|
566
|
result.statisticalValues.add(newData);
|
567
|
}
|
568
|
|
569
|
return result;
|
570
|
//no changes to: unit
|
571
|
} catch (CloneNotSupportedException e) {
|
572
|
logger.warn("Object does not implement cloneable");
|
573
|
e.printStackTrace();
|
574
|
return null;
|
575
|
}
|
576
|
}
|
577
|
|
578
|
}
|